@article{
 title = {SIMPATHIC: Accelerating drug repurposing for rare diseases by exploiting SIMilarities in clinical and molecular PATHology},
 type = {article},
 year = {2025},
 pages = {109073},
 websites = {https://linkinghub.elsevier.com/retrieve/pii/S1096719225000642},
 month = {3},
 publisher = {Academic Press},
 day = {1},
 id = {8e19aab6-d250-392e-8a74-bb7de43179d5},
 created = {2025-03-03T07:31:36.236Z},
 accessed = {2025-03-03},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-03-03T07:32:54.550Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {van Karnebeek, Clara D.M. and Müller, Annelieke R. and Benkemoun, Laura and Boussaad, Ibrahim and Cornel, Martina C. and IntHout, Joanna and de Kort, Martin and de Oliveira Martins, Sofia and Prigione, Alessandro and Rigter, Tessel and Roes, Kit C.B. and Sanchez, Anna and Schipper, Raymond and Wilkinson, Mark D. and ’t Hoen, Peter A.C.},
 doi = {10.1016/J.YMGME.2025.109073},
 journal = {Molecular Genetics and Metabolism}
}

@article{
 title = {FLAIR-GG -Evolution of Germplasm Banks From Seed Keepers and Providers to FAIR Data Centers},
 type = {article},
 year = {2025},
 keywords = {federated queries,integrated conservation,linked data,wild species},
 websites = {https://www.authorea.com/users/895724/articles/1272510-flair-gg-evolution-of-germplasm-banks-from-seed-keepers-and-providers-to-fair-data-centers},
 month = {2},
 publisher = {Authorea},
 day = {28},
 institution = {Authorea Inc.},
 id = {bec16795-1e5d-3d87-8ba0-79078cd0367b},
 created = {2025-03-05T09:50:53.868Z},
 accessed = {2025-03-05},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-03-05T09:52:44.531Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {Informed ex situ conservation strategies require data from germplasm banks about both the breadth and depth of sampling for any given species to answer a key question: are samples available for most natural occurrences of each species spanning the breadth of soil, topography and climate types? When this is so, the germplasm bank is likely to have a rich representation of genome adaptations. Importantly, and especially for wild species, germplasm is held in a widely disparate and distributed array of germplasm banks that have limited resources and limited data exploration interfaces. This has led to germplasm banks being used primarily as seed providers, in spite of the fact that the rich information they contain is critical for developing data-driven conservation and use strategies. The FLAIR-GG initiative intends to assist germplasm banks to evolve from just seed keepers and distributors to independent data centers. The FLAIR-GG platform deploys tools and standards —based on the FAIR Principles— that facilitate both inter-bank collaborations as well as connections to eco-geographical databases, and also “vertical” connections with international germplasm catalogues. FLAIR-GG establishes a stepwise approach to enhancing data discovery and sharing with a minimum of training or resources required, in an attempt to minimize the barrier-to-entry to this critical migration from bank to data center. Here we discuss the objectives, methodology, and current outcomes of the ongoing roll-out of the FLAIR-GG Network and Virtual Platform, and invite other participants to join the initiative.},
 bibtype = {article},
 author = {Torres, Elena and Cámara Ballesteros, Alberto and Wilkinson, Mark D and Aguayo Jara, Elena and Pastor Del Olmo, Germán and Moreno-Vázquez, Santiago and Ballesteros, Cámara and Jara, Aguayo and del Olmo, Pastor},
 doi = {10.22541/AU.174077736.65133189/V1},
 journal = {Authorea Preprints}
}

Informed ex situ conservation strategies require data from germplasm banks about both the breadth and depth of sampling for any given species to answer a key question: are samples available for most natural occurrences of each species spanning the breadth of soil, topography and climate types? When this is so, the germplasm bank is likely to have a rich representation of genome adaptations. Importantly, and especially for wild species, germplasm is held in a widely disparate and distributed array of germplasm banks that have limited resources and limited data exploration interfaces. This has led to germplasm banks being used primarily as seed providers, in spite of the fact that the rich information they contain is critical for developing data-driven conservation and use strategies. The FLAIR-GG initiative intends to assist germplasm banks to evolve from just seed keepers and distributors to independent data centers. The FLAIR-GG platform deploys tools and standards —based on the FAIR Principles— that facilitate both inter-bank collaborations as well as connections to eco-geographical databases, and also “vertical” connections with international germplasm catalogues. FLAIR-GG establishes a stepwise approach to enhancing data discovery and sharing with a minimum of training or resources required, in an attempt to minimize the barrier-to-entry to this critical migration from bank to data center. Here we discuss the objectives, methodology, and current outcomes of the ongoing roll-out of the FLAIR-GG Network and Virtual Platform, and invite other participants to join the initiative.

@article{
 title = {The FLAIR-GG federated network of FAIR germplasm data resources},
 type = {article},
 year = {2024},
 pages = {1386},
 volume = {11},
 month = {12},
 day = {18},
 id = {f96751dd-e722-3d97-94f6-3aa11c2571b2},
 created = {2025-01-16T14:03:10.543Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:27:50.552Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Cámara Ballesteros, Alberto and Aguayo Jara, Elena and Verykaki, Evrykleia Sofia and Pastor del Olmo, Germán and Moreno Vázquez, Santiago and Torres, Elena and Wilkinson, Mark D.},
 doi = {10.1038/s41597-024-04243-7},
 journal = {Scientific Data},
 number = {1}
}

@article{
 title = {607P A patient-centered registry for rare neuromuscular disorders with federated FAIR infrastructure: the EURO-NMD Registry Hub},
 type = {article},
 year = {2024},
 pages = {104441.556},
 volume = {43},
 month = {10},
 id = {5fe7f58a-7872-31bb-9b90-993ab0c6dca4},
 created = {2025-01-16T14:04:09.671Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:27:59.733Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Atalaia, A. and Wandrei, D. and Lalout, N. and Tassoni, A. and ’t Hoen P, A.C. and Athanasiou, D. and D'Angelo, C. and Mancuso, M. and Kornblum, C. and Kirschner, J. and Pareyson, D. and Bassez, G. and Lamy, F. and de Visser, M. and Silani, V. and Vroom, E. and Wilkinson, M.D. and Lochmuller, H. and Evangelista, T.},
 doi = {10.1016/j.nmd.2024.07.565},
 journal = {Neuromuscular Disorders}
}

@article{
 title = {Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time},
 type = {article},
 year = {2024},
 pages = {27},
 volume = {260},
 month = {7},
 day = {12},
 id = {0e9061c1-ec32-30ea-94cc-4e60f0e2da31},
 created = {2025-01-16T14:05:39.490Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:28:07.311Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Poza-Viejo, Laura and Payá-Milans, Miriam and Wilkinson, Mark D. and Piñeiro, Manuel and Jarillo, José A. and Crevillén, Pedro},
 doi = {10.1007/s00425-024-04454-7},
 journal = {Planta},
 number = {1}
}

@article{
 title = {Common conditions of use elements. Atomic concepts for consistent and effective information governance},
 type = {article},
 year = {2024},
 pages = {465},
 volume = {11},
 month = {5},
 day = {8},
 id = {44c8e371-d15a-33f8-8816-a9010947138e},
 created = {2025-01-16T14:06:23.813Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:28:12.273Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {<p>Myriad policy, ethical and legal considerations underpin the sharing of biological resources, implying the need for standardised and yet flexible ways to digitally represent diverse ‘use conditions’. We report a core lexicon of terms that are atomic, non-directional ‘concepts of use’, called Common Conditions of use Elements. This work engaged biobanks and registries relevant to the European Joint Programme for Rare Diseases and aimed to produce a lexicon that would have generalised utility. Seventy-six concepts were initially identified from diverse real-world settings, and via iterative rounds of deliberation and user-testing these were optimised and condensed down to 20 items. To validate utility, support software and training information was provided to biobanks and registries who were asked to create Sharing Policy Profiles. This succeeded and involved adding standardised directionality and scope annotations to the employed terms. The addition of free-text parameters was also explored. The approach is now being adopted by several real-world projects, enabling this standard to evolve progressively into a universal basis for representing and managing conditions of use.</p>},
 bibtype = {article},
 author = {Sanchez Gonzalez, Maria del Carmen and Kamerling, Pim and Iermito, Mariapia and Casati, Sara and Riaz, Umar and Veal, Colin D. and Maini, Monika and Jeanson, Francis and Benhamed, Oussama Mohammed and van Enckevort, Esther and Landi, Annalisa and Mimouni, Yanis and Le Cornec, Clèmence and Coviello, Domenico A. and Franchin, Tiziana and Fusco, Francesca and Ramírez García, Jose Antonio and van der Zanden, Loes F. M. and Bernier, Alexander and Wilkinson, Mark D. and Mueller, Heimo and Gibson, Spencer J. and Brookes, Anthony J.},
 doi = {10.1038/s41597-024-03279-z},
 journal = {Scientific Data},
 number = {1}
}

Myriad policy, ethical and legal considerations underpin the sharing of biological resources, implying the need for standardised and yet flexible ways to digitally represent diverse ‘use conditions’. We report a core lexicon of terms that are atomic, non-directional ‘concepts of use’, called Common Conditions of use Elements. This work engaged biobanks and registries relevant to the European Joint Programme for Rare Diseases and aimed to produce a lexicon that would have generalised utility. Seventy-six concepts were initially identified from diverse real-world settings, and via iterative rounds of deliberation and user-testing these were optimised and condensed down to 20 items. To validate utility, support software and training information was provided to biobanks and registries who were asked to create Sharing Policy Profiles. This succeeded and involved adding standardised directionality and scope annotations to the employed terms. The addition of free-text parameters was also explored. The approach is now being adopted by several real-world projects, enabling this standard to evolve progressively into a universal basis for representing and managing conditions of use.

@article{
 title = {Getting your DUCs in a row - standardising the representation of Digital Use Conditions},
 type = {article},
 year = {2024},
 pages = {464},
 volume = {11},
 month = {5},
 day = {8},
 id = {5610e796-3a8d-37ad-94b0-c61803aeb192},
 created = {2025-01-16T14:08:39.806Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:28:17.038Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {<p>Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.</p>},
 bibtype = {article},
 author = {Jeanson, Francis and Gibson, Spencer J. and Alper, Pinar and Bernier, Alexander and Woolley, J. Patrick and Mietchen, Daniel and Strug, Andrzej and Becker, Regina and Kamerling, Pim and Sanchez Gonzalez, Maria del Carmen and Mah, Nancy and Novakowski, Ann and Wilkinson, Mark D. and Benhamed, Oussama Mohammed and Landi, Annalisa and Krog, Georg Philip and Müller, Heimo and Riaz, Umar and Veal, Colin and Holub, Petr and van Enckevort, Esther and Brookes, Anthony J.},
 doi = {10.1038/s41597-024-03280-6},
 journal = {Scientific Data},
 number = {1}
}

Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.

@article{
 title = {FAIR Header Reference genome: a TRUSTworthy standard},
 type = {article},
 year = {2024},
 volume = {25},
 month = {3},
 day = {27},
 id = {57ea5b58-9a5c-38ef-a551-7f6d4a381845},
 created = {2025-01-16T14:09:16.793Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:28:21.440Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {<p>The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR’s design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.</p>},
 bibtype = {article},
 author = {Wright, Adam and Wilkinson, Mark D and Mungall, Christopher and Cain, Scott and Richards, Stephen and Sternberg, Paul and Provin, Ellen and Jacobs, Jonathan L and Geib, Scott and Raciti, Daniela and Yook, Karen and Stein, Lincoln and Molik, David C},
 doi = {10.1093/bib/bbae122},
 journal = {Briefings in Bioinformatics},
 number = {3}
}

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR’s design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

@article{
 title = {Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution},
 type = {article},
 year = {2024},
 pages = {429-456},
 volume = {6},
 month = {5},
 day = {1},
 id = {363b116b-90f5-326f-9ff8-3f94d7649d3e},
 created = {2025-01-16T14:10:09.348Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:27:22.605Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {<p>Since 2014, “Bring Your Own Data” workshops (BYODs) have been organised to inform people about the process and benefits of making resources Findable, Accessible, Interoperable, and Reusable (FAIR, and the FAIRification process). The BYOD workshops’ content and format differ depending on their goal, context, and the background and needs of participants. Data-focused BYODs educate domain experts on how to make their data FAIR to find new answers to research questions. Management-focused BYODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification projects. Software-focused BYODs gather software developers and experts on FAIR to implement or improve software resources that are used to support FAIRification. Overall, these BYODs intend to foster collaboration between different types of stakeholders involved in data management, curation, and reuse (e.g. domain experts, trainers, developers, data owners, data analysts, FAIR experts). The BYODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and experience. In this paper, we detail the three different structures of the BYODs and describe examples of early BYODs related to plant breeding data, and rare disease registries and biobanks, which have shaped the structure of the workshops. We discuss the latest insights into making BYODs more productive by leveraging our almost ten years of training experience in these workshops, including successes and encountered challenges. Finally, we examine how the participants’ feedback has motivated the research on FAIR, including the development of workflows and software.</p>},
 bibtype = {article},
 author = {Bernabé, César H. and Thielemans, Lieze and Kaliyaperumal, Rajaram and Carta, Claudio and Zhang, Shuxin and van Gelder, Celia W.G. and Benis, Nirupama and da Silva Santos, Luiz Olavo Bonino and Cornet, Ronald and dos Santos Vieira, Bruna and Lalout, Nawel and Henriques, Ines and Ballesteros, Alberto Cámara and Burger, Kees and Kersloot, Martijn G. and Ehrhart, Friederike and van Enckevort, Esther and Evelo, Chris T. and Gray, Alasdair J. G. and Hanauer, Marc and Hettne, Kristina and de Ligt, Joep and Pereira, Arnaldo and Queralt-Rosinach, Núria and Schultes, Erik and Taruscio, Domenica and Waagmeester, Andra and Wilkinson, Mark D. and Willighagen, Egon L. and Jansen, Mascha and Mons, Barend and Roos, Marco and Jacobsen, Annika},
 doi = {10.1162/dint_a_00236},
 journal = {Data Intelligence},
 number = {2}
}

Since 2014, “Bring Your Own Data” workshops (BYODs) have been organised to inform people about the process and benefits of making resources Findable, Accessible, Interoperable, and Reusable (FAIR, and the FAIRification process). The BYOD workshops’ content and format differ depending on their goal, context, and the background and needs of participants. Data-focused BYODs educate domain experts on how to make their data FAIR to find new answers to research questions. Management-focused BYODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification projects. Software-focused BYODs gather software developers and experts on FAIR to implement or improve software resources that are used to support FAIRification. Overall, these BYODs intend to foster collaboration between different types of stakeholders involved in data management, curation, and reuse (e.g. domain experts, trainers, developers, data owners, data analysts, FAIR experts). The BYODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and experience. In this paper, we detail the three different structures of the BYODs and describe examples of early BYODs related to plant breeding data, and rare disease registries and biobanks, which have shaped the structure of the workshops. We discuss the latest insights into making BYODs more productive by leveraging our almost ten years of training experience in these workshops, including successes and encountered challenges. Finally, we examine how the participants’ feedback has motivated the research on FAIR, including the development of workflows and software.

@article{
 title = {EURO-NMD registry: federated FAIR infrastructure, innovative technologies and concepts of a patient-centred registry for rare neuromuscular disorders},
 type = {article},
 year = {2024},
 pages = {66},
 volume = {19},
 month = {2},
 day = {14},
 id = {7e27c972-de4e-3fd7-b5ee-54a65fc38219},
 created = {2025-01-16T14:10:50.604Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:27:27.676Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Atalaia, Antonio and Wandrei, Dagmar and Lalout, Nawel and Thompson, Rachel and Tassoni, Adrian and ’t Hoen, Peter A. C. and Athanasiou, Dimitrios and Baker, Suzie-Ann and Sakellariou, Paraskevi and Paliouras, Georgios and D’Angelo, Carla and Horvath, Rita and Mancuso, Michelangelo and van der Beek, Nadine and Kornblum, Cornelia and Kirschner, Janbernd and Pareyson, Davide and Bassez, Guillaume and Blacas, Laura and Jacoupy, Maxime and Eng, Catherine and Lamy, François and Plançon, Jean-Philippe and Haberlova, Jana and Brusse, Esther and Hoeijmakers, Janneke G. J. and de Visser, Marianne and Claeys, Kristl G. and Paradas, Carmen and Toscano, Antonio and Silani, Vincenzo and Gyenge, Melinda and Reviers, Evy and Hamroun, Dalil and Vroom, Elisabeth and Wilkinson, Mark D. and Lochmuller, Hanns and Evangelista, Teresinha},
 doi = {10.1186/s13023-024-03059-3},
 journal = {Orphanet Journal of Rare Diseases},
 number = {1}
}

@inbook{
 type = {inbook},
 year = {2024},
 month = {8},
 day = {22},
 id = {76a42a7d-aca7-33db-a60f-c0c771dde690},
 created = {2025-01-16T14:11:34.551Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:26:59.850Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {inbook},
 author = {Hayn, Dieter and Sandner, Emanuel and Vengadeswaran, Abishaa and Tãtaru, Elena-Alexandra and Wilkinson, Mark and Hanauer, Marc and Kreiner, Karl and Schreier, Guenter},
 doi = {10.3233/SHTI240683},
 chapter = {Privacy-Preserving Linkage of Distributed Pseudonymised Datasets in a Virtual European Rare Disease Platform}
}

@article{
 title = {FAIR Data Point: A FAIR-Oriented Approach for Metadata Publication},
 type = {article},
 year = {2023},
 pages = {163-183},
 volume = {5},
 websites = {https://direct.mit.edu/dint/article/5/1/163/112599/FAIR-Data-Point-A-FAIR-Oriented-Approach-for},
 month = {3},
 day = {8},
 id = {a3a37cbd-061d-35c2-9dc2-50afae31f8d4},
 created = {2022-08-26T07:26:00.913Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2023-10-11T09:32:24.556Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {<p>Metadata, data about other digital objects, play an important role in FAIR with a direct relation to all FAIR principles. In this paper we present and discuss the FAIR Data Point (FDP), a software architecture aiming to define a common approach to publish semantically-rich and machine-actionable metadata according to the FAIR principles. We present the core components and features of the FDP, its approach to metadata provision, the criteria to evaluate whether an application adheres to the FDP specifications and the service to register, index and allow users to search for metadata content of available FDPs.</p>},
 bibtype = {article},
 author = {da Silva Santos, Luiz Olavo Bonino and Burger, Kees and Kaliyaperumal, Rajaram and Wilkinson, Mark D.},
 doi = {10.1162/dint_a_00160},
 journal = {Data Intelligence},
 number = {1}
}

Metadata, data about other digital objects, play an important role in FAIR with a direct relation to all FAIR principles. In this paper we present and discuss the FAIR Data Point (FDP), a software architecture aiming to define a common approach to publish semantically-rich and machine-actionable metadata according to the FAIR principles. We present the core components and features of the FDP, its approach to metadata provision, the criteria to evaluate whether an application adheres to the FDP specifications and the service to register, index and allow users to search for metadata content of available FDPs.

@article{
 title = {The FAIR Data Point: Interfaces and Tooling},
 type = {article},
 year = {2023},
 pages = {184-201},
 volume = {5},
 websites = {https://direct.mit.edu/dint/article/5/1/184/113181/The-FAIR-Data-Point-Interfaces-and-Tooling},
 month = {3},
 day = {8},
 id = {e43e1e38-66dc-368c-807d-54ea5cc2e1c7},
 created = {2022-10-10T09:53:21.433Z},
 file_attached = {true},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2023-07-17T04:35:30.329Z},
 read = {true},
 starred = {false},
 authored = {true},
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 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
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 abstract = {<p>While the FAIR Principles do not specify a technical solution for ‘FAIRness’, it was clear from the outset of the FAIR initiative that it would be useful to have commodity software and tooling that would simplify the creation of FAIR-compliant resources. The FAIR Data Point is a metadata repository that follows the DCAT(2) schema, and utilizes the Linked Data Platform to manage the hierarchical metadata layers as LDP Containers. There has been a recent flurry of development activity around the FAIR Data Point that has significantly improved its power and ease-of-use. Here we describe five specific tools—an installer, a loader, two Web-based interfaces, and an indexer—aimed at maximizing the uptake and utility of the FAIR Data Point.</p>},
 bibtype = {article},
 author = {Benhamed, Oussama Mohammed and Burger, Kees and Kaliyaperumal, Rajaram and da Silva Santos, Luiz Olavo Bonino and Suchánek, Marek and Slifka, Jan and Wilkinson, Mark D.},
 doi = {10.1162/dint_a_00161},
 journal = {Data Intelligence},
 number = {1}
}

While the FAIR Principles do not specify a technical solution for ‘FAIRness’, it was clear from the outset of the FAIR initiative that it would be useful to have commodity software and tooling that would simplify the creation of FAIR-compliant resources. The FAIR Data Point is a metadata repository that follows the DCAT(2) schema, and utilizes the Linked Data Platform to manage the hierarchical metadata layers as LDP Containers. There has been a recent flurry of development activity around the FAIR Data Point that has significantly improved its power and ease-of-use. Here we describe five specific tools—an installer, a loader, two Web-based interfaces, and an indexer—aimed at maximizing the uptake and utility of the FAIR Data Point.

@inbook{
 type = {inbook},
 year = {2023},
 pages = {627-640},
 month = {4},
 publisher = {WORLD SCIENTIFIC},
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 author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Wilkinson, Mark and Harland, Lee},
 doi = {10.1142/9789811265679_0033},
 chapter = {FAIR: Making Data AI-Ready},
 title = {Artificial Intelligence for Science}
}

@article{
 title = {Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert},
 type = {article},
 year = {2023},
 pages = {24},
 volume = {18},
 month = {3},
 day = {28},
 id = {95f2cf59-caf2-3d9d-a212-d2f871752db4},
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 bibtype = {article},
 author = {Mandakovic, Dinka and Aguado-Norese, Constanza and García-Jiménez, Beatriz and Hodar, Christian and Maldonado, Jonathan E. and Gaete, Alexis and Latorre, Mauricio and Wilkinson, Mark D. and Gutiérrez, Rodrigo A. and Cavieres, Lohengrin A. and Medina, Joaquín and Cambiazo, Verónica and Gonzalez, Mauricio},
 doi = {10.1186/s40793-023-00486-w},
 journal = {Environmental Microbiome},
 number = {1}
}

@article{
 title = {Leveraging Biolink as a “Rosetta Stone” Between C-Path and EJP-RD Semantic Models Provides Emergent Interoperability},
 type = {article},
 year = {2023},
 volume = {2},
 month = {4},
 day = {14},
 id = {e9f492e2-c58e-3406-b4a9-0344a0d335ce},
 created = {2023-04-18T10:08:39.952Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2023-04-18T10:52:44.559Z},
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 starred = {false},
 authored = {true},
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 hidden = {false},
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 abstract = {<p>Interoperability between clinical datasets is challenging due to, in part, the number of data models and vocabularies in use and the variety of implementations. Here we describe the first steps in an ongoing effort to achieve interoperability between two clinical datasets currently being constructed within independent international projects. Both are utilizing the FAIR Principles but have constructed their data models independently and have selected different ontologies. In this initial exploratory experiment, we examined the degree to which a mapping of both models into an independent schema, Biolink, can increase interoperability. Mapping was achieved by categorizing the key nodes in both data models as “types” of concepts in the Biolink schema. We found that with this very thin mapping in place, and without changing either model, queries could be constructed that extracted data from both datasets, demonstrating that at least some degree of interoperability had been achieved. Our results support the use of FAIR-compliant data representations, which are, by nature, more interoperable than legacy clinical data representations, even when the models have not been coordinated upfront.</p>},
 bibtype = {article},
 author = {Alarcon, Pablo and Braun, Ian and Hartley, Emily and Olson, Daniel and Benis, Nirupama and Cornet, Ronald and Wilkinson, Mark and Walls, Ramona L.},
 doi = {10.47912/jscdm.130},
 journal = {Journal of the Society for Clinical Data Management},
 number = {3}
}

Interoperability between clinical datasets is challenging due to, in part, the number of data models and vocabularies in use and the variety of implementations. Here we describe the first steps in an ongoing effort to achieve interoperability between two clinical datasets currently being constructed within independent international projects. Both are utilizing the FAIR Principles but have constructed their data models independently and have selected different ontologies. In this initial exploratory experiment, we examined the degree to which a mapping of both models into an independent schema, Biolink, can increase interoperability. Mapping was achieved by categorizing the key nodes in both data models as “types” of concepts in the Biolink schema. We found that with this very thin mapping in place, and without changing either model, queries could be constructed that extracted data from both datasets, demonstrating that at least some degree of interoperability had been achieved. Our results support the use of FAIR-compliant data representations, which are, by nature, more interoperable than legacy clinical data representations, even when the models have not been coordinated upfront.

@inproceedings{
 title = {Meeting abstracts from the 11th edition of the European conference on Rare Diseases & Orphan Products (ECRD) 2022},
 type = {inproceedings},
 year = {2023},
 pages = {118},
 volume = {18},
 issue = {S1 (P36)},
 websites = {https://ojrd.biomedcentral.com/articles/10.1186/s13023-023-02707-4},
 month = {6},
 day = {2},
 id = {8550151d-5e55-3200-a577-9d3c3c6f97b4},
 created = {2023-06-07T08:01:20.407Z},
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 authored = {true},
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 private_publication = {false},
 abstract = {P36 Innovative FAIRification solution for a Rare Disease Patient-led Registry: The Duchenne Data Platform Background: The first Duchenne patient-led registry to undertake a FAIRification process is the Duchenne Data Platform (DDP), managed by the Duchenne Parent Project, a patient organization in the Netherlands. The reality for patients with Duchenne and Becker Muscular Dystrophy (DMD/BMD) is that, after diagnosis, they are seen by different healthcare professionals. Consequently, a wide range of health data is produced. These are kept in different data systems and their (re)use is prevented by silo mentalities. The adoption of FAIR data practices [1] by all stakeholders who build, manage, and own these data systems can address this usage problem. As such, the DMD/BMD patient community pledged to make DMD/BMD-related data FAIR, i.e., Findable, Accessible, Interoperable, and Reusable for humans and machines. Methods: The FAIRification solution called ‘FAIR-in-a-Box’ consists of an automated FAIR transformation workflow, where cloud-based servers communicate with each other through secure API calls. Variables to be collected corresponded to the Set of common data elements for Rare Diseases Registrations (CDEs) [2] and Patient Reported Outcomes (PROs). The Recommended International Standards by the European Joint Programme on Rare Diseases (EJPRD) [3] were essential to annotate, map and transform data elements into a machine-readable format. The project required a multidisciplinary team of domain and FAIR experts, supported by a dedicated FAIR project manager. Results: The successful deployment of the FAIR-in-a-Box solution saw DDP reach a FAIR status within 12 months. It is innovative because: 1. It provided minimal disturbances to the source data capture and publishing system by adding a FAIR layer on top of an existing infrastructure 2. It is modular and template-based, allowing individual components to be added, removed, or synchronized with other registries, sometimes without any software changes 3. It used a generic FAIRification process, based on international standards and deployed by other registries such as VASCA Registry for Vascular Anomalies [4] Conclusions: The adoption of FAIR data practices enables efficient and real-time analysis across multiple data sources. To foster change and support others with similar FAIR projects, the Duchenne Parent Project made the FAIR-in-a-Box solution open source [5]. We’re now upscaling our FAIR efforts to make DDP interoperable with other rare disease registries as well as with the European Reference Network (ERN) EURO-NMD for all rare neuromuscular diseases. Consequently, DDP FAIR data can be used, under well defined conditions, by researchers, health care providers, regulators and patients to accelerate discoveries for early diagnosis and innovative treatments. Acknowledgements We would like to express our gratitude to the FAIR experts involved directly or indirectly with the positive outcomes of our first FAIRification process. In particular to the EJPRD technical experts who contributed their time in-kind at different stages of the project. DDP FAIR project was self-funded.},
 bibtype = {inproceedings},
 author = {Lalout, Nawel and Prieto, Mario and Camara, Alberto and Quemada, Eduardo and Rosinach, Núria Queralt and dos Santos Vieira, Bruna and Roos, Marco and ‘t Hoen, Peter A.C. and Vroom, Elizabeth and Franken, Mirjam and Kaliyaperumal, Rajaram and Wilkinson, Mark D.},
 doi = {10.1186/s13023-023-02707-4},
 booktitle = {Orphanet Journal of Rare Diseases}
}

P36 Innovative FAIRification solution for a Rare Disease Patient-led Registry: The Duchenne Data Platform Background: The first Duchenne patient-led registry to undertake a FAIRification process is the Duchenne Data Platform (DDP), managed by the Duchenne Parent Project, a patient organization in the Netherlands. The reality for patients with Duchenne and Becker Muscular Dystrophy (DMD/BMD) is that, after diagnosis, they are seen by different healthcare professionals. Consequently, a wide range of health data is produced. These are kept in different data systems and their (re)use is prevented by silo mentalities. The adoption of FAIR data practices [1] by all stakeholders who build, manage, and own these data systems can address this usage problem. As such, the DMD/BMD patient community pledged to make DMD/BMD-related data FAIR, i.e., Findable, Accessible, Interoperable, and Reusable for humans and machines. Methods: The FAIRification solution called ‘FAIR-in-a-Box’ consists of an automated FAIR transformation workflow, where cloud-based servers communicate with each other through secure API calls. Variables to be collected corresponded to the Set of common data elements for Rare Diseases Registrations (CDEs) [2] and Patient Reported Outcomes (PROs). The Recommended International Standards by the European Joint Programme on Rare Diseases (EJPRD) [3] were essential to annotate, map and transform data elements into a machine-readable format. The project required a multidisciplinary team of domain and FAIR experts, supported by a dedicated FAIR project manager. Results: The successful deployment of the FAIR-in-a-Box solution saw DDP reach a FAIR status within 12 months. It is innovative because: 1. It provided minimal disturbances to the source data capture and publishing system by adding a FAIR layer on top of an existing infrastructure 2. It is modular and template-based, allowing individual components to be added, removed, or synchronized with other registries, sometimes without any software changes 3. It used a generic FAIRification process, based on international standards and deployed by other registries such as VASCA Registry for Vascular Anomalies [4] Conclusions: The adoption of FAIR data practices enables efficient and real-time analysis across multiple data sources. To foster change and support others with similar FAIR projects, the Duchenne Parent Project made the FAIR-in-a-Box solution open source [5]. We’re now upscaling our FAIR efforts to make DDP interoperable with other rare disease registries as well as with the European Reference Network (ERN) EURO-NMD for all rare neuromuscular diseases. Consequently, DDP FAIR data can be used, under well defined conditions, by researchers, health care providers, regulators and patients to accelerate discoveries for early diagnosis and innovative treatments. Acknowledgements We would like to express our gratitude to the FAIR experts involved directly or indirectly with the positive outcomes of our first FAIRification process. In particular to the EJPRD technical experts who contributed their time in-kind at different stages of the project. DDP FAIR project was self-funded.

@article{
 title = {P203 Proven interoperability of five neuromuscular rare disease registries},
 type = {article},
 year = {2023},
 pages = {S145},
 volume = {33},
 month = {10},
 id = {5557d33a-cf57-3416-be17-5e2fd026bc98},
 created = {2025-01-16T14:12:51.443Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2025-01-16T14:26:22.604Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {'t Hoen, P. and Lalout, N. and Vroom, E. and Franken, M. and Jäger, D. and Tassoni, A. and Kampowski, T. and Delattre, H. and Hamroun, D. and Molthof, R. and de Jong, I. and Quemada, E. and Atalaia, A. and Evangelista, T. and Wilkinson, M.},
 doi = {10.1016/j.nmd.2023.07.312},
 journal = {Neuromuscular Disorders}
}

@article{
 title = {Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa},
 type = {article},
 year = {2022},
 websites = {https://onlinelibrary.wiley.com/doi/10.1111/pce.14258},
 month = {2},
 day = {9},
 id = {565481b2-4d7a-3d07-aab4-98df770716e3},
 created = {2022-02-10T09:18:35.092Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2022-02-10T09:19:29.081Z},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
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 bibtype = {article},
 author = {Poza‐Viejo, Laura and Payá‐Milans, Miriam and San Martín‐Uriz, Patxi and Castro‐Labrador, Laura and Lara‐Astiaso, David and Wilkinson, Mark D. and Piñeiro, Manuel and Jarillo, José A. and Crevillén, Pedro},
 doi = {10.1111/pce.14258},
 journal = {Plant, Cell & Environment}
}

@article{
 title = {Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data},
 type = {article},
 year = {2022},
 pages = {9},
 volume = {13},
 month = {12},
 day = {15},
 id = {afd69365-ee27-3d25-9bbd-526e8ba77a18},
 created = {2022-05-31T10:14:52.129Z},
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 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2023-04-18T10:56:26.911Z},
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 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {Kaliyaperumal, Rajaram and Wilkinson, Mark D. and Moreno, Pablo Alarcón and Benis, Nirupama and Cornet, Ronald and dos Santos Vieira, Bruna and Dumontier, Michel and Bernabé, César Henrique and Jacobsen, Annika and Le Cornec, Clémence M. A. and Godoy, Mario Prieto and Queralt-Rosinach, Núria and Schultze Kool, Leo J. and Swertz, Morris A. and van Damme, Philip and van der Velde, K. Joeri and Lalout, Nawel and Zhang, Shuxin and Roos, Marco},
 doi = {10.1186/s13326-022-00264-6},
 journal = {Journal of Biomedical Semantics},
 number = {1}
}

@article{
 title = {The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses},
 type = {article},
 year = {2022},
 volume = {13},
 websites = {https://www.frontiersin.org/article/10.3389/fpls.2022.928386},
 id = {fe696c92-6a29-362a-bf00-a99eb14cc5e9},
 created = {2022-07-14T08:42:23.035Z},
 file_attached = {false},
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 last_modified = {2022-07-14T08:42:23.337Z},
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 authored = {true},
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 citation_key = {10.3389/fpls.2022.928386},
 source_type = {article},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {The accumulation of the auxin precursor indole-3-acetamide (IAM) in the ami1 mutant has recently been reported to reduce plant growth and to trigger abiotic stress responses in Arabidopsis thaliana. The observed response includes the induction of abscisic acid (ABA) biosynthesis through the promotion of NCED3 expression. The mechanism by which plant growth is limited, however, remained largely unclear. Here, we investigated the transcriptional responses evoked by the exogenous application of IAM using comprehensive RNA-sequencing (RNA-seq) and reverse genetics approaches. The RNA-seq results highlighted the induction of a small number of genes, including the R2R3 MYB transcription factor genes MYB74 and MYB102. The two MYB factors are known to respond to various stress cues and to ABA. Consistent with a role as negative plant growth regulator, conditional MYB74 overexpressor lines showed a considerable growth reduction. RNA-seq analysis of MYB74 mutants indicated an association of MYB74 with responses to osmotic stress, water deprivation, and seed development, which further linked MYB74 with the observed ami1 osmotic stress and seed phenotype. Collectively, our findings point toward a role for MYB74 in plant growth control and in responses to abiotic stress stimuli.},
 bibtype = {article},
 author = {Ortiz-García, Paloma and Pérez-Alonso, Marta-Marina and González Ortega-Villaizán, Adrián and Sánchez-Parra, Beatriz and Ludwig-Müller, Jutta and Wilkinson, Mark D and Pollmann, Stephan},
 doi = {10.3389/fpls.2022.928386},
 journal = {Frontiers in Plant Science}
}

The accumulation of the auxin precursor indole-3-acetamide (IAM) in the ami1 mutant has recently been reported to reduce plant growth and to trigger abiotic stress responses in Arabidopsis thaliana. The observed response includes the induction of abscisic acid (ABA) biosynthesis through the promotion of NCED3 expression. The mechanism by which plant growth is limited, however, remained largely unclear. Here, we investigated the transcriptional responses evoked by the exogenous application of IAM using comprehensive RNA-sequencing (RNA-seq) and reverse genetics approaches. The RNA-seq results highlighted the induction of a small number of genes, including the R2R3 MYB transcription factor genes MYB74 and MYB102. The two MYB factors are known to respond to various stress cues and to ABA. Consistent with a role as negative plant growth regulator, conditional MYB74 overexpressor lines showed a considerable growth reduction. RNA-seq analysis of MYB74 mutants indicated an association of MYB74 with responses to osmotic stress, water deprivation, and seed development, which further linked MYB74 with the observed ami1 osmotic stress and seed phenotype. Collectively, our findings point toward a role for MYB74 in plant growth control and in responses to abiotic stress stimuli.

@article{
 title = {Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries},
 type = {article},
 year = {2022},
 pages = {436},
 volume = {17},
 websites = {https://ojrd.biomedcentral.com/articles/10.1186/s13023-022-02558-5},
 month = {12},
 day = {14},
 id = {5d85b7ca-3d95-3ca1-8bbd-b6b71c785674},
 created = {2023-01-30T12:21:40.056Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2023-04-18T10:52:45.332Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {dos Santos Vieira, Bruna and Bernabé, César H. and Zhang, Shuxin and Abaza, Haitham and Benis, Nirupama and Cámara, Alberto and Cornet, Ronald and Le Cornec, Clémence M. A. and ’t Hoen, Peter A. C. and Schaefer, Franz and van der Velde, K. Joeri and Swertz, Morris A. and Wilkinson, Mark D. and Jacobsen, Annika and Roos, Marco},
 doi = {10.1186/s13023-022-02558-5},
 journal = {Orphanet Journal of Rare Diseases},
 number = {1}
}

@techreport{
 title = {Community-driven Governance of FAIRness Assessment: An Open Issue, an Open Discussion Authorship Community},
 type = {techreport},
 year = {2022},
 month = {12},
 institution = {EOSC},
 id = {5d37aeda-e908-3795-ac6f-7112623d061a},
 created = {2023-04-18T10:12:03.927Z},
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 bibtype = {techreport},
 author = {Mark D Wilkinson, undefined and Susanna-Assunta Sansone, undefined and Eva Méndez, undefined and Romain David, undefined and Richard Dennis, undefined and David Hecker, undefined and Mari Kleemola, undefined and Carlo Lacagnina, undefined and Anastasija Nikiforova, undefined},
 doi = {10.5281/zenodo.7390482}
}

@techreport{
 title = {FAIR Assessment Tools: Towards an "Apples to Apples" Comparisons},
 type = {techreport},
 year = {2022},
 month = {12},
 id = {d103fe63-faa3-3dc7-a3dd-08881cace0ca},
 created = {2023-04-18T10:33:52.720Z},
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 bibtype = {techreport},
 author = {Wilkinson, Mark D and Sansone, Susanna-Assunta and Grootveld Marjan, undefined and Nordling, Josefine and Dennis, Richard and Hecker, David},
 doi = {10.5281/zenodo.7463421}
}

@article{
 title = {Predicting microbiomes through a deep latent space},
 type = {article},
 year = {2021},
 pages = {1444-1451},
 volume = {37},
 websites = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa971/5988714,https://academic.oup.com/bioinformatics/article/37/10/1444/5988714},
 month = {6},
 day = {16},
 id = {c467687d-616f-393d-9251-48d732e29b5b},
 created = {2020-12-01T10:10:41.382Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2021-08-25T15:31:54.873Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Garcia-Jimenez2020},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {García-Jiménez, Beatriz and Muñoz, Jorge and Cabello, Sara and Medina, Joaquín and Wilkinson, Mark D},
 editor = {Jonathan, Wren},
 doi = {10.1093/bioinformatics/btaa971},
 journal = {Bioinformatics},
 number = {10}
}

@article{
 title = {Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis},
 type = {article},
 year = {2021},
 pages = {459-475},
 volume = {72},
 websites = {https://academic.oup.com/jxb/article/72/2/459/5928899},
 month = {2},
 day = {2},
 id = {12f5f83b-e084-3fad-8bb3-7c620ba2446b},
 created = {2021-03-03T10:05:14.406Z},
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 last_modified = {2021-03-03T10:05:15.340Z},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Perez-Alonso2020},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {The evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid, salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyse the physiological role of AMIDASE 1 (AMI1) in Arabidopsis plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalysing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plant’s stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including jasmonic acid and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin and ABA homeostasis.},
 bibtype = {article},
 author = {Pérez-Alonso, Marta-Marina and Ortiz-García, Paloma and Moya-Cuevas, José and Lehmann, Thomas and Sánchez-Parra, Beatriz and Björk, Robert G and Karim, Sazzad and Amirjani, Mohammad R and Aronsson, Henrik and Wilkinson, Mark D and Pollmann, Stephan},
 editor = {Napier, Richard},
 doi = {10.1093/jxb/eraa485},
 journal = {Journal of Experimental Botany},
 number = {2}
}

The evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid, salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyse the physiological role of AMIDASE 1 (AMI1) in Arabidopsis plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalysing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plant’s stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including jasmonic acid and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin and ABA homeostasis.

@inproceedings{
 title = {Reuse of Design Pattern Measurements for Health Data},
 type = {inproceedings},
 year = {2021},
 websites = {https://ceur-ws.org/Vol-2969/paper14-DEMO.pdf,https://ceur-ws.org/Vol-2969/},
 city = {Bolzano, Italy, September 11-18},
 id = {26b6f146-ca73-3c24-8bd1-3859abd348a7},
 created = {2021-10-24T07:49:32.126Z},
 accessed = {2023-07-13},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2023-07-13T08:02:30.841Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Queralt-Rosinach2021},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Queralt-Rosinach, Núria and Wilkinson, Mark D and Kaliyaperumal, Rajaram and Bernabé, César and Long, Qinqin and Dumontier, Michel and Schofield, Paul and Roos, Marco},
 editor = {Sanfilippo, Emilio M. and Kutz, Oliver and Troquard, Nicolas and Hahmann., Torsten and Masolo, Claudio and Hoehndorf, Robert and Vita, Randi},
 booktitle = {12th International Conference on Formal Ontology in Information Systems (FOIS 2021) Demonstrations}
}

@article{
 title = {FAIR Principles for Research Software (FAIR4RS Principles)},
 type = {article},
 year = {2021},
 websites = {https://zenodo.org/record/6623556#.YqCJTJNBwlw},
 publisher = {Research Data Alliance},
 id = {572a15aa-a4b8-3e5f-8171-068a787c88b7},
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 file_attached = {false},
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 starred = {false},
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 citation_key = {https://doi.org/10.15497/rda00068},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Chue Hong, Neil P and Katz, Daniel S and Barker, Michelle and Lamprecht, Anna-Lena and Martinez, Carlos and Psomopoulos, Fotis E and Harrow, Jen and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and Honeyman, Tom},
 doi = {10.15497/RDA00068}
}

@misc{
 title = {RO-Crate Metadata Specification 1.1.1},
 type = {misc},
 year = {2021},
 websites = {https://doi.org/10.5281/zenodo.4541002},
 month = {2},
 id = {caf6d176-6091-393d-9f32-091416d5ce64},
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 starred = {false},
 authored = {true},
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 hidden = {false},
 citation_key = {peter_sefton_2021_4541002},
 source_type = {manual},
 notes = {Recommendation published by researchobject.org - <br/>see https://w3id.org/ro/crate/1.1 for web version.},
 private_publication = {false},
 bibtype = {misc},
 author = {Sefton, Peter and Carragáin, Eoghan Ó and Soiland-Reyes, Stian and Corcho, Oscar and Garijo, Daniel and Palma, Raul and Coppens, Frederik and Goble, Carole and Fernández, José María and Chard, Kyle and Gomez-Perez, Jose Manuel and Crusoe, Michael R and Eguinoa, Ignacio and Juty, Nick and Holmes, Kristi and Clark, Jason A and Capella-Gutierrez, Salvador and Gray, Alasdair J G and Owen, Stuart and Williams, Alan R and Tartari, Giacomo and Bacall, Finn and Thelen, Thomas and Ménager, Hervé and Rodríguez-Navas, Laura and Walk, Paul and brandon whitehead, undefined and Wilkinson, Mark and Groth, Paul and Bremer, Erich and Castro, L J Garcia and Sebby, Karl and Kanitz, Alexander and Trisovic, Ana and Kennedy, Gavin and Graves, Mark and Koehorst, Jasper and Leo, Simone and Portier, Marc},
 doi = {10.5281/zenodo.4541002}
}

@misc{
 title = {A Fresh Look at FAIR for Research Software},
 type = {misc},
 year = {2021},
 keywords = {FOS: Computer and information sciences,Software Engineering (cs.SE)},
 websites = {https://arxiv.org/abs/2101.10883},
 publisher = {arXiv},
 id = {9256d0ac-8f75-3e57-97e9-4c91d6cf7319},
 created = {2022-07-14T09:01:21.081Z},
 file_attached = {false},
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 last_modified = {2022-07-14T09:01:21.081Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {https://doi.org/10.48550/arxiv.2101.10883},
 source_type = {misc},
 private_publication = {false},
 bibtype = {misc},
 author = {Katz, Daniel S and Gruenpeter, Morane and Honeyman, Tom and Hwang, Lorraine and Wilkinson, Mark D and Sochat, Vanessa and Anzt, Hartwig and Goble, Carole and 1, for FAIR4RS Subgroup},
 doi = {10.48550/ARXIV.2101.10883}
}

@article{
 title = {BioHackathon 2015: Semantics of data for life sciences and reproducible research},
 type = {article},
 year = {2020},
 pages = {136},
 volume = {9},
 websites = {https://f1000research.com/articles/9-136/v1},
 month = {2},
 day = {24},
 id = {68a7fa20-e2c3-331d-a8d2-b7c17bb746f1},
 created = {2020-02-25T08:55:52.881Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2020-07-10T11:55:06.907Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vos2020},
 private_publication = {false},
 abstract = {We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.},
 bibtype = {article},
 author = {Vos, Rutger A. and Katayama, Toshiaki and Mishima, Hiroyuki and Kawano, Shin and Kawashima, Shuichi and Kim, Jin-Dong and Moriya, Yuki and Tokimatsu, Toshiaki and Yamaguchi, Atsuko and Yamamoto, Yasunori and Wu, Hongyan and Amstutz, Peter and Antezana, Erick and Aoki, Nobuyuki P. and Arakawa, Kazuharu and Bolleman, Jerven T. and Bolton, Evan and Bonnal, Raoul J. P. and Bono, Hidemasa and Burger, Kees and Chiba, Hirokazu and Cohen, Kevin B. and Deutsch, Eric W. and Fernández-Breis, Jesualdo T. and Fu, Gang and Fujisawa, Takatomo and Fukushima, Atsushi and García, Alexander and Goto, Naohisa and Groza, Tudor and Hercus, Colin and Hoehndorf, Robert and Itaya, Kotone and Juty, Nick and Kawashima, Takeshi and Kim, Jee-Hyub and Kinjo, Akira R. and Kotera, Masaaki and Kozaki, Kouji and Kumagai, Sadahiro and Kushida, Tatsuya and Lütteke, Thomas and Matsubara, Masaaki and Miyamoto, Joe and Mohsen, Attayeb and Mori, Hiroshi and Naito, Yuki and Nakazato, Takeru and Nguyen-Xuan, Jeremy and Nishida, Kozo and Nishida, Naoki and Nishide, Hiroyo and Ogishima, Soichi and Ohta, Tazro and Okuda, Shujiro and Paten, Benedict and Perret, Jean-Luc and Prathipati, Philip and Prins, Pjotr and Queralt-Rosinach, Núria and Shinmachi, Daisuke and Suzuki, Shinya and Tabata, Tsuyosi and Takatsuki, Terue and Taylor, Kieron and Thompson, Mark and Uchiyama, Ikuo and Vieira, Bruno and Wei, Chih-Hsuan and Wilkinson, Mark and Yamada, Issaku and Yamanaka, Ryota and Yoshitake, Kazutoshi and Yoshizawa, Akiyasu C. and Dumontier, Michel and Kosaki, Kenjiro and Takagi, Toshihisa},
 doi = {10.12688/f1000research.18236.1},
 journal = {F1000Research}
}

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

@article{
 title = {Data-driven classification of the certainty of scholarly assertions},
 type = {article},
 year = {2020},
 pages = {e8871},
 volume = {8},
 websites = {https://peerj.com/articles/8871},
 month = {4},
 day = {21},
 id = {0b32f8c2-f0a8-3480-bb74-cde89e8d0992},
 created = {2020-05-12T12:13:44.995Z},
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 last_modified = {2020-07-10T11:55:06.849Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Prieto2020},
 private_publication = {false},
 abstract = {The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation—a Nanopublication—where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.},
 bibtype = {article},
 author = {Prieto, Mario and Deus, Helena and de Waard, Anita and Schultes, Erik and García-Jiménez, Beatriz and Wilkinson, Mark D.},
 doi = {10.7717/peerj.8871},
 journal = {PeerJ}
}

The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation—a Nanopublication—where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.

@article{
 title = {FAIR Principles: Interpretations and Implementation Considerations},
 type = {article},
 year = {2020},
 pages = {10-29},
 volume = {2},
 websites = {https://www.mitpressjournals.org/doi/abs/10.1162/dint_r_00024},
 month = {1},
 id = {bfeb8cec-d455-3ef0-acf5-1b2e0ad24181},
 created = {2020-07-20T08:38:47.818Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2020-12-01T10:10:42.667Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Jacobsen2020},
 private_publication = {false},
 abstract = {The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 FAIR guiding principles do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability and Reusability of digital resources. This has likely contributed to the broad adoption of the FAIR principles, because individual stakeholder communities can implement their own FAIR solutions. However, it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations. Thus, while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways, for true interoperability we need to support convergence in implementation choices that are widely accessible and (re)-usable. We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible, robust, widespread and consistent FAIR implementations. Any self-identified stakeholder community may either choose to reuse solutions from existing implementations, or when they spot a gap, accept the challenge to create the needed solution, which, ideally, can be used again by other communities in the future. Here, we provide interpretations and implementation considerations (choices and challenges) for each FAIR principle.},
 bibtype = {article},
 author = {Jacobsen, Annika and de Miranda Azevedo, Ricardo and Juty, Nick and Batista, Dominique and Coles, Simon and Cornet, Ronald and Courtot, Mélanie and Crosas, Mercè and Dumontier, Michel and Evelo, Chris T. and Goble, Carole and Guizzardi, Giancarlo and Hansen, Karsten Kryger and Hasnain, Ali and Hettne, Kristina and Heringa, Jaap and Hooft, Rob W.W. and Imming, Melanie and Jeffery, Keith G. and Kaliyaperumal, Rajaram and Kersloot, Martijn G. and Kirkpatrick, Christine R. and Kuhn, Tobias and Labastida, Ignasi and Magagna, Barbara and McQuilton, Peter and Meyers, Natalie and Montesanti, Annalisa and van Reisen, Mirjam and Rocca-Serra, Philippe and Pergl, Robert and Sansone, Susanna-Assunta and da Silva Santos, Luiz Olavo Bonino and Schneider, Juliane and Strawn, George and Thompson, Mark and Waagmeester, Andra and Weigel, Tobias and Wilkinson, Mark D. and Willighagen, Egon L. and Wittenburg, Peter and Roos, Marco and Mons, Barend and Schultes, Erik},
 doi = {10.1162/dint_r_00024},
 journal = {Data Intelligence},
 number = {1-2}
}

The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 FAIR guiding principles do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability and Reusability of digital resources. This has likely contributed to the broad adoption of the FAIR principles, because individual stakeholder communities can implement their own FAIR solutions. However, it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations. Thus, while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways, for true interoperability we need to support convergence in implementation choices that are widely accessible and (re)-usable. We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible, robust, widespread and consistent FAIR implementations. Any self-identified stakeholder community may either choose to reuse solutions from existing implementations, or when they spot a gap, accept the challenge to create the needed solution, which, ideally, can be used again by other communities in the future. Here, we provide interpretations and implementation considerations (choices and challenges) for each FAIR principle.

@article{
 title = {Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering},
 type = {article},
 year = {2020},
 websites = {https://www.researchsquare.com/article/rs-14990/v1},
 id = {850be0cc-e34c-37d9-be56-0322bfdc90f0},
 created = {2020-11-25T09:30:01.860Z},
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 citation_key = {Garcia-Jimenez2020a},
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 private_publication = {false},
 bibtype = {article},
 author = {García-Jiménez, Beatriz and Carrasco, Jorge and Medina, Joaquín and Wilkinson, Mark D},
 doi = {10.21203/rs.2.24431/v1},
 journal = {Research Square Preprints}
}

@article{
 title = {Perturbations of the AMI1 IAM-amidohydrolase expression trigger plant stress responses in Arabidopsis thaliana},
 type = {article},
 year = {2020},
 websites = {https://doi.org/10.1101%2F2020.08.31.275206},
 month = {8},
 publisher = {Cold Spring Harbor Laboratory},
 id = {69a6b313-1dcf-31d9-bb92-5b2d07ad83bc},
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 author = {Pérez-Alonso, Marta Marina and Ortiz-Gárcia, Paloma and Moya-Cuevas, José and Lehmann, Thomas and Sanchez-Parra, Beatriz and Björk, Robert G and Karim, Sazzad and Amirjani, Mohammad R and Aronsson, Henrik and Wilkinson, Mark D and Pollmann, Stephan},
 doi = {10.1101/2020.08.31.275206}
}

@article{
 title = {Robust and automatic definition of microbiome states},
 type = {article},
 year = {2019},
 pages = {e6657},
 volume = {7},
 websites = {https://peerj.com/articles/6657},
 month = {3},
 day = {26},
 id = {1b9224c1-99b1-3935-96f6-2b7cb5e00505},
 created = {2019-04-24T09:53:40.994Z},
 file_attached = {false},
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 last_modified = {2020-07-10T11:55:07.004Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Garcia-Jimenez2019},
 private_publication = {false},
 abstract = {Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.},
 bibtype = {article},
 author = {García-Jiménez, Beatriz and Wilkinson, Mark D.},
 doi = {10.7717/peerj.6657},
 journal = {PeerJ}
}

Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.

@article{
 title = {Data-driven classification of the certainty of scholarly assertions},
 type = {article},
 year = {2019},
 keywords = {FAIR Data,certainty,machine learning,scholarly communication,text mining},
 pages = {e27829v1},
 volume = {7},
 websites = {https://doi.org/10.7287/peerj.preprints.27829v1},
 month = {6},
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 confirmed = {true},
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 abstract = {
The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty. However, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three categories of certainty perceived by readers: one level of high certainty, and two levels of lower certainty that are somewhat less distinct, but nevertheless show a significant degree of inter-annotator agreement. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.
},
 bibtype = {article},
 author = {Prieto, Mario and Deus, Helena and De Waard, Anita and Schultes, Erik and García-Jiménez, Beatriz and Wilkinson, Mark D},
 doi = {10.7287/peerj.preprints.27829v1},
 journal = {PeerJ Preprints}
}

The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty. However, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three categories of certainty perceived by readers: one level of high certainty, and two levels of lower certainty that are somewhat less distinct, but nevertheless show a significant degree of inter-annotator agreement. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.

@article{
 title = {The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data},
 type = {article},
 year = {2019},
 volume = {arXiv:1902},
 websites = {http://arxiv.org/abs/1902.11162},
 month = {2},
 day = {26},
 id = {f39a4f13-5b8c-3244-bf01-a974ea4ad345},
 created = {2019-09-06T09:36:15.367Z},
 accessed = {2019-03-01},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2020-07-10T11:55:06.930Z},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wittenburg2019},
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 abstract = {There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.},
 bibtype = {article},
 author = {Wittenburg, P. and Sustkova, H. Pergl and Montesanti, A. and Bloemers, S. M. and de Waard, S. H. and Musen, M. A. and Graybeal, J. B. and Hettne, K. M. and Jacobsen, A. and Pergl, R. and Hooft, R. W. W. and Staiger, C. and van Gelder, C. W. G. and Knijnenburg, S. L. and van Arkel, A. C. and Meerman, B. and Wilkinson, M. D. and Sansone, S-A and Rocca-Serra, P. and McQuilton, P. and Gonzalez-Beltran, A. N. and Aben, G. J. C. and Henning, P. and Alencar, S. and Ribeiro, C. and Silva, C. R. L. and Sayao, L. and Sales, L. and Veiga, V. and Lima, J. and Dib, S. and Xavier, P. and Murtinho, R. and Tendel, J. and Schaap, B. F. and Brouwer, P. M. and Gavai, A. K. and Bouzembrak, Y. and Marvin, H. J. P. and Mons, A. and Kuhn, T. and Gambardella, A. A. and Azevedo, R. de Miranda and Muhonen, V. and van der Naald, M. and Smit, N. W. and Buys, M. J. and de Bruin, T. F. and Schoots, F. and Goodson, H. J. E. and Rzepa, H. S. and Jeffery, K. G. and Shanahan, H. P. and Axton, M. and Tkachenko, V. and Maya, A. D. and Meyers, N. K. and Conlon, M. and Haak, L. L. and Schultes, E. A.},
 journal = {arXiv}
}

There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.

@article{
 title = {Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework},
 type = {article},
 year = {2019},
 websites = {https://www.biorxiv.org/content/early/2019/05/28/649202},
 publisher = {Cold Spring Harbor Laboratory},
 id = {eb8c11c4-3bc8-3dcc-ac4d-fbf3fcf87f10},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson649202},
 source_type = {article},
 private_publication = {false},
 abstract = {Transparent evaluations of FAIRness are increasingly required by a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers. We propose a scalable, automatable framework to evaluate digital resources that encompasses measurable indicators, open source tools, and participation guidelines, which come together to accommodate domain relevant community-defined FAIR assessments. The components of the framework are: (1) Maturity Indicators - community-authored specifications that delimit a specific automatically-measurable FAIR behavior; (2) Compliance Tests - small Web apps that test digital resources against individual Maturity Indicators; and (3) the Evaluator, a Web application that registers, assembles, and applies community-relevant sets of Compliance Tests against a digital resource, and provides a detailed report about what a machine \textquotedblleftsees\textquotedblright when it visits that resource. We discuss the technical and social considerations of FAIR assessments, and how this translates to our community-driven infrastructure. We then illustrate how the output of the Evaluator tool can serve as a roadmap to assist data stewards to incrementally and realistically improve the FAIRness of their resources.},
 bibtype = {article},
 author = {Wilkinson, Mark D and Dumontier, Michel and Sansone, Susanna-Assunta and da Silva Santos, Luiz Olavo Bonino and Prieto, Mario and Batista, Dominique and McQuilton, Peter and Kuhn, Tobias and Rocca-Serra, Philippe and Crosas, Mercè and Schultes, Erik},
 doi = {10.1101/649202},
 journal = {bioRxiv}
}

Transparent evaluations of FAIRness are increasingly required by a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers. We propose a scalable, automatable framework to evaluate digital resources that encompasses measurable indicators, open source tools, and participation guidelines, which come together to accommodate domain relevant community-defined FAIR assessments. The components of the framework are: (1) Maturity Indicators - community-authored specifications that delimit a specific automatically-measurable FAIR behavior; (2) Compliance Tests - small Web apps that test digital resources against individual Maturity Indicators; and (3) the Evaluator, a Web application that registers, assembles, and applies community-relevant sets of Compliance Tests against a digital resource, and provides a detailed report about what a machine \textquotedblleftsees\textquotedblright when it visits that resource. We discuss the technical and social considerations of FAIR assessments, and how this translates to our community-driven infrastructure. We then illustrate how the output of the Evaluator tool can serve as a roadmap to assist data stewards to incrementally and realistically improve the FAIRness of their resources.

@article{
 title = {Evaluating FAIR maturity through a scalable, automated, community-governed framework},
 type = {article},
 year = {2019},
 pages = {174},
 volume = {6},
 websites = {http://www.nature.com/articles/s41597-019-0184-5},
 month = {12},
 day = {20},
 id = {82fd6792-a170-36f2-a24b-681cb4b0030c},
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 author = {Wilkinson, Mark D. and Dumontier, Michel and Sansone, Susanna-Assunta and Bonino da Silva Santos, Luiz Olavo and Prieto, Mario and Batista, Dominique and McQuilton, Peter and Kuhn, Tobias and Rocca-Serra, Philippe and Crosas, Mercѐ and Schultes, Erik},
 doi = {10.1038/s41597-019-0184-5},
 journal = {Scientific Data},
 number = {1}
}

@article{
 title = {BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services},
 type = {article},
 year = {2019},
 pages = {1677},
 volume = {8},
 websites = {https://f1000research.com/articles/8-1677/v1},
 month = {9},
 day = {23},
 id = {9671f940-ee07-31d4-9f88-f1f5f588e123},
 created = {2019-09-24T07:01:57.153Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2019-09-24T07:01:58.345Z},
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 authored = {true},
 confirmed = {true},
 hidden = {false},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.},
 bibtype = {article},
 author = {Katayama, Toshiaki and Kawashima, Shuichi and Micklem, Gos and Kawano, Shin and Kim, Jin-Dong and Kocbek, Simon and Okamoto, Shinobu and Wang, Yue and Wu, Hongyan and Yamaguchi, Atsuko and Yamamoto, Yasunori and Antezana, Erick and Aoki-Kinoshita, Kiyoko F. and Arakawa, Kazuharu and Banno, Masaki and Baran, Joachim and Bolleman, Jerven T. and Bonnal, Raoul J.P. and Bono, Hidemasa and Fernández-Breis, Jesualdo T. and Buels, Robert and Campbell, Matthew P. and Chiba, Hirokazu and Cock, Peter J. A. and Cohen, Kevin B. and Dumontier, Michel and Fujisawa, Takatomo and Fujiwara, Toyofumi and Garcia, Leyla and Gaudet, Pascale and Hattori, Emi and Hoehndorf, Robert and Itaya, Kotone and Ito, Maori and Jamieson, Daniel and Jupp, Simon and Juty, Nick and Kalderimis, Alex and Kato, Fumihiro and Kawaji, Hideya and Kawashima, Takeshi and Kinjo, Akira R. and Komiyama, Yusuke and Kotera, Masaaki and Kushida, Tatsuya and Malone, James and Matsubara, Masaaki and Mizuno, Satoshi and Mizutani, Sayaka and Mori, Hiroshi and Moriya, Yuki and Murakami, Katsuhiko and Nakazato, Takeru and Nishide, Hiroyo and Nishimura, Yosuke and Ogishima, Soichi and Ohta, Tazro and Okuda, Shujiro and Ono, Hiromasa and Perez-Riverol, Yasset and Shinmachi, Daisuke and Splendiani, Andrea and Strozzi, Francesco and Suzuki, Shinya and Takehara, Junichi and Thompson, Mark and Tokimatsu, Toshiaki and Uchiyama, Ikuo and Verspoor, Karin and Wilkinson, Mark D. and Wimalaratne, Sarala and Yamada, Issaku and Yamamoto, Nozomi and Yarimizu, Masayuki and Kawamoto, Shoko and Takagi, Toshihisa},
 doi = {10.12688/f1000research.18238.1},
 journal = {F1000Research}
}

Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.

@article{
 title = {Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa},
 type = {article},
 year = {2019},
 volume = {8},
 websites = {https://doi.org/10.1093/gigascience/giz147,https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giz147/5652252},
 month = {12},
 day = {1},
 id = {ec5a6ab6-8387-313f-9991-ac1bbbedb081},
 created = {2019-12-11T07:07:49.276Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2020-02-03T07:06:34.461Z},
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 starred = {false},
 authored = {true},
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 citation_key = {10.1093/gigascience/giz147},
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 abstract = {Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide.We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3′-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci.We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.},
 bibtype = {article},
 author = {Payá-Milans, Miriam and Poza-Viejo, Laura and Martín-Uriz, Patxi San and Lara-Astiaso, David and Wilkinson, Mark D and Crevillén, Pedro},
 doi = {10.1093/gigascience/giz147},
 journal = {GigaScience},
 number = {12}
}

Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide.We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3′-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci.We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.

@article{
 title = {Conserved Roles of the H3K27ME3 Epigenome on Plant Development},
 type = {article},
 year = {2019},
 pages = {28},
 websites = {http://www.sebiology.org/docs/default-source/event-documents/seb_nucleus-impact_satellite-programme_nov19-digital.pdf},
 publisher = {The Society for Experimental Biology},
 city = {Madrid, 9-11 DECEMBER, 2019},
 id = {5605f7fd-24d3-3a23-af75-c34d6865aece},
 created = {2019-12-11T09:00:00.443Z},
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 read = {false},
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 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Crevillen2019},
 private_publication = {false},
 abstract = {The study of the epigenome and its relation with the underlying genome sequence has become a central question in Biology nowadays. Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. We have developed a Reproducible Epigenomics Analysis (REA) pipeline combining a Galaxy environment for data analysis and Jupyter notebooks for results visualization composed into Docker. We successfully applied this REA pipeline to study of the H3K27m3 epigenome on leaves and flowers of plant model (Arabidopsis thaliana) and crop (Brassica rapa) species. The comparative analysis between leaves and inflorescences genomic datasets suggested that the expression of various floral regulatory genes during development is controlled by H3K27 methylation. H3K27me3 is a repressive epigenetic mark set by Polycomb protein complexes and counteracted by the histone demethylase activity of specific Jumonji domain proteins. We are also studying the role of these epigenetic factors in A. thaliana and B. rapa. Mutant analyses have shown that these epigenetic factors regulate a wide range of developmental responses including flowering time. The similarities and differences between model and crop systems on the role of H3K27me},
 bibtype = {article},
 author = {Crevillén, Pedro and Poza-Viejo, Laura and Payá-Milans, Miriam and Del Olmo, IVÁN and Wilkinson​, Mark D},
 journal = {IMPACT OF CHROMATIN DOMAINS ON PLANT PHENOTYPES}
}

The study of the epigenome and its relation with the underlying genome sequence has become a central question in Biology nowadays. Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. We have developed a Reproducible Epigenomics Analysis (REA) pipeline combining a Galaxy environment for data analysis and Jupyter notebooks for results visualization composed into Docker. We successfully applied this REA pipeline to study of the H3K27m3 epigenome on leaves and flowers of plant model (Arabidopsis thaliana) and crop (Brassica rapa) species. The comparative analysis between leaves and inflorescences genomic datasets suggested that the expression of various floral regulatory genes during development is controlled by H3K27 methylation. H3K27me3 is a repressive epigenetic mark set by Polycomb protein complexes and counteracted by the histone demethylase activity of specific Jumonji domain proteins. We are also studying the role of these epigenetic factors in A. thaliana and B. rapa. Mutant analyses have shown that these epigenetic factors regulate a wide range of developmental responses including flowering time. The similarities and differences between model and crop systems on the role of H3K27me

@article{
 title = {Erratum: Addendum: The FAIR Guiding Principles for scientific data management and stewardship (Scientific data (2016) 3 (160018))},
 type = {article},
 year = {2019},
 volume = {6},
 id = {2aeacd52-ca87-3b7d-810d-ddaed2736630},
 created = {2019-04-01T23:59:00.000Z},
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 last_modified = {2021-02-05T08:40:11.317Z},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Wilkinson, M.D. and Dumontier, M. and Jan Aalbersberg, I. and Appleton, G. and Axton, M. and Baak, A. and Blomberg, N. and Boiten, J.-W. and da Silva Santos, L.B. and Bourne, P.E. and Bouwman, J. and Brookes, A.J. and Clark, T. and Crosas, M. and Dillo, I. and Dumon, O. and Edmunds, S. and Evelo, C.T. and Finkers, R. and Gonzalez-Beltran, A. and Gray, A.J.G. and Groth, P. and Goble, C. and Grethe, J.S. and Heringa, J. and Hoen, P.A.C.'. and Hooft, R. and Kuhn, T. and Kok, R. and Kok, J. and Lusher, S.J. and Martone, M.E. and Mons, A. and Packer, A.L. and Persson, B. and Rocca-Serra, P. and Roos, M. and van Schaik, R. and Sansone, S.-A. and Schultes, E. and Sengstag, T. and Slater, T. and Strawn, G. and Swertz, M.A. and Thompson, M. and van der Lei, J. and van Mulligen, E. and Jan Velterop, undefined and Waagmeester, A. and Wittenburg, P. and Wolstencroft, K. and Zhao, J. and Mons, B.},
 doi = {10.1038/s41597-019-0009-6},
 journal = {Scientific data},
 number = {1}
}

@article{
 title = {Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework (Scientific Data, (2019), 6, 1, (174), 10.1038/s41597-019-0184-5)},
 type = {article},
 year = {2019},
 volume = {6},
 id = {45031bc9-d260-31ff-95c0-63730ccf2c36},
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 abstract = {The affiliation of Mark Wilkinson and Mario Prieto was incompletely stated in the original publication. It is: Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain This has now been corrected in the HTML and PDF versions.},
 bibtype = {article},
 author = {Wilkinson, Mark D. and Dumontier, Michel and Sansone, Susanna Assunta and Bonino da Silva Santos, Luiz Olavo and Prieto, Mario and Batista, Dominique and McQuilton, Peter and Kuhn, Tobias and Rocca-Serra, Philippe and Crosas, Mercѐ and Schultes, Erik},
 doi = {10.1038/s41597-019-0248-6},
 journal = {Scientific Data},
 number = {1}
}

The affiliation of Mark Wilkinson and Mario Prieto was incompletely stated in the original publication. It is: Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain This has now been corrected in the HTML and PDF versions.

@inproceedings{
 title = {Enrichment of rare disease patient registries by FAIRification},
 type = {inproceedings},
 year = {2018},
 pages = {POSTER},
 id = {2a9d7868-3741-3e08-aa7c-f485ea8b4f5b},
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 citation_key = {Jacobsen2018a},
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 bibtype = {inproceedings},
 author = {Jacobsen, Annika and Thompson, Mark and Schultes, Erik A. and Cornet, Ronald and Wilkinson, Mark and Thompson, Rachel and Mordenti, Marina and Sangiorgi, Luca and Carta, Claudio and Groenen, Karlijn and Kersloot, Martijn and Schultze Kool, Leo and van Enckevort, David and Roos, Marco},
 booktitle = {ECRD 2018}
}

@inproceedings{
 title = {FAIRification of rare disease patient registries},
 type = {inproceedings},
 year = {2018},
 city = {Athens, Greece, April 16-18, 2018},
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 bibtype = {inproceedings},
 author = {Jacobsen, Annika and Thompson, Mark and Sernadela, Pedro and Ehrhart, Friederike and Carta, Claudio and Groenen, Karlijn and Kersloot, Martijn and Kool, Leo Schultze and Mordenti, Marina and Locatelli, Manuela and Sangiorgi, Luca and Schultes, Erik A. and Cornet, Ronald and Wilkinson, Mark D and Taruscio, Domenica and Thompson, Rachel and van Enckevort, David and Evelo, Chris and Roos, Marco},
 booktitle = {Proceedings of the 2018 Annual Partner Meeting of RD Connect}
}

@article{
 title = {A design framework and exemplar metrics for FAIRness},
 type = {article},
 year = {2018},
 pages = {180118},
 volume = {5},
 websites = {http://www.nature.com/articles/sdata2018118},
 month = {6},
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 bibtype = {article},
 author = {Wilkinson, Mark D. and Sansone, Susanna-Assunta and Schultes, Erik and Doorn, Peter and Bonino da Silva Santos, Luiz Olavo and Dumontier, Michel},
 doi = {10.1038/sdata.2018.118},
 journal = {Scientific Data}
}

@article{
 title = {MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases},
 type = {article},
 year = {2018},
 pages = {914-924},
 volume = {39},
 websites = {http://doi.wiley.com/10.1002/humu.23542},
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 author = {Townend, Gillian S. and Ehrhart, Friederike and van Kranen, Henk J. and Wilkinson, Mark and Jacobsen, Annika and Roos, Marco and Willighagen, Egon L. and van Enckevort, David and Evelo, Chris T. and Curfs, Leopold M. G.},
 doi = {10.1002/humu.23542},
 journal = {Human Mutation},
 number = {7}
}

@article{
 title = {Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus},
 type = {article},
 year = {2018},
 websites = {http://doi.wiley.com/10.1111/nph.15405},
 month = {8},
 day = {31},
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 author = {Rodríguez-Romero, Julio and Marconi, Marco and Ortega-Campayo, Víctor and Demuez, Marie and Wilkinson, Mark D. and Sesma, Ane},
 doi = {10.1111/nph.15405},
 journal = {New Phytologist}
}

@article{
 title = {MDPbiome: microbiome engineering through prescriptive perturbations},
 type = {article},
 year = {2018},
 pages = {i838-i847},
 volume = {34},
 websites = {https://academic.oup.com/bioinformatics/article/34/17/i838/5093255},
 month = {9},
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 author = {García-Jiménez, Beatriz and de la Rosa, Tomás and Wilkinson, Mark Denis},
 doi = {10.1093/bioinformatics/bty562},
 journal = {Bioinformatics},
 number = {17}
}

@article{
 title = {Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework},
 type = {article},
 year = {2018},
 websites = {http://biorxiv.org/content/early/2018/09/16/418376.abstract},
 month = {1},
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 abstract = {With the increased adoption of the FAIR Principles, a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers, are seeking ways to transparently evaluate resource FAIRness. We describe the FAIR Evaluator, a software infrastructure to register and execute tests of compliance with the recently published FAIR Metrics. The Evaluator enables digital resources to be assessed objectively and transparently. We illustrate its application to three widely used generalist repositories - Dataverse, Dryad, and Zenodo - and report their feedback. Evaluations allow communities to select relevant Metric subsets to deliver FAIRness measurements in diverse and specialized applications. Evaluations are executed in a semi-automated manner through Web Forms filled-in by a user, or through a JSON-based API. A comparison of manual vs automated evaluation reveals that automated evaluations are generally stricter, resulting in lower, though more accurate, FAIRness scores. Finally, we highlight the need for enhanced infrastructure such as standards registries, like FAIRsharing, as well as additional community involvement in domain-specific data infrastructure creation.},
 bibtype = {article},
 author = {Wilkinson, Mark D and Dumontier, Michel and Sansone, Susanna-Assunta and Bonino da Silva Santos, Luiz Olavo and Prieto, Mario and Gautier, Julian and McQuilton, Peter and Murphy, Derek and Crosas, Merce and Schultes, Erik},
 journal = {bioRxiv}
}

With the increased adoption of the FAIR Principles, a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers, are seeking ways to transparently evaluate resource FAIRness. We describe the FAIR Evaluator, a software infrastructure to register and execute tests of compliance with the recently published FAIR Metrics. The Evaluator enables digital resources to be assessed objectively and transparently. We illustrate its application to three widely used generalist repositories - Dataverse, Dryad, and Zenodo - and report their feedback. Evaluations allow communities to select relevant Metric subsets to deliver FAIRness measurements in diverse and specialized applications. Evaluations are executed in a semi-automated manner through Web Forms filled-in by a user, or through a JSON-based API. A comparison of manual vs automated evaluation reveals that automated evaluations are generally stricter, resulting in lower, though more accurate, FAIRness scores. Finally, we highlight the need for enhanced infrastructure such as standards registries, like FAIRsharing, as well as additional community involvement in domain-specific data infrastructure creation.

@article{
 title = {Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae},
 type = {article},
 year = {2018},
 pages = {180271},
 volume = {5},
 websites = {http://www.nature.com/articles/sdata2018271},
 month = {11},
 day = {27},
 id = {e45f5172-2841-3e2a-a9f0-df5ad2524122},
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 bibtype = {article},
 author = {Marconi, Marco and Sesma, Ane and Rodríguez-Romero, Julio Luis and González, María Lourdes Rosano and Wilkinson, Mark D.},
 doi = {10.1038/sdata.2018.271},
 journal = {Scientific Data}
}

@article{
 title = {Automatic definition of robust microbiome sub-states in longitudinal data},
 type = {article},
 year = {2018},
 keywords = {Clustering,Longitudinal dataset,Machine Learning,Metagenomics,Microbiome,Sub-states},
 pages = {e26657v1},
 volume = {6},
 websites = {https://doi.org/10.7287/peerj.preprints.26657v1},
 month = {3},
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 abstract = {
The analysis of microbiome dynamics would allow us to elucidate patterns within microbial community evolution; however, microbiome state-transition dynamics have been scarcely studied. This is in part because a necessary first-step in such analyses has not been well-defined: how to deterministically describe a microbiome’s ”state”. Clustering in states have been widely studied, although no standard has been concluded yet. We propose a generic, domain-independent and automatic procedure to determine a reliable set of microbiome sub-states within a specific dataset, and with respect to the conditions of the study. The robustness of sub-state identification is established by the combination of diverse techniques for stable cluster verification. We reuse four distinct longitudinal microbiome datasets to demonstrate the broad applicability of our method, analysing results with different taxa subset allowing to adjust it depending on the application goal, and showing that the methodology provides a set of robust sub-states to examine in downstream studies about dynamics in microbiome.
},
 bibtype = {article},
 author = {García-Jiménez, Beatriz and Wilkinson, Mark D},
 doi = {10.7287/peerj.preprints.26657v1},
 journal = {PeerJ Preprints}
}

The analysis of microbiome dynamics would allow us to elucidate patterns within microbial community evolution; however, microbiome state-transition dynamics have been scarcely studied. This is in part because a necessary first-step in such analyses has not been well-defined: how to deterministically describe a microbiome’s ”state”. Clustering in states have been widely studied, although no standard has been concluded yet. We propose a generic, domain-independent and automatic procedure to determine a reliable set of microbiome sub-states within a specific dataset, and with respect to the conditions of the study. The robustness of sub-state identification is established by the combination of diverse techniques for stable cluster verification. We reuse four distinct longitudinal microbiome datasets to demonstrate the broad applicability of our method, analysing results with different taxa subset allowing to adjust it depending on the application goal, and showing that the methodology provides a set of robust sub-states to examine in downstream studies about dynamics in microbiome.

@article{
 title = {FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies},
 type = {article},
 year = {2018},
 websites = {https://www.biorxiv.org/content/early/2018/09/26/245183},
 publisher = {Cold Spring Harbor Laboratory},
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 abstract = {In this modern, data-driven age, governments, funders and publishers expect greater transparency and reuse of research data, as well as greater access to and preservation of the data that supports research findings. Community-developed standards, such as those for the identification and reporting of data, underpin reproducible and reusable research, aid scholarly publishing, and drive both the discovery and evolution of scientific practice. The number of these standardization efforts, driven by large organizations or at the grass root level, has been on the rise since the early 2000s. Thousands of community-developed standards are available (across all disciplines), many of which have been created and/or implemented by several thousand data repositories. Nevertheless, their uptake by the research community, however, has been slow and uneven. This is mainly because investigators lack incentives to follow and adopt standards. The situation is exacerbated if standards are not promptly implemented by databases, repositories and other research tools, or endorsed by infrastructures. Furthermore, the fragmentation of community efforts results in the development of arbitrarily different, incompatible standards. In turn, this leads to standards becoming rapidly obsolete in fast-evolving research areas. As with any other digital object, standards, databases and repositories are dynamic in nature, with a life cycle that encompasses formulation, development and maintenance; their status in this cycle may vary depending on the level of activity of the developing group or community. There is an urgent need for a service that enhances the information available on the evolving constellation of heterogeneous standards, databases and repositories, guides users in the selection of these resources, and that works with developers and maintainers of these resources to foster collaboration and promote harmonization. Such an informative and educational service is vital to reduce the knowledge gap among those involved in producing, managing, serving, curating, preserving, publishing or regulating data. A diverse set of stakeholders-representing academia, industry, funding agencies, standards organizations, infrastructure providers and scholarly publishers, both national and domain-specific as well global and general organizations, have come together as a community, representing the core adopters, advisory board members, and/or key collaborators of the FAIRsharing resource. Here, we introduce its mission and community network. We present an evaluation of the standards landscape, focusing on those for reporting data and metadata - the most diverse and numerous of the standards - and their implementation by databases and repositories. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We present guidelines that highlight the role each stakeholder group must play to maximize the visibility and adoption of standards, databases and repositories.},
 bibtype = {article},
 author = {Sansone, Susanna-Assunta and McQuilton, Peter and Rocca-Serra, Philippe and Gonzalez-Beltran, Alejandra and Izzo, Massimiliano and Lister, Allyson and Thurston, Milo and Batista, Dominique and Granell, Ramon and Adekale, Melanie and Dauga, Delphine and Ganley, Emma and Hodson, Simon and Lawrence, Rebecca and Khodiyar, Varsha and Tenenbaum, Jessica and Axton, J Myles and Ball, Michael and Besson, Sebastien and Bloom, Theodora and Bonazzi, Vivien and Jimenez, Rafael and Carr, David and Chan, Wei Mun and Chung, Caty and Clement-Stoneham, Geraldine and Cousijn, Helena and Dayalan, Saravanan and Dumontier, Michel and Dzale Yeumo, Esther and Edmunds, Scott and Everitt, Nicholas and Fripp, Dom and Goble, Carole and Golebiewski, Martin and Hall, Neil and Hanisch, Robert and Hucka, Michael and Huerta, Michael and Kenall, Amye and Kiley, Robert and Klenk, Juergen and Koureas, Dimitrios and Larkin, Jennie and Lemberger, Thomas and Lynch, Nick and Schriml, Lynn and Ma\textquoterightayan, Avi and MacCallum, Catriona and Mons, Barend and Moore, Josh and Muller, Wolfgang and Murray, Hollydawn and Nobusada, Tomoe and Noesgaard, Daniel and Paxton-Boyd, Jennifer and Orchard, Sandra and Rustici, Gabriella and Schurer, Stephan and Sharples, Kathryn and e Silva, Marina and Stanford, Natalie J and Subirats-Coll, Inmaculada and Swedlow, Jason and Tong, Weida and Wilkinson, Mark and Wise, John and Yilmaz, Pelin},
 doi = {10.1101/245183},
 journal = {bioRxiv}
}

In this modern, data-driven age, governments, funders and publishers expect greater transparency and reuse of research data, as well as greater access to and preservation of the data that supports research findings. Community-developed standards, such as those for the identification and reporting of data, underpin reproducible and reusable research, aid scholarly publishing, and drive both the discovery and evolution of scientific practice. The number of these standardization efforts, driven by large organizations or at the grass root level, has been on the rise since the early 2000s. Thousands of community-developed standards are available (across all disciplines), many of which have been created and/or implemented by several thousand data repositories. Nevertheless, their uptake by the research community, however, has been slow and uneven. This is mainly because investigators lack incentives to follow and adopt standards. The situation is exacerbated if standards are not promptly implemented by databases, repositories and other research tools, or endorsed by infrastructures. Furthermore, the fragmentation of community efforts results in the development of arbitrarily different, incompatible standards. In turn, this leads to standards becoming rapidly obsolete in fast-evolving research areas. As with any other digital object, standards, databases and repositories are dynamic in nature, with a life cycle that encompasses formulation, development and maintenance; their status in this cycle may vary depending on the level of activity of the developing group or community. There is an urgent need for a service that enhances the information available on the evolving constellation of heterogeneous standards, databases and repositories, guides users in the selection of these resources, and that works with developers and maintainers of these resources to foster collaboration and promote harmonization. Such an informative and educational service is vital to reduce the knowledge gap among those involved in producing, managing, serving, curating, preserving, publishing or regulating data. A diverse set of stakeholders-representing academia, industry, funding agencies, standards organizations, infrastructure providers and scholarly publishers, both national and domain-specific as well global and general organizations, have come together as a community, representing the core adopters, advisory board members, and/or key collaborators of the FAIRsharing resource. Here, we introduce its mission and community network. We present an evaluation of the standards landscape, focusing on those for reporting data and metadata - the most diverse and numerous of the standards - and their implementation by databases and repositories. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We present guidelines that highlight the role each stakeholder group must play to maximize the visibility and adoption of standards, databases and repositories.

@article{
 title = {Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae},
 type = {article},
 year = {2017},
 pages = {891-895},
 volume = {162},
 websites = {http://link.springer.com/10.1007/s00705-016-3144-9},
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 doi = {10.1007/s00705-016-3144-9},
 journal = {Archives of Virology},
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@article{
 title = {Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud},
 type = {article},
 year = {2017},
 pages = {49-56},
 volume = {37},
 websites = {http://www.medra.org/servlet/aliasResolver?alias=iospress&doi=10.3233/ISU-170824},
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 author = {Mons, Barend and Neylon, Cameron and Velterop, Jan and Dumontier, Michel and da Silva Santos, Luiz Olavo Bonino and Wilkinson, Mark D},
 doi = {10.3233/ISU-170824},
 journal = {Information Services & Use},
 number = {1}
}

@article{
 title = {Identifying Bioinformatics Subworkflows with SCOFF: Semantic Clustering Of Functional Fragments},
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}

@inproceedings{
 title = {Boosting health care and life science research on rare diseases by creating a robust infrastructure of independently Findable, Accessible, Interoperable, and Reusable (FAIR) biobanks, registries, and molecular data resources},
 type = {inproceedings},
 year = {2017},
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 author = {Enckevort, David van and Thompson, Rachel and Carta, Claudio and Wilkinson, Mark and Roos, Marco},
 booktitle = {IRDiRC 2017}
}

@inproceedings{
 title = {Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies},
 type = {inproceedings},
 year = {2017},
 websites = {http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=d9a7502e-a4d5-4bde-8329-8e609d95cd6f&cKey=1f9e2b9b-3380-44c6-928d-03e1a9914236&mKey=%7B15A3630E-7769-4D64-A80A-47F190AC2F4F%7D},
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 author = {Enckevort, David van and Carta, Claudio and Thompson, Rachel and Thompson, Mark and Ehrhart, Friederieke and Kaliyaperumal, Rajaram and Sernadela, Pedro and Reihs, Robert and Jacobsen, Annika and da Silva Santos, Luiz Olavo Bonino and Wilkinson, Mark D and Muller, Heimo and Oliviera, Jose Luis and Evelo, Chris T. and Taruscio, Domenica and ‘t Hoen, Peter A.C. and Roos, Marco},
 booktitle = {ESHG 2017}
}

@techreport{
 title = {Findable, Accessible, Interoperable and Reusable data resources to speed up research on rare diseases.},
 type = {techreport},
 year = {2017},
 pages = {Poster 94, p19},
 websites = {http://docplayer.it/60979940-Poster-76-il-controllo-microbiologico-delle-acque-obiettivi-antichi-tecniche-sempre-nuove.html},
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 abstract = {CELEBRATION OF 83 YEARS OF CNMR-ISS, ITALY},
 bibtype = {techreport},
 author = {Carta, Claudio and Roos, Marco and Jansen, Mascha and Enckevort, David van and Wilkinson, Mark D and Kaliyaperumal, Rajaram and Thompson, Mark and Torreri, Paola and da Silva Santos, Luiz Olavo Bonino and Cornet, Ronald and Kodra, Yllka and Taruscio, Domenica}
}

CELEBRATION OF 83 YEARS OF CNMR-ISS, ITALY

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@article{
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Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.

@inproceedings{
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@inproceedings{
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@inproceedings{
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@techreport{
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@inproceedings{
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@article{
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@article{
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Motivation: There are few tools that allow longitudinal analysis of metagenomic data subjected to distinct perturbations. Methods: This study examines longitudinal metagenomics data modelled as a Markov Decision Process (MDP). Given an external perturbation, the MDP predicts the next microbiome state in a temporal sequence, selected from a finite set of possible microbiome states. Results: We examined three distinct datasets to demonstrate this approach. An MDP created for a vaginal microbiome time series generates a variety of behaviour policies. For example, that moving from a state associated with bacterial vaginosis to a healthier one, requires avoiding perturbations such as lubricant, sex toys, tampons and anal sex. The flexibility of our proposal is verified after applying MDPs to human gut and chick gut microbiomes, taking nutritional intakes, or salmonella and probiotic treatments, respectively, as perturbations. In the latter case, MDPs provided a quantitative explanation for why salmonella vaccine accelerates microbiome maturation in chicks. This novel analytical approach has applications in, for example, medicine where the MDP could suggest the sequence of perturbations (e.g. clinical interventions) to apply to follow the best path from any given starting state, to a desired (healthy) state, avoiding strongly negative states.

@article{
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@inproceedings{
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@inproceedings{
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 citation_key = {Roos2016},
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 bibtype = {inproceedings},
 author = {Roos, Marco and Wilkinson, Mark D and Kaliyaperumal, Rajaram and Thompson, Mark and Carta, Claudio and Cornet, Ronald and van Enckevort, David and Bonino, Luiz},
 editor = {Paschke, Adrian and Burger, Albert and Splendiani, Andrea and Marshall, M. Scott and Romano, Paolo},
 booktitle = {Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences}
}

@article{
 title = {<b><i>VPS13D</i></b> Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock},
 type = {article},
 year = {2015},
 pages = {545-553},
 volume = {7},
 websites = {http://www.karger.com/?doi=10.1159/000381265},
 month = {4},
 day = {17},
 id = {6aa7ec52-052d-37db-abac-d975e80746a3},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Nakada2015},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {Nakada, Taka-aki and Boyd, John H. and Russell, James A. and Aguirre-Hern�ndez, Rosal�a and Wilkinson, Mark D. and Thair, Simone A. and Nakada, Emiri and McConechy, Melissa K. and Fjell, Christopher D. and Walley, Keith R.},
 doi = {10.1159/000381265},
 journal = {Journal of Innate Immunity},
 number = {5}
}

@article{
 title = {Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples.},
 type = {article},
 year = {2015},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/25577362},
 month = {1},
 day = {11},
 id = {a6e0ca44-2856-387a-a4c4-a5d769948c12},
 created = {2014-12-09T11:42:19.000Z},
 accessed = {2015-01-13},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Pawluczyk2015},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {Unbiased identification of organisms by PCR reactions using universal primers followed by DNA sequencing assumes positive amplification. We used six universal loci spanning 48 plant species and quantified the bias at each step of the identification process from end point PCR to next-generation sequencing. End point amplification was significantly different for single loci and between species. Quantitative PCR revealed that Cq threshold for various loci, even within a single DNA extraction, showed 2,000-fold differences in DNA quantity after amplification. Next-generation sequencing (NGS) experiments in nine species showed significant biases towards species and specific loci using adaptor-specific primers. NGS sequencing bias may be predicted to some extent by the Cq values of qPCR amplification.},
 bibtype = {article},
 author = {Pawluczyk, Marta and Weiss, Julia and Links, Matthew G and Egaña Aranguren, Mikel and Wilkinson, Mark D and Egea-Cortines, Marcos},
 doi = {10.1007/s00216-014-8435-y},
 journal = {Analytical and bioanalytical chemistry}
}

Unbiased identification of organisms by PCR reactions using universal primers followed by DNA sequencing assumes positive amplification. We used six universal loci spanning 48 plant species and quantified the bias at each step of the identification process from end point PCR to next-generation sequencing. End point amplification was significantly different for single loci and between species. Quantitative PCR revealed that Cq threshold for various loci, even within a single DNA extraction, showed 2,000-fold differences in DNA quantity after amplification. Next-generation sequencing (NGS) experiments in nine species showed significant biases towards species and specific loci using adaptor-specific primers. NGS sequencing bias may be predicted to some extent by the Cq values of qPCR amplification.

@inbook{
 type = {inbook},
 year = {2015},
 pages = {79-87},
 websites = {http://link.springer.com/10.1007/978-3-319-19776-0_9},
 publisher = {Springer International Publishing},
 id = {8b1a9673-9669-341b-a1b7-4ca59c97cb8d},
 created = {2015-07-09T11:49:42.000Z},
 file_attached = {false},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Rodriguez-Gonzalez2015},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {In the creation of diagnostic decision support systems (DDSS) it is crucial to have validated and precise knowledge in order to create accurate systems. Typically, medical experts are the source of this knowledge, but it is not always possible to obtain all the desired information from them. Another valuable source could be medical books or articles describing the diagnosis of diseases managed by the DDSS, but again, it is not easy to extract this information. In this paper we present the results of our research, in which we have used Web scraping and a combination of natural language processing techniques to extract diagnostic criteria from MedlinePlus articles about infectious diseases.},
 bibtype = {inbook},
 author = {Rodríguez-González, Alejandro and Martínez-Romero, Marcos and Costumero, Roberto and Wilkinson, Mark D. and Menasalvas-Ruiz, Ernestina},
 editor = {Overbeek, Ross and Rocha, Miguel P. and Fdez-Riverola, Florentino and Paz, Juan F. De},
 doi = {10.1007/978-3-319-19776-0_9},
 chapter = {Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases},
 title = {9th International Conference on Practical Applications of Computational Biology and Bioinformatics}
}

In the creation of diagnostic decision support systems (DDSS) it is crucial to have validated and precise knowledge in order to create accurate systems. Typically, medical experts are the source of this knowledge, but it is not always possible to obtain all the desired information from them. Another valuable source could be medical books or articles describing the diagnosis of diseases managed by the DDSS, but again, it is not easy to extract this information. In this paper we present the results of our research, in which we have used Web scraping and a combination of natural language processing techniques to extract diagnostic criteria from MedlinePlus articles about infectious diseases.

@misc{
 title = {DataFairPort: The Perl libraries version 0.231},
 type = {misc},
 year = {2015},
 websites = {http://dx.doi.org/10.5281/zenodo.33584},
 month = {11},
 id = {5a073330-f305-33ec-8a6d-a80920d586d2},
 created = {2015-11-18T07:53:57.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {mark_wilkinson_2015_33584},
 source_type = {misc},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {misc},
 author = {Wilkinson, Mark and Dumontier, Michel and Durbin, Philip},
 doi = {10.5281/zenodo.33584}
}

@article{
 title = {Enhanced reproducibility of SADI web service workflows with Galaxy and Docker},
 type = {article},
 year = {2015},
 pages = {59},
 volume = {4},
 websites = {http://www.gigasciencejournal.com/content/4/1/59},
 month = {12},
 day = {3},
 id = {cb951481-aff2-3792-8db0-af7e7f4815f9},
 created = {2015-12-09T08:08:36.000Z},
 file_attached = {false},
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 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Aranguren2015},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {Aranguren, Mikel Egaña and Wilkinson, Mark D.},
 doi = {10.1186/s13742-015-0092-3},
 journal = {GigaScience},
 number = {1}
}

@book{
 title = {Erratum to: Diagnostic knowledge extraction from MedlinePlus: An application for infectious diseases (9th International Conference on Practical Applications of Computational Biology and Bioinformatics, Advances in Intelligent Systems and Computing 375, 10},
 type = {book},
 year = {2015},
 source = {Advances in Intelligent Systems and Computing},
 volume = {375},
 id = {96af3c35-b93e-35ef-8a35-ebbbd853e963},
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 author = {Rodríguez-González, A. and Martínez-Romero, M. and Costumero, R. and Wilkinson, M.D. and Menasalvas-Ruiz, E.},
 doi = {10.1007/978-3-319-19776-0_16}
}

@article{
 title = {Executing SADI services in Galaxy},
 type = {article},
 year = {2014},
 pages = {42},
 volume = {5},
 websites = {http://www.jbiomedsem.com/content/5/1/42},
 id = {95e6db0a-202a-3397-bbeb-27bb4afa9634},
 created = {2013-12-12T11:12:08.000Z},
 accessed = {2014-09-23},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {EganaAranguren2014},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {Egaña Aranguren, Mikel and Rodríguez González, Alejandro and Wilkinson, Mark D.},
 doi = {10.1186/2041-1480-5-42},
 journal = {Journal of Biomedical Semantics},
 number = {1}
}

@inproceedings{
 title = {Nanopublishing clinical diagnoses: tracking diagnostic knowledge base content and utilization},
 type = {inproceedings},
 year = {2014},
 pages = {335-340},
 id = {d20b763e-810c-303e-a692-19f9a5035867},
 created = {2014-01-23T08:32:49.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Rodriguez-Gonzalez2014},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Rodríguez-González, Alejandro and Martinez-Romero, Marcos and Aranguren, Mikel Egaña and Wilkinson, Mark D.},
 doi = {10.1109/CBMS.2014.82},
 booktitle = {CBMS '14 Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical Systems}
}

@inbook{
 type = {inbook},
 year = {2014},
 pages = {371-391},
 websites = {http://link.springer.com/chapter/10.1007/978-3-319-05687-6_15},
 publisher = {Springer International Publishing},
 chapter = {Bioinformatics Tools for Next-Generation RNA Sequencing Analysis},
 id = {8a36acd0-ce7f-3168-b83d-2da0a2c5f4bb},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Marconi2014},
 private_publication = {false},
 abstract = {The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools.},
 bibtype = {inbook},
 author = {Marconi, Marco and Rodriguez-Romero, Julio and Sesma, Ane and Wilkinson, Mark D.},
 editor = {Sesma, Ane and von der Haar, T.},
 doi = {10.1007/978-3-319-05687-6_15},
 title = {Fungal RNA biology}
}

The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools.

@inproceedings{
 title = {The Crop Ontology, a resource for enabling access to breeders'data},
 type = {inproceedings},
 year = {2014},
 pages = {W352},
 websites = {https://pag.confex.com/pag/xxii/webprogram/Paper11073.html},
 city = {San Diego},
 id = {566e1b72-8841-3d10-a14b-65cb74e92a6b},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Arnaud2014},
 private_publication = {false},
 abstract = {The Crop Ontology (CO) (www.cropontology.org) is a service of the Integrated Breeding Platform (IBP), Generation Challenge Programme (GCP). CO currently includes reference lists of breeders’traits with measurement methods and scales for 14 crops – with work ongoing to add barley, lentil and sweet potato – as well as environmental and experimental design concepts. The objective is to provide a controlled vocabulary enabling harmonized annotations of evaluation data and metadata. The crop communities of practice, coordinated by the Crop Lead Centers, validate the concepts compiled in the CO trait dictionary template. CO trait concepts are cross-referenced to Plant Ontology (PO) and Trait Ontology (TO). The environmental and trial management concepts will be improved by a group of experts in agronomy and crop modelling. The Integrated Breeding Fieldbook and the Chado schema of the GCP crop databases both use the CO concepts for the capture and annotation of breeders’data. The Programmatic Application Interface (API) of CO enables direct download of the concepts by third-party web sites like: the international cassava database (http://www.cassavabase.org/), the Global Agricultural Trial Repository (Agtrials) (http://agtrials.org/), Eu-Solanaceae database at Wageningen University (https://www.eu-sol.wur.nl/), and the Phenomics Ontology Driven Database (PODD: http://150.229.2.236/podd/about) of the Australian Plant Phenomics Facility (APPF). CO is available in RDF format (Resource Description Framework) using the SKOS vocabulary (Simple Knowledge Organization System) for the purpose of publishing it in the Linked Open Data (LOD) Cloud. CO will be aligned with the AGROVOC thesaurus (FAO;http://www.fao.org/agrovoc) to test the integration of crop data into the mashup site of Agris (http://agris.fao.org/).},
 bibtype = {inproceedings},
 author = {Arnaud, Elizabeth and Matteis, Luca and Laporte, Marie Angelique and Espinosa, Herlin and Hyman, Glenn and Shrestha, Rosemary and Portugal, Arlett and Chibon, Pierre Yves and Devare, Medha and Akintunde, Akinnola and White, Jeffrey W and Wilkinson, Mark and Caracciolo, Caterina and Celli, Fabrizio and Mclaren, Graham},
 booktitle = {In proceeding of: Plant and Animal Genome XXII}
}

The Crop Ontology (CO) (www.cropontology.org) is a service of the Integrated Breeding Platform (IBP), Generation Challenge Programme (GCP). CO currently includes reference lists of breeders’traits with measurement methods and scales for 14 crops – with work ongoing to add barley, lentil and sweet potato – as well as environmental and experimental design concepts. The objective is to provide a controlled vocabulary enabling harmonized annotations of evaluation data and metadata. The crop communities of practice, coordinated by the Crop Lead Centers, validate the concepts compiled in the CO trait dictionary template. CO trait concepts are cross-referenced to Plant Ontology (PO) and Trait Ontology (TO). The environmental and trial management concepts will be improved by a group of experts in agronomy and crop modelling. The Integrated Breeding Fieldbook and the Chado schema of the GCP crop databases both use the CO concepts for the capture and annotation of breeders’data. The Programmatic Application Interface (API) of CO enables direct download of the concepts by third-party web sites like: the international cassava database (http://www.cassavabase.org/), the Global Agricultural Trial Repository (Agtrials) (http://agtrials.org/), Eu-Solanaceae database at Wageningen University (https://www.eu-sol.wur.nl/), and the Phenomics Ontology Driven Database (PODD: http://150.229.2.236/podd/about) of the Australian Plant Phenomics Facility (APPF). CO is available in RDF format (Resource Description Framework) using the SKOS vocabulary (Simple Knowledge Organization System) for the purpose of publishing it in the Linked Open Data (LOD) Cloud. CO will be aligned with the AGROVOC thesaurus (FAO;http://www.fao.org/agrovoc) to test the integration of crop data into the mashup site of Agris (http://agris.fao.org/).

@article{
 title = {The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.},
 type = {article},
 year = {2014},
 pages = {14},
 volume = {5},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/24602174},
 month = {3},
 day = {6},
 id = {2e66e828-3bd8-3772-abc5-ecfaceda8d06},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2014-03-19},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Dumontier2014},
 private_publication = {false},
 abstract = {The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and associate qualities, capabilities, functions, quantities, and informational entities including textual, geometrical, and mathematical entities, and provides specific extensions in the domains of chemistry, biology, biochemistry, and bioinformatics. SIO provides an ontological foundation for the Bio2RDF linked data for the life sciences project and is used for semantic integration and discovery for SADI-based semantic web services. SIO is freely available to all users under a creative commons by attribution license. See website for further information: http://sio.semanticscience.org .},
 bibtype = {article},
 author = {Dumontier, Michel and Baker, Christopher Jo and Baran, Joachim and Callahan, Alison and Chepelev, Leonid and Cruz-Toledo, José and Del Rio, Nicholas R and Duck, Geraint and Furlong, Laura I. and Keath, Nichealla and Klassen, Dana and McCusker, James P. and Queralt-Rosinach, Núria and Samwald, Matthias and Villanueva-Rosales, Natalia and Wilkinson, Mark D and Hoehndorf, Robert},
 doi = {10.1186/2041-1480-5-14},
 journal = {Journal of biomedical semantics},
 number = {1}
}

The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and associate qualities, capabilities, functions, quantities, and informational entities including textual, geometrical, and mathematical entities, and provides specific extensions in the domains of chemistry, biology, biochemistry, and bioinformatics. SIO provides an ontological foundation for the Bio2RDF linked data for the life sciences project and is used for semantic integration and discovery for SADI-based semantic web services. SIO is freely available to all users under a creative commons by attribution license. See website for further information: http://sio.semanticscience.org .

@inproceedings{
 title = {Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies},
 type = {inproceedings},
 year = {2014},
 pages = {464-478},
 volume = {8803},
 websites = {http://arxiv.org/abs/1407.0165,http://link.springer.com/10.1007/978-3-662-45231-8},
 publisher = {Springer Berlin Heidelberg},
 city = {Berlin, Heidelberg},
 series = {Lecture Notes in Computer Science},
 id = {f1ab1039-e253-39df-a88c-d0a192291b6e},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2014-10-17},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Garcia-Jimenez2014},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {García-Jiménez, Beatriz and Wilkinson, Mark D},
 editor = {Margaria, Tiziana and Steffen, Bernhard},
 doi = {10.1007/978-3-662-45231-8},
 booktitle = {Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications - 6th International Symposium, ISoLA 2014, Imperial, Corfu, Greece, October 8-11, 2014, Proceedings, Part II}
}

@article{
 title = {BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains},
 type = {article},
 year = {2014},
 pages = {5},
 volume = {5},
 websites = {http://www.jbiomedsem.com/content/5/1/5},
 id = {f01f7c02-6823-3028-bae7-0e021618384c},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2014-02-05},
 file_attached = {true},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Katayama2014},
 private_publication = {false},
 abstract = {The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.},
 bibtype = {article},
 author = {Katayama, Toshiaki and Wilkinson, Mark and Aoki-Kinoshita, Kiyoko and Kawashima, Shuichi and Yamamoto, Yasunori and Yamaguchi, Atsuko and Okamoto, Shinobu and Kawano, Shin and Kim, Jin-Dong and Wang, Yue and Wu, Hongyan and Kano, Yoshinobu and Ono, Hiromasa and Bono, Hidemasa and Kocbek, Simon and Aerts, Jan and Akune, Yukie and Antezana, Erick and Arakawa, Kazuharu and Aranda, Bruno and Baran, Joachim and Bolleman, Jerven and Bonnal, Raoul and Buttigieg, Pier and Campbell, Matthew and Chen, Yi-an and Chiba, Hirokazu and Cock, Peter and Cohen, Kevin and Constantin, Alexandru},
 doi = {10.1186/2041-1480-5-5},
 journal = {Journal of Biomedical Semantics},
 number = {1},
 keywords = {biohackathon}
}

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.

@article{
 title = {Automatic detection and resolution of measurement-unit conflicts in aggregated data},
 type = {article},
 year = {2014},
 keywords = {Clinical Research,Measurement-units,Ontologies,Semantic Web Services},
 pages = {S12},
 volume = {7},
 websites = {http://www.biomedcentral.com/1755-8794/7/S1/S12},
 id = {d6595cdd-d461-3d5b-826b-b438ee9c39cd},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2014-05-08},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Samadian},
 private_publication = {false},
 abstract = {Motivation: Measurement-unit conflicts are a perennial problem in integrative research domains such as clinical meta-analysis. As multi-national collaborations grow, as new measurement instruments appear, and as Linked Open Data infrastructures become increasingly pervasive, the number of such conflicts will similarly increase. We propose a generic approach to the problem of (a) encoding measurement units in datasets in a machine-readable manner, (b) detecting when a dataset contained mixtures of measurement units, and (c) automatically converting any conflicting units into a desired unit, as defined for a given study. Results: We utilized existing ontologies and standards for scientific data representation, measurement unit definition, and data manipulation to build a simple and flexible Semantic Web Service-based approach to measurement-unit harmonization. A cardiovascular patient cohort in which clinical measurements were recorded in a number of different units (e.g., mmHg and cmHg for blood pressure) was automatically classified into a number of clinical phenotypes, semantically defined using different measurement units. Conclusion: We demonstrate that through a combination of semantic standards and frameworks, unit integration problems can be automatically detected and resolved.},
 bibtype = {article},
 author = {Samadian, Soroush and McManus, Bruce and Wilkinson, Mark},
 doi = {10.1186/1755-8794-7-S1-S12},
 journal = {BMC Medical Genomics},
 number = {Suppl 1}
}

Motivation: Measurement-unit conflicts are a perennial problem in integrative research domains such as clinical meta-analysis. As multi-national collaborations grow, as new measurement instruments appear, and as Linked Open Data infrastructures become increasingly pervasive, the number of such conflicts will similarly increase. We propose a generic approach to the problem of (a) encoding measurement units in datasets in a machine-readable manner, (b) detecting when a dataset contained mixtures of measurement units, and (c) automatically converting any conflicting units into a desired unit, as defined for a given study. Results: We utilized existing ontologies and standards for scientific data representation, measurement unit definition, and data manipulation to build a simple and flexible Semantic Web Service-based approach to measurement-unit harmonization. A cardiovascular patient cohort in which clinical measurements were recorded in a number of different units (e.g., mmHg and cmHg for blood pressure) was automatically classified into a number of clinical phenotypes, semantically defined using different measurement units. Conclusion: We demonstrate that through a combination of semantic standards and frameworks, unit integration problems can be automatically detected and resolved.

@article{
 title = {Automatically exposing OpenLifeData via SADI semantic Web Services},
 type = {article},
 year = {2014},
 keywords = {Bio2RDF,Galaxy,OpenLifeData,SADI,SHARE,SPARQL,Semantic Web Services,Sentient Knowledge Explorer},
 pages = {46},
 volume = {5},
 websites = {http://www.jbiomedsem.com/content/5/1/46},
 id = {8d17d73b-aeeb-397e-a9f7-c938fd66efbd},
 created = {2014-07-17T12:27:47.000Z},
 accessed = {2014-11-20},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Gonzalez2014},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {Background Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.},
 bibtype = {article},
 author = {González, Alejandro Rodríguez and Callahan, Alison and Cruz-Toledo, José and Garcia, Adrian and Egaña Aranguren, Mikel and Dumontier, Michel and Wilkinson, Mark D},
 doi = {10.1186/2041-1480-5-46},
 journal = {Journal of Biomedical Semantics},
 number = {1}
}

Background Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

@article{
 title = {The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus.},
 type = {article},
 year = {2014},
 pages = {e1004492},
 volume = {10},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4223077&tool=pmcentrez&rendertype=abstract},
 month = {11},
 id = {34bc6727-ebd8-3192-849d-bfccd8739e2f},
 created = {2014-07-29T08:56:57.000Z},
 accessed = {2015-01-09},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Hily2014a},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {Identification of the determinants of pathogen reservoir potential is central to understand disease emergence. It has been proposed that host lifespan is one such determinant: short-lived hosts will invest less in costly defenses against pathogens, so that they will be more susceptible to infection, more competent as sources of infection and/or will sustain larger vector populations, thus being effective reservoirs for the infection of long-lived hosts. This hypothesis is sustained by analyses of different hosts of multihost pathogens, but not of different genotypes of the same host species. Here we examined this hypothesis by comparing two genotypes of the plant Arabidopsis thaliana that differ largely both in life-span and in tolerance to its natural pathogen Cucumber mosaic virus (CMV). Experiments with the aphid vector Myzus persicae showed that both genotypes were similarly competent as sources for virus transmission, but the short-lived genotype was more susceptible to infection and was able to sustain larger vector populations. To explore how differences in defense against CMV and its vector relate to reservoir potential, we developed a model that was run for a set of experimentally-determined parameters, and for a realistic range of host plant and vector population densities. Model simulations showed that the less efficient defenses of the short-lived genotype resulted in higher reservoir potential, which in heterogeneous host populations may be balanced by the longer infectious period of the long-lived genotype. This balance was modulated by the demography of both host and vector populations, and by the genetic composition of the host population. Thus, within-species genetic diversity for lifespan and defenses against pathogens will result in polymorphisms for pathogen reservoir potential, which will condition within-population infection dynamics. These results are relevant for a better understanding of host-pathogen co-evolution, and of the dynamics of pathogen emergence.},
 bibtype = {article},
 author = {Hily, Jean Michel and García, Adrián and Moreno, Arancha and Plaza, María and Wilkinson, Mark D and Fereres, Alberto and Fraile, Aurora and García-Arenal, Fernando},
 doi = {10.1371/journal.ppat.1004492},
 journal = {PLoS pathogens},
 number = {11}
}

Identification of the determinants of pathogen reservoir potential is central to understand disease emergence. It has been proposed that host lifespan is one such determinant: short-lived hosts will invest less in costly defenses against pathogens, so that they will be more susceptible to infection, more competent as sources of infection and/or will sustain larger vector populations, thus being effective reservoirs for the infection of long-lived hosts. This hypothesis is sustained by analyses of different hosts of multihost pathogens, but not of different genotypes of the same host species. Here we examined this hypothesis by comparing two genotypes of the plant Arabidopsis thaliana that differ largely both in life-span and in tolerance to its natural pathogen Cucumber mosaic virus (CMV). Experiments with the aphid vector Myzus persicae showed that both genotypes were similarly competent as sources for virus transmission, but the short-lived genotype was more susceptible to infection and was able to sustain larger vector populations. To explore how differences in defense against CMV and its vector relate to reservoir potential, we developed a model that was run for a set of experimentally-determined parameters, and for a realistic range of host plant and vector population densities. Model simulations showed that the less efficient defenses of the short-lived genotype resulted in higher reservoir potential, which in heterogeneous host populations may be balanced by the longer infectious period of the long-lived genotype. This balance was modulated by the demography of both host and vector populations, and by the genetic composition of the host population. Thus, within-species genetic diversity for lifespan and defenses against pathogens will result in polymorphisms for pathogen reservoir potential, which will condition within-population infection dynamics. These results are relevant for a better understanding of host-pathogen co-evolution, and of the dynamics of pathogen emergence.

@article{
 title = {Health Web Science},
 type = {article},
 year = {2014},
 pages = {269-419},
 volume = {4},
 websites = {http://dx.doi.org/10.1561/1800000019},
 id = {a24fcb08-f3e3-3cb2-aafc-c24dbff0317d},
 created = {2014-10-17T10:05:32.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {WEB-019},
 source_type = {article},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {Luciano, Joanne S and Cumming, Grant P and Kahana, Eva and Wilkinson, Mark D and Brooks, Elizabeth H and Jarman, Holly and McGuinness, Deborah L and Levine, Minna S},
 doi = {10.1561/1800000019},
 journal = {Foundations and Trends® in Web Science},
 number = {4}
}

@inbook{
 type = {inbook},
 year = {2014},
 websites = {http://ceur-ws.org/Vol-1320/paper_36.pdf},
 publisher = {CEUR Workshop Proceedings},
 city = {Berlin},
 edition = {Volume 132},
 id = {043d46b4-75d6-3318-8fdd-5845f1071a93},
 created = {2014-10-29T07:19:00.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Roos2014},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {inbook},
 author = {Roos, Marco and Gray, Alasdair J G and Waagmeester, Andra and Thompson, Mark and Kaliyaperumal, Rajaram and Horst, Eelke van der and Mons, Barend and Wilkinson, Mark D},
 editor = {Paschke, Adrian and Burger, Albert and Romano, Paolo and Marshall, M. Scott and Andrea, Splendiani},
 chapter = {Bring Your Own Data workshops: a mechanism to aid data owners to comply with Linked Data best practices},
 title = {Proceedings of Semantic Web Applications and Tools for Life Sciences 2014}
}

@book{
 title = {Automatic annotation of bioinformatics workflows with biomedical ontologies},
 type = {book},
 year = {2014},
 source = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
 keywords = {Bioinformatics,Ontologies,Scientific workflows,Semantic annotation,Tags,Term extraction,Text mining,Web services},
 volume = {8803},
 id = {6fcf84a2-c4b9-3eb0-8476-a57a62dc7cb6},
 created = {2017-12-03T10:44:25.364Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.060Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {© Springer-Verlag Berlin Heidelberg 2014. Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 my- Experiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.},
 bibtype = {book},
 author = {García-Jiménez, B. and Wilkinson, M.D.}
}

© Springer-Verlag Berlin Heidelberg 2014. Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 my- Experiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.

@article{
 title = {Plant Pathogen Interactions Ontology (PPIO)},
 type = {article},
 year = {2013},
 pages = {695-702},
 id = {ff09fc56-2b1a-3679-811a-a24295a2e5da},
 created = {2013-01-21T13:41:57.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Iglesias2013},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 bibtype = {article},
 author = {Iglesias, Alejandro Rodríguez and Aranguren, Mikel Egaña and Gonzalez, Alejandro Rodríguez and Wilkinson, Mark D.},
 journal = {Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering}
}

@article{
 title = {The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions},
 type = {article},
 year = {2013},
 pages = {e14},
 volume = {2},
 websites = {http://www.researchprotocols.org/2013/1/e14/},
 month = {4},
 day = {5},
 id = {4d66f145-86f5-39d8-a4f0-32de018507e4},
 created = {2013-03-06T10:37:55.000Z},
 accessed = {2013-04-06},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2013},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
 private_publication = {false},
 abstract = {Background: The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. Objective: The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. Methods: We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. Results: A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. Conclusions: The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain (drug/drug interactions), the proposed architecture is generalizable, and could act as the foundation for much richer personalized-health-Web clients, while importantly providing a novel and personalizable mechanism for clinical experts to inject their expertise into the browsing experience of their patients in the form of customized semantic queries and ontologies.},
 bibtype = {article},
 author = {Vandervalk, Ben and McCarthy, E. Luke and Cruz-Toledo, José and Klein, Artjom and Baker, Christopher J. O. and Dumontier, Michel and Wilkinson, Mark D.},
 doi = {10.2196/resprot.2315},
 journal = {JMIR Research Protocols},
 number = {1}
}

Background: The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. Objective: The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. Methods: We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. Results: A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. Conclusions: The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain (drug/drug interactions), the proposed architecture is generalizable, and could act as the foundation for much richer personalized-health-Web clients, while importantly providing a novel and personalizable mechanism for clinical experts to inject their expertise into the browsing experience of their patients in the form of customized semantic queries and ontologies.

@inproceedings{
 title = {Plant Pathogen Interactions Ontology (PPIO)},
 type = {inproceedings},
 year = {2013},
 pages = {695-702},
 id = {8e0b5cc5-fbe3-3c81-ac4b-7f5a738bdd05},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Iglesias2013},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Iglesias, Alejandro Rodríguez and Aranguren, Mikel Egaña and Gonzalez, Alejandro Rodríguez and Wilkinson, Mark D.},
 booktitle = {Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering}
}

@article{
 title = {The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions},
 type = {article},
 year = {2013},
 pages = {e14},
 volume = {2},
 websites = {http://www.researchprotocols.org/2013/1/e14/},
 month = {4},
 day = {5},
 id = {11a86057-6fdf-33e0-a89f-271a5a02a07e},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2013-04-06},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2013},
 private_publication = {false},
 bibtype = {article},
 author = {Vandervalk, Ben and McCarthy, E. Luke and Cruz-Toledo, José and Klein, Artjom and Baker, Christopher J. O. and Dumontier, Michel and Wilkinson, Mark D.},
 doi = {10.2196/resprot.2315},
 journal = {JMIR Research Protocols},
 number = {1}
}

@article{
 title = {OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.},
 type = {article},
 year = {2013},
 pages = {2},
 volume = {4},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/23286517},
 month = {1},
 day = {4},
 id = {af463206-f23e-30d0-8384-53d9b2ff3736},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2013-01-06},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {EganaAranguren2013},
 private_publication = {false},
 abstract = {ABSTRACT: BACKGROUND: Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. RESULTS: We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedicalontologies. CONCLUSIONS: Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.},
 bibtype = {article},
 author = {Egaña Aranguren, Mikel and Fernández-Breis, Jesualdo Tomás and Antezana, Erick and Mungall, Chris and Rodríguez González, Alejandro and Wilkinson, Mark D},
 doi = {10.1186/2041-1480-4-2},
 journal = {Journal of biomedical semantics},
 number = {1}
}

ABSTRACT: BACKGROUND: Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. RESULTS: We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedicalontologies. CONCLUSIONS: Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

@article{
 title = {The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies},
 type = {article},
 year = {2013},
 pages = {6},
 volume = {4},
 websites = {http://www.jbiomedsem.com/content/4/1/6},
 id = {f73616d0-42da-3a16-bd6c-b6de41efbc9c},
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 citation_key = {Katayama2013},
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 bibtype = {article},
 author = {Katayama, Toshiaki and Wilkinson, Mark D. and Micklem, Gos and Kawashima, Shuichi and Yamaguchi, Atsuko and Nakao, Mitsuteru and Yamamoto, Yasunori and Okamoto, Shinobu and Oouchida, Kenta and Chun, Hong-Woo and Aerts, Jan and Afzal, Hammad and Antezana, Erick and Arakawa, Kazuharu and Aranda, Bruno and Belleau, Francois and Bolleman, Jerven and Bonnal, Raoul Jean and Chapman, Brad and Cock, Peter and Eriksson, Tore and Gordon, Paul and Goto, Naohisa and Hayashi, Kazuhiro and Horn, Heiko and Ishiwata, Ryosuke and Kaminuma, Eli and Kasprzyk, Arek and Kawaji, Hideya and Kido, Nobuhiro and Kim, Young Joo and Kinjo, Akira R. and Konishi, Fumikazu and Kwon, Kyung-Hoon and Labarga, Alberto and Lamprecht, Anna-Lena and Lin, Yu and Lindenbaum, Pierre and McCarthy, Luke and Morita, Hideyuki and Murakami, Katsuhiko and Nagao, Koji and Nishida, Kozo and Nishimura, Kunihiro and Nishizawa, Tatsuya and Ogishima, Soichi and Ono, Keiichiro and Oshita, Kazuki and Park, Keun-Joon and Prins, Pjotr and Saito, Taro L. and Samwald, Matthias and Satagopam, Venkata P. and Shigemoto, Yasumasa and Smith, Richard and Splendiani, Andrea and Sugawara, Hideaki and Taylor, James and Vos, Rutger and Withers, David and Yamasaki, Chisato and Zmasek, Christian M. and Kawamoto, Shoko and Okubo, Kosaku and Asai, Kiyoshi and Takagi, Toshihisa},
 doi = {10.1186/2041-1480-4-6},
 journal = {Journal of Biomedical Semantics},
 number = {1}
}

@inbook{
 type = {inbook},
 year = {2013},
 keywords = {Personalized Web,Reproducibility,SADI,SHARE,Semantic Web Services,Transparency,Workflow Orchestration},
 pages = {71-74},
 websites = {http://www.thinkmind.org/index.php?view=article&articleid=service_computation_2013_4_20_10017},
 publisher = {Copyright (c) IARIA, 2013},
 city = {Valencia, Spain},
 id = {380be731-07ba-31cf-ad48-52da4bfafd62},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2013},
 private_publication = {false},
 abstract = {The emergent domain of Web Science has a number of as-yet unrealized goals. Among these are: to facilitate scientific discourse by supporting the explicit comparison and evaluation of hypotheses; to simplify in silico experiments by providing an ecosystem of expert analytical strategies that can be automatically assembled; to enhance scientific rigor by reducing bias, and improving reproducibility; and to integrate the knowledge gained from the experiment back into the Web. SHARE is a novel orchestration system that automatically chains-together Semantic Automated Discovery and Integration (SADI)–style Semantic Web Services. During development of SHARE, we noted that many requirements of such an end-to-end Web Science research environment were being realized. These include formally-defined, machine-readable, Web-embedded research hypotheses; an explicit, transparent, rigorous, and reproducible research methodology utilizing the most up-to-date data and expert-knowledge from the community; immediate dissemination and re-use of the resulting data and knowledge; and enhanced support for peer-review. This manuscript describes how SHARE is now being tested as a prototype Web Science framework. (Best Paper Award: http://www.iaria.org/conferences2013/AwardsSERVICECOMPUTATION13.html)},
 bibtype = {inbook},
 author = {Wilkinson, Mark D.},
 chapter = {Web Science Studies into Semantic Web Service-Based Research Environments (Awarded "Best Paper")},
 title = {The Fifth International Conferences on Advanced Service Computing, SERVICE COMPUTATION 2013}
}

The emergent domain of Web Science has a number of as-yet unrealized goals. Among these are: to facilitate scientific discourse by supporting the explicit comparison and evaluation of hypotheses; to simplify in silico experiments by providing an ecosystem of expert analytical strategies that can be automatically assembled; to enhance scientific rigor by reducing bias, and improving reproducibility; and to integrate the knowledge gained from the experiment back into the Web. SHARE is a novel orchestration system that automatically chains-together Semantic Automated Discovery and Integration (SADI)–style Semantic Web Services. During development of SHARE, we noted that many requirements of such an end-to-end Web Science research environment were being realized. These include formally-defined, machine-readable, Web-embedded research hypotheses; an explicit, transparent, rigorous, and reproducible research methodology utilizing the most up-to-date data and expert-knowledge from the community; immediate dissemination and re-use of the resulting data and knowledge; and enhanced support for peer-review. This manuscript describes how SHARE is now being tested as a prototype Web Science framework. (Best Paper Award: http://www.iaria.org/conferences2013/AwardsSERVICECOMPUTATION13.html)

@article{
 title = {The emergent discipline of health web science.},
 type = {article},
 year = {2013},
 keywords = {Delivery of Health Care,Information Storage and Retrieval,Internet},
 pages = {e166},
 volume = {15},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3758025&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {e564924d-1419-317f-89d4-ce36d6ef68d6},
 created = {2014-07-11T11:52:32.000Z},
 accessed = {2014-07-11},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Luciano2013},
 private_publication = {false},
 abstract = {The transformative power of the Internet on all aspects of daily life, including health care, has been widely recognized both in the scientific literature and in public discourse. Viewed through the various lenses of diverse academic disciplines, these transformations reveal opportunities realized, the promise of future advances, and even potential problems created by the penetration of the World Wide Web for both individuals and for society at large. Discussions about the clinical and health research implications of the widespread adoption of information technologies, including the Internet, have been subsumed under the disciplinary label of Medicine 2.0. More recently, however, multi-disciplinary research has emerged that is focused on the achievement and promise of the Web itself, as it relates to healthcare issues. In this paper, we explore and interrogate the contributions of the burgeoning field of Web Science in relation to health maintenance, health care, and health policy. From this, we introduce Health Web Science as a subdiscipline of Web Science, distinct from but overlapping with Medicine 2.0. This paper builds on the presentations and subsequent interdisciplinary dialogue that developed among Web-oriented investigators present at the 2012 Medicine 2.0 Conference in Boston, Massachusetts.},
 bibtype = {article},
 author = {Luciano, Joanne S and Cumming, Grant P and Wilkinson, Mark D and Kahana, Eva},
 doi = {10.2196/jmir.2499},
 journal = {Journal of medical Internet research},
 number = {8}
}

The transformative power of the Internet on all aspects of daily life, including health care, has been widely recognized both in the scientific literature and in public discourse. Viewed through the various lenses of diverse academic disciplines, these transformations reveal opportunities realized, the promise of future advances, and even potential problems created by the penetration of the World Wide Web for both individuals and for society at large. Discussions about the clinical and health research implications of the widespread adoption of information technologies, including the Internet, have been subsumed under the disciplinary label of Medicine 2.0. More recently, however, multi-disciplinary research has emerged that is focused on the achievement and promise of the Web itself, as it relates to healthcare issues. In this paper, we explore and interrogate the contributions of the burgeoning field of Web Science in relation to health maintenance, health care, and health policy. From this, we introduce Health Web Science as a subdiscipline of Web Science, distinct from but overlapping with Medicine 2.0. This paper builds on the presentations and subsequent interdisciplinary dialogue that developed among Web-oriented investigators present at the 2012 Medicine 2.0 Conference in Boston, Massachusetts.

@article{
 title = {Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web.},
 type = {article},
 year = {2012},
 pages = {6},
 volume = {3},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22818710},
 month = {7},
 day = {20},
 id = {2c11d236-dafd-35e0-b030-ec34f6b2701c},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2012-07-25},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Samadian2012},
 private_publication = {false},
 abstract = {ABSTRACT: BACKGROUND: Clinical phenotypes and disease-risk stratification are most often determined through the direct observations of clinicians in conjunction with published standards and guidelines, where the clinical expert is the final arbiter of the patient's classification. While this "human" approach is highly desirable in the context of personalized and optimal patient care, it is problematic in a healthcare research setting because the basis for the patient's classification is not transparent, and likely not reproducible from one clinical expert to another. This sits in opposition to the rigor required to execute, for example, Genome-wide association analyses and other high-throughput studies where a large number of variables are being compared to a complex disease phenotype. Most clinical classification systems and are not structured for automated classification, and similarly, clinical data is generally not represented in a form that lends itself to automated integration and interpretation. Here we apply Semantic Web technologies to the problem of automated, transparent interpretation of clinical data for use in high-throughput research environments, and explore migration-paths for existing data and legacy semantic standards. RESULTS: Using a dataset from a cardiovascular cohort collected two decades ago, we present a migration path - both for the terminologies/classification systems and the data - that enables rich automated clinical classification using well-established standards. This is achieved by establishing a simple and flexible core data model, which is combined with a layered ontological framework utilizing both logical reasoning and analytical algorithms to iteratively "lift" clinical data through increasingly complex layers of interpretation and classification. We compare our automated analysis to that of the clinical expert, and discrepancies are used to refine the ontological models, finally arriving at ontologies that mirror the expert opinion of the individual clinical researcher. Other discrepancies, however, could not be as easily modeled, and we evaluate what information we are lacking that would allow these discrepancies to be resolved in an automated manner. CONCLUSIONS: We demonstrate that the combination of semantically-explicit data, logically rigorous models of clinical guidelines, and publicly-accessible Semantic Web Services, can be used to execute automated, rigorous and reproducible clinical classifications with an accuracy approaching that of an expert. Discrepancies between the manual and automatic approaches reveal, as expected, that clinicians do not always rigorously follow established guidelines for classification; however, we demonstrate that "personalized" ontologies may represent a re-usable and transparent approach to modeling individual clinical expertise, leading to more reproducible science.},
 bibtype = {article},
 author = {Samadian, Soroush and McManus, Bruce and Wilkinson, Mark D},
 doi = {10.1186/2041-1480-3-6},
 journal = {Journal of biomedical semantics},
 number = {1}
}

ABSTRACT: BACKGROUND: Clinical phenotypes and disease-risk stratification are most often determined through the direct observations of clinicians in conjunction with published standards and guidelines, where the clinical expert is the final arbiter of the patient's classification. While this "human" approach is highly desirable in the context of personalized and optimal patient care, it is problematic in a healthcare research setting because the basis for the patient's classification is not transparent, and likely not reproducible from one clinical expert to another. This sits in opposition to the rigor required to execute, for example, Genome-wide association analyses and other high-throughput studies where a large number of variables are being compared to a complex disease phenotype. Most clinical classification systems and are not structured for automated classification, and similarly, clinical data is generally not represented in a form that lends itself to automated integration and interpretation. Here we apply Semantic Web technologies to the problem of automated, transparent interpretation of clinical data for use in high-throughput research environments, and explore migration-paths for existing data and legacy semantic standards. RESULTS: Using a dataset from a cardiovascular cohort collected two decades ago, we present a migration path - both for the terminologies/classification systems and the data - that enables rich automated clinical classification using well-established standards. This is achieved by establishing a simple and flexible core data model, which is combined with a layered ontological framework utilizing both logical reasoning and analytical algorithms to iteratively "lift" clinical data through increasingly complex layers of interpretation and classification. We compare our automated analysis to that of the clinical expert, and discrepancies are used to refine the ontological models, finally arriving at ontologies that mirror the expert opinion of the individual clinical researcher. Other discrepancies, however, could not be as easily modeled, and we evaluate what information we are lacking that would allow these discrepancies to be resolved in an automated manner. CONCLUSIONS: We demonstrate that the combination of semantically-explicit data, logically rigorous models of clinical guidelines, and publicly-accessible Semantic Web Services, can be used to execute automated, rigorous and reproducible clinical classifications with an accuracy approaching that of an expert. Discrepancies between the manual and automatic approaches reveal, as expected, that clinicians do not always rigorously follow established guidelines for classification; however, we demonstrate that "personalized" ontologies may represent a re-usable and transparent approach to modeling individual clinical expertise, leading to more reproducible science.

@article{
 title = {SPARQL Assist language-neutral query composer.},
 type = {article},
 year = {2012},
 pages = {S2},
 volume = {13 Suppl 1},
 websites = {http://www.biomedcentral.com/1471-2105/13/S1/S2,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3471353&tool=pmcentrez&rendertype=abstract},
 month = {1},
 day = {25},
 id = {464527e6-eae7-3479-b92b-ec67ed83e46f},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2013-03-06},
 file_attached = {true},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {McCarthy2011},
 private_publication = {false},
 abstract = {BACKGROUND: SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. RESULTS: We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. CONCLUSIONS: To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources.},
 bibtype = {article},
 author = {McCarthy, Luke and Vandervalk, Ben and Wilkinson, Mark},
 doi = {10.1186/1471-2105-13-S1-S2},
 journal = {BMC bioinformatics},
 number = {Suppl 1},
 keywords = {SPARQL Assist,natural language,query composer,sparql}
}

BACKGROUND: SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. RESULTS: We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. CONCLUSIONS: To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources.

@inbook{
 type = {inbook},
 year = {2012},
 pages = {489-511},
 volume = {856},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22399472},
 month = {1},
 id = {76668a90-5a62-3d5a-9fb5-bb7b0a4c90e1},
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 hidden = {false},
 citation_key = {Wilkinson2012},
 private_publication = {false},
 abstract = {The emergence of genomics tools for the evolutionary and comparative biology community led to a rapid explosion in the number of online resources targeted at this specialized community, including Web-based comparative genomics software, such as the Artemis Comparison Tool (WebACT); databases, such as PaleoDB, Global Biodiversity Information Facility, and TreeBase; and knowledge frameworks, such as the Evolution Ontology. Unfortunately, these providers are largely independent of one another and therefore the individual resources do not share any centralized plan for how the data or tools would or should be provided. As a result, there are a myriad of often incompatible technologies and frameworks being used by this community of providers. In this chapter, we explore approaches to online resource publication, both those already in use by the community, as well as new and emergent frameworks and standards. Exploration of the strengths and weaknesses of each approach, together with a brief exploration of the philosophy or informatics theory behind the varying approaches, will hopefully help readers as they navigate this data space. The discussion is constructed such that it lays the groundwork for exploration of a new global standard for data and knowledge representation--"The Semantic Web"--that holds promise of providing solutions to many of the complexities users face in their attempts to discover and integrate biodiversity data, and examples are provided.},
 bibtype = {inbook},
 author = {Wilkinson, Mark D},
 doi = {10.1007/978-1-61779-585-5_20},
 chapter = {Genomics data resources: frameworks and standards.},
 title = {Methods in molecular biology (Clifton, N.J.)}
}

The emergence of genomics tools for the evolutionary and comparative biology community led to a rapid explosion in the number of online resources targeted at this specialized community, including Web-based comparative genomics software, such as the Artemis Comparison Tool (WebACT); databases, such as PaleoDB, Global Biodiversity Information Facility, and TreeBase; and knowledge frameworks, such as the Evolution Ontology. Unfortunately, these providers are largely independent of one another and therefore the individual resources do not share any centralized plan for how the data or tools would or should be provided. As a result, there are a myriad of often incompatible technologies and frameworks being used by this community of providers. In this chapter, we explore approaches to online resource publication, both those already in use by the community, as well as new and emergent frameworks and standards. Exploration of the strengths and weaknesses of each approach, together with a brief exploration of the philosophy or informatics theory behind the varying approaches, will hopefully help readers as they navigate this data space. The discussion is constructed such that it lays the groundwork for exploration of a new global standard for data and knowledge representation--"The Semantic Web"--that holds promise of providing solutions to many of the complexities users face in their attempts to discover and integrate biodiversity data, and examples are provided.

@inbook{
 type = {inbook},
 year = {2012},
 pages = {56-66},
 publisher = {Springer Berlin/Heidelberg},
 id = {b7a08242-7958-3a0a-aecd-0cb6d75d1e62},
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 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {wood2012owl},
 source_type = {article},
 private_publication = {false},
 bibtype = {inbook},
 author = {Wood, I and Vandervalk, B and McCarthy, L and Wilkinson, Mark D},
 editor = {Margaria, Tiziana and Steffen, Bernhard},
 doi = {10.1007/978-3-642-34032-1_6},
 chapter = {OWL-DL Domain-Models as Abstract Workflows},
 title = {Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies}
}

@article{
 title = {Bioscientific Data Processing and Modeling},
 type = {article},
 year = {2012},
 pages = {7-11},
 publisher = {Springer Berlin/Heidelberg},
 id = {97f9c50d-cf32-35b0-a516-aeab4fe58e7a},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {kok2012bioscientific},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Kok, J and Lamprecht, A L and Verbeek, F and Wilkinson, M},
 doi = {10.1007/978-3-642-34032-1_2},
 journal = {Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies}
}

@article{
 title = {Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study},
 type = {article},
 year = {2012},
 pages = {1-9},
 volume = {2012},
 websites = {http://www.hindawi.com/journals/cmmm/2012/367345/},
 id = {058acd6a-ed57-3dcc-8456-36558ccca976},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2012-12-27},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Rodriguez-Gonzalez2012},
 private_publication = {false},
 bibtype = {article},
 author = {Rodríguez-González, Alejandro and Torres-Niño, Javier and Mayer, Miguel A. and Alor-Hernandez, Giner and Wilkinson, Mark D.},
 doi = {10.1155/2012/367345},
 journal = {Computational and Mathematical Methods in Medicine}
}

@inproceedings{
 title = {A data-driven approach to automatic discovery of prescription drugs in cardiovascular risk management},
 type = {inproceedings},
 year = {2012},
 pages = {14-17},
 websites = {http://goo.gl/JAnh2},
 id = {e07bde1d-b1ea-3e5b-9dfa-b9455adbd312},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Samadian2012},
 private_publication = {false},
 abstract = {Objectives: To evaluate a data-driven approach for automatically identifying medications used in the treatment of cardiovascular disease, and consider how these learned rules might be applied to ontology curation, and evaluation. Methods: We mined the clinical records of a large cardiovascular patient cohort, focusing on their clinical phenotype and their prescribed medications. Machine learning algorithms from WEKA detected rules linking medications to patient’s treatment-status. These rules were then compared to axioms encoded in the NDF-RT Ontology. Results: For most medications in the dataset we were able to re-discover, with high precision, the prescriptive rules present in the NDF-RT; however, we discovered only 4/19 possible rules for medications linked to Chronic Heart Failure, and no rules for medications linked to Hypertension. We also show that, in some cases, these rules contain more detailed information than is present in the NDF-RT itself. Conclusion: This experiment demonstrates how data-driven approaches might be used to ameliorate the knowledge acquisition problem for ontology design. We show that the learned rules could be used to evaluate and improve an existing ontology (NDF-RT). We propose that these rules could be used to automatically construct ontological axioms, thus semi-automating the process of de novo ontology construction for a given domain.},
 bibtype = {inproceedings},
 author = {Samadian, Soroush and Good, Benjamin M. and McManus, Bruce and Wilkinson, Mark D.},
 booktitle = {Proceedings of The BioOntologies SIG, ISMB 2012}
}

Objectives: To evaluate a data-driven approach for automatically identifying medications used in the treatment of cardiovascular disease, and consider how these learned rules might be applied to ontology curation, and evaluation. Methods: We mined the clinical records of a large cardiovascular patient cohort, focusing on their clinical phenotype and their prescribed medications. Machine learning algorithms from WEKA detected rules linking medications to patient’s treatment-status. These rules were then compared to axioms encoded in the NDF-RT Ontology. Results: For most medications in the dataset we were able to re-discover, with high precision, the prescriptive rules present in the NDF-RT; however, we discovered only 4/19 possible rules for medications linked to Chronic Heart Failure, and no rules for medications linked to Hypertension. We also show that, in some cases, these rules contain more detailed information than is present in the NDF-RT itself. Conclusion: This experiment demonstrates how data-driven approaches might be used to ameliorate the knowledge acquisition problem for ontology design. We show that the learned rules could be used to evaluate and improve an existing ontology (NDF-RT). We propose that these rules could be used to automatically construct ontological axioms, thus semi-automating the process of de novo ontology construction for a given domain.

@article{
 title = {Coherent 100G field trial over installed fiber links: Investigating key network scenarios and applications [Invited]},
 type = {article},
 year = {2012},
 keywords = {Optical fiber communication,Phase modulation,WDM networks,Wavelength division multiplexing},
 volume = {4},
 id = {dab6eb26-3a63-3428-a07a-23c751388373},
 created = {2017-12-03T10:44:26.170Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.352Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {We report a successful coherent 100G field trial over installed fiber links of a total of 769 km, investigating the performance of coherent technology for key network scenarios and applications including network upgrade, a new dispersion-compensation-module-less network design, polarization mode dispersion tolerance and support for alien wavelengths. In addition, we evaluated the end to end transport performance of 100GE and 10GE client signals. © 2012 Optical Society of America.},
 bibtype = {article},
 author = {Zhou, Y.R. and Smith, K. and Wilkinson, M. and Payne, R. and Lord, A. and Bennett, T. and Frankel, M.},
 doi = {10.1364/JOCN.4.000B35},
 journal = {Journal of Optical Communications and Networking},
 number = {11}
}

We report a successful coherent 100G field trial over installed fiber links of a total of 769 km, investigating the performance of coherent technology for key network scenarios and applications including network upgrade, a new dispersion-compensation-module-less network design, polarization mode dispersion tolerance and support for alien wavelengths. In addition, we evaluated the end to end transport performance of 100GE and 10GE client signals. © 2012 Optical Society of America.

@inproceedings{
 title = {Coherent 100G field trial over installed fiber links: Investigating key network scenarios and applications},
 type = {inproceedings},
 year = {2012},
 id = {59892d56-b1f6-3762-a924-3a184af4acaa},
 created = {2017-12-03T10:44:26.234Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.504Z},
 read = {false},
 starred = {false},
 authored = {true},
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 hidden = {false},
 private_publication = {false},
 abstract = {We report successful coherent 100G field trial over installed fiber links of total 769km, investigating performance of coherent technology for key network scenarios and applications including upgrade, new DCM-less design, PMD issue and alien wavelength. © 2012 OSA.},
 bibtype = {inproceedings},
 author = {Zhou, Y.R. and Smith, K. and Wilkinson, M. and Payne, R. and Lord, A. and Bennett, T. and Frankel, M.},
 booktitle = {National Fiber Optic Engineers Conference, NFOEC 2012}
}

We report successful coherent 100G field trial over installed fiber links of total 769km, investigating performance of coherent technology for key network scenarios and applications including upgrade, new DCM-less design, PMD issue and alien wavelength. © 2012 OSA.

@inproceedings{
 title = {Preface},
 type = {inproceedings},
 year = {2012},
 volume = {930},
 id = {d5e2cce3-02e6-3964-b1c2-430cc9a87477},
 created = {2017-12-03T10:44:26.326Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.732Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Rodríguez-González, A. and Pathak, J. and Wilkinson, M.D. and Shah, N.H. and Stevens, R. and Boyce, R. and García-Crespo, Á.},
 booktitle = {CEUR Workshop Proceedings}
}

@inproceedings{
 title = {Coherent 100G field trial over installed fiber links: Investigating key network scenarios and applications},
 type = {inproceedings},
 year = {2012},
 id = {1b7be891-f480-3c08-bffc-70f87402fad5},
 created = {2017-12-03T10:44:26.382Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.853Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {We report successful coherent 100G field trial over installed fiber links of total 769km, investigating performance of coherent technology for key network scenarios and applications including upgrade, new DCM-less design, PMD issue and alien wavelength. © 2012 OSA.},
 bibtype = {inproceedings},
 author = {Zhou, Y.R. and Smith, K. and Wilkinson, M. and Payne, R. and Lord, A. and Bennett, T. and Frankel, M.},
 booktitle = {National Fiber Optic Engineers Conference, NFOEC 2012}
}

We report successful coherent 100G field trial over installed fiber links of total 769km, investigating performance of coherent technology for key network scenarios and applications including upgrade, new DCM-less design, PMD issue and alien wavelength. © 2012 OSA.

@inproceedings{
 title = {The SADI plug-in to IO informatics' sentient knowledge explorer},
 type = {inproceedings},
 year = {2011},
 pages = {116-118},
 institution = {ACM},
 id = {7bec755d-07b2-376e-9d7d-bfe2d1080e46},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {wilkinson2011sadi},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Wilkinson, M D and McCarthy, L},
 booktitle = {Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences}
}

@article{
 title = {The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.},
 type = {article},
 year = {2011},
 pages = {8},
 volume = {2},
 websites = {http://www.jbiomedsem.com/content/2/1/8/abstract},
 month = {10},
 publisher = {BioMed Central Ltd},
 day = {24},
 id = {cd541f6d-50d0-3b3d-b227-87fd7594643f},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2011-10-31},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2011},
 language = {en},
 private_publication = {false},
 abstract = {ABSTRACT:  BACKGROUND: The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration.  There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics  community.  Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains.  Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices.  In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. CONCLUSIONS: SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users.  In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system.  Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.},
 bibtype = {article},
 author = {Wilkinson, Mark D and Vandervalk, Benjamin and McCarthy, Luke},
 doi = {10.1186/2041-1480-2-8},
 journal = {Journal of biomedical semantics},
 number = {1}
}

ABSTRACT: BACKGROUND: The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. CONCLUSIONS: SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.

@article{
 title = {The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications},
 type = {article},
 year = {2011},
 keywords = {review},
 pages = {4},
 volume = {2},
 websites = {http://dx.doi.org/10.1186/2041-1480-2-4},
 id = {cc43fc7b-8d22-35f8-9d12-1bf93251bd8d},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Katayama2011},
 source_type = {article},
 notes = {10.1186/2041-1480-2-4},
 private_publication = {false},
 bibtype = {article},
 author = {Katayama, Toshiaki and Wilkinson, Mark and Vos, Rutger and Kawashima, Takeshi and Kawashima, Shuichi and Nakao, Mitsuteru and Yamamoto, Yasunori and Chun, Hong-Woo and Yamaguchi, Atsuko and Kawano, Shin and Aerts, Jan and Aoki-Kinoshita, Kiyoko and Arakawa, Kazuharu and Aranda, Bruno and Bonnal, Raoul and Fernandez, Jose and Fujisawa, Takatomo and Gordon, Paul and Goto, Naohisa and Haider, Syed and Harris, Todd and Hatakeyama, Takashi and Ho, Isaac and Itoh, Masumi and Kasprzyk, Arek and Kido, Nobuhiro and Kim, Young-Joo and Kinjo, Akira and Konishi, Fumikazu and Kovarskaya, Yulia and von Kuster, Greg and Labarga, Alberto and Limviphuvadh, Vachiranee and McCarthy, Luke and Nakamura, Yasukazu and Nam, Yunsun and Nishida, Kozo and Nishimura, Kunihiro and Nishizawa, Tatsuya and Ogishima, Soichi and Oinn, Tom and Okamoto, Shinobu and Okuda, Shujiro and Ono, Keiichiro and Oshita, Kazuki and Park, Keun-Joon and Putnam, Nicholas and Senger, Martin and Severin, Jessica and Shigemoto, Yasumasa and Sugawara, Hideaki and Taylor, James and Trelles, Oswaldo and Yamasaki, Chisato and Yamashita, Riu and Satoh, Noriyuki and Takagi, Toshihisa},
 doi = {10.1186/2041-1480-2-4},
 journal = {Journal of Biomedical Semantics},
 number = {1}
}

@inproceedings{
 title = {SADI for GMOD: Semantic Web Services for Model Organism Databases},
 type = {inproceedings},
 year = {2011},
 websites = {http://ceur-ws.org/Vol-774/ben.pdf},
 city = {Vancouver, BC},
 id = {bf5c8fc4-86a9-3fef-aeee-77a4111d0cc3},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2011a},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Vandervalk, Ben and Dumontier, Michel and McCarthy, E Luke and Wilkinson, Mark D},
 booktitle = {Proceedings of the Canadian Semantic Web Symposium 2011}
}

@inproceedings{
 title = {SADI for GMOD:  Bringing Model Organism Data onto the Semantic Web},
 type = {inproceedings},
 year = {2011},
 pages = {36},
 websites = {http://www.oboedit.org/BOSC2011/BOSC2011-program.pdf},
 city = {Vienna, Austria},
 id = {0e4afb87-3819-31ce-8867-5cdacd1561f3},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2011},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Vandervalk, Ben and McCarthy, Luke and Wilkinson, Mark},
 booktitle = {Proceedings of Bio Open Source Conference (BOSC) 2011}
}

@inproceedings{
 title = {SADI for GMOD: Semantic web services for model organism databases},
 type = {inproceedings},
 year = {2011},
 keywords = {Bioinformatics,GMOD,Model organ- ism databases,SADI,Semantic Web,Sequence features,Web services},
 volume = {774},
 id = {6e56ff90-280e-3a76-b3f7-18931ff7a293},
 created = {2017-12-03T10:44:25.738Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.895Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Here we describe work-in-progress on the SADI for GMOD project (SADI: Semantic Automated Discovery and Integration; GMOD: Generic Model Organism Database), a distribution of ready-made Web services that will bring additional model organism data onto the Seman- tic Web. SADI is a lightweight standard for implementing Web services that natively consume and generate RDF, while GMOD is a widely-used toolkit for building model organism databases (e.g. FlyBase, Parameci- umDB). The SADI for GMOD services will provide a novel mechanism for analyzing data across GMOD sites, as well as other bioinformatics resources that publish their data using SADI.},
 bibtype = {inproceedings},
 author = {Vandervalk, B. and Dumontier, M. and McCarthy, E.L. and Wilkinson, M.D.},
 booktitle = {CEUR Workshop Proceedings}
}

Here we describe work-in-progress on the SADI for GMOD project (SADI: Semantic Automated Discovery and Integration; GMOD: Generic Model Organism Database), a distribution of ready-made Web services that will bring additional model organism data onto the Seman- tic Web. SADI is a lightweight standard for implementing Web services that natively consume and generate RDF, while GMOD is a widely-used toolkit for building model organism databases (e.g. FlyBase, Parameci- umDB). The SADI for GMOD services will provide a novel mechanism for analyzing data across GMOD sites, as well as other bioinformatics resources that publish their data using SADI.

@article{
 title = {SADI, SHARE, and the in silico scientific method},
 type = {article},
 year = {2010},
 keywords = {Mark Wilkinson},
 pages = {S7},
 volume = {11},
 websites = {http://dx.doi.org/10.1186/1471-2105-11-s12-s7,http://www.biomedcentral.com/1471-2105/11/S12/S7},
 id = {2ccdc128-ed60-35a1-9153-3eb9cffdd25c},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2010},
 source_type = {article},
 notes = {10.1186/1471-2105-11-s12-s7},
 private_publication = {false},
 abstract = {Background The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in �the new way�, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies. Results Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries. Conclusions The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the �semantification� of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.},
 bibtype = {article},
 author = {Wilkinson, Mark D and McCarthy, Luke and Vandervalk, Benjamin and Withers, David and Kawas, Edward and Samadian, Soroush},
 doi = {10.1186/1471-2105-11-S12-S7},
 journal = {BMC Bioinformatics},
 number = {Suppl 12}
}

Background The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in �the new way�, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies. Results Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries. Conclusions The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the �semantification� of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.

@inproceedings{
 title = {Tools in Scientific Workflow Composition},
 type = {inproceedings},
 year = {2010},
 keywords = {workflows},
 pages = {258-260},
 volume = {6415},
 websites = {http://www.springerlink.com/content/788740348072h439/},
 id = {1d181afa-cb38-3cdf-b82b-3d850d56712a},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kok2010},
 source_type = {inproceedings},
 notes = {10.1007/978-3-642-16558-0_22},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Kok, Joost and Lamprecht, Anna-Lena and Wilkinson, Mark},
 booktitle = {Leveraging Applications of Formal Methods, Verification, and Validation Lecture Notes in Computer Science}
}

@inproceedings{
 title = {SHARE & The Semantic Web - This Time it's Personal!},
 type = {inproceedings},
 year = {2010},
 keywords = {Mark Wilkinson},
 websites = {http://www.webont.org/owled/2010/papers/owled2010_submission_22.pdf},
 id = {e589a4a1-da43-307c-8bef-5cb37a1b5b8a},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2010},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Vandervalk, Benjamin and McCarthy, Luke and Wilkinson, Mark},
 booktitle = {Proceedings of OWLED 2010, San Francisco, California, USA 21-22 June 2010}
}

@inproceedings{
 title = {Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins},
 type = {inproceedings},
 year = {2010},
 keywords = {biomoby,plug-ins,taverna,workflows},
 pages = {301-312},
 volume = {6415},
 websites = {doi:10.1007/978-3-642-16558-0_26},
 id = {18acd740-1a25-3b41-80ca-66b61f657b9b},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Withers2010},
 source_type = {inproceedings},
 notes = {10.1007/978-3-642-16558-0_26},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Withers, David and Kawas, Edward and McCarthy, Luke and Vandervalk, Benjamin and Wilkinson, Mark},
 booktitle = {Leveraging Applications of Formal Methods, Verification, and Validation 4th International Symposium on Leveraging Applications, Lecture Notes in Computer Science}
}

@inproceedings{
 title = {SADI Semantic Web Services - 'cause you can't always GET what you want!},
 type = {inproceedings},
 year = {2010},
 keywords = {semantic web},
 pages = {13-18},
 websites = {http://dx.doi.org/10.1109/APSCC.2009.5394148},
 month = {1},
 id = {2ec3ea00-78bc-3482-a13a-1e407bd2c539},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {MD2010},
 source_type = {inproceedings},
 notes = {10.1109/APSCC.2009.5394148},
 private_publication = {false},
 abstract = {SADI-semantic automated discovery and integration- is a set of standards-compliant semantic Web service design patterns that exploit the relatively straightforward interfaces exposed by most bioinformatics services to simplify and partially automate service design and deployment. The SADI design explicitly exposes an important service feature -the semantic relationship between input and output data. SADI services consume and produce instances of OWL classes, where the service's function is to add properties onto the input class until it fulfills the class-membership requirements of the output class. Indexing services based on the properties they add enables discovery of Services that generate the biological features of interest relative to a piece of in-hand data. We show that this design pattern can be used to create a client application with strikingly rich semantic behaviors, such as automated discovery of distributed data resources and the automated orchestration of chains of Web services into complex workflows.},
 bibtype = {inproceedings},
 author = {MD, Wilkinson and B, Vandervalk and L, McCarthy},
 doi = {10.1109/APSCC.2009.5394148},
 booktitle = {Services Computing Conference, 2009. APSCC 2009. IEEE Asia-Pacific}
}

SADI-semantic automated discovery and integration- is a set of standards-compliant semantic Web service design patterns that exploit the relatively straightforward interfaces exposed by most bioinformatics services to simplify and partially automate service design and deployment. The SADI design explicitly exposes an important service feature -the semantic relationship between input and output data. SADI services consume and produce instances of OWL classes, where the service's function is to add properties onto the input class until it fulfills the class-membership requirements of the output class. Indexing services based on the properties they add enables discovery of Services that generate the biological features of interest relative to a piece of in-hand data. We show that this design pattern can be used to create a client application with strikingly rich semantic behaviors, such as automated discovery of distributed data resources and the automated orchestration of chains of Web services into complex workflows.

@inproceedings{
 title = {SPARQL Assist Language-Neutral Query Composer},
 type = {inproceedings},
 year = {2010},
 keywords = {Mark Wilkinson},
 websites = {http://arxiv.org/abs/1012.1666v1},
 id = {1bda307b-7cba-302c-9257-14be65f20293},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {McCarthy2010},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: a web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.},
 bibtype = {inproceedings},
 author = {McCarthy, Luke and Vandervalk, Ben and Wilkinson, Mark},
 booktitle = {Proceedings of Semantic Web Applications and Tools for Life Sciences 2010}
}

SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: a web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.

@article{
 title = {OWL2Perl: Creating Perl modules from OWL class definitions.},
 type = {article},
 year = {2010},
 keywords = {perl},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20628074},
 month = {7},
 id = {5c80b3b9-fabe-3393-bba4-1ea2152d0932},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kawas2010},
 source_type = {article},
 notes = {10.1093/bioinformatics/btq416},
 private_publication = {false},
 abstract = {SUMMARY: Support for utilizing OWL ontologies in Perl is extremely limited, despite the growing importance of the Semantic Web in Healthcare and Life Sciences. Here we present a Perl framework that generates Perl modules based on OWL Class definitions. These modules can then be used by other software applications to create RDF data compliant with these OWL models. AVAILABILITY: OWL2Perl is available for download from CPAN, under the module name OWL2Perl. It is released under the new BSD license. CONTACT: markw@illuminae.com; edward.kawas@gmail.com.},
 bibtype = {article},
 author = {Kawas, Edward and Wilkinson, Mark},
 journal = {Bioinformatics (Oxford, England)}
}

SUMMARY: Support for utilizing OWL ontologies in Perl is extremely limited, despite the growing importance of the Semantic Web in Healthcare and Life Sciences. Here we present a Perl framework that generates Perl modules based on OWL Class definitions. These modules can then be used by other software applications to create RDF data compliant with these OWL models. AVAILABILITY: OWL2Perl is available for download from CPAN, under the module name OWL2Perl. It is released under the new BSD license. CONTACT: markw@illuminae.com; edward.kawas@gmail.com.

@article{
 title = {The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.},
 type = {article},
 year = {2010},
 pages = {8},
 volume = {1},
 id = {bd4393d2-9c5c-3229-bdf8-2833362c9772},
 created = {2015-01-29T12:42:44.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Katayama2010},
 private_publication = {false},
 abstract = {Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.},
 bibtype = {article},
 author = {Katayama, Toshiaki and Arakawa, Kazuharu and Nakao, Mitsuteru and Ono, Keiichiro and Aoki-Kinoshita, Kiyoko F and Yamamoto, Yasunori and Yamaguchi, Atsuko and Kawashima, Shuichi and Chun, Hong-Woo and Aerts, Jan and Aranda, Bruno and Barboza, Lord Hendrix and Bonnal, Raoul Jp and Bruskiewich, Richard and Bryne, Jan C and Fernández, José M and Funahashi, Akira and Gordon, Paul Mk and Goto, Naohisa and Groscurth, Andreas and Gutteridge, Alex and Holland, Richard and Kano, Yoshinobu and Kawas, Edward A and Kerhornou, Arnaud and Kibukawa, Eri and Kinjo, Akira R and Kuhn, Michael and Lapp, Hilmar and Lehvaslaiho, Heikki and Nakamura, Hiroyuki and Nakamura, Yasukazu and Nishizawa, Tatsuya and Nobata, Chikashi and Noguchi, Tamotsu and Oinn, Thomas M and Okamoto, Shinobu and Owen, Stuart and Pafilis, Evangelos and Pocock, Matthew and Prins, Pjotr and Ranzinger, René and Reisinger, Florian and Salwinski, Lukasz and Schreiber, Mark and Senger, Martin and Shigemoto, Yasumasa and Standley, Daron M and Sugawara, Hideaki and Tashiro, Toshiyuki and Trelles, Oswaldo and Vos, Rutger A and Wilkinson, Mark D and York, William and Zmasek, Christian M and Asai, Kiyoshi and Takagi, Toshihisa},
 doi = {10.1186/2041-1480-1-8},
 journal = {Journal of biomedical semantics}
}

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

@inproceedings{
 title = {SHARE & the semantic web - This time it's personal!},
 type = {inproceedings},
 year = {2010},
 keywords = {OWL,RDF,SADI,SHARE,SPARQL,Semantic web,Semantic web services,Workflow,Workflow orchestration},
 volume = {614},
 id = {6e467549-da6a-3985-b73e-12a80b876a32},
 created = {2017-12-03T10:44:25.600Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.189Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Currently, in the Semantic Web in Healthcare and Life Sciences large ontologies representing a "consensus" world-view are selected, then data relevant to those ontologies is manually located and aggregated prior to reasoning. This approach presents challenges in addition to the real-world limitations of reasoning over such large-scale data: data critical to discovery in the life sciences must often be generated dynamically by analytical algorithms. Here we describe a prototype system - SHARE - That consumes ontologies and queries and automatically discovers, retrieves, and reasons over information relevant to that ontological world view by locating and executing Web Services. The SHARE system exhibits what we believe are crucial characteristics of the Semantic Web vision: Relevant information is dynamically discovered and/or generated from distributed resources, and is interpreted, updated, or re-interpreted as the over-laid local ontology changes.},
 bibtype = {inproceedings},
 author = {Vandervalk, B. and McCarthy, L. and Wilkinson, M.},
 booktitle = {CEUR Workshop Proceedings}
}

Currently, in the Semantic Web in Healthcare and Life Sciences large ontologies representing a "consensus" world-view are selected, then data relevant to those ontologies is manually located and aggregated prior to reasoning. This approach presents challenges in addition to the real-world limitations of reasoning over such large-scale data: data critical to discovery in the life sciences must often be generated dynamically by analytical algorithms. Here we describe a prototype system - SHARE - That consumes ontologies and queries and automatically discovers, retrieves, and reasons over information relevant to that ontological world view by locating and executing Web Services. The SHARE system exhibits what we believe are crucial characteristics of the Semantic Web vision: Relevant information is dynamically discovered and/or generated from distributed resources, and is interpreted, updated, or re-interpreted as the over-laid local ontology changes.

@book{
 title = {Tools in scientific workflow composition},
 type = {book},
 year = {2010},
 source = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
 volume = {6415 LNCS},
 issue = {PART 1},
 id = {39576430-3e69-3a71-9289-2fa0dbd78c5b},
 created = {2017-12-03T10:44:25.647Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.947Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Scientific workflows are combinations of activities and computations in order to solve scientific problems. In contrast to, for instance, business workflows that implement business processes involving different persons and information systems, scientific workflows are used to carry out computational experiments, possibly confirming or invalidating scientific hypotheses [1]. Scientific workflow systems [2] [3] support and automate the execution of error-prone, repetitive tasks such as data access, transformation, and analysis. Several systems for different purposes and following different approaches have been developed in the last decade, and research in this comparatively new field is currently going into many different directions. This ISoLA 2010 special track is devoted to "Tools in Scientific Workflow Composition". Its papers comprise subjects such as tools and frameworks for workflow composition, semantically aware workflow development, and automatic workflow composition, as well as some case studies, examples, and experiences. The contributions are primarily from the bioinformatics domain, but do also contain examples from other (scientific) application domains. © 2010 Springer-Verlag.},
 bibtype = {book},
 author = {Kok, J.N. and Lamprecht, A.-L. and Wilkinson, M.D.},
 doi = {10.1007/978-3-642-16558-0_22}
}

Scientific workflows are combinations of activities and computations in order to solve scientific problems. In contrast to, for instance, business workflows that implement business processes involving different persons and information systems, scientific workflows are used to carry out computational experiments, possibly confirming or invalidating scientific hypotheses [1]. Scientific workflow systems [2] [3] support and automate the execution of error-prone, repetitive tasks such as data access, transformation, and analysis. Several systems for different purposes and following different approaches have been developed in the last decade, and research in this comparatively new field is currently going into many different directions. This ISoLA 2010 special track is devoted to "Tools in Scientific Workflow Composition". Its papers comprise subjects such as tools and frameworks for workflow composition, semantically aware workflow development, and automatic workflow composition, as well as some case studies, examples, and experiences. The contributions are primarily from the bioinformatics domain, but do also contain examples from other (scientific) application domains. © 2010 Springer-Verlag.

@inproceedings{
 title = {SPARQL assist language-neutral query composer},
 type = {inproceedings},
 year = {2010},
 keywords = {I18n,OWL,RDF,SPARQL,Semantic web,Semantic web services},
 volume = {698},
 id = {9f9a8f52-14f4-34bd-b5f0-3c0b7842f137},
 created = {2017-12-03T10:44:25.693Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.809Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: A web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.},
 bibtype = {inproceedings},
 author = {McCarthy, L. and Vandervalk, B. and Wilkinson, M.},
 booktitle = {CEUR Workshop Proceedings}
}

SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: A web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.

@inbook{
 type = {inbook},
 year = {2009},
 keywords = {semantic web},
 pages = {367-369},
 volume = {5926},
 websites = {http://dx.doi.org/10.1007/978-3-642-10871-6_27,http://link.springer.com/10.1007/978-3-642-10871-6_27},
 id = {56aedf48-4bde-385c-a8e6-e0526b184d73},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2009b},
 source_type = {inproceedings},
 notes = {10.1007/978-3-642-10871-6_27},
 private_publication = {false},
 abstract = {Driven by the goal of automating data analyses in the field of bioinformatics, SHARE (Semantic Health and Research Environment) is a specialized SPARQL engine that resolves queries against Web Services and SPARQL endpoints. Developed in conjunction with SHARE, SADI (Semantic Automated Discovery and Integration) is a standard for native-RDF services that facilitates the automated assembly of services into workflows, thereby eliminating the need for ad hoc scripting in the construction of a bioinformatics analysis pipeline.},
 bibtype = {inbook},
 author = {Vandervalk, Ben P. and McCarthy, E. Luke and Wilkinson, Mark D.},
 doi = {10.1007/978-3-642-10871-6_27},
 chapter = {SHARE: A Semantic Web Query Engine for Bioinformatics},
 title = {The Semantic Web, Lecture Notes in Computer Science proceedings of the ASWC 2009}
}

Driven by the goal of automating data analyses in the field of bioinformatics, SHARE (Semantic Health and Research Environment) is a specialized SPARQL engine that resolves queries against Web Services and SPARQL endpoints. Developed in conjunction with SHARE, SADI (Semantic Automated Discovery and Integration) is a standard for native-RDF services that facilitates the automated assembly of services into workflows, thereby eliminating the need for ad hoc scripting in the construction of a bioinformatics analysis pipeline.

@article{
 title = {Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics},
 type = {article},
 year = {2009},
 keywords = {metadata},
 pages = {313},
 volume = {10},
 websites = {http://dx.doi.org/10.1186/1471-2105-10-313},
 month = {9},
 id = {26b49111-9e09-3305-8d8e-13539f040e1f},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Good2009},
 source_type = {article},
 notes = {10.1186/1471-2105-10-313},
 private_publication = {false},
 abstract = {Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. Results We assessed the metadata that users of CiteULike and Connotea associated with citations in PubMed with the following metrics: coverage of the document space, density of metadata (tags) per document, rates of inter-annotator agreement, and rates of agreement with MeSH indexing. CiteULike and Connotea were very similar on all of the measurements. In comparison to PubMed, document coverage and per-document metadata density were much lower for the social tagging systems. Inter-annotator agreement within the social tagging systems and the agreement between the aggregated social tagging metadata and MeSH indexing was low though the latter could be increased through voting. Conclusion The most promising uses of metadata from current academic social tagging repositories will be those that find ways to utilize the novel relationships between users, tags, and documents exposed through these systems. For more traditional kinds of indexing-based applications (such as keyword-based search) to benefit substantially from socially generated metadata in the life sciences, more documents need to be tagged and more tags are needed for each document. These issues may be addressed both by finding ways to attract more users to current systems and by creating new user interfaces that encourage more collectively useful individual tagging behaviour.},
 bibtype = {article},
 author = {Good, Benjamin and Tennis, Joseph and Wilkinson, Mark},
 journal = {BMC Bioinformatics},
 number = {1}
}

Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. Results We assessed the metadata that users of CiteULike and Connotea associated with citations in PubMed with the following metrics: coverage of the document space, density of metadata (tags) per document, rates of inter-annotator agreement, and rates of agreement with MeSH indexing. CiteULike and Connotea were very similar on all of the measurements. In comparison to PubMed, document coverage and per-document metadata density were much lower for the social tagging systems. Inter-annotator agreement within the social tagging systems and the agreement between the aggregated social tagging metadata and MeSH indexing was low though the latter could be increased through voting. Conclusion The most promising uses of metadata from current academic social tagging repositories will be those that find ways to utilize the novel relationships between users, tags, and documents exposed through these systems. For more traditional kinds of indexing-based applications (such as keyword-based search) to benefit substantially from socially generated metadata in the life sciences, more documents need to be tagged and more tags are needed for each document. These issues may be addressed both by finding ways to attract more users to current systems and by creating new user interfaces that encourage more collectively useful individual tagging behaviour.

@article{
 title = {Moby and Moby 2: Creatures of the Deep (Web)},
 type = {article},
 year = {2009},
 keywords = {Mark Wilkinson},
 pages = {114},
 volume = {10},
 websites = {http://dx.doi.org/10.1093/bib/bbn051},
 month = {1},
 id = {dce43e07-67ce-364c-93ca-5c1ad836da31},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2009c},
 source_type = {article},
 notes = {10.1093/bib/bbn051},
 private_publication = {false},
 abstract = {Facile and meaningful integration of data from disparate resources is the ‘holy grail’ of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized ‘semantic warehouses’ that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the ‘Deep Web’—that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine ‘The State of the Union’ for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.},
 bibtype = {article},
 author = {Vandervalk, Ben and McCarthy, E and Wilkinson, Mark},
 journal = {Briefings in Bioinformatics},
 number = {2}
}

Facile and meaningful integration of data from disparate resources is the ‘holy grail’ of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized ‘semantic warehouses’ that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the ‘Deep Web’—that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine ‘The State of the Union’ for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

@inproceedings{
 title = {Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm},
 type = {inproceedings},
 year = {2009},
 keywords = {Mark Wilkinson},
 pages = {330-337},
 volume = {1},
 websites = {http://dx.doi.org/10.1109/cse.2009.144},
 id = {73017c99-6506-304a-a8a6-f10d99f0075a},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vandervalk2009a},
 source_type = {inproceedings},
 notes = {10.1109/cse.2009.144},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Vandervalk, Ben and McCarthy, Luke and Wilkinson, Mark},
 booktitle = {IEEE International Conference on Computational Science and Engineering}
}

@inproceedings{
 title = {Optimization of distributed SPARQL queries using edmonds' algorithm and prim's algorithm},
 type = {inproceedings},
 year = {2009},
 volume = {1},
 id = {cd66cd4a-0ef2-31c7-baf0-efdccdc01b96},
 created = {2017-12-03T10:44:25.790Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.569Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Here we describe the application of two well known graph algorithms, Edmonds' algorithm and Prim's algorithm, to the problem of optimizing distributed SPARQL queries. In the context of this paper, a "distributed SPARQL query" is a SPARQL query which is resolved by contacting any number of remote SPARQL endpoints. Two optimization approaches are described. In the first approach, a static query plan is computed in advance of query execution, using one of two standard graph algorithms for finding minimum spanning trees (Edmonds' algorithm and Prim's algorithm). In the second approach, the planning and execution of the query are interleaved, so that as each potential solution is expanded it is permitted to follow an independent query plan. Our optimization approach requires basic statistics regarding RDF predicates which must be obtained prior to the user's query, through automated querying of the remote SPARQL endpoints.},
 bibtype = {inproceedings},
 author = {Vandervalk, B.P. and McCarthy, E.L. and Wilkinson, M.D.},
 doi = {10.1109/CSE.2009.144},
 booktitle = {Proceedings - 12th IEEE International Conference on Computational Science and Engineering, CSE 2009}
}

Here we describe the application of two well known graph algorithms, Edmonds' algorithm and Prim's algorithm, to the problem of optimizing distributed SPARQL queries. In the context of this paper, a "distributed SPARQL query" is a SPARQL query which is resolved by contacting any number of remote SPARQL endpoints. Two optimization approaches are described. In the first approach, a static query plan is computed in advance of query execution, using one of two standard graph algorithms for finding minimum spanning trees (Edmonds' algorithm and Prim's algorithm). In the second approach, the planning and execution of the query are interleaved, so that as each potential solution is expanded it is permitted to follow an independent query plan. Our optimization approach requires basic statistics regarding RDF predicates which must be obtained prior to the user's query, through automated querying of the remote SPARQL endpoints.

@inproceedings{
 title = {Effect of dynamic strain aging on fracture in aluminum alloy sheet materials AA5754},
 type = {inproceedings},
 year = {2009},
 volume = {8},
 id = {c460de6e-454b-3417-b7b5-37a8969afb1c},
 created = {2017-12-03T10:44:25.986Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.360Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Solid-solution alloys such as Al-Mg alloy AA5754 often display serrated flow during tensile deformation due to dynamic strain aging over a range of temperatures and strain rates. The effect of dynamic strain aging on fracture properties has been an important concern in addition to surface quality and formability. In this paper, we present the results for double-edge-notched samples tested at room temperature. Digital image correlation was utilized to follow the deformation pattern during the tensile processes. The results show that the plasticity bursts are not limited to the notch tip causing the plastic zone to be finger-like. This cannot be predicted using conventional elastic-plastic fracture models. The results show that the fracture strain increases with increasing strain rate. We have also used 45 degree offset-edge notched samples also tested at room temperature. The results here show that the ductile crack propagates along the original crack line leading to the final failure.},
 bibtype = {inproceedings},
 author = {Kang, J. and Wilkinson, M.D.S. and Beaudoin, A.J. and Embury, J.D. and Mishra, R.K.},
 booktitle = {12th International Conference on Fracture 2009, ICF-12}
}

Solid-solution alloys such as Al-Mg alloy AA5754 often display serrated flow during tensile deformation due to dynamic strain aging over a range of temperatures and strain rates. The effect of dynamic strain aging on fracture properties has been an important concern in addition to surface quality and formability. In this paper, we present the results for double-edge-notched samples tested at room temperature. Digital image correlation was utilized to follow the deformation pattern during the tensile processes. The results show that the plasticity bursts are not limited to the notch tip causing the plastic zone to be finger-like. This cannot be predicted using conventional elastic-plastic fracture models. The results show that the fracture strain increases with increasing strain rate. We have also used 45 degree offset-edge notched samples also tested at room temperature. The results here show that the ductile crack propagates along the original crack line leading to the final failure.

@article{
 title = {Interoperability with Moby 1.0--it's better than sharing your toothbrush!},
 type = {article},
 year = {2008},
 keywords = {Computational Biology,Computational Biology: methods,Database Management Systems,Databases,Factual,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Programming Languages,Systems Integration},
 pages = {220-31},
 volume = {9},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/18238804},
 month = {5},
 id = {71d6e1bc-7dd3-346d-b61a-5ee54fcb5e81},
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 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
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 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2008},
 private_publication = {false},
 abstract = {The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.},
 bibtype = {article},
 author = {Wilkinson, Mark D and Senger, Martin and Kawas, Edward and Bruskiewich, Richard and Gouzy, Jerome and Noirot, Celine and Bardou, Philippe and Ng, Ambrose and Haase, Dirk and Saiz, Enrique de Andres and Wang, Dennis and Gibbons, Frank and Gordon, Paul M K and Sensen, Christoph W and Carrasco, Jose Manuel Rodriguez and Fernández, José M and Shen, Lixin and Links, Matthew and Ng, Michael and Opushneva, Nina and Neerincx, Pieter B T and Leunissen, Jack A M and Ernst, Rebecca and Twigger, Simon and Usadel, Bjorn and Good, Benjamin and Wong, Yan and Stein, Lincoln and Crosby, William and Karlsson, Johan and Royo, Romina and Párraga, Iván and Ramírez, Sergio and Gelpi, Josep Lluis and Trelles, Oswaldo and Pisano, David G and Jimenez, Natalia and Kerhornou, Arnaud and Rosset, Roman and Zamacola, Leire and Tarraga, Joaquin and Huerta-Cepas, Jaime and Carazo, Jose María and Dopazo, Joaquin and Guigo, Roderic and Navarro, Arcadi and Orozco, Modesto and Valencia, Alfonso and Claros, M Gonzalo and Pérez, Antonio J and Aldana, Jose and Rojano, M Mar and Fernandez-Santa Cruz, Raul and Navas, Ismael and Schiltz, Gary and Farmer, Andrew and Gessler, Damian and Schoof, Heiko and Groscurth, Andreas},
 doi = {10.1093/bib/bbn003},
 journal = {Briefings in bioinformatics},
 number = {3}
}

The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.

@article{
 title = {Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework},
 type = {article},
 year = {2008},
 keywords = {semantic web},
 pages = {837},
 volume = {41},
 websites = {http://dx.doi.org/10.1016/j.jbi.2008.02.005},
 id = {8ef16910-3990-38b8-825a-bbffa45fb360},
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 hidden = {false},
 citation_key = {DiBernardo2008},
 source_type = {article},
 notes = {10.1016/j.jbi.2008.02.005},
 private_publication = {false},
 abstract = {Researchers in the life-sciences are currently limited to small-scale informatics experiments and analyses because of the lack of interoperability among life-sciences web services. This limitation can be addressed by annotating services and their interfaces with semantic information, so that interoperability problems can be reasoned about programmatically. The Moby semantic web framework is a popular and mature platform that is used for this purpose. However, the number of services that are available to select from when building a workflow is becoming unmanageable for users. As such, attempts have been made to assist with service selection and composition. These tasks fall under the general label of automated service composition. We present a prototype workflow assembly client that reduces the number of choices that users have to make by (1) restricting the overall set of services presented to them and (2) ranking services so that the the most desirable ones are presented first. We demonstrate via an evaluation of this prototype that a unification of relatively simple techniques can rank desirable services highly while maintaining interactive response times.},
 bibtype = {article},
 author = {DiBernardo, undefined and M, undefined and Pottinger, undefined and R, undefined and Wilkinson, M},
 journal = {Journal of Biomedical Informatics},
 number = {5}
}

Researchers in the life-sciences are currently limited to small-scale informatics experiments and analyses because of the lack of interoperability among life-sciences web services. This limitation can be addressed by annotating services and their interfaces with semantic information, so that interoperability problems can be reasoned about programmatically. The Moby semantic web framework is a popular and mature platform that is used for this purpose. However, the number of services that are available to select from when building a workflow is becoming unmanageable for users. As such, attempts have been made to assist with service selection and composition. These tasks fall under the general label of automated service composition. We present a prototype workflow assembly client that reduces the number of choices that users have to make by (1) restricting the overall set of services presented to them and (2) ranking services so that the the most desirable ones are presented first. We demonstrate via an evaluation of this prototype that a unification of relatively simple techniques can rank desirable services highly while maintaining interactive response times.

@article{
 title = {The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science},
 type = {article},
 year = {2008},
 keywords = {genomics},
 pages = {369601},
 volume = {2008},
 websites = {http://dx.doi.org/10.1155/2008/369601},
 month = {4},
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 abstract = {The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.},
 bibtype = {article},
 author = {R, Bruskiewich and M, Senger and G, Davenport and M, Ruiz and M, Rouard and T, Hazekamp and M, Takeya and K, Doi and K, Satoh and M, Costa and R, Simon and J, Balaji and A, Akintunde and R, Mauleon and S, Wanchana and T, Shah and M, Anacleto and A, Portugal and Vj, Ulat and S, Thongjuea and K, Braak and S, Ritter and A, Dereeper and M, Skofic and E, Rojas and N, Martins and G, Pappas and R, Alamban and R, Almodiel and Lh, Barboza and J, Detras and K, Manansala and Mj, Mendoza and J, Morales and B, Peralta and R, Valerio and Y, Zhang and S, Gregorio and J, Hermocilla and M, Echavez and Jm, Yap and A, Farmer and G, Schiltz and J, Lee and T, Casstevens and P, Jaiswal and A, Meintjes and M, Wilkinson and B, Good and J, Wagner and J, Morris and D, Marshall and A, Collins and S, Kikuchi and T, Metz and G, McLaren and Hintum, Van},
 journal = {International Journal of Plant Genomics}
}

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

@article{
 title = {DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data},
 type = {article},
 year = {2008},
 keywords = {Bioinformatics},
 pages = {233-236},
 volume = {1},
 websites = {http://www.omicsonline.com/ArchiveJPB/2008/July/03/JPB1.233.php},
 month = {7},
 day = {17},
 id = {fcb60693-c4e0-33bd-8ae7-d3f1671f30ea},
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 citation_key = {Chan2008},
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 abstract = {Here we describe DataBiNS-Viz – a visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data gathered by the BioMoby-based DataBiNS workflow. DataBiNSViz enables execution of the DataBiNS workflow on proteins described by KEGG, PubMed, or OMIM identifiers, followed by manual exploration of the integrated structure/function and pathway data for those proteins, with a particular focus on nsSNP data in-context. The tool can be freely accessed at http://bioinfo.icapture.ubc.ca:8090/DataBiNS (please use the Firefox or Safari web browsers). Examples of the retrieved data are given under the “Help on inputs” option. Detailed documentation can be accessed at: http://bioinfo.icapture.ubc.ca/mywiki/DataBiNS.},
 bibtype = {article},
 author = {Chan, Fong Chun and Kawas, Edward A. and Wilkinson, Mark D. and Tebbutt, Scott J.},
 doi = {10.4172/jpb.1000029},
 journal = {Journal of Proteomics & Bioinformatics},
 number = {4}
}

Here we describe DataBiNS-Viz – a visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data gathered by the BioMoby-based DataBiNS workflow. DataBiNSViz enables execution of the DataBiNS workflow on proteins described by KEGG, PubMed, or OMIM identifiers, followed by manual exploration of the integrated structure/function and pathway data for those proteins, with a particular focus on nsSNP data in-context. The tool can be freely accessed at http://bioinfo.icapture.ubc.ca:8090/DataBiNS (please use the Firefox or Safari web browsers). Examples of the retrieved data are given under the “Help on inputs” option. Detailed documentation can be accessed at: http://bioinfo.icapture.ubc.ca/mywiki/DataBiNS.

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 title = {Encyclopedia of Database Systems}
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@techreport{
 title = {CardioSHARE: Web Services for the Semantic Web},
 type = {techreport},
 year = {2008},
 keywords = {semantic web},
 websites = {http://cardioshare.icapture.ubc.ca/SWChallenge.pdf},
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@inproceedings{
 title = {Structured Representation of Biomedical Experiments: A Bottom-Up Approach},
 type = {inproceedings},
 year = {2008},
 keywords = {annotation},
 websites = {http://bioinfo.icapture.ubc.ca:8090/PubmedAnnotator/IKE2008.pdf},
 id = {904f7e35-ee80-3a45-b565-d477c3d3d181},
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 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kothari2008b},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {Scientific publications are currently the only means to disseminate the details of biomedical experiments across the life sciences research community. With the ever increasing volume of scientific publications, life scientists and curators of life science knowledge bases are often confronted with the daunting task of sifting through hundreds of relevant publications to apprise themselves of the latest experimental techniques and research findings in their area of interest. The use of concise, structured annotations to describe the salient features of experiments would alleviate this difficulty. For this purpose, minimum information standards and controlled vocabularies for experiment representation are in development to be used by biologists to annotate their experiments. This paper presents the initial results from a methodology to manually annotate descriptions of experiments in scientific publications; and discusses the utility of these annotations in a bottom-up approach to creating an ontology of biomedical experiments.},
 bibtype = {inproceedings},
 author = {Kothari, Cartik and Wilkinson, Mark},
 booktitle = {Proceedings of the 2008 International Conference on Information & Knowledge Engineering, IKE 2008. Las Vegas Nevada, USA}
}

Scientific publications are currently the only means to disseminate the details of biomedical experiments across the life sciences research community. With the ever increasing volume of scientific publications, life scientists and curators of life science knowledge bases are often confronted with the daunting task of sifting through hundreds of relevant publications to apprise themselves of the latest experimental techniques and research findings in their area of interest. The use of concise, structured annotations to describe the salient features of experiments would alleviate this difficulty. For this purpose, minimum information standards and controlled vocabularies for experiment representation are in development to be used by biologists to annotate their experiments. This paper presents the initial results from a methodology to manually annotate descriptions of experiments in scientific publications; and discusses the utility of these annotations in a bottom-up approach to creating an ontology of biomedical experiments.

@inproceedings{
 title = {The Semantic Health and Research Environment: SHARE-ing Deep Web Data on the Semantic Web},
 type = {inproceedings},
 year = {2008},
 keywords = {semantic web},
 pages = {127-128},
 websites = {http://research.microsoft.com/en-us/events/escience2008/},
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 citation_key = {Vandervalk2008a},
 source_type = {inproceedings},
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 abstract = {Proceedings of the Microsoft eScience Workshop 2008. December 6-10, 2008, Indianapolis, Indiana},
 bibtype = {inproceedings},
 author = {Vandervalk, Benjamin and McCarthy, Luke and Wilkinson, Mark},
 booktitle = {Proceedings of the 2008 Microsoft eScience Workshop}
}

Proceedings of the Microsoft eScience Workshop 2008. December 6-10, 2008, Indianapolis, Indiana

@inproceedings{
 title = {SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web},
 type = {inproceedings},
 year = {2008},
 pages = {69-78},
 websites = {http://arxiv.org/abs/1305.4455},
 month = {5},
 day = {20},
 city = {Bangkok, Thailand},
 id = {2c721224-2152-3b2d-a5ef-c3de427bc143},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2013-05-21},
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 confirmed = {true},
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 genre = {Digital Libraries; Artificial Intelligence; Software Engineering},
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 abstract = {Here we describe the SHARE system, a web service based framework for distributed querying and reasoning on the semantic web. The main innovations of SHARE are: (1) the extension of a SPARQL query engine to perform on-demand data retrieval from web services, and (2) the extension of an OWL reasoner to test property restrictions by means of web service invocations. In addition to enabling queries across distributed datasets, the system allows for a target dataset that is significantly larger than is possible under current, centralized approaches. Although the architecture is equally applicable to all types of data, the SHARE system targets bioinformatics, due to the large number of interoperable web services that are already available in this area. SHARE is built entirely on semantic web standards, and is the successor of the BioMOBY project.},
 bibtype = {inproceedings},
 author = {Vandervalk, Ben P and McCarthy, E Luke and Wilkinson, Mark D},
 booktitle = {Third Asian Semantic Web Conference, ASWC2008, Workshops Proceedings (NEFORS2008)}
}

Here we describe the SHARE system, a web service based framework for distributed querying and reasoning on the semantic web. The main innovations of SHARE are: (1) the extension of a SPARQL query engine to perform on-demand data retrieval from web services, and (2) the extension of an OWL reasoner to test property restrictions by means of web service invocations. In addition to enabling queries across distributed datasets, the system allows for a target dataset that is significantly larger than is possible under current, centralized approaches. Although the architecture is equally applicable to all types of data, the SHARE system targets bioinformatics, due to the large number of interoperable web services that are already available in this area. SHARE is built entirely on semantic web standards, and is the successor of the BioMOBY project.

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@unpublished{
 title = {OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web},
 type = {unpublished},
 year = {2008},
 websites = {http://arxiv.org/abs/1502.06025},
 revision = {arXiv:1502.06025 [q-bio.QM]},
 id = {c4c6768b-1dc6-3111-8bac-b589bbeeef1f},
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 citation_key = {Good2008},
 folder_uuids = {ec2ec352-fa41-43db-919d-f96649955c40},
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 abstract = {The delineation of logical definitions for each class in an ontology and the consistent application of these definitions to the assignment of instances to classes are important criteria for ontology evaluation. If ontologies are specified with property-based restrictions on class membership, then such consistency can be checked automatically. If no such logical restrictions are applied, as is the case with many biological ontologies, there are currently no automated methods for measuring the semantic consistency of instance assignment on an ontology-wide scale, nor for inferring the patterns of properties that might define a particular class. We constructed a program that takes as its input an OWL/RDF knowledge base containing an ontology, instances associated with each of the classes in the ontology, and properties of those instances. For each class, it outputs: 1) a rule for determining class membership based on the properties of the instances and 2) a quantitative score for the class that reflects the ability of the identified rule to correctly predict class membership for the instances in the knowledge base. We evaluated this program using both artificial knowledge bases of known quality and real, widely used ontologies. The results indicate that the suggested method can be used to conduct objective, automatic, data-driven evaluations of biological ontologies without formal class definitions in regards to the property-based consistency of instance-assignment. This inductive method complements existing, purely deductive approaches to automatic consistency checking, offering not just the potential to help in the ontology engineering process but also in the knowledge discovery process.},
 bibtype = {unpublished},
 author = {Good, Benjamin M. and Ha, Gavin and Ho, Chi K. and Wilkinson, Mark D.},
 keywords = {ontology engineering,ontoloki}
}

The delineation of logical definitions for each class in an ontology and the consistent application of these definitions to the assignment of instances to classes are important criteria for ontology evaluation. If ontologies are specified with property-based restrictions on class membership, then such consistency can be checked automatically. If no such logical restrictions are applied, as is the case with many biological ontologies, there are currently no automated methods for measuring the semantic consistency of instance assignment on an ontology-wide scale, nor for inferring the patterns of properties that might define a particular class. We constructed a program that takes as its input an OWL/RDF knowledge base containing an ontology, instances associated with each of the classes in the ontology, and properties of those instances. For each class, it outputs: 1) a rule for determining class membership based on the properties of the instances and 2) a quantitative score for the class that reflects the ability of the identified rule to correctly predict class membership for the instances in the knowledge base. We evaluated this program using both artificial knowledge bases of known quality and real, widely used ontologies. The results indicate that the suggested method can be used to conduct objective, automatic, data-driven evaluations of biological ontologies without formal class definitions in regards to the property-based consistency of instance-assignment. This inductive method complements existing, purely deductive approaches to automatic consistency checking, offering not just the potential to help in the ontology engineering process but also in the knowledge discovery process.

@inproceedings{
 title = {Structured representation of biomedical experiments: A bottom-up approach},
 type = {inproceedings},
 year = {2008},
 keywords = {Annotation,Experiments,Framework,Representation,Structure},
 id = {19ec058f-6546-33d2-a5f8-526c3b68561a},
 created = {2017-12-03T10:44:25.468Z},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Scientific publications are currently the only means to disseminate the details of biomedical experiments across the life sciences research community. With the ever increasing volume of scientific publications, life scientists and curators of life science knowledge bases are often confronted with the daunting task of sifting through hundreds of relevant publications to apprise themselves of the latest experimental techniques and research findings in their area of interest. The use of concise, structured annotations to describe the salient features of experiments would alleviate this difficulty. For this purpose, minimum information standards and controlled vocabularies for experiment representation are in development to be used by biologists to annotate their experiments. This paper presents the initial results from a methodology to manually annotate descriptions of experiments in scientific publications; and discusses the utility of these annotations in a bottom-up approach to creating an ontology of biomedical experiments.},
 bibtype = {inproceedings},
 author = {Kothari, C.R. and Wilkinson, M.D.},
 booktitle = {Proceedings of the 2008 International Conference on Information and Knowledge Engineering, IKE 2008}
}

Scientific publications are currently the only means to disseminate the details of biomedical experiments across the life sciences research community. With the ever increasing volume of scientific publications, life scientists and curators of life science knowledge bases are often confronted with the daunting task of sifting through hundreds of relevant publications to apprise themselves of the latest experimental techniques and research findings in their area of interest. The use of concise, structured annotations to describe the salient features of experiments would alleviate this difficulty. For this purpose, minimum information standards and controlled vocabularies for experiment representation are in development to be used by biologists to annotate their experiments. This paper presents the initial results from a methodology to manually annotate descriptions of experiments in scientific publications; and discusses the utility of these annotations in a bottom-up approach to creating an ontology of biomedical experiments.

@inproceedings{
 title = {Restoration of ethernet services over a dual-homed GPON system - Operator requirements and practical demonstration},
 type = {inproceedings},
 year = {2008},
 id = {9e409d1e-6b39-3dc2-85f9-0a6074afbc6b},
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 abstract = {Restoration requirements for Ethernet services in FTTx deployments are discussed. An initial demonstration of a dual-homed GPON offering layer 2 resilience is reported along with measurements of the service disruption time. © 2007 Optical Society of America.},
 bibtype = {inproceedings},
 author = {Kang, J. and Wilkinson, M. and Smith, K. and Nesset, D.},
 doi = {10.1109/OFC.2008.4528316},
 booktitle = {OFC/NFOEC 2008 - 2008 Conference on Optical Fiber Communication/National Fiber Optic Engineers Conference}
}

Restoration requirements for Ethernet services in FTTx deployments are discussed. An initial demonstration of a dual-homed GPON offering layer 2 resilience is reported along with measurements of the service disruption time. © 2007 Optical Society of America.

@inproceedings{
 title = {Restoration of ethernet services over a dual-homed GPON system - Operator and practical demonstration},
 type = {inproceedings},
 year = {2008},
 id = {f980936f-fb8f-3cd5-b139-0daf50bf30c6},
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 abstract = {Restoration requirements for Ethernet services in FTTx deployments are discussed. An initial demonstration of a dual-homed GPON offering layer 2 resilience is reported along with measurements of the service disruption time. © 2007 Optical Society of America.},
 bibtype = {inproceedings},
 author = {Kang, J. and Wilkinson, N. and Smith, K. and Nesset, D.},
 booktitle = {Optics InfoBase Conference Papers}
}

Restoration requirements for Ethernet services in FTTx deployments are discussed. An initial demonstration of a dual-homed GPON offering layer 2 resilience is reported along with measurements of the service disruption time. © 2007 Optical Society of America.

@article{
 title = {The generation challenge programme platform: Semantic standards and workbench for crop science},
 type = {article},
 year = {2008},
 volume = {2008},
 id = {68dadb36-1641-3586-bb87-75b7f978fd89},
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 abstract = {The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.},
 bibtype = {article},
 author = {Bruskiewich, R. and Senger, M. and Davenport, G. and Ruiz, M. and Rouard, M. and Hazekamp, T. and Takeya, M. and Doi, K. and Satoh, K. and Costa, M. and Simon, R. and Balaji, J. and Akintunde, A. and Mauleon, R. and Wanchana, S. and Shah, T. and Anacleto, M. and Portugal, A. and Ulat, V.J. and Thongjuea, S. and Braak, K. and Ritter, S. and Dereeper, A. and Skofic, M. and Rojas, E. and Martins, N. and Pappas, G. and Alamban, R. and Almodiel, R. and Barboza, L.H. and Detras, J. and Manansala, K. and Mendoza, M.J. and Morales, J. and Peralta, B. and Valerio, R. and Zhang, Y. and Gregorio, S. and Hermocilla, J. and Echavez, M. and Yap, J.M. and Farmer, A. and Schiltz, G. and Lee, J. and Casstevens, T. and Jaiswal, P. and Meintjes, A. and Wilkinson, M. and Good, B. and Wagner, J. and Morris, J. and Marshall, D. and Collins, A. and Kikuchi, S. and Metz, T. and McLaren, G. and Van Hintum, T.},
 doi = {10.1155/2008/369601},
 journal = {International Journal of Plant Genomics}
}

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

@inproceedings{
 title = {Tag clouds for summarizing web search results},
 type = {inproceedings},
 year = {2007},
 keywords = {evaluation},
 pages = {1203},
 websites = {http://www.cs.bell-labs.com/cm/cs/who/pfps/temp/web/www2007.org/posters/poster1046.pdf,http://portal.acm.org/citation.cfm?doid=1242572.1242766},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {507dec13-9e8e-36f9-97e9-e93258a864d8},
 created = {2014-07-02T09:11:39.000Z},
 accessed = {2015-01-15},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kuo2007},
 source_type = {inproceedings},
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 abstract = {In this paper, we describe an application, PubCloud that uses tag clouds for the summarization of results from queries over the PubMed database of biomedical literature. PubCloud responds to queries of this database with tag clouds generated from words extracted from the abstracts returned by the query. The results of a user study comparing the PubCloud tag-cloud summarization of query results with the standard result list provided by PubMed indicated that the tag cloud interface is advantageous in presenting descriptive information and in reducing user frustration but that it is less effective at the task of enabling users to discover relations between concepts.},
 bibtype = {inproceedings},
 author = {Kuo, Byron Y-L and Hentrich, Thomas and Good, Benjamin M . and Wilkinson, Mark D.},
 doi = {10.1145/1242572.1242766},
 booktitle = {Proceedings of the 16th international conference on World Wide Web - WWW '07}
}

In this paper, we describe an application, PubCloud that uses tag clouds for the summarization of results from queries over the PubMed database of biomedical literature. PubCloud responds to queries of this database with tag clouds generated from words extracted from the abstracts returned by the query. The results of a user study comparing the PubCloud tag-cloud summarization of query results with the standard result list provided by PubMed indicated that the tag cloud interface is advantageous in presenting descriptive information and in reducing user frustration but that it is less effective at the task of enabling users to discover relations between concepts.

@inproceedings{
 title = {Using a novel data transformation technique to provide the EMBOSS software suite as Semantic Web Services},
 type = {inproceedings},
 year = {2007},
 keywords = {web services},
 websites = {http://www.cis.drexel.edu/faculty/thu/bibm/BIBM07-paperlist.htm},
 month = {11},
 id = {d27477c0-e317-3ba3-80cd-86dab00781a1},
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 file_attached = {false},
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 citation_key = {Gordon2007},
 source_type = {inproceedings},
 notes = {Gordon P.M.K., Kawas E., Wilkinson M.D., Sensen C.W. (2007) Using a novel data transformation technique to provide the EMBOSS software suite as Semantic Web Services. To appear in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (San Jose, California), November 2-4, 2007 (mwilkinson 2007-10-31 17:02:49)},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Gordon, P and Kawas, E and Wilkinson, M and Sensen, C},
 booktitle = {Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine}
}

@article{
 title = {DataBiNS: Data Mining Tool for Biological Pathways and Non-Synonymous SNPs.},
 type = {article},
 year = {2007},
 keywords = {snp},
 pages = {780-782},
 volume = {23},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=17237074&dopt=Abstract},
 month = {1},
 id = {46eeb9fa-11e5-3f46-a335-969f0e91afcf},
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 citation_key = {Song2007},
 source_type = {article},
 notes = {10.1093/bioinformatics/btl648},
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 abstract = {DataBiNS is a custom-designed BioMOBY Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations, and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow Services. The use of an automated BioMOBY workflow, rather than manual ``surfing'', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMOBY Services enables fine-grained reusing of each Service in other workflows, thus reducing the effort required to achieve similar investigations in the future. AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.},
 bibtype = {article},
 author = {Song, Young and Kawas, Edward and Good, Ben and Wilkinson, Mark and Tebbutt, Scott},
 journal = {Bioinformatics},
 number = {6}
}

DataBiNS is a custom-designed BioMOBY Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations, and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow Services. The use of an automated BioMOBY workflow, rather than manual ``surfing'', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMOBY Services enables fine-grained reusing of each Service in other workflows, thus reducing the effort required to achieve similar investigations in the future. AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.

@inproceedings{
 title = {Ontology Engineering Using Volunteer Labor},
 type = {inproceedings},
 year = {2007},
 keywords = {Mark Wilkinson},
 websites = {http://www.cs.bell-labs.com/cm/cs/who/pfps/temp/web/www2007.org/posters/poster898.pdf},
 id = {678790a2-4bc5-3920-9145-23b4f956722b},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Good2007},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {We describe an approach designed to reduce the costs of ontology development through the use of untrained, volunteer knowledge engineers. Results are provided from an experiment in which volunteers were asked to judge the correctness of automatically inferred subsumption relationships in the biomedical domain. The experiment indicated that volunteers can be recruited fairly easily but that their attention is difficult to hold, that most do not understand the subsumption relationship without training, and that incorporating learned estimates of trust into voting systems is beneficial to aggregate performance},
 bibtype = {inproceedings},
 author = {Good, Benjamin and Wilkinson, Mark},
 booktitle = {Proceedings of the World Wide Web Conference (WWW2007)}
}

We describe an approach designed to reduce the costs of ontology development through the use of untrained, volunteer knowledge engineers. Results are provided from an experiment in which volunteers were asked to judge the correctness of automatically inferred subsumption relationships in the biomedical domain. The experiment indicated that volunteers can be recruited fairly easily but that their attention is difficult to hold, that most do not understand the subsumption relationship without training, and that incorporating learned estimates of trust into voting systems is beneficial to aggregate performance

@inproceedings{
 title = {From chaos to order: A generic, distributed, ontology based annotation system},
 type = {inproceedings},
 year = {2007},
 keywords = {metadata},
 pages = {141-145},
 websites = {http://bioinfo.icapture.ubc.ca/publications/ike2007_submission.pdf},
 id = {66355719-dd4d-3098-b0b0-67558ab9122c},
 created = {2014-07-02T09:11:39.000Z},
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 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
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 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kothari2007},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {This paper presents a proposed methodology for Semantic Web compatible data annotation that may be used with ontologies created using syntactic constructs provided by the Web Ontology Language (OWL). In this approach, the definitions of concepts in the ontology are used to elicit annotations for previously unordered or unclassified data instances. At every step of this iterative annotation process, the user answers a very specific question about a data instance to incrementally annotate it. This incremental annotation has the effect of iteratively classifying the instance into increasingly specialized concepts. Each question is extracted from the necessary and sufficient conditions for the concepts defined in the OWL ontology, and only “relevant” questions are posed based on the current state of annotation of that instance. The system is therefore, a proof-of-concept of the use of ontologies to guide the annotation and classification of previously unordered data. Importantly, this approach lends itself well to use in mass collaborative environments in much the same way as popular collaborative-tagging environments such as Flickr and Delicious; thus it is likely to be an extremely costeffective approach to the annotation of large volumes of instance data. A prototype application with a test OWL ontology is also discussed.},
 bibtype = {inproceedings},
 author = {Kothari, Cartik and Wilkinson, Mark},
 booktitle = {Proceedings of the 2007 International Conference on Information & Knowledge Engineering, IKE 2007, June 25-28, 2007. Las Vegas Nevada, USA}
}

This paper presents a proposed methodology for Semantic Web compatible data annotation that may be used with ontologies created using syntactic constructs provided by the Web Ontology Language (OWL). In this approach, the definitions of concepts in the ontology are used to elicit annotations for previously unordered or unclassified data instances. At every step of this iterative annotation process, the user answers a very specific question about a data instance to incrementally annotate it. This incremental annotation has the effect of iteratively classifying the instance into increasingly specialized concepts. Each question is extracted from the necessary and sufficient conditions for the concepts defined in the OWL ontology, and only “relevant” questions are posed based on the current state of annotation of that instance. The system is therefore, a proof-of-concept of the use of ontologies to guide the annotation and classification of previously unordered data. Importantly, this approach lends itself well to use in mass collaborative environments in much the same way as popular collaborative-tagging environments such as Flickr and Delicious; thus it is likely to be an extremely costeffective approach to the annotation of large volumes of instance data. A prototype application with a test OWL ontology is also discussed.

@article{
 title = {Vcsa1 Gene Peptides for the Treatment of Inflammatory and Allergic Reactions},
 type = {article},
 year = {2007},
 keywords = {patents},
 pages = {124-132},
 volume = {1},
 websites = {http://193.63.84.41/content/ben/iad/2007/00000001/00000002/art00004},
 id = {ae900436-d4bd-353d-83c2-e497f87d271b},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
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 authored = {true},
 confirmed = {true},
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 citation_key = {Morris2007},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Morris, Katherine and Kuo, Byron and Wilkinson, Mark and Davison, Joseph and Befus, Dean and Mathison, Ronald},
 journal = {Recent Patents on Inflammation & Allergy Drug Discovery},
 number = {2}
}

@inproceedings{
 title = {Ontology engineering using volunteer labor},
 type = {inproceedings},
 year = {2007},
 keywords = {Knowledge acquisition,Ontology engineering,Semantic web},
 id = {a1a93888-b19b-3f5a-a1ed-20fefb70166b},
 created = {2017-12-03T10:44:25.418Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.538Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {We describe an approach designed to reduce the costs of ontology development through the use of untrained, volunteer knowledge engineers. Results are provided from an experiment in which volunteers were asked to judge the correctness of automatically inferred subsumption relationships in the biomedical domain. The experiment indicated that volunteers can be recruited fairly easily but that their attention is difficult to hold, that most do not understand the subsumption relationship without training, and that incorporating learned estimates of trust into voting systems is beneficial to aggregate performance.},
 bibtype = {inproceedings},
 author = {Good, B.M. and Wilkinson, M.D.},
 doi = {10.1145/1242572.1242787},
 booktitle = {16th International World Wide Web Conference, WWW2007}
}

We describe an approach designed to reduce the costs of ontology development through the use of untrained, volunteer knowledge engineers. Results are provided from an experiment in which volunteers were asked to judge the correctness of automatically inferred subsumption relationships in the biomedical domain. The experiment indicated that volunteers can be recruited fairly easily but that their attention is difficult to hold, that most do not understand the subsumption relationship without training, and that incorporating learned estimates of trust into voting systems is beneficial to aggregate performance.

@article{
 title = {DataBiNS: A BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs},
 type = {article},
 year = {2007},
 volume = {23},
 id = {1c964f19-5bf6-3813-b20a-c47a285c24b6},
 created = {2017-12-03T10:44:26.037Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.498Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Summary: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual 'surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. © 2007 Oxford University Press.},
 bibtype = {article},
 author = {Song, Y.C. and Kawas, E. and Good, B.M. and Wilkinson, M.D. and Tebbutt, S.J.},
 doi = {10.1093/bioinformatics/btl648},
 journal = {Bioinformatics},
 number = {6}
}

Summary: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual 'surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. © 2007 Oxford University Press.

@article{
 title = {Designing a 21st and 22nd century fibre broadband access network},
 type = {article},
 year = {2007},
 volume = {25},
 id = {69730548-df7d-3c36-80c1-e1c6643a244c},
 created = {2017-12-03T10:44:26.095Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.234Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {DSL technology has been incredibly successful at allowing copper telephony wires to deliver broadband services. However, the physics of copper dictate that as speeds increase further it will be necessary to push optical fibre closer to the customer - to the cabinet, and ultimately to the premises. Deploying optical fibre to the mass consumer is well known as representing a significant capital investment and will take many years to deploy. It would be fair to say that putting fibre in the residential access network is a 'once in a century' investment. There are many different choices of 'high fibre' broadband access systems and as technology develops further, this situation is likely to continue. When operators deploy fibre in the access network, it is therefore vital that they do so in a future-proof manner which can support technologies and architectures yet to come, and allow migration and further evolution. © Springer Science+Business Media, Inc. 2007.},
 bibtype = {article},
 author = {Davey, R.P. and Payne, D. and Barker, P. and Smith, K. and Wilkinson, M. and Gunning, P.},
 doi = {10.1007/s10550-007-0062-0},
 journal = {BT Technology Journal},
 number = {3-4}
}

DSL technology has been incredibly successful at allowing copper telephony wires to deliver broadband services. However, the physics of copper dictate that as speeds increase further it will be necessary to push optical fibre closer to the customer - to the cabinet, and ultimately to the premises. Deploying optical fibre to the mass consumer is well known as representing a significant capital investment and will take many years to deploy. It would be fair to say that putting fibre in the residential access network is a 'once in a century' investment. There are many different choices of 'high fibre' broadband access systems and as technology develops further, this situation is likely to continue. When operators deploy fibre in the access network, it is therefore vital that they do so in a future-proof manner which can support technologies and architectures yet to come, and allow migration and further evolution. © Springer Science+Business Media, Inc. 2007.

@article{
 title = {Low boil-off HTS current leads},
 type = {article},
 year = {2007},
 keywords = {Cryogen free magnet,Current leads,High temperature superconductors},
 volume = {17},
 id = {459ca7e8-4eb4-3d07-8ded-756bfe1c5767},
 created = {2017-12-03T10:44:26.547Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.084Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {HTS based leads have established themselves for high current carrying applications. This work revisits the issues for commercial magnets with a view to minimizing heat load and space for both the resistive and HTS parts. The paper describes the experimental work carried out to develop up to 300 A HTS current leads for Oxford Instruments' Cryofree and liquid helium cooled magnets. The current-voltage, temperature, and quench measurements are reported. The leads make use of BSCCO-2223 HTS wire and have been characterized at 4.2 K, 77 K, and some intermediate temperatures for quench purposes to test their robustness. The leads are in thermal equilibrium with their environment and require no additional cooling, unlike in the case of large current leads for accelerator magnets. The current work on the combined resistive and HTS parts has achieved a boil-off of 20 ml/hr in a liquid cooled cryostat. © 2007 IEEE.},
 bibtype = {article},
 author = {Lakrimi, M. and Brown, J. and Cetnik, P. and Wilkinson, M. and Clapton, D. and Fair, R. and Smith, K. and Noonan, P.},
 doi = {10.1109/TASC.2007.898102},
 journal = {IEEE Transactions on Applied Superconductivity},
 number = {2}
}

HTS based leads have established themselves for high current carrying applications. This work revisits the issues for commercial magnets with a view to minimizing heat load and space for both the resistive and HTS parts. The paper describes the experimental work carried out to develop up to 300 A HTS current leads for Oxford Instruments' Cryofree and liquid helium cooled magnets. The current-voltage, temperature, and quench measurements are reported. The leads make use of BSCCO-2223 HTS wire and have been characterized at 4.2 K, 77 K, and some intermediate temperatures for quench purposes to test their robustness. The leads are in thermal equilibrium with their environment and require no additional cooling, unlike in the case of large current leads for accelerator magnets. The current work on the combined resistive and HTS parts has achieved a boil-off of 20 ml/hr in a liquid cooled cryostat. © 2007 IEEE.

@article{
 title = {Vcsa1 gene peptides for the treatment of inflammatory and allergic reactions.},
 type = {article},
 year = {2007},
 volume = {1},
 id = {88de51dc-3aa1-3b47-bf3f-c7fa52732889},
 created = {2018-04-19T19:34:46.775Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2018-07-06T08:42:56.715Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The recently emerged Vcsa1 gene is one member of the variable coding sequence (VCS) multigene family of Rattus norvegicus. This gene encodes the precursor prohormone SMR1 (submandibular rat-1), which on enzymatic processing gives rise to several 5 to 11 amino acid peptides that modulate a variety of physiological functions. The analgesic pentapeptide sialorphin and anti-inflammatory heptapeptide submandibular gland peptide-T (TDIFEGG) are the most intensively studied. Although the Vcsa1 gene and its protein product are unique to rats, TDIFEGG or a derivative acts on all species examined to date, including human cells, in functions related to allergic reactions and inflammation. In this review, the patent and academic literature on SMR1 and its natural peptides and their derivatives are reviewed for consideration of biological targets and relevance to the development of novel therapeutic agents. The VCS gene family is discussed and we speculate on possible human homologs of these potent anti-inflammatory rat-derived peptides. The biologically active peptide products of SMR1 are considered and the mechanism of action and structure-activity relationships of the anti-inflammatory submandibular gland peptide-T and its derivatives are discussed.},
 bibtype = {article},
 author = {Morris, K. and Kuo, B. and Wilkinson, M.D. and Davison, J.S. and Befus, A.D. and Mathison, R.D.},
 journal = {Recent patents on inflammation & allergy drug discovery},
 number = {2}
}

The recently emerged Vcsa1 gene is one member of the variable coding sequence (VCS) multigene family of Rattus norvegicus. This gene encodes the precursor prohormone SMR1 (submandibular rat-1), which on enzymatic processing gives rise to several 5 to 11 amino acid peptides that modulate a variety of physiological functions. The analgesic pentapeptide sialorphin and anti-inflammatory heptapeptide submandibular gland peptide-T (TDIFEGG) are the most intensively studied. Although the Vcsa1 gene and its protein product are unique to rats, TDIFEGG or a derivative acts on all species examined to date, including human cells, in functions related to allergic reactions and inflammation. In this review, the patent and academic literature on SMR1 and its natural peptides and their derivatives are reviewed for consideration of biological targets and relevance to the development of novel therapeutic agents. The VCS gene family is discussed and we speculate on possible human homologs of these potent anti-inflammatory rat-derived peptides. The biologically active peptide products of SMR1 are considered and the mechanism of action and structure-activity relationships of the anti-inflammatory submandibular gland peptide-T and its derivatives are discussed.

@article{
 title = {Gbrowse Moby: A Web-based browser for BioMOBY Services},
 type = {article},
 year = {2006},
 keywords = {Mark Wilkinson},
 pages = {4},
 volume = {1},
 websites = {http://www.scfbm.org/content/1/1/4},
 month = {10},
 id = {8e2b1a45-65ab-3959-af90-e478cda2c7ec},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2006},
 source_type = {article},
 notes = {10.1186/1751-0473-1-4},
 private_publication = {false},
 abstract = {The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of October, 2006, approximately 850 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client - Gbrowse Moby - that allows users to discover and surf from one bioinformatics service to the next using a semantically-aided browsing interface.},
 bibtype = {article},
 author = {Wilkinson, Mark},
 journal = {Source Code for Biology and Medicine},
 number = {1}
}

The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of October, 2006, approximately 850 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client - Gbrowse Moby - that allows users to discover and surf from one bioinformatics service to the next using a semantically-aided browsing interface.

@article{
 title = {iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website},
 type = {article},
 year = {2006},
 keywords = {Mark Wilkinson},
 pages = {534},
 volume = {7},
 websites = {http://www.biomedcentral.com/1471-2105/7/534/abstract},
 month = {12},
 id = {04d62303-5d23-339f-ac66-67d2cdea37d0},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Good2006c},
 source_type = {article},
 notes = {10.1186/1471-2105-7-534},
 private_publication = {false},
 bibtype = {article},
 author = {Good, Benjamin and Kawas, Edward and Kuo, Byron and Wilkinson, Mark},
 journal = {BMC Bioinformatics},
 number = {1}
}

@article{
 title = {BioMoby extensions to the Taverna workflow management and enactment software},
 type = {article},
 year = {2006},
 keywords = {Mark Wilkinson},
 pages = {523},
 volume = {7},
 websites = {http://www.biomedcentral.com/1471-2105/7/523/abstract},
 month = {11},
 id = {0a134973-cdc9-30ed-974b-65c5c7f2c910},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kawas2006},
 source_type = {article},
 notes = {10.1186/1471-2105-7-523},
 private_publication = {false},
 abstract = {As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.},
 bibtype = {article},
 author = {Kawas, Edward and Senger, Martin and Wilkinson, Mark},
 journal = {BMC Bioinformatics},
 number = {1}
}

As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.

@article{
 title = {Fast, cheap and out of control: a zero curation model for ontology development.},
 type = {article},
 year = {2006},
 keywords = {curation},
 pages = {128-139},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17094234&query_hl=5&itool=pubmed_docsum},
 id = {eeb77893-ef79-375c-be58-e27257c78b6f},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Good2006b},
 source_type = {article},
 private_publication = {false},
 abstract = {During two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. These volunteers created a shared vocabulary of 661 terms, linking these terms to each other and to a pre-existing upper ontology by adding 245 hyponym relationships and 340 synonym relationships. While ontology-building has proved to be an expensive and labor-intensive process using most existing methodologies, the rudimentary ontology constructed in this study was composed in only two days at a cost of only 3 t-shirts, 4 coffee mugs, and one chocolate moose. The protocol used to create and evaluate this ontology involved a targeted, web-based interface. The design and implementation of this protocol is discussed along with quantitative and qualitative assessments of the constructed ontology.},
 bibtype = {article},
 author = {Good, Benjamin and Tranfield, Erin and Tan, Poh and Shehata, Marlene and Singhera, Gurpreet and Gosselink, John and Okon, Elena and Wilkinson, Mark},
 journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}
}

During two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. These volunteers created a shared vocabulary of 661 terms, linking these terms to each other and to a pre-existing upper ontology by adding 245 hyponym relationships and 340 synonym relationships. While ontology-building has proved to be an expensive and labor-intensive process using most existing methodologies, the rudimentary ontology constructed in this study was composed in only two days at a cost of only 3 t-shirts, 4 coffee mugs, and one chocolate moose. The protocol used to create and evaluate this ontology involved a targeted, web-based interface. The design and implementation of this protocol is discussed along with quantitative and qualitative assessments of the constructed ontology.

@article{
 title = {The Life Sciences Semantic Web is Full of Creeps!},
 type = {article},
 year = {2006},
 keywords = {semantic web},
 pages = {275-286},
 volume = {7},
 websites = {http://bib.oxfordjournals.org/cgi/content/abstract/bbl025?ijkey=QgZhvAQ4xvjfqzK&},
 month = {8},
 id = {a3b59294-812c-32f5-8862-138d26435245},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Good2006a},
 source_type = {article},
 notes = {10.1093/bib/bbl025},
 private_publication = {false},
 abstract = {The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as ‘semantic creep’—timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers.},
 bibtype = {article},
 author = {Good, Benjamin and Wilkinson, Mark},
 journal = {Briefings in bioinformatics},
 number = {3}
}

The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as ‘semantic creep’—timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers.

@article{
 title = {Designing an 'adaptive' enterprise architecture},
 type = {article},
 year = {2006},
 volume = {24},
 id = {68111a53-e2cd-3144-a4fd-54fa21361001},
 created = {2017-12-03T10:44:25.316Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.329Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Businesses today are under ever more intense pressure, that extends beyond just increasing shareholder value. Commoditisation in core businesses is a problem, compounded further by regulatory requirements and controls, and increased competition. With new opportunities in diverse markets and geographies, information technology (IT) needs to once again become the business's saviour. Core to the new IT is an enterprise architecture spanning people, processes and technology. In this paper we introduce the aspects of governance, process and technology required to successfully transform IT into the business's champion. © Springer Science+Business Media, Inc. 2006.},
 bibtype = {article},
 author = {Wilkinson, M.},
 doi = {10.1007/s10550-006-0099-5},
 journal = {BT Technology Journal},
 number = {4}
}

Businesses today are under ever more intense pressure, that extends beyond just increasing shareholder value. Commoditisation in core businesses is a problem, compounded further by regulatory requirements and controls, and increased competition. With new opportunities in diverse markets and geographies, information technology (IT) needs to once again become the business's saviour. Core to the new IT is an enterprise architecture spanning people, processes and technology. In this paper we introduce the aspects of governance, process and technology required to successfully transform IT into the business's champion. © Springer Science+Business Media, Inc. 2006.

@article{
 title = {Meeting business objectives through adaptive information and communications technology},
 type = {article},
 year = {2006},
 volume = {24},
 id = {4ba331d2-9809-3424-8a7a-8a05052a9ffa},
 created = {2017-12-03T10:44:25.512Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.118Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Today's information and communications technology infrastructure can be used by businesses in a much more flexible and dynamic manner allowing elements of the infrastructure to be dynamically allocated to business processes as they are needed. This has the effect of increasing the efficiency of the underlying infrastructure and making better use of the available resources. Some challenges still remain, however, in linking the performance of the underlying infrastructure to the business objectives. In order to provide this linkage, there is a need to integrate the control of all the elements (from network to application) in the infrastructure. This integrated monitoring and control is still at an early stage of maturity. This paper considers the challenges that these requirements present and examines some of the independent work that has been done in both BT and HP and which has already led to product developments, as well as highlighting some of the challenges that still remain to be solved in the industry. © Springer Science+Business Media, Inc. 2006.},
 bibtype = {article},
 author = {Di Vitantonio, G. and Legh-Smith, J. and Millar, W. and Wilkinson, M.},
 doi = {10.1007/s10550-006-0101-2},
 journal = {BT Technology Journal},
 number = {4}
}

Today's information and communications technology infrastructure can be used by businesses in a much more flexible and dynamic manner allowing elements of the infrastructure to be dynamically allocated to business processes as they are needed. This has the effect of increasing the efficiency of the underlying infrastructure and making better use of the available resources. Some challenges still remain, however, in linking the performance of the underlying infrastructure to the business objectives. In order to provide this linkage, there is a need to integrate the control of all the elements (from network to application) in the infrastructure. This integrated monitoring and control is still at an early stage of maturity. This paper considers the challenges that these requirements present and examines some of the independent work that has been done in both BT and HP and which has already led to product developments, as well as highlighting some of the challenges that still remain to be solved in the industry. © Springer Science+Business Media, Inc. 2006.

@article{
 title = {Multiservice Ethernet access},
 type = {article},
 year = {2006},
 volume = {24},
 id = {2cb2baa3-8ce1-3231-9346-9356d49730f6},
 created = {2017-12-03T10:44:25.941Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.790Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Ethernet is evolving from its origins in the local area network into a cost-effective and reliable wide area network technology. Market research shows that business customers are moving away from traditional leased lines and selecting Ethernet as the access network technology of choice due to its low cost, simplicity and flexibility. Developments in Ethernet technology are now offering service providers the opportunity to deliver cost-effective carrier class Ethernet services. In particular, a new generation of Ethernet network termination equipment (NTE) is emerging which provides remote management, flexible bandwidth and fault diagnosis while supporting access to multiple services delivered over a single physical connection. This paper describes the a dvantages and potential cost savings of using Ethernet in the access network. A case study for a city demonstrates significant capital expenditure cost savings and highlights the advantages of using new Ethernet NTEs, which can be up to ten times cheaper than SDH technology, delivering equivalent bandwidth. Remote management and fault diagnosis features can also reduce operational expenditure by avoiding unnecessary site visits. A network architecture is presented which supports delivery of Ethernet services over a combination of circuit-switched and packet-switched domains. New standards which are maturing in the IETF, IEEE and ITU to support Ethernet delivery of interoperable services with carrier class reliability are also discussed. © Springer Science+Business Media, Inc. 2006.},
 bibtype = {article},
 author = {Gunning, P. and Wilkinson, M. and Rragami, L. and Semnani, S. and Smith, K.},
 doi = {10.1007/s10550-006-0041-x},
 journal = {BT Technology Journal},
 number = {2}
}

Ethernet is evolving from its origins in the local area network into a cost-effective and reliable wide area network technology. Market research shows that business customers are moving away from traditional leased lines and selecting Ethernet as the access network technology of choice due to its low cost, simplicity and flexibility. Developments in Ethernet technology are now offering service providers the opportunity to deliver cost-effective carrier class Ethernet services. In particular, a new generation of Ethernet network termination equipment (NTE) is emerging which provides remote management, flexible bandwidth and fault diagnosis while supporting access to multiple services delivered over a single physical connection. This paper describes the a dvantages and potential cost savings of using Ethernet in the access network. A case study for a city demonstrates significant capital expenditure cost savings and highlights the advantages of using new Ethernet NTEs, which can be up to ten times cheaper than SDH technology, delivering equivalent bandwidth. Remote management and fault diagnosis features can also reduce operational expenditure by avoiding unnecessary site visits. A network architecture is presented which supports delivery of Ethernet services over a combination of circuit-switched and packet-switched domains. New standards which are maturing in the IETF, IEEE and ITU to support Ethernet delivery of interoperable services with carrier class reliability are also discussed. © Springer Science+Business Media, Inc. 2006.

@article{
 title = {Erratum: In situ experimental technique for measurement of temperature and current distribution in proton exchange membrane fuel cells (Electrochemical and Solid-State Letters (2006) 9 (A507))},
 type = {article},
 year = {2006},
 volume = {9},
 id = {36f3c91b-a371-3540-ba7f-01dd5efe45ad},
 created = {2017-12-03T10:44:26.277Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:53.551Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Wilkinson, M. and Blanco, M. and Gu, E. and Martin, J.J. and Wilkinson, D.P. and Zhang, J.J. and Wang, H.},
 doi = {10.1149/1.2357872},
 journal = {Electrochemical and Solid-State Letters},
 number = {11}
}

@article{
 title = {In situ experimental technique for measurement of temperature and current distribution in proton exchange membrane fuel cells},
 type = {article},
 year = {2006},
 volume = {9},
 id = {ef406561-1105-3902-9322-fb73f433972c},
 created = {2017-12-03T10:44:26.439Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:55.486Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Current distribution data is vital for improved fuel cell designs and improved performance. However, none of the common current mapping techniques is simple to perform and often compromise the design and operation of the fuel cell. By comparison, local temperature measurements with thermocouples are easier to set up and can be done in an unobtrusive way with minimal impact on the fuel cell. Our results show that current mapping can be indirectly conducted through local temperature measurements and have the potential to provide in situ high-resolution data capable of following load cycling and use in real applications. © 2006 The Electrochemical Society. All rights reserved.},
 bibtype = {article},
 author = {Wilkinson, M. and Blanco, M. and Gu, E. and Martin, J.J. and Wilkinson, D.P. and Zhang, J.J. and Wang, H.},
 doi = {10.1149/1.2338769},
 journal = {Electrochemical and Solid-State Letters},
 number = {11}
}

Current distribution data is vital for improved fuel cell designs and improved performance. However, none of the common current mapping techniques is simple to perform and often compromise the design and operation of the fuel cell. By comparison, local temperature measurements with thermocouples are easier to set up and can be done in an unobtrusive way with minimal impact on the fuel cell. Our results show that current mapping can be indirectly conducted through local temperature measurements and have the potential to provide in situ high-resolution data capable of following load cycling and use in real applications. © 2006 The Electrochemical Society. All rights reserved.

@article{
 title = {Designing a 21st and 22nd century fibre broadband access network},
 type = {article},
 year = {2006},
 volume = {24},
 id = {cb835af5-a6df-3f2f-977e-02273f064b2d},
 created = {2017-12-03T10:44:26.496Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.410Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {DSL technology has been incredibly successful at allowing copper telephony wires to deliver broadband services. However, the physics of copper dictates that as speeds increase further it will be necessary to push optical fibre closer to the customer - to the cabinet, and ultimately to the premises. Deploying optical fibre to the mass consumer is well known as representing a significant capital investment and will take many years to deploy. It would be fair to say that putting fibre in the residential access network is a 'once in a century' investment. There are many different choices of 'high fibre' broadband access systems and as technology develops further, this situation is likely to continue. When operators deploy fibre in the access network, it is therefore vital that they do so in a future-proof manner which can support technologies and architectures yet to come, and allow migration and further evolution. © Springer Science+Business Media, Inc. 2006.},
 bibtype = {article},
 author = {Davey, R. and Payne, D. and Barker, P. and Smith, K. and Wilkinson, M. and Gunning, P.},
 doi = {10.1007/s10550-006-0039-4},
 journal = {BT Technology Journal},
 number = {2}
}

DSL technology has been incredibly successful at allowing copper telephony wires to deliver broadband services. However, the physics of copper dictates that as speeds increase further it will be necessary to push optical fibre closer to the customer - to the cabinet, and ultimately to the premises. Deploying optical fibre to the mass consumer is well known as representing a significant capital investment and will take many years to deploy. It would be fair to say that putting fibre in the residential access network is a 'once in a century' investment. There are many different choices of 'high fibre' broadband access systems and as technology develops further, this situation is likely to continue. When operators deploy fibre in the access network, it is therefore vital that they do so in a future-proof manner which can support technologies and architectures yet to come, and allow migration and further evolution. © Springer Science+Business Media, Inc. 2006.

@article{
 title = {BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case.},
 type = {article},
 year = {2005},
 keywords = {Mark Wilkinson},
 pages = {5-17},
 volume = {138},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15888673},
 month = {5},
 id = {2b3052bb-0186-3283-bd6e-1638d443f1d0},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2005},
 source_type = {article},
 notes = {10.1104/pp.104.059170},
 private_publication = {false},
 bibtype = {article},
 author = {Wilkinson, Mark and Schoof, Heiko and Ernst, Rebecca and Haase, Dirk},
 journal = {Plant physiology.},
 number = {1}
}

@article{
 title = {Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum},
 type = {article},
 year = {2004},
 keywords = {Mark Wilkinson},
 pages = {3},
 volume = {4},
 websites = {http://www.biomedcentral.com/1471-2229/4/3/},
 month = {3},
 id = {cbeed114-9d2b-3d6d-aecd-8b6bfe814b84},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Henry2004},
 source_type = {article},
 notes = {10.1186/1471-2229-4-3},
 private_publication = {false},
 bibtype = {article},
 author = {Henry, Isabelle and Wilkinson, Mark and Hernandez, J and Schwarz-Sommer, Zsuzsanna and Grotewold, Erich and Mandoli, Dina},
 journal = {BMC Plant Biology},
 number = {1}
}

@article{
 title = {Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt},
 type = {article},
 year = {2004},
 keywords = {Mark Wilkinson},
 pages = {350-364},
 volume = {3298},
 websites = {http://www.springerlink.com/openurl.asp?genre=article&id=1B7B409W0LW92326},
 month = {1},
 id = {fcde783a-b5ac-3dcf-97b6-161c9a03ceff},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Lord2004},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Lord, Phillip and Bechhofer, Sean and Wilkinson, Mark and Schiltz, Gary and Gessler, Damian and Hull, Duncan and Goble, Carole and Stein, Lincoln},
 journal = {Lecture Notes in Computer Science}
}

@inproceedings{
 title = {The BioMOBY Project Explores Open-Source, Simple, Extensible Protocols for Enabling Biological Database Interoperability},
 type = {inproceedings},
 year = {2003},
 keywords = {moby 1.0},
 pages = {16-26},
 volume = {3},
 websites = {http://biomoby.org/VCGB_130.pdf},
 id = {afa83b09-c9f5-35f2-8541-8c0ac408d0eb},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2003},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Wilkinson, Mark and Gessler, Damian and Farmer, Andrew and Sten, Lincoln},
 booktitle = {Proceedings of the Virtual Conference on Genomics and Bioinformatics, 2003}
}

@article{
 title = {BioMOBY: an open source biological web services proposal.},
 type = {article},
 year = {2002},
 keywords = {moby 1.0},
 pages = {331-341},
 volume = {3},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12511062&query_hl=1&itool=pubmed_docsum},
 month = {12},
 id = {49c87398-686d-3d93-84c5-07b3e24b42f6},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2002b},
 source_type = {article},
 private_publication = {false},
 abstract = {The original BioMOBY paper},
 bibtype = {article},
 author = {Wilkinson, Mark and Links, Matthew},
 doi = {10.1093/bib/3.4.331},
 journal = {Briefings in Bioinformatics},
 number = {4}
}

The original BioMOBY paper

@article{
 title = {Genquire: genome annotation browser/editor},
 type = {article},
 year = {2002},
 keywords = {bioperl},
 pages = {1398},
 volume = {18},
 websites = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1398},
 id = {340be55a-3ca8-308a-a346-186fab37260a},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
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 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2002a},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Wilkinson, M and Block, D and Crosby, W},
 journal = {Bioinformatics},
 number = {10}
}

@article{
 title = {The Bioperl Toolkit: Perl Modules for the Life Sciences},
 type = {article},
 year = {2002},
 keywords = {bioperl},
 pages = {1611-1618},
 volume = {12},
 websites = {http://www.genome.org/cgi/content/abstract/12/10/1611},
 month = {10},
 id = {faafab33-d70e-37c8-9b3e-a0aeb2830f16},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Stajich2002},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Stajich, Jason and Block, David and Boulez, Kris and Brenner, Steven and Chervitz, Stephen and Dagdigian, Chris and Fuellen, Georg and Gilbert, James and Korf, Ian and Lapp, Hilmar and Lehvaslaiho, Heikki and Matsalla, Chad and Mungall, Chris and Osborne, Brian and Pocock, Matthew and Schattner, Peter and Senger, Martin and Stein, Lincoln and Stupka, Elia and Wilkinson, Mark and Birney, Ewan},
 journal = {Genome Research},
 number = {10}
}

@article{
 title = {CHORIPETALA and DESPENTEADO: general regulators during plant development and potential floral targets of FIMBRIATA-mediated degradation},
 type = {article},
 year = {2000},
 keywords = {antirrhinum},
 pages = {3725-3734},
 volume = {127},
 websites = {http://dev.biologists.org/cgi/content/abstract/127/17/3725},
 month = {9},
 id = {d1c13421-4295-3189-83a3-1611e84d8656},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson2000},
 source_type = {article},
 private_publication = {false},
 abstract = {Two Antirrhinum majus mutants, choripetala (cho) and despenteado (desp), exhibit identical highly pleiotropic phenotypes including petaloid transformation of first whorl floral organs, narrowing of both vegetative and floral organs, reduction in carpel size and fertility and delayed germination. The petaloid first whorl results from ectopic expression of the class B genes DEFICIENS and GLOBOSA and is correlated with the ectopic expression of the proposed class B/C gene regulator FIMBRIATA (FIM). Ectopic class B gene expression is apparent from the earliest point at which class B gene transcription can be detected in the wild type, indicating that the pre-patterning of the class B domain has been disrupted in these mutants. Single and double mutant analyses indicate that CHO and DESP also play a role in regulation of the class C domain. Interestingly, the cho and desp mutations partially suppress the phenotype of fim null mutants, suggesting that the F-box protein FIM may target a member of the CHO/DESP pathway for degradation. We propose that CHO and DESP are members of a 'basal regulatory function' influencing many processes throughout plant development and in particular are directly or indirectly required for the repression of class B and C genes during early stages of flower development.},
 bibtype = {article},
 author = {Wilkinson, M and Silva, Eda and Zachgo, S and Saedler, H and Schwarz-Sommer, Z},
 journal = {Development},
 number = {17}
}

Two Antirrhinum majus mutants, choripetala (cho) and despenteado (desp), exhibit identical highly pleiotropic phenotypes including petaloid transformation of first whorl floral organs, narrowing of both vegetative and floral organs, reduction in carpel size and fertility and delayed germination. The petaloid first whorl results from ectopic expression of the class B genes DEFICIENS and GLOBOSA and is correlated with the ectopic expression of the proposed class B/C gene regulator FIMBRIATA (FIM). Ectopic class B gene expression is apparent from the earliest point at which class B gene transcription can be detected in the wild type, indicating that the pre-patterning of the class B domain has been disrupted in these mutants. Single and double mutant analyses indicate that CHO and DESP also play a role in regulation of the class C domain. Interestingly, the cho and desp mutations partially suppress the phenotype of fim null mutants, suggesting that the F-box protein FIM may target a member of the CHO/DESP pathway for degradation. We propose that CHO and DESP are members of a 'basal regulatory function' influencing many processes throughout plant development and in particular are directly or indirectly required for the repression of class B and C genes during early stages of flower development.

@article{
 title = {Floral meristem identity and the A function in Antirrhinum},
 type = {article},
 year = {1998},
 keywords = {antirrhinum},
 pages = {41-43},
 volume = {25},
 websites = {http://www.ulg.ac.be/fnl/fnl25/fnl25abstr6.html},
 id = {f13d3d6e-25eb-3234-941c-ee1fcc6a55cd},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Motte1998},
 source_type = {article},
 private_publication = {false},
 abstract = {Class A activity, as defined in the Arabidopsis ABC model, has so far not been observed in Antirrhinum. Although the Antirrhinum class A homologues exhibit both FLIP (Floral Initiation Process) and cadastral functions, no loss-of-function phenotype has so far been identified which can separate the determination of the first floral whorl from the determination of the flower itself. Thus it would appear that, in this species, these 2 functions are linked.},
 bibtype = {article},
 author = {Motte, P and Wilkinson, M and Schwarz-Sommer, Z},
 journal = {The Flowering Newsletter},
 number = {6}
}

Class A activity, as defined in the Arabidopsis ABC model, has so far not been observed in Antirrhinum. Although the Antirrhinum class A homologues exhibit both FLIP (Floral Initiation Process) and cadastral functions, no loss-of-function phenotype has so far been identified which can separate the determination of the first floral whorl from the determination of the flower itself. Thus it would appear that, in this species, these 2 functions are linked.

@article{
 title = {Different Roles of Flowering-Time Genes in the Activation of Floral Initiation Genes in Arabidopsis},
 type = {article},
 year = {1997},
 keywords = {Arabidopsis},
 pages = {1921-1934},
 volume = {9},
 websites = {http://www.plantcell.org/cgi/content/abstract/9/11/1921},
 month = {11},
 id = {c019cba5-07ca-32b3-99b8-dca1b61b691c},
 created = {2014-07-02T09:11:39.000Z},
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 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Ruiz-Garcia1997},
 source_type = {article},
 notes = {10.1105/tpc.9.11.1921},
 private_publication = {false},
 abstract = {We have analyzed double mutants that combine late-flowering mutations at four flowering-time loci (FVE, FPA, FWA, and FT) with mutations at the LEAFY (LFY), APETALA1 (AP1), and TERMINAL FLOWER1 (TFL1) loci involved in the floral initiation process (FLIP). Double mutants between ft-1 or fwa-1 and lfy-6 completely lack flowerlike structures, indicating that both FWA and FT act redundantly with LFY to control AP1. Moreover, the phenotypes of ft-1 ap1-1 and fwa-1 ap1-1 double mutants are reminiscent of the phenotype of ap1-1 cal-1 double mutants, suggesting that FWA and FT could also be involved in the control of other FLIP genes. Such extreme phenotypes were not observed in double mutants between fve-2 or fpa-1 and lfy-6 or ap1-1. Each of these showed a phenotype similar to that of ap1-1 or lfy-6 mutants grown under noninductive photoperiods, suggesting a redundant interaction with FLIP genes. Finally, the phenotype of double mutants combining the late-flowering mutations with tfl1-2 were also consistent with the different roles of flowering-time genes.},
 bibtype = {article},
 author = {Ruiz-Garcia, L and Madueno, F and Wilkinson, M and Haughn, G and Salinas, J and Martinez-Zapater, J M},
 journal = {THE PLANT CELL},
 number = {11}
}

We have analyzed double mutants that combine late-flowering mutations at four flowering-time loci (FVE, FPA, FWA, and FT) with mutations at the LEAFY (LFY), APETALA1 (AP1), and TERMINAL FLOWER1 (TFL1) loci involved in the floral initiation process (FLIP). Double mutants between ft-1 or fwa-1 and lfy-6 completely lack flowerlike structures, indicating that both FWA and FT act redundantly with LFY to control AP1. Moreover, the phenotypes of ft-1 ap1-1 and fwa-1 ap1-1 double mutants are reminiscent of the phenotype of ap1-1 cal-1 double mutants, suggesting that FWA and FT could also be involved in the control of other FLIP genes. Such extreme phenotypes were not observed in double mutants between fve-2 or fpa-1 and lfy-6 or ap1-1. Each of these showed a phenotype similar to that of ap1-1 or lfy-6 mutants grown under noninductive photoperiods, suggesting a redundant interaction with FLIP genes. Finally, the phenotype of double mutants combining the late-flowering mutations with tfl1-2 were also consistent with the different roles of flowering-time genes.

@inproceedings{
 title = {Continuous wave CO<inf>2</inf>laser induced damage thresholds in optical components},
 type = {inproceedings},
 year = {1997},
 keywords = {CO laser 2,Damage threshold,High power,Infra-red,Optical components,Surface absorption},
 volume = {3244},
 id = {c1a73a3f-03d6-328c-a040-c0f55c68ef93},
 created = {2017-12-03T10:44:26.651Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-12-12T09:00:54.050Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The measurement of intrinsic laser induced damage thresholds (LIDT) in optical components for continuous wave (CW) CO 2 radiation has been investigated. A combination of analytical and numerical models showed that the temperature rise is mainly determined by the surface absorption in transmissive as well as reflective components, and is proportional to the ratio of power to linear dimension (P/d) of the irradiated spot rather than to the conventional power/area (P/d 2 ) parameter. The former ratio therefore represents the correct power scaling law for LIDT measurement in CW laser systems. The precise time domain within which this law holds is a function of spot diameter. This prediction has been confirmed by experimental LIDT tests on well characterised uncoated ZnSe substrates and copper mirrors, and on coated ZnSe windows and copper mirrors. Measured P/d values, though lower than predicted by modelling are considerably higher than those inferred from the technical literature, and show that transmissive components may be used at much higher powers than are at present believed. The results indicate that surface absorption occurs primarily in the sub-surface processing layer. This has been shown by transmission electron microscopy and spectroscopic ellipsometry to be a few hundred nm in depth.},
 bibtype = {inproceedings},
 author = {Puttick, K. and Holm, R. and Ristau, D. and Natzschka, U. and Kiriakidis, G. and Garawal, N. and Judd, E. and Holland, D. and Greening, D. and Ellis, N. and Wilkinson, M. and Pamies, M.G. and Sanviti, C.},
 doi = {10.1117/12.307045},
 booktitle = {Proceedings of SPIE - The International Society for Optical Engineering}
}

The measurement of intrinsic laser induced damage thresholds (LIDT) in optical components for continuous wave (CW) CO 2 radiation has been investigated. A combination of analytical and numerical models showed that the temperature rise is mainly determined by the surface absorption in transmissive as well as reflective components, and is proportional to the ratio of power to linear dimension (P/d) of the irradiated spot rather than to the conventional power/area (P/d 2 ) parameter. The former ratio therefore represents the correct power scaling law for LIDT measurement in CW laser systems. The precise time domain within which this law holds is a function of spot diameter. This prediction has been confirmed by experimental LIDT tests on well characterised uncoated ZnSe substrates and copper mirrors, and on coated ZnSe windows and copper mirrors. Measured P/d values, though lower than predicted by modelling are considerably higher than those inferred from the technical literature, and show that transmissive components may be used at much higher powers than are at present believed. The results indicate that surface absorption occurs primarily in the sub-surface processing layer. This has been shown by transmission electron microscopy and spectroscopic ellipsometry to be a few hundred nm in depth.

@article{
 title = {Different roles of flowering-time genes in the activation of floral initiation genes in Arabidopsis},
 type = {article},
 year = {1997},
 volume = {9},
 id = {33b793ad-379e-35ac-9e2c-27b585fb4238},
 created = {2018-04-21T01:44:54.170Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2018-07-06T08:42:56.713Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {We have analyzed double mutants that combine late-flowering mutations at four flowering-time loci (FVE, FPA, FWA, and FT) with mutations at the LEAFY (LFY), APETALA 1 (AP1), and TERMINAL FLOWER1 (TFL 1) loci involved in the floral initiation process (FLIP). Double mutants between ft-1 or fwa-1 and lfy-6 completely lack flowerlike structures, indicating that both FWA and FT act redundantly with LFY to control AP1. Moreover, the phenotypes of ft-1 ap1-1 and fwa-1 apt-1 double mutants are reminiscent of the phenotype of ap1-1 cal-1 double routants, suggesting that FWA and FT could also  be involved in the control of other FLIP genes. Such extreme phenotypes were not observed in double mutants between fve-2 or fpa-1 and lfy-6 or ap1-1. Each of these showed a phenotype similar to that of ap1-1 or lfy-6 mutants grown under noninductive photoperiods, suggesting a redundant interaction with FLIP genes. Finally, the phenotype of double mutants combining the late-flowering mutations with tfl1-2 were also consistent with the different roles of flowering-time genes.},
 bibtype = {article},
 author = {Ruiz-García, L. and Madueño, F. and Wilkinson, M. and Haughn, G. and Saunas, J. and Martínez-Zapater, J.M.},
 doi = {10.1105/tpc.9.11.1921},
 journal = {Plant Cell},
 number = {11}
}

We have analyzed double mutants that combine late-flowering mutations at four flowering-time loci (FVE, FPA, FWA, and FT) with mutations at the LEAFY (LFY), APETALA 1 (AP1), and TERMINAL FLOWER1 (TFL 1) loci involved in the floral initiation process (FLIP). Double mutants between ft-1 or fwa-1 and lfy-6 completely lack flowerlike structures, indicating that both FWA and FT act redundantly with LFY to control AP1. Moreover, the phenotypes of ft-1 ap1-1 and fwa-1 apt-1 double mutants are reminiscent of the phenotype of ap1-1 cal-1 double routants, suggesting that FWA and FT could also be involved in the control of other FLIP genes. Such extreme phenotypes were not observed in double mutants between fve-2 or fpa-1 and lfy-6 or ap1-1. Each of these showed a phenotype similar to that of ap1-1 or lfy-6 mutants grown under noninductive photoperiods, suggesting a redundant interaction with FLIP genes. Finally, the phenotype of double mutants combining the late-flowering mutations with tfl1-2 were also consistent with the different roles of flowering-time genes.

@phdthesis{
 title = {Genetic and molecular analyses of the role of the UNUSUAL FLORAL ORGANS gene in regulation of shoot and organ identity in Arabidopsis thaliana},
 type = {phdthesis},
 year = {1996},
 keywords = {phd thesis},
 websites = {https://open.library.ubc.ca/cIRcle/collections/ubctheses/831/items/1.0087899},
 id = {7ec540fe-0add-357e-917e-89bfff131d7f},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson1996},
 source_type = {phdthesis},
 private_publication = {false},
 abstract = {My PhD Thesis},
 bibtype = {phdthesis},
 author = {Wilkinson, M}
}

My PhD Thesis

@article{
 title = {Parallels between UNUSUAL FLORAL ORGANS and FIMBRIATA, Genes Controlling Flower Development in Arabidopsis and Antirrhinum},
 type = {article},
 year = {1995},
 keywords = {Mark Wilkinson},
 pages = {1501-1510},
 volume = {7},
 websites = {http://www.plantcell.org/cgi/content/abstract/7/9/1501?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=ingram&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT},
 month = {9},
 id = {3e532ad5-5939-3879-b33f-a7d239c1d7dc},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Ingram1995},
 source_type = {article},
 notes = {10.1105/tpc.7.9.1501},
 private_publication = {false},
 abstract = {The unusual floral organs (ufo) mutant of Arabidopsis has flowers with variable homeotic organ transformations and inflorescence-like characteristics. To determine the relationship between UFO and previously characterized meristem and organ identity genes, we cloned UFO and determined its expression pattern. The UFO gene shows extensive homology with FIMBRIATA (FIM), a gene mediating between meristem and organ identity genes in Antirrhinum. All three UFO mutant alleles that we sequenced are predicted to produce truncated proteins. UFO transcripts were first detected in early floral meristems, before organ identity genes had been activated. At later developmental stages, UFO expression is restricted to the junction between sepal and petal primordia. Phenotypic, genetic, and expression pattern comparisons between UFO and FIM suggest that they are cognate homologs and play a similar role in mediating between meristem and organ identity genes. However, some differences in the functions and genetic interactions of UFO and FIM were apparent, indicating that changes in partially redundant pathways have occurred during the evolutionary divergence of Arabidopsis and Antirrhinum.},
 bibtype = {article},
 author = {Ingram, G C and Goodrich, J and Wilkinson, M D and Simon, R and Haughn, G W and Coen, E S},
 journal = {THE PLANT CELL},
 number = {9}
}

The unusual floral organs (ufo) mutant of Arabidopsis has flowers with variable homeotic organ transformations and inflorescence-like characteristics. To determine the relationship between UFO and previously characterized meristem and organ identity genes, we cloned UFO and determined its expression pattern. The UFO gene shows extensive homology with FIMBRIATA (FIM), a gene mediating between meristem and organ identity genes in Antirrhinum. All three UFO mutant alleles that we sequenced are predicted to produce truncated proteins. UFO transcripts were first detected in early floral meristems, before organ identity genes had been activated. At later developmental stages, UFO expression is restricted to the junction between sepal and petal primordia. Phenotypic, genetic, and expression pattern comparisons between UFO and FIM suggest that they are cognate homologs and play a similar role in mediating between meristem and organ identity genes. However, some differences in the functions and genetic interactions of UFO and FIM were apparent, indicating that changes in partially redundant pathways have occurred during the evolutionary divergence of Arabidopsis and Antirrhinum.

@article{
 title = {UNUSUAL FLORAL ORGANS Controls Meristem Identity and Organ Primordia Fate in Arabidopsis},
 type = {article},
 year = {1995},
 keywords = {developmental biology},
 pages = {1485-1499},
 volume = {7},
 websites = {http://www.plantcell.org/cgi/content/abstract/7/9/1485},
 month = {9},
 id = {a82e1739-ba67-3a72-8920-03fbe8cbf7fa},
 created = {2014-07-02T09:11:39.000Z},
 file_attached = {false},
 profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
 last_modified = {2017-03-22T07:45:59.566Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilkinson1995},
 source_type = {article},
 notes = {10.1105/tpc.7.9.1485},
 private_publication = {false},
 abstract = {A novel gene that is involved in regulating flower initiation and development has been identified in Arabidopsis. This gene has been designated UNUSUAL FLORAL ORGANS (UFO), with five corresponding nuclear recessive alleles designated ufo[middot]1 to ufo[middot]5. Under short day-length conditions, ufo homozygotes generate more coflorescences than do the wild type, and coflorescences often appear apical to the first floral shoot, resulting in a period of inflorescence development in which regions of floral and coflorescence shoots are produced alternately. ufo enhances the phenotype of weak leafy alleles, and the double mutant Ufo-1 Apetala1-1 produces only coflorescence-like shoots, suggesting that these two genes control different aspects of floral initiation. Floral development was also altered in Ufo plants. Ufo flowers have an altered organ number in all whorls, and organs in the first, second, and third whorls exhibit variable homeotic transformations. Ufo single and double mutant phenotypes suggest that the floral changes result from reduction in class B floral homeotic gene expression and fluctuations in the expression boundaries of class C function and FLO10. Surprisingly, in situ hybridization analysis revealed no obvious differences in expression pattern or level in developing Ufo flowers compared with that of the wild type for any class B or C gene studied. We propose that UFO acts in concert with known floral initiation genes and regulates the domains of floral homeotic gene function},
 bibtype = {article},
 author = {Wilkinson, M D and Haughn, G W},
 journal = {THE PLANT CELL},
 number = {9}
}

A novel gene that is involved in regulating flower initiation and development has been identified in Arabidopsis. This gene has been designated UNUSUAL FLORAL ORGANS (UFO), with five corresponding nuclear recessive alleles designated ufo[middot]1 to ufo[middot]5. Under short day-length conditions, ufo homozygotes generate more coflorescences than do the wild type, and coflorescences often appear apical to the first floral shoot, resulting in a period of inflorescence development in which regions of floral and coflorescence shoots are produced alternately. ufo enhances the phenotype of weak leafy alleles, and the double mutant Ufo-1 Apetala1-1 produces only coflorescence-like shoots, suggesting that these two genes control different aspects of floral initiation. Floral development was also altered in Ufo plants. Ufo flowers have an altered organ number in all whorls, and organs in the first, second, and third whorls exhibit variable homeotic transformations. Ufo single and double mutant phenotypes suggest that the floral changes result from reduction in class B floral homeotic gene expression and fluctuations in the expression boundaries of class C function and FLO10. Surprisingly, in situ hybridization analysis revealed no obvious differences in expression pattern or level in developing Ufo flowers compared with that of the wild type for any class B or C gene studied. We propose that UFO acts in concert with known floral initiation genes and regulates the domains of floral homeotic gene function

@article{
 title = {Gene expression during imaginal disc regeneration detected using enhancer-sensitive P-elements},
 type = {article},
 year = {1993},
 keywords = {genetics},
 pages = {1287-1297},
 volume = {117},
 websites = {http://dev.biologists.org/cgi/content/abstract/117/4/1287},
 month = {4},
 id = {762400ff-ec79-3618-97e7-5c36f4087597},
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 abstract = {When imaginal disc fragments from Drosophila are cultured in adult female hosts, they either duplicate the part of the pattern specified by the fate map, or regenerate to replace the missing part. The new tissue is added by proliferation of a small number of cells from the cut edge, brought together when the wound heals to form a regeneration blastema. Specification of the new pattern has been explained by assuming interactions among cells of different positional value in the regeneration blastema. In order to identify genes which might mediate these events, we screened over eight hundred independently isolated autosomal insertions of an enhancer-sensitive P-element, for altered lac-z expression in regenerating discs following cell death induced by a temperature-sensitive cell-lethal mutation. Two further screens divided the positive lines into four groups based on appropriate timing of the lac-z response in the cell-lethal mutant background and the expected response to an alternate source of cell death. Expression in wing disc fragments cultured in vivo was most frequent in the target class defined by the screens. In this direct test, lac-z expression was found in 23 lines and in most cases was spatially and temporally correlated with the formation of the regeneration blastema. Our results suggest a very substantial transcriptional response during the early stages of imaginal disc regeneration. lac-z expression in control imaginal discs, embryos and adult ovaries of the positive lines was also assayed. The selected insertions included: a small class expressed only in discs undergoing regeneration and apparently not at any other stage, possibly representing genes active exclusively in regeneration; a larger class expressed in the embryo or during oogenesis, but not normally in imaginal discs, as expected for functions recruited from earlier stages of the developmental program; and finally a class with spatially patterned expression in normal discs. This class included several insertions with expression associated with compartment boundaries, including one at the decapentaplegic (dpp), and one at the crumbs (crb) locus, a growth factor homologue, and an EGF-repeat gene respectively. Some of the expression patterns observed in cultured disc fragments provide evidence for cell communication in the regeneration blastema.},
 bibtype = {article},
 author = {Brook, W and Ostafichuk, L and Piorecky, J and Wilkinson, M and Hodgetts, D and Russell, M},
 journal = {Development},
 number = {4}
}

When imaginal disc fragments from Drosophila are cultured in adult female hosts, they either duplicate the part of the pattern specified by the fate map, or regenerate to replace the missing part. The new tissue is added by proliferation of a small number of cells from the cut edge, brought together when the wound heals to form a regeneration blastema. Specification of the new pattern has been explained by assuming interactions among cells of different positional value in the regeneration blastema. In order to identify genes which might mediate these events, we screened over eight hundred independently isolated autosomal insertions of an enhancer-sensitive P-element, for altered lac-z expression in regenerating discs following cell death induced by a temperature-sensitive cell-lethal mutation. Two further screens divided the positive lines into four groups based on appropriate timing of the lac-z response in the cell-lethal mutant background and the expected response to an alternate source of cell death. Expression in wing disc fragments cultured in vivo was most frequent in the target class defined by the screens. In this direct test, lac-z expression was found in 23 lines and in most cases was spatially and temporally correlated with the formation of the regeneration blastema. Our results suggest a very substantial transcriptional response during the early stages of imaginal disc regeneration. lac-z expression in control imaginal discs, embryos and adult ovaries of the positive lines was also assayed. The selected insertions included: a small class expressed only in discs undergoing regeneration and apparently not at any other stage, possibly representing genes active exclusively in regeneration; a larger class expressed in the embryo or during oogenesis, but not normally in imaginal discs, as expected for functions recruited from earlier stages of the developmental program; and finally a class with spatially patterned expression in normal discs. This class included several insertions with expression associated with compartment boundaries, including one at the decapentaplegic (dpp), and one at the crumbs (crb) locus, a growth factor homologue, and an EGF-repeat gene respectively. Some of the expression patterns observed in cultured disc fragments provide evidence for cell communication in the regeneration blastema.

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 title = {BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services Toshiaki Katayama Journal of Biomedical Semantics},
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