@InProceedings{10.1145/3643991.3644876,
    author="Garijo, Daniel and Arroyo, Miguel and Gonzalez, Esteban and Treude, Christoph and Tarocco, Nicola",
    title="Bidirectional Paper-Repository Tracing in Software Engineering",
    booktitle="To appear in 21st International Conference on Mining Software Repositories",
    year="2024",
    publisher="ACM",
    address="Cham",
    doi="10.1145/3643991.3644876",
    url= {https://dgarijo.com/papers/msr_2024.pdf}
}

@article{arenas2023morph,
  title={Morph-KGC^{star}: declarative generation of RDF-star graphs from heterogeneous data},
  author={Arenas-Guerrero, Juli{\'a}n and Iglesias-Molina, Ana and Chaves-Fraga, David and Garijo, Daniel and Corcho, Oscar and Dimou, Anastasia},
  journal={Semantic Web},
  url={https://dgarijo.com/papers/swj_arenas_2024.pdf},
  volume={24},
  year={2023}
}

@article{bolinches2023saltbot,
  title		   = {SALTBot: Linking Software and Articles in Wikidata},
  author	   = {Bolinches, Jorge and Garijo, Daniel},
  year         = {2023},
  booktitle    = {Proceedings of the Wikidata Workshop 2023 co-located with 22nd International Semantic Web Conference (ISWC 2023)},
  publisher    = {CEUR-WS.org},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {3640},
  url          = {https://ceur-ws.org/Vol-3640/paper12.pdf}
}

@InProceedings{10.1007/978-3-031-47243-5_5,
    author="Markovic, Milan and Garijo, Daniel and Germano, Stefano and Naja, Iman",
    editor="Payne, Terry R. and Presutti, Valentina and Qi, Guilin and Poveda-Villal{\'o}n, Mar{\'i}a and Stoilos, Giorgos and Hollink, Laura and Kaoudi, Zoi and Cheng, Gong and Li, Juanzi",
    title="TEC: Transparent Emissions Calculation Toolkit",
    booktitle="The Semantic Web -- ISWC 2023",
    year="2023",
    publisher="Springer Nature Switzerland",
    address="Cham",
    pages="76--93",
    doi="10.1007/978-3-031-47243-5_5",
    url= {https://dgarijo.com/papers/TEC_Toolkit_ISWC_2023.pdf}
}

@misc{leo2023recording,
      title={Recording provenance of workflow runs with RO-Crate}, 
      author={Simone Leo and Michael R. Crusoe and Laura Rodríguez-Navas and Raül Sirvent and Alexander Kanitz and Paul De Geest and Rudolf Wittner and Luca Pireddu and Daniel Garijo and José M. Fernández and Iacopo Colonnelli and Matej Gallo and Tazro Ohta and Hirotaka Suetake and Salvador Capella-Gutierrez and Renske de Wit and Bruno P. Kinoshita and Stian Soiland-Reyes},
      year={2023},
      eprint={2312.07852},
      url = {https://arxiv.org/pdf/2312.07852.pdf}
}

@techreport{david:hal-04184377,
  title = {{Task Force Sub Group 3 - Review of Software Quality Attributes and Characteristics}},
  author = {David, Mario and Colom, Miguel and Garijo, Daniel and Castro, Leyla Jael and Louvet, Violaine and Ronchieri, Elisabetta and Torquati, Massimo and del Ca{\~n}o, Laura and Leong, Siew Hoon and van den Bossche, Maxime and Campos, Isabel and Di Cosmo, Roberto},
  url = {https://hal.science/hal-04184377},
  publisher = {{Zenodo}},
  pages = {https://zenodo.org/record/8221384},
  institution = {{European Comission}},
  year = {2023},
  month = Aug,
  doi = {10.5281/zenodo.8221384},
  keywords = {Software Quality ; Research Software ; EOSC},
  pdf = {https://hal.science/hal-04184377/file/review-sqaatributes-v1.0.0.pdf}
}

@article{iglesias2023towards,
  title        = {Towards Assessing FAIR Research Software Best Practices in an Organization Using RDF-star},
  author       = {Iglesias-Molina, Ana and Garijo, Daniel},
  year         = {2023},
  booktitle    = {Proceedings of the Posters and Demo Track of the 19th International Conference on Semantic Systems co-located with 19th International Conference on Semantic Systems (SEMANTiCS 2023)},
  publisher    = {CEUR-WS.org},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {3526},
  url          = {https://ceur-ws.org/Vol-3526/paper-09.pdf}
}

@article{softalias2023,
  title        = {Softalias-KG: Reconciling Software Mentions in Scientific Literature},
  author       = {Gonzalez Guardia, Esteban and Lopez, Hector and Garijo, Daniel},
  year         = 2023,
  booktitle    = {International Semantic Web Conference (ISWC) 2023: Posters, Demos, and Industry Tracks},
  publisher    = {CEUR-WS.org},
  series       = {{CEUR} Workshop Proceedings},
  url          = {https://dgarijo.com/papers/ISWC2023_demo_softalias.pdf}
}

@misc{ya2ro,
	title        = {Ya2ro: A tool for creating Research Objects from minimum metadata},
	author       = {Pavel, Floriana Antonia and Garijo, Daniel},
	booktitle    = {Workshop on Metadata and Research (objects) Management for Linked Open Science (DAMALOS 2023)},
	doi          = {10.4126/FRL01-006444984},
	year 		 = {2023},
	url          = {https://repository.publisso.de/resource/frl:6452739/data}
}

@misc{gonzalez_damalos_2023,
	title        = {FAIR Research Object Assessment: A landscape analysis},
	author       = {Gonzalez, Esteban and Garijo, Daniel and Corcho, Oscar and Palma, Raul and Wolniewicz, Malgorzata and Rynkiewicz, Aron},
	booktitle    = {Workshop on Metadata and Research (objects) Management for Linked Open Science (DAMALOS 2023)},
	doi          = {10.4126/FRL01-006444989},
	year 		 = {2023},
	url          = {https://repository.publisso.de/resource/frl:6452748/data}
}

@misc{dasoulas2023declarative,
	title        = {Declarative RDF construction from in-memory data structures with RML},
	author       = {Dasoulas, Ioannis and Chaves-Fraga, David and Garijo, Daniel and Dimou, Anastasia},
	year         = 2023,
	booktitle    = {Knowledge Graph Construction Workshop, co-located with ESWC 2023},
	url          = {https://dgarijo.com/papers/KGC_ESWC_2023.pdf}
}

@misc{da_silva_wf_2023,
	title        = {Workflows Community Summit 2022: A Roadmap Revolution},
	author       = {Da Silva, Rafael Ferreira and Badia, Rosa M. and Bala, Venkat and Bard, Debbie and Bremer, Peer-Timo and Buckley, Ian and Caino-Lores, Silvina and Chard, Kyle and Goble, Carole and Jha, Shantenu and Katz, Daniel S. and Laney, Daniel and Parashar, Manish and Suter, Frederic and Tyler, Nick and Uram, Thomas and Altintas, Ilkay and Andersson, Stefan and Arndt, William and Aznar, Juan and Bader, Jonathan and Balis, Bartosz and Blanton, Chris and Braghetto, Kelly Rosa and Brodutch, Aharon and Brunk, Paul and Casanova, Henri and Lierta, Alba Cervera and Chigu, Justin and Coleman, Taina and Collier, Nick and Colonnelli, Iacopo and Coppens, Frederik and Crusoe, Michael and Cunningham, Will and De Paula Kinoshita, Bruno and Di Tommaso, Paolo and Doutriaux, Charles and Downton, Matthew and Elwasif, Wael and Enders, Bjoern and Erdmann, Chris and Fahringer, Thomas and Figueiredo, Ludmilla and Filgueira, Rosa and Foltin, Martin and Fouilloux, Anne and Gadelha, Luiz and Gallo, Andy and Saez, Artur Garcia and Garijo, Daniel and Gerlach, Roman and Grant, Ryan and Grayson, Samuel and Grubel, Patricia and Gustafsson, Johan and Hayot-Sasson, Valerie and Hernandez, Oscar and Hilbrich, Marcus and {AnnMary Justine} and Laflotte, Ian and Lehmann, Fabian and Luckow, Andre and Luettgau, Jakob and Maheshwari, Ketan and Matsuda, Motohiko and Medic, Doriana and Mendygral, Pete and Michalewicz, Marek and {Jorji Nonaka} and Pawlik, Maciej and Pottier, Loic and Pouchard, Line and Putz, Mathias and Radha, Santosh Kumar and Ramakrishnan, Lavanya and Ristov, Sashko and Romano, Paul and Rosendo, Daniel and Ruefenacht, Martin and Rycerz, Katarzyna and {Nishant Saurabh} and Savchenko, Volodymyr and Schulz, Martin and Simpson, Christine and Sirvent, Raul and Skluzacek, Tyler and Soiland-Reyes, Stian and Souza, Renan and Sukumar, Sreenivas Rangan and Sun, Ziheng and Sussman, Alan and Thain, Douglas and Titov, Mikhail and Tovar, Benjamin and Tripathy, Aalap and Turilli, Matteo and Tuznik, Bartosz and Van Dam, Hubertus and Vivas, Aurelio and Ward, Logan and Widener, Patrick and Wilkinson, Sean and Zawalska, Justyna and {Mahnoor Zulfiqar}},
	year         = 2023,
	publisher    = {Zenodo},
	doi          = {10.5281/ZENODO.7750670},
	url          = {https://zenodo.org/record/7750670},
	copyright    = {Creative Commons Attribution 4.0 International},
	keywords     = {scientific workflows, high performance computing, cloud computing, edge computing, artificial intelligence, quantum computing, FAIR, AI workflows},
	language     = {en}
}

@article{SCHAFFHAUSER2023105695,
  title = {A framework for the broad dissemination of hydrological models for non-expert users},
  journal = {Environmental Modelling & Software},
  pages = {105695},
  year = {2023},
  issn = {1364-8152},
  doi = {10.1016/j.envsoft.2023.105695},
  url = {https://dgarijo.com/papers/MINT_MIC_Paper_Submitted.pdf},
  author = {Timo Schaffhauser and Daniel Garijo and Maximiliano Osorio and Daniel Bittner and Suzanne Pierce and Hernán Vargas and Markus Disse and Yolanda Gil},
  keywords = {Software metadata, Model metadata, Model encapsulation, Model catalogs, MINT, Hydrological models}
}

@inproceedings{navas2022,
  author = {Navas-Loro, Maria and Garijo, Daniel and Corcho, Oscar},
  title = {Multi-label Text Classification for Public Procurement in Spanish},
  journal = {Procesamiento del Lenguaje Natural},
  volume = {69},
  number = {0},
  year = {2022},
  abstract = {Public procurement accounts for a 14% of the annual budget of the different governments of the European Union. In Europe, contracting processes are classified using Common Procurement Vocabulary codes (CPVs), a taxonomy designed to facilitate statistical reporting, search and the creation of alerts that can be used by potential bidders. CPVs are commonly assigned manually by public employees in charge of contracting processes. However, CPV classification is not a trivial task, as there are more than 9,000 different CPV categories, which are often assigned following heterogeneous criteria. In this paper we have created a CPV classifier that uses as an input the textual description of the contracting process, and assigns CPVs from the 45 top-level CPV categories. We work only with texts in Spanish, although our approach may be easily extended to other languages. Our results improve the state of the art (10% F1-score improvement) and are available online.},
  issn = {1989-7553},
  url = {http://journal.sepln.org/sepln/ojs/ojs/index.php/pln/article/view/6429},
  pages = {73--82}
}

Public procurement accounts for a 14% of the annual budget of the different governments of the European Union. In Europe, contracting processes are classified using Common Procurement Vocabulary codes (CPVs), a taxonomy designed to facilitate statistical reporting, search and the creation of alerts that can be used by potential bidders. CPVs are commonly assigned manually by public employees in charge of contracting processes. However, CPV classification is not a trivial task, as there are more than 9,000 different CPV categories, which are often assigned following heterogeneous criteria. In this paper we have created a CPV classifier that uses as an input the textual description of the contracting process, and assigns CPVs from the 45 top-level CPV categories. We work only with texts in Spanish, although our approach may be easily extended to other languages. Our results improve the state of the art (10% F1-score improvement) and are available online.

@article{garijo_nine_2022,
	title = {Nine best practices for research software registries and repositories},
	volume = {8},
	issn = {2376-5992},
	url = {https://dgarijo.com/papers/nine_best_practices.pdf},
	doi = {10.7717/peerj-cs.1023},
	journal = {PeerJ Computer Science},
	author = {Garijo, Daniel and Ménager, Hervé and Hwang, Lorraine and Trisovic, Ana and Hucka, Michael and Morrell, Thomas and Allen, Alice and {Task Force on Best Practices for Software Registries} and {SciCodes Consortium}},
	month = aug,
	year = {2022},
	pages = {e1023},
}

@inproceedings{10.1007/978-3-031-16802-4_6,
author="Gonz{\'a}lez, Esteban and Ben{\'i}tez, Alejandro and Garijo, Daniel",
editor="Silvello, Gianmaria and Corcho, Oscar and Manghi, Paolo and Di Nunzio, Giorgio Maria and Golub, Koraljka and Ferro, Nicola and Poggi, Antonella",
title="FAIROs: Towards FAIR Assessment in Research Objects",
booktitle="Linking Theory and Practice of Digital Libraries",
year="2022",
publisher="Springer International Publishing",
address="Cham",
pages="68--80",
abstract="The FAIR principles have become a popular means to guide researchers when publishing their research outputs (i.e., data, software, etc.) in a Findable, Accessible, Interoperable and Reusable manner. In order to ease compliance with FAIR, different frameworks have been developed by the scientific community, offering guidance and suggestions to researchers. However, scientific outputs are rarely published in isolation. Research Objects have been proposed as a framework to capture the relationships and context of all constituents of an investigation. In this paper we present FAIROs, a framework for assessing the compliance of a Research Object (and its constituents) against the FAIR principles. FAIROs reuses existing FAIR validators for individual resources and proposes i) two scoring methods for assessing the fairness of Research Objects, ii) an initial implementation of the scoring methods in the FAIROs framework, and iii) an explanation-based approach designed to visualize the obtained scores. We validate FAIROs against 165 Research Objects, and discuss the advantages and limitations of different scoring systems.",
isbn="978-3-031-16802-4",
doi={10.1007/978-3-031-16802-4_6},
url = {https://dgarijo.com/papers/TPDL2022_gonzalez.pdf}
}

The FAIR principles have become a popular means to guide researchers when publishing their research outputs (i.e., data, software, etc.) in a Findable, Accessible, Interoperable and Reusable manner. In order to ease compliance with FAIR, different frameworks have been developed by the scientific community, offering guidance and suggestions to researchers. However, scientific outputs are rarely published in isolation. Research Objects have been proposed as a framework to capture the relationships and context of all constituents of an investigation. In this paper we present FAIROs, a framework for assessing the compliance of a Research Object (and its constituents) against the FAIR principles. FAIROs reuses existing FAIR validators for individual resources and proposes i) two scoring methods for assessing the fairness of Research Objects, ii) an initial implementation of the scoring methods in the FAIROs framework, and iii) an explanation-based approach designed to visualize the obtained scores. We validate FAIROs against 165 Research Objects, and discuss the advantages and limitations of different scoring systems.

@article{10.1145/3557785.3557789,
author = {Guerzhoy, Michael and Neumann, Marion and Johnson, Emmanuel and Johnson, David and Chai, Henry and Garijo, Daniel and Lyu, Zhuoyue and MacLellan, Christopher J.},
title = {EAAI-22 Blue Sky Ideas in Artificial Intelligence Education from the AAAI/ACM SIGAI New and Future AI Educator Program},
year = {2022},
issue_date = {June 2022},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {8},
number = {2},
url = {https://dgarijo.com/papers/blue_sky_cr.pdf},
doi = {10.1145/3557785.3557789},
abstract = {The 12th Symposium on Educational Advances in Artificial Intelligence (EAAI-22, cochaired by Michael Guerzhoy and Marion Neumann) continued the AAAI/ACM SIGAI New and Future AI Educator Program to support the training of early-career university faculty, secondary school faculty, and future educators (PhD candidates or postdocs who intend a career in academia). As part of the program, awardees were asked to address one of the following "blue sky" questions:•How could/should AI courses incorporate AI Ethics into the curriculum?•How could we teach AI topics at an early undergraduate or a secondary school level?•AI has the potential for broad impact to numerous disciplines. How could we make AI education more interdisciplinary, specifically to benefit non-engineering fields?•How should standard AI courses evolve?•How could we leverage AI education to promote diversity in the field?This paper is a collection of their responses, intended to help motivate discussion around these issues in AI education.},
journal = {AI Matters},
month = {nov},
pages = {16–21},
numpages = {6}
}

The 12th Symposium on Educational Advances in Artificial Intelligence (EAAI-22, cochaired by Michael Guerzhoy and Marion Neumann) continued the AAAI/ACM SIGAI New and Future AI Educator Program to support the training of early-career university faculty, secondary school faculty, and future educators (PhD candidates or postdocs who intend a career in academia). As part of the program, awardees were asked to address one of the following "blue sky" questions:•How could/should AI courses incorporate AI Ethics into the curriculum?•How could we teach AI topics at an early undergraduate or a secondary school level?•AI has the potential for broad impact to numerous disciplines. How could we make AI education more interdisciplinary, specifically to benefit non-engineering fields?•How should standard AI courses evolve?•How could we leverage AI education to promote diversity in the field?This paper is a collection of their responses, intended to help motivate discussion around these issues in AI education.

@inproceedings{espinoza2022extending,
  title={Extending Ontology Engineering Practices to Facilitate Application Development},
  author={Espinoza-Arias, Paola and Garijo, Daniel and Corcho, Oscar},
  booktitle={Proceedings of the 23rd International Conference Knowledge on Engineering and Knowledge Management (EKAW 2022)},
  pages={19--35},
  year={2022},
  doi={10.1007/978-3-031-17105-5_2},
  url = {https://dgarijo.com/papers/EKAW2022_espinoza.pdf},
  organization={Springer}
}

@inproceedings{gil2022towards,
  title={Towards Capturing Scientific Reasoning to Automate Data Analysis},
  author={Gil, Yolanda and Khider, Deborah and Osorio, Maximiliano and Ratnakar, Varun and Vargas, Hernan and Garijo, Daniel and Pierce, Suzanne},
  booktitle={Proceedings of the Annual Meeting of the Cognitive Science Society},
  year={2022},
  url = {https://dgarijo.com/papers/gil_et_al_cogsci_2022.pdf},
}

@inproceedings{FilgueiraG22,
  author    = {Rosa Filgueira and
               Daniel Garijo},
  title     = {Inspect4py: {A} Knowledge Extraction Framework for Python Code Repositories},
  booktitle = {{IEEE/ACM} 19th International Conference on Mining Software Repositories,
               {MSR} 2022, Pittsburgh, PA, USA, May 23-24, 2022},
  pages     = {232--236},
  publisher = {{IEEE}},
  year      = {2022},
  url       = {https://dgarijo.com/papers/inspect4py_MSR2022.pdf},
  doi       = {10.1145/3524842.3528497}
}

@book{751dfce356e5441f8e3f8c1401e0a1e0,
  title = "FAIR Principles for Research Software (FAIR4RS Principles)",
  author = "Hong, {Neil P. Chue} and Katz, {Daniel S.} and Michelle Barker and Anna-Lena Lamprecht and Carlos Martinez and Psomopoulos, {Fotis E.} and Jen Harrow and Castro, {Leyla Jael} and Morane Gruenpeter and Martinez, {Paula Andrea} and Tom Honeyman and Alexander Struck and Allen Lee and Axel Loewe and Werkhoven, {Ben van} and Daniel Garijo and Esther Plomp and Francoise Genova and Hugh Shanahan and Maggie Hellstr{\"o}m and Malin Sandstr{\"o}m and Manodeep Sinha and Mateusz Kuzak and Patricia Herterich and Sharif Islam and Susanna-Assunta Sansone and Tom Pollard and Atmojo, {Udayanto Dwi} and Alan Williams and Andreas Czerniak and Anna Niehues and Fouilloux, {Anne Claire} and Bala Desinghu and Carole Goble and C{\'e}line Richard and Charles Gray and Chris Erdmann and Daniel N{\"u}st and Daniele Tartarini and Elena Ranguelova and Hartwig Anzt and Ilian Todorov and James McNally and Jessica Burnett and Juli{\'a}n Garrido-S{\'a}nchez and Khalid Belhajjame and Laurents Sesink and Lorraine Hwang and Tovani-Palone, {Marcos Roberto} and Wilkinson, {Mark D.} and Mathieu Servillat and Matthias Liffers and Merc Fox and Nadica Miljkovi{\'c} and Nick Lynch and Lavanchy, {Paula Martinez} and Sandra Gesing and Sarah Stevens and Cuesta, {Sergio Martinez} and Silvio Peroni and Stian Soiland-Reyes and Tom Bakker and Tovo Rabemanantsoa and Vanessa Sochat and Yo Yehudi and FAIR4RS WG",
  year = "2022",
  month = mar,
  day = "16",
  doi = "10.15497/RDA00065",
  url = {https://dgarijo.com/papers/FAIR4RS_2022.pdf},
  language = "English"
}

@article{osorio_dockerpedia_2022,
	title = {{DockerPedia}: {A} {Knowledge} {Graph} of {Software} {Images} and {Their} {Metadata}},
	volume = {32},
	issn = {0218-1940, 1793-6403},
	shorttitle = {{DockerPedia}},
	url = {https://dgarijo.com/papers/reproducibility_docker.pdf},
	doi = {10.1142/S0218194022500036},
	abstract = {An increasing amount of researchers use software images to capture the requirements and code dependencies needed to carry out computational experiments. Software images preserve the computational environment required to execute a scientific experiment and have become a crucial asset for reproducibility. However, software images are usually not properly documented and described, making it challenging for scientists to find, reuse and understand them. In this paper, we propose a framework for automatically describing software images in a machine-readable manner by (i) creating a vocabulary to describe software images; (ii) developing an annotation framework designed to automatically document the underlying environment of software images and (iii) creating DockerPedia, a Knowledge Graph with over 150,000 annotated software images, automatically described using our framework. We illustrate the usefulness of our approach in finding images with specific software dependencies, comparing similar software images, addressing versioning problems when running computational experiments; and flagging problems with vulnerable software dependencies.},
	language = {en},
	number = {01},
	urldate = {2022-03-02},
	journal = {International Journal of Software Engineering and Knowledge Engineering},
	author = {Osorio, Maximiliano and Buil-Aranda, Carlos and Santana-Perez, Idafen and Garijo, Daniel},
	month = jan,
	year = {2022},
	pages = {71--89},
}

An increasing amount of researchers use software images to capture the requirements and code dependencies needed to carry out computational experiments. Software images preserve the computational environment required to execute a scientific experiment and have become a crucial asset for reproducibility. However, software images are usually not properly documented and described, making it challenging for scientists to find, reuse and understand them. In this paper, we propose a framework for automatically describing software images in a machine-readable manner by (i) creating a vocabulary to describe software images; (ii) developing an annotation framework designed to automatically document the underlying environment of software images and (iii) creating DockerPedia, a Knowledge Graph with over 150,000 annotated software images, automatically described using our framework. We illustrate the usefulness of our approach in finding images with specific software dependencies, comparing similar software images, addressing versioning problems when running computational experiments; and flagging problems with vulnerable software dependencies.

@article{SHENOY2022100679,
  title = {A study of the quality of Wikidata},
  journal = {Journal of Web Semantics},
  volume = {72},
  pages = {100679},
  year = {2022},
  issn = {1570-8268},
  doi = {10.1016/j.websem.2021.100679},
  url = {https://dgarijo.com/papers/a_study_wikidata_2022.pdf},
  author = {Kartik Shenoy and Filip Ilievski and Daniel Garijo and Daniel Schwabe and Pedro Szekely},
  keywords = {Wikidata, Data quality, Knowledge graphs, Constraints, Crowdsourcing},
  abstract = {Wikidata has been increasingly adopted by many communities for a wide variety of applications, which demand high-quality knowledge to deliver successful results. In this paper, we develop a framework to detect and analyze low-quality statements in Wikidata by shedding light on the current practices exercised by the community. We explore three indicators of data quality in Wikidata, based on: (1) community consensus on the currently recorded knowledge, assuming that statements that have been removed and not added back are implicitly agreed to be of low quality; (2) statements that have been deprecated; and (3) constraint violations in the data. We combine these indicators to detect low-quality statements, revealing challenges with duplicate entities, missing triples, violated type rules, and taxonomic distinctions. Our findings complement ongoing efforts by the Wikidata community to improve data quality, aiming to make it easier for users and editors to find and correct mistakes.}
}

Wikidata has been increasingly adopted by many communities for a wide variety of applications, which demand high-quality knowledge to deliver successful results. In this paper, we develop a framework to detect and analyze low-quality statements in Wikidata by shedding light on the current practices exercised by the community. We explore three indicators of data quality in Wikidata, based on: (1) community consensus on the currently recorded knowledge, assuming that statements that have been removed and not added back are implicitly agreed to be of low quality; (2) statements that have been deprecated; and (3) constraint violations in the data. We combine these indicators to detect low-quality statements, revealing challenges with duplicate entities, missing triples, violated type rules, and taxonomic distinctions. Our findings complement ongoing efforts by the Wikidata community to improve data quality, aiming to make it easier for users and editors to find and correct mistakes.

@article{soiland2021packaging,
  title={Packaging research artefacts with RO-Crate},
  author={Soiland-Reyes, Stian and Sefton, Peter and Crosas, Merc{\`e} and Castro, Leyla Jael and Coppens, Frederik and Fern{\'a}ndez, Jos{\'e} M and Garijo, Daniel and Gr{\"u}ning, Bj{\"o}rn and La Rosa, Marco and Leo, Simone and others},
  journal={Data Science},
  doi={10.3233/DS-210053},
  url={https://dgarijo.com/papers/ro_crate_data_science.pdf},
  pages={1--42},
  volume={Pre-press},
  year={2022}
}

@article{10.1162/qss_a_00167,
    author = {Kelley, Aidan and Garijo, Daniel},
    title = "{A Framework for Creating Knowledge Graphs of Scientific Software Metadata}",
    journal = {Quantitative Science Studies},
    pages = {1-37},
    year = {2021},
    month = {11},
    issn = {2641-3337},
    doi = {10.1162/qss_a_00167},
    url = {https://doi.org/10.1162/qss_a_00167},
    eprint = {https://direct.mit.edu/qss/article-pdf/doi/10.1162/qss_a_00167/1971225/qss_a_00167.pdf},
}

@misc{chalupsky2021creating,
      title={Creating and Querying Personalized Versions of Wikidata on a Laptop},
      author={Hans Chalupsky and Pedro Szekely and Filip Ilievski and Daniel Garijo and Kartik Shenoy},
      year={2021},
      eprint={2108.07119},
      archivePrefix={arXiv},
      url={http://ceur-ws.org/Vol-2982/paper-4.pdf}
}

@misc{dasilva2021community,
      title={A Community Roadmap for Scientific Workflows Research and Development},
      author={Rafael Ferreira da Silva and Henri Casanova and Kyle Chard and Ilkay Altintas and Rosa M Badia and Bartosz Balis and Tainã Coleman and Frederik Coppens and Frank Di Natale and Bjoern Enders and Thomas Fahringer and Rosa Filgueira and Grigori Fursin and Daniel Garijo and Carole Goble and Dorran Howell and Shantenu Jha and Daniel S. Katz and Daniel Laney and Ulf Leser and Maciej Malawski and Kshitij Mehta and Loïc Pottier and Jonathan Ozik and J. Luc Peterson and Lavanya Ramakrishnan and Stian Soiland-Reyes and Douglas Thain and Matthew Wolf},
      year={2021},
      eprint={2110.02168},
      archivePrefix={arXiv},
      url={https://arxiv.org/pdf/2110.02168}
}

@article{foops2021,
  title        = {FOOPS!: An Ontology Pitfall Scanner for the FAIR Principles},
  author       = {Garijo, Daniel and Corcho, Oscar and Poveda-Villal{\'o}n, Mar{\i}a},
  year         = 2021,
  booktitle    = {International Semantic Web Conference (ISWC) 2021: Posters, Demos, and Industry Tracks},
  publisher    = {CEUR-WS.org},
  series       = {{CEUR} Workshop Proceedings},
  volume       = 2980,
  url          = {http://ceur-ws.org/Vol-2980/paper321.pdf}
}

@article{da2021workflows,
  title        = {Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development},
  author       = {da Silva, Rafael Ferreira and Casanova, Henri and Chard, Kyle and Coleman, Tain{\~a} and Laney, Dan and Ahn, Dong and Jha, Shantenu and Howell, Dorran and Soiland-Reys, Stian and Altintas, Ilkay and others},
  journal      = {arXiv preprint},
	url          = {https://arxiv.org/abs/2106.05177},
  year         = {2021}
}

@article{ESPINOZAARIAS2021,
title          = {Crossing the chasm between ontology engineering and application development: A survey},
journal        = {Journal of Web Semantics},
pages          = {100655},
year           = {2021},
issn           = {1570-8268},
doi            = {10.1016/j.websem.2021.100655},
url            = {https://dgarijo.com/papers/jws_survey_2021.pdf},
author         = {Paola Espinoza-Arias and Daniel Garijo and Oscar Corcho},
keywords       = {Ontology, OWL, Ontology engineering, Web API, Application development, Knowledge graph},
abstract       = {The adoption of Knowledge Graphs (KGs) by public and private organizations to integrate and publish data has increased in recent years. Ontologies play a crucial role in providing the structure for KGs, but are usually disregarded when designing Application Programming Interfaces (APIs) to enable browsing KGs in a developer-friendly manner. In this paper we provide a systematic review of the state of the art on existing approaches to ease access to ontology-based KG data by application developers. We propose two comparison frameworks to understand specifications, technologies and tools responsible for providing APIs for KGs. Our results reveal several limitations on existing API-based specifications, technologies and tools for KG consumption, which outline exciting research challenges including automatic API generation, API resource path prediction, ontology-based API versioning, and API validation and testing.}
}

The adoption of Knowledge Graphs (KGs) by public and private organizations to integrate and publish data has increased in recent years. Ontologies play a crucial role in providing the structure for KGs, but are usually disregarded when designing Application Programming Interfaces (APIs) to enable browsing KGs in a developer-friendly manner. In this paper we provide a systematic review of the state of the art on existing approaches to ease access to ontology-based KG data by application developers. We propose two comparison frameworks to understand specifications, technologies and tools responsible for providing APIs for KGs. Our results reveal several limitations on existing API-based specifications, technologies and tools for KG consumption, which outline exciting research challenges including automatic API generation, API resource path prediction, ontology-based API versioning, and API validation and testing.

@article{tiis2021,
	title        = {Artificial Intelligence for Modeling Complex Systems: Taming the Complexity of Expert Models to Improve Decision Making},
	author       = {Yolanda Gil and Daniel Garijo and Deborah Khider and Craig A. Knoblock and Varun Ratnakar and Maximiliano Osorio and Hernán Vargas and Minh Pham and Jay Pujara and Basel Shbita and  Binh Vu and Yao-Yi Chiang and Dan Feldman and Yijun Lin and Hayley Song and Vipin Kumar and Ankush Khandelwal and Michael Steinbach and Kshitij Tayal and Shaoming Xu and Suzanne A. Pierce and Lissa Pearson and Daniel Hardesty-Lewis and Ewa Deelman and Rafael Ferreira da Silva and Rajiv Mayani and Armen R. Kemanian and Yuning Shi and Lorne Leonard and Scott Peckham and Maria Stoica and Kelly Cobourn and Zeya Zhang and Christopher Duffy and Lele Shu},
  year = {2021},
  issue_date = {July 2021},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  volume = {11},
  number = {2},
  issn = {2160-6455},
  doi = {10.1145/3453172},
  journal = {ACM Trans. Interact. Intell. Syst.},
  month = jul,
  articleno = {11},
  numpages = {49},
	url          = {https://dgarijo.com/papers/MINT-tiis.pdf}
}

@inproceedings{inbook_2020,
	title        = {Mapping the Web Ontology Language to the OpenAPI Specification},
	author       = {Espinoza{-}Arias, Paola and Garijo, Daniel and Corcho, Oscar},
	year         = 2020,
	month        = 12,
	booktitle    = {2nd Workshop on Conceptual Modeling, Ontologies and (Meta)data Management for Findable, Accessible, Interoperable and Reusable (FAIR) Data (CMOMM4FAIR) Colocated with the 2020 Conference on Advances in Conceptual Modeling},
	pages        = {117--127},
	doi          = {10.1007/978-3-030-65847-2_11},
	url          = {https://dgarijo.com/papers/mapping_owl_to_oas_2020.pdf}
}

@article{monteil2020nine,
	title        = {Nine Best Practices for Research Software Registries and Repositories: A Concise Guide},
	author       = {Monteil, Alain and Gonzalez-Beltran, Alejandra and Ioannidis, Alexandros and Allen, Alice and Lee, Allen and Bandrowski, Anita and Wilson, Bruce E and Mecum, Bryce and Du, Cai Fan and Robinson, Carly and Daniel Garijo and others},
	year         = 2020,
	journal      = {arXiv preprint},
	url          = {https://dgarijo.com/papers/nine_best_2020.pdf}
}

@inproceedings{DBLP:conf/semweb/GarijoYSS20,
	title        = {A Template-Based Approach for Annotating Long-Tail Datasets},
	author       = {Daniel Garijo and Ke{-}Thia Yao and Amandeep Singh and Pedro A. Szekely},
	year         = 2020,
	booktitle    = {Joint Proceedings of Workshops AI4LEGAL2020, NLIWOD, {PROFILES} 2020, QuWeDa 2020 and {SEMIFORM2020} Colocated with the 19th International Semantic Web Conference {(ISWC} 2020), Virtual Conference, November, 2020},
	publisher    = {CEUR-WS.org},
	series       = {{CEUR} Workshop Proceedings},
	volume       = 2722,
	pages        = {97--102},
	url          = {http://ceur-ws.org/Vol-2722/profiles2020-paper-3.pdf}
}

@inproceedings{garijo2020OBA,
	title        = {{OBA}: An Ontology-Based Framework for Creating REST APIs for Knowledge Graphs},
	author       = {Garijo, Daniel and Osorio, Maximiliano},
	booktitle={International Semantic Web Conference},
	pages={48--64},
	year={2020},
	doi={10.1007/978-3-030-62466-8_4},
	isbn={978-3-030-62466-8},
	url          = {https://dgarijo.com/papers/OBA__Ontology_Based_APIs.pdf},
	organization = {Springer, Cham}
}

@inproceedings{garijo2020KGTK,
	title        = {{KGTK}: A Toolkit for Large Knowledge Graph Manipulation and Analysis},
	author       = {Ilievski, Filip and Garijo, Daniel and Chalupsky, Hans and Teja Divvala, Naren and Yao, Yixiang and Rogers, Craig and Li, Ronpeng  and Liu,  and  Singh, Amandeep and Schwabe, Daniel and Szekely, Pedro},
	booktitle={International Semantic Web Conference},
  pages={278--293},
  year={2020},
	url          = {https://dgarijo.com/papers/Camera_ready_ISWC__KGTK.pdf},
	organization = {Springer, Cham}
}

@inproceedings{garijo2020EKAW,
	title        = {Coming to terms with FAIR ontologies: A position paper},
	author       = {Poveda-Villalón, María and Espinoza-Arias, Paola and Garijo, Daniel and Corcho, Oscar},
	year         = 2020,
	month        = September,
  pages        = {255-270},
	booktitle    = {Proceedings of the 22nd International Conference on Knowledge Engineering and Knowledge Management (EKAW 2020)},
  doi          = {10.1007/978-3-030-61244-3_18},
	url          = {https://dgarijo.com/papers/EKAW2020_Coming_to_Terms_with_FAIR_Ontologies.pdf}
}

@article{goble_2020,
	title        = {FAIR Computational Workflows},
	author       = {Goble, Carole and Cohen-Boulakia, Sarah and Soiland-Reyes, Stian and Garijo, Daniel and Gil, Yolanda and Crusoe, Michael R. and Peters, Kristian and Schober, Daniel},
	year         = 2020,
	journal      = {Data Intelligence},
	volume       = 2,
	number       = {1-2},
	pages        = {108--121},
	doi          = {10.1162/dint_a_00033},
	url          = {https://dgarijo.com/papers/fair_wfs2019.pdf},
	eprint       = {https://doi.org/10.1162/dint_a_00033}
}

@article{grasby2020genetic,
	title        = {The genetic architecture of the human cerebral cortex},
	author       = {Grasby, Katrina L and Jahanshad, Neda and Painter, Jodie N and Colodro-Conde, Luc{\'\i}a and Bralten, Janita and Hibar, Derrek P and Lind, Penelope A and Pizzagalli, Fabrizio and Ching, Christopher RK and McMahon, Mary Agnes B and others},
	year         = 2020,
	journal      = {Science},
	publisher    = {American Association for the Advancement of Science},
	volume       = 367,
	number       = 6484,
	url          = {https://dgarijo.com/papers/genetic_architecture_of_the_human_cerebral_cor.pdf}
}

@incollection{garijo2020,
	title        = {Best Practices for Implementing FAIR Vocabularies and Ontologies on the Web},
	author       = {Daniel Garijo and Maria Poveda-Villalón},
	year         = 2020,
	booktitle    = {Applications and Practices in Ontology Design, Extraction, and Reasoning},
	publisher    = {{IOS} Press},
	address      = {Netherlands},
	doi          = {10.3233/SSW200034},
	url          = {https://dgarijo.com/papers/best_practices2020.pdf},
	editor       = {Giuseppe Cota, Marilena Daquino and Gian Luca Pozzato}
}

@article{Thompson2020,
	title        = {ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries},
	author       = {Thompson, Paul M. and Jahanshad, Neda and Ching, Christopher R. K. and Salminen, Lauren E. and Thomopoulos, Sophia I. and Bright, Joanna and Baune, Bernhard T. and Bertol{\'i}n, Sara and Bralten, Janita and Bruin, Willem B. and B{\"u}low, Robin and Chen, Jian and Chye, Yann and Dannlowski, Udo and de Kovel, Carolien G. F. and Donohoe, Gary and Eyler, Lisa T. and Faraone, Stephen V. and Favre, Pauline and Filippi, Courtney A. and Frodl, Thomas and Garijo, Daniel and Gil, Yolanda and Grabe, Hans J. and Grasby, Katrina L. and Hajek, Tomas and Han, Laura K. M. and Hatton, Sean N. and Hilbert, Kevin and Ho, Tiffany C. and Holleran, Laurena and Homuth, Georg and Hosten, Norbert and Houenou, Josselin and Ivanov, Iliyan and Jia, Tianye and Kelly, Sinead and Klein, Marieke and Kwon, Jun Soo and Laansma, Max A. and Leerssen, Jeanne and Lueken, Ulrike and Nunes, Abraham and Neill, Joseph O' and Opel, Nils and Piras, Fabrizio and Piras, Federica and Postema, Merel C. and Pozzi, Elena and Shatokhina, Natalia and Soriano-Mas, Carles and Spalletta, Gianfranco and Sun, Daqiang and Teumer, Alexander and Tilot, Amanda K. and Tozzi, Leonardo and van der Merwe, Celia and Van Someren, Eus J. W. and van Wingen, Guido A. and V{\"o}lzke, Henry and Walton, Esther and Wang, Lei and Winkler, Anderson M. and Wittfeld, Katharina and Wright, Margaret J. and Yun, Je-Yeon and Zhang, Guohao and Zhang-James, Yanli and Adhikari, Bhim M. and Agartz, Ingrid and Aghajani, Moji and Aleman, Andr{\'e} and Althoff, Robert R. and Altmann, Andre and Andreassen, Ole A. and Baron, David A. and Bartnik-Olson, Brenda L. and Marie Bas-Hoogendam, Janna and Baskin-Sommers, Arielle R. and Bearden, Carrie E. and Berner, Laura A. and Boedhoe, Premika S. W. and Brouwer, Rachel M. and Buitelaar, Jan K. and Caeyenberghs, Karen and Cecil, Charlotte A. M. and Cohen, Ronald A. and Cole, James H. and Conrod, Patricia J. and De Brito, Stephane A. and de Zwarte, Sonja M. C. and Dennis, Emily L. and Desrivieres, Sylvane and Dima, Danai and Ehrlich, Stefan and Esopenko, Carrie and Fairchild, Graeme and Fisher, Simon E. and Fouche, Jean-Paul and Francks, Clyde and Frangou, Sophia and Franke, Barbara and Garavan, Hugh P. and Glahn, David C. and Groenewold, Nynke A. and Gurholt, Tiril P. and Gutman, Boris A. and Hahn, Tim and Harding, Ian H. and Hernaus, Dennis and Hibar, Derrek P. and Hillary, Frank G. and Hoogman, Martine and Hulshoff Pol, Hilleke E. and Jalbrzikowski, Maria and Karkashadze, George A. and Klapwijk, Eduard T. and Knickmeyer, Rebecca C. and Kochunov, Peter and Koerte, Inga K. and Kong, Xiang-Zhen and Liew, Sook-Lei and Lin, Alexander P. and Logue, Mark W. and Luders, Eileen and Macciardi, Fabio and Mackey, Scott and Mayer, Andrew R. and McDonald, Carrie R. and McMahon, Agnes B. and Medland, Sarah E. and Modinos, Gemma and Morey, Rajendra A. and Mueller, Sven C. and Mukherjee, Pratik and Namazova-Baranova, Leyla and Nir, Talia M. and Olsen, Alexander and Paschou, Peristera and Pine, Daniel S. and Pizzagalli, Fabrizio and Renter{\'i}a, Miguel E. and Rohrer, Jonathan D. and S{\"a}mann, Philipp G. and Schmaal, Lianne and Schumann, Gunter and Shiroishi, Mark S. and Sisodiya, Sanjay M. and Smit, Dirk J. A. and S{\o}nderby, Ida E. and Stein, Dan J. and Stein, Jason L. and Tahmasian, Masoud and Tate, David F. and Turner, Jessica A. and van den Heuvel, Odile A. and van der Wee, Nic J. A. and van der Werf, Ysbrand D. and van Erp, Theo G. M. and van Haren, Neeltje E. M. and van Rooij, Daan and van Velzen, Laura S. and Veer, Ilya M. and Veltman, Dick J. and Villalon-Reina, Julio E. and Walter, Henrik and Whelan, Christopher D. and Wilde, Elisabeth A. and Zarei, Mojtaba and Zelman, Vladimir and the ENIGMA Consortium},
	year         = 2020,
	month        = mar,
	day          = 20,
	journal      = {Translational Psychiatry},
	volume       = 10,
	number       = 1,
	pages        = 100,
	doi          = {10.1038/s41398-020-0705-1},
	issn         = {2158-3188},
	url          = {https://dgarijo.com/papers/enigma_global.pdf}
}

@inproceedings{9006447,
	title        = {SoMEF: A Framework for Capturing Scientific Software Metadata from its Documentation},
	author       = {A. {Mao} and D. {Garijo} and S. {Fakhraei}},
	year         = 2019,
	booktitle    = {2019 IEEE International Conference on Big Data (Big Data)},
	pages        = {3032--3037},
  doi          = {10.1109/BigData47090.2019.9006447},
	url          = {https://dgarijo.com/papers/SoMEF.pdf}
}

@inproceedings{Garijo:2019:III:3308557.3308711,
	title        = {An Intelligent Interface for Integrating Climate, Hydrology, Agriculture, and Socioeconomic Models},
	author       = {Garijo, Daniel and Khider, Deborah and Ratnakar, Varun and Gil, Yolanda and Deelman, Ewa and da Silva, Rafael Ferreira and Knoblock, Craig and Chiang, Yao-Yi and Pham, Minh and Pujara, Jay and Vu, Binh and Feldman, Dan and Mayani, Rajiv and Cobourn, Kelly and Duffy, Chris and Kemanian, Armen and Shu, Lele and Kumar, Vipin and Khandelwal, Ankush and Tayal, Kshitij and Peckham, Scott and Stoica, Maria and Dabrowski, Anna and Hardesty-Lewis, Daniel and Pierce, Suzanne},
	year         = 2019,
	booktitle    = {Proceedings of the 24th International Conference on Intelligent User Interfaces: Companion},
	location     = {Marina del Ray, California},
	publisher    = {ACM},
	address      = {New York, NY, USA},
	series       = {IUI '19},
	pages        = {111--112},
	doi          = {10.1145/3308557.3308711},
	isbn         = {978-1-4503-6673-1},
	url          = {https://dgarijo.com/papers/iuiDemo2019.pdf},
	numpages     = 2,
	acmid        = 3308711,
	keywords     = {environmental modeling, intelligent workflow systems, model integration, scientific discovery}
}

@inproceedings{Gil:2019:THM:3301275.3302324,
	title        = {Towards Human-guided Machine Learning},
	author       = {Gil, Yolanda and Honaker, James and Gupta, Shikhar and Ma, Yibo and D'Orazio, Vito and Garijo, Daniel and Gadewar, Shruti and Yang, Qifan and Jahanshad, Neda},
	year         = 2019,
	booktitle    = {Proceedings of the 24th International Conference on Intelligent User Interfaces},
	location     = {Marina del Ray, California},
	publisher    = {ACM},
	address      = {New York, NY, USA},
	series       = {IUI '19},
	pages        = {614--624},
	doi          = {10.1145/3301275.3302324},
	isbn         = {978-1-4503-6272-6},
	url          = {https://dgarijo.com/papers/iui2019.pdf},
	numpages     = 11,
	acmid        = 3302324,
	keywords     = {automated machine learning (AutoML), human-guided machine learning, scientific workflows, task analysis}
}

@inproceedings{srivastava-etal-psb19,
	title        = {Semantic Workflows for Benchmark Challenges: Enhancing Comparability, Reusability and Reproducibility},
	author       = {Arunima Srivastava and Ravali Adusumilli and Hunter Boyce and Daniel Garijo and Varun Ratnakar and Rajiv Mayani and Thomas Yu and Raghu Machiraju and Yolanda Gil and Parag Mallick},
	year         = 2019,
	booktitle    = {Proceedings of the Pacific Symposium on Biocomputing (PSB)},
	url          = {http://www.isi.edu/~gil/papers/srivastava-etal-psb19.pdf}
}

@inproceedings{szekely-garijo-et-al2019,
	title        = {T2WML: Table To Wikidata Mapping Language},
	author       = {Szekely, Pedro and Garijo, Daniel and Bhatia, Divij and Wu, Jiasheng and Yao, Yixiang and Pujara, Jay},
	year         = 2019,
	booktitle    = {Proceedings of the 10th International Conference on Knowledge Capture},
	location     = {Marina Del Rey, CA, USA},
	publisher    = {Association for Computing Machinery},
	address      = {New York, NY, USA},
	series       = {K-CAP ’19},
	pages        = {267–270},
	doi          = {10.1145/3360901.3364448},
	isbn         = 9781450370080,
	url          = {https://dgarijo.com/papers/t2wmlKCAP2019.pdf},
	numpages     = 4,
	keywords     = {entity linking, wikidata, rdf, knowledge graphs}
}

@inproceedings{markovic-et-al2019,
	title        = {Semantic Modelling of Plans and Execution Traces for Enhancing Transparency of IoT Systems},
	author       = {M. {Markovic} and D. {Garijo} and P. {Edwards} and W. {Vasconcelos}},
	year         = 2019,
	month        = oct,
	booktitle    = {2019 Sixth International Conference on Internet of Things: Systems, Management and Security (IOTSMS)},
	volume       = {},
	number       = {},
	pages        = {110--115},
	doi          = {10.1109/IOTSMS48152.2019.8939260},
	url          = {https://dgarijo.com/papers/IoT_Systems_AAM2019.pdf},
	keywords     = {}
}

@inproceedings{Szekely2019T2WMLAC,
	title        = {T2WML: A Cell-Based Language to Map Tables into Wikidata Records},
	author       = {Pedro A. Szekely and Daniel Garijo and Jay Pujara and Divij Bhatia and Jiasheng Wu},
	year         = 2019,
	booktitle    = {ISWC Satellites},
	url          = {http://ceur-ws.org/Vol-2456/paper12.pdf}
}

@inproceedings{carrillo-et-al-sciknow2019,
	title        = {Semantic Workflows and Machine Learning for the Assessment of Carbon Storage by Urban Trees},
	author       = {Juan Manuel Carrillo Garcia and Daniel Garijo and Mark Crowley and Rober Carrillo and Yolanda Gil and Katherine Borda},
	year         = 2019,
	booktitle    = {Proceedings of the Third Workshop on Capturing Scientific Knowledge (SciKnow 2019), held in conjunction with the 2019 ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Los Angeles, California},
	volume       = 2526,
	issn         = {1613-0073},
	url          = {http://ceur-ws.org/Vol-2526/paper1.pdf}
}

@inproceedings{markovic-et-al-sciknow2019,
	title        = {Linking Abstract Plans of Scientific Experiments to their Corresponding Execution Traces},
	author       = {Milan Markovic and Daniel Garijo and Peter Edwards},
	year         = 2019,
	booktitle    = {Proceedings of the Third Workshop on Capturing Scientific Knowledge (SciKnow 2019), held in conjunction with the 2019 ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Los Angeles, California},
	volume       = 2526,
	issn         = {1613-0073},
	url          = {http://ceur-ws.org/Vol-2526/short1.pdf}
}

@inproceedings{garijo-and-szekely-sciknow2019,
	title        = {WDPlus: Leveraging Wikidata to Link and Extend Tabular Data},
	author       = {Daniel Garijo and Pedro Szekely},
	year         = 2019,
	booktitle    = {Proceedings of the Third Workshop on Capturing Scientific Knowledge (SciKnow 2019), held in conjunction with the 2019 ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Los Angeles, California},
	volume       = 2526,
	issn         = {1613-0073},
	url          = {http://ceur-ws.org/Vol-2526/short4.pdf}
}

@article{ALOBAID2019100472,
	title        = {Automating ontology engineering support activities with OnToology},
	author       = {Ahmad Alobaid and Daniel Garijo and María Poveda-Villalón and Idafen Santana-Perez and Alba Fernández-Izquierdo and Oscar Corcho},
	year         = 2019,
	journal      = {Journal of Web Semantics},
	volume       = 57,
	pages        = 100472,
	doi          = {10.1016/j.websem.2018.09.003},
	issn         = {1570-8268},
	url          = {https://dgarijo.com/papers/JWSsupporting.pdf},
	keywords     = {Ontology engineering, Ontology evaluation, Ontology documentation, Ontology publication},
	abstract     = {Due to the increasing uptake of semantic technologies, ontologies are now part of a good number of information systems. As a result, software development teams that have to combine ontology engineering activities with software development practices are facing several challenges, since these two areas have evolved, in general, separately. In this paper we present OnToology, an approach to manage ontology engineering support activities (i.e., documentation, evaluation, releasing and versioning). OnToology is a web-based application that builds on top of Git-based environments and integrates existing semantic web technologies. We have validated OnToology against a set of representative requirements for ontology development support activities in distributed environments, and report on a survey of the system to assess its usefulness and usability.}
}

Due to the increasing uptake of semantic technologies, ontologies are now part of a good number of information systems. As a result, software development teams that have to combine ontology engineering activities with software development practices are facing several challenges, since these two areas have evolved, in general, separately. In this paper we present OnToology, an approach to manage ontology engineering support activities (i.e., documentation, evaluation, releasing and versioning). OnToology is a web-based application that builds on top of Git-based environments and integrates existing semantic web technologies. We have validated OnToology against a set of representative requirements for ontology development support activities in distributed environments, and report on a survey of the system to assess its usefulness and usability.

@inproceedings{ref10.1007/978-3-030-33752-0_18,
	title        = {Towards Automated Hypothesis Testing in Neuroscience},
	author       = {Garijo, Daniel and Fakhraei, Shobeir and Ratnakar, Varun and Yang, Qifan and Endrias, Hanna and Ma, Yibo and Wang, Regina and Bornstein, Michael and Bright, Joanna and Gil, Yolanda and Jahanshad, Neda},
	year         = 2019,
	booktitle    = {Heterogeneous Data Management, Polystores, and Analytics for Healthcare},
	publisher    = {Springer International Publishing},
	address      = {Cham},
	pages        = {249--257},
	isbn         = {978-3-030-33752-0},
	url          = {https://dgarijo.com/papers/Enigma_Disk_2019.pdf},
	editor       = {Gadepally, Vijay and Mattson, Timothy and Stonebraker, Michael and Wang, Fusheng and Luo, Gang and Laing, Yanhui and Dubovitskaya, Alevtina}
}

@article{doi:10.1029/2019PA003632,
	title        = {PaCTS 1.0: A Crowdsourced Reporting Standard for Paleoclimate Data},
	author       = {Khider, D. and Emile-Geay, J. and McKay, N. P. and Gil, Y. and Garijo, D. and Ratnakar, V. and Alonso-Garcia, M. and Bertrand, S. and Bothe, O. and Brewer, P. and Bunn, A. and Chevalier, M. and Comas-Bru, L. and Csank, A. and Dassié, E. and DeLong, K. and Felis, T. and Francus, P. and Frappier, A. and Gray, W. and Goring, S. and Jonkers, L. and Kahle, M. and Kaufman, D. and Kehrwald, N. M. and Martrat, B. and McGregor, H. and Richey, J. and Schmittner, A. and Scroxton, N. and Sutherland, E. and Thirumalai, K. and Allen, K. and Arnaud, F. and Axford, Y. and Barrows, T. and Bazin, L. and Pilaar Birch, S. E. and Bradley, E. and Bregy, J. and Capron, E. and Cartapanis, O. and Chiang, H.-W. and Cobb, K. M. and Debret, M. and Dommain, R. and Du, J. and Dyez, K. and Emerick, S. and Erb, M. P. and Falster, G. and Finsinger, W. and Fortier, D. and Gauthier, Nicolas and George, S. and Grimm, E. and Hertzberg, J. and Hibbert, F. and Hillman, A. and Hobbs, W. and Huber, M. and Hughes, A. L. C. and Jaccard, S. and Ruan, J. and Kienast, M. and Konecky, B. and Le Roux, G. and Lyubchich, V. and Novello, V. F. and Olaka, L. and Partin, J. W. and Pearce, C. and Phipps, S. J. and Pignol, C. and Piotrowska, N. and Poli, M.-S. and Prokopenko, A. and Schwanck, F. and Stepanek, C. and Swann, G. E. A. and Telford, R. and Thomas, E. and Thomas, Z. and Truebe, S. and von Gunten, L. and Waite, A. and Weitzel, N. and Wilhelm, B. and Williams, J. and Williams, J. J. and Winstrup, M. and Zhao, N. and Zhou, Y.},
	year         = 2019,
	journal      = {Paleoceanography and Paleoclimatology},
	volume       = 34,
	number       = 10,
	pages        = {1570--1596},
	doi          = {10.1029/2019PA003632},
	url          = {https://dgarijo.com/papers/agu_2019.pdf},
	keywords     = {standards, FAIR, paleoclimate, paleoceanography, data, best practices},
	eprint       = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019PA003632}
}

@inproceedings{garijo_okg-soft_2019,
	title        = {{OKG}-{Soft}: {An} {Open} {Knowledge} {Graph} with {Machine} {Readable} {Scientific} {Software} {Metadata}},
	shorttitle   = {{OKG}-{Soft}},
	author       = {Garijo, Daniel and Osorio, Maximiliano and Khider, Deborah and Ratnakar, Varun and Gil, Yolanda},
	year         = 2019,
	month        = sep,
	booktitle    = {2019 15th {International} {Conference} on {eScience} ({eScience})},
	publisher    = {IEEE},
	address      = {San Diego, CA, USA},
	pages        = {349--358},
	doi          = {10.1109/eScience.2019.00046},
	isbn         = {978-1-72812-451-3},
	url          = {https://dgarijo.com/papers/OKG-SoftEscience2019.pdf},
	urldate      = {2020-04-08}
}

@inproceedings{DBLP:conf/psb/SrivastavaABGRM19,
	title        = {Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility},
	author       = {Arunima Srivastava and Ravali Adusumilli and Hunter Boyce and Daniel Garijo and Varun Ratnakar and Rajiv Mayani and Thomas Yu and Raghu Machiraju and Yolanda Gil and Parag Mallick},
	year         = 2019,
	booktitle    = {Biocomputing 2019: Proceedings of the Pacific Symposium, The Big Island of Hawaii, Hawaii, USA, January 3-7, 2019},
	pages        = {208--219},
	url          = {http://psb.stanford.edu/psb-online/proceedings/psb19/srivastava.pdf},
	editor       = {Russ B. Altman and A. Keith Dunker and Lawrence Hunter and Marylyn D. Ritchie and Teri E. Klein},
	timestamp    = {Thu, 12 Mar 2020 11:38:57 +0100},
	biburl       = {https://dblp.org/rec/conf/psb/SrivastavaABGRM19.bib},
	bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{carvalho-etal-escience18,
	title        = {Semantic Software Metadata for Workflow Exploration and Evolution},
	author       = {Lucas Carvalho and Daniel Garijo and Claudia Bauzer Medeiros and Yolanda Gil},
	year         = 2018,
	booktitle    = {Proceedings of the Fourteenth IEEE International Conference on eScience},
	address      = {Amsterdam, The Netherlands},
	url          = {https://www.isi.edu/~gil/papers/carvalho-etal-escience18.pdf}
}

@inproceedings{ferreira-etal-iemss18,
	title        = {Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution},
	author       = {Rafael Ferreira da Silva and Daniel Garijo and Scott D. Peckham and Yolanda Gil and Ewa Deelman and Varun Ratnakar},
	year         = 2018,
	booktitle    = {Proceedings of the Ninth International Congress on Environmental Modeling and Software},
	address      = {Ft Collins, CO},
	url          = {http://www.isi.edu/~gil/papers/ferreira-etal-iemss18.pdf}
}

@inproceedings{gil2018mint,
	title        = {MINT: Model Integration Through Knowledge-Powered Data and Process Composition},
	author       = {Yolanda  Gil and Kelly Cobourn and Ewa Deelman and Chris Duffy and Rafael Ferreira da Silva and Armen Kemanian and Craig Knoblock and Vipin Kumar and Scott Peckham and Lucas Carvalho and Yao-Yi Chiang and Daniel Garijo and Deborah Khider and Ankush Khandelwal and Minh Pahm and Jay Pujara and Varun Ratnakar and Maria Stoica and Binh Vu},
	year         = 2018,
	booktitle    = {Proceedings of the 9th International Congress on Environmental Modelling and Software},
	url          = {https://dgarijo.com/papers/iemss2018-MINT.pdf}
}

@inproceedings{garijo2018ontosoft,
	title        = {A Semantic Model Catalog to Support Comparison and Reuse},
	author       = {Daniel Garijo and Deborah Khider and Yolanda Gil and Lucas Carvalho and Bakinam Essawy and Suzanne Pierce and Daniel Hardesty Lewis and Varun Ratnakar and Scott Peckham and Chris Duffy and Jonathan Goodal},
	year         = 2018,
	booktitle    = {Proceedings of the 9th International Congress on Environmental Modelling and Software},
	url          = {https://dgarijo.com/papers/IEMSs2018-OntoSoft.pdf}
}

@inproceedings{gil2018p4ml,
	title        = {P4ML: A Phased Performance-Based Pipeline Planner for Automated Machine Learning},
	author       = {Yolanda Gil and Ke-Thia Yao and Varun Ratnakar and Daniel Garijo and Greg Ver Steeg and Pedro Szekely and Rob Brekelmans and Mayank Kejriwal and Fanghao Luo and I-Hui Huang},
	year         = 2018,
	booktitle    = {Proceedings of Machine Learning Research, ICML 2018 AutoML Workshop},
	url          = {https://dgarijo.com/papers/AutoML2018.pdf}
}

@inproceedings{DBLP:conf/webi/CheongGCG18,
	title        = {PSM-Flow: Probabilistic Subgraph Mining for Discovering Reusable Fragments in Workflows},
	author       = {Chin Wang Cheong and Daniel Garijo and Kwok{-}Wai Cheung and Yolanda Gil},
	year         = 2018,
	booktitle    = {2018 {IEEE/WIC/ACM} International Conference on Web Intelligence, {WI} 2018, Santiago, Chile, December 3-6, 2018},
	pages        = {166--173},
	doi          = {10.1109/WI.2018.00-93},
	url          = {https://dgarijo.com/papers/psmFlow.pdf},
	crossref     = {DBLP:conf/webi/2018},
	biburl       = {https://dblp.org/rec/bib/conf/webi/CheongGCG18},
	bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{garijo-etal-sciknow2017,
	title        = {The DISK Hypothesis Ontology: Capturing Hypothesis Evolution for Automated Discovery},
	author       = {Daniel Garijo and Yolanda Gil and Varun Ratnakar},
	year         = 2017,
	booktitle    = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Austin, Texas},
	url          = {https://dgarijo.com/papers/garijo_sciknow17.pdf},
	funding      = {DARPA W911NF-15-1-0555, NIH 1R01GM117097}
}

@inproceedings{carvalho-etal-sciknow2017b,
	title        = {NiW: Converting Notebooks into Workflows to Capture Dataflow and Provenance},
	author       = {Lucas A. M. C. Carvalho and Regina Wang and Yolanda Gil and Daniel Garijo},
	year         = 2017,
	booktitle    = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Austin, Texas},
	url          = {https://dgarijo.com/papers/carvalho_niw.pdf},
	funding      = {USNSF ICER-1440323, SPRF 2017/03570-3}
}

@inproceedings{carvalho-etal-sciknow2017a,
	title        = {Requirements for Supporting the Iterative Exploration of Scientific Workflow Variants},
	author       = {Lucas A. M. C. Carvalho and Bakinam T. Essawy and Daniel Garijo and Claudia Bauzer Medeiros and Yolanda Gil},
	year         = 2017,
	booktitle    = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Austin, Texas},
	url          = {https://dgarijo.com/papers/carvalho_sciknow17.pdf},
	funding      = {USNSF ICER-1440323, SPRF 2017/03570-3}
}

@inproceedings{gil-etal-sciknow2017,
	title        = {Improving Publication and Reproducibility of Computational Experiments through Workflow Abstractions},
	author       = {Yolanda Gil and Daniel Garijo and Margaret Knoblock and Alyssa Deng and Ravali Adusumilli and Varun Ratnakar and Parag Mallick},
	year         = 2017,
	booktitle    = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
	address      = {Austin, Texas},
	url          = {https://dgarijo.com/papers/gil_sciknow17.pdf},
	funding      = {DARPA W911NF-15-1-0555, NIH 1U01CA196387}
}

@inproceedings{jang-etal-semsci17,
	title        = {Towards Automatic Generation of Portions of Scientific Papers for Large Multi-Institutional Collaborations Based on Semantic Metadata},
	author       = {MiHyun Jang and Tejal Patted and Yolanda Gil and Daniel Garijo and Varun Ratnakar and Jie Ji and Prince Wang and Aggie McMahon and Paul M. Thompson and Neda Jahanshad},
	year         = 2017,
	booktitle    = {Proceedings of the Workshop on Enabling Open Semantic Science, co-located with the Sixteenth International Semantic Web Conference (ISWC)},
	address      = {Vienna, Austria},
	url          = {http://www.isi.edu/~gil/papers/jang-etal-semsci17.pdf},
	ee           = {http://ceur-ws.org/Vol-1931/paper-09.pdf},
	funding      = {NSF IIS-1344272, NIHBD U54EB020403}
}

@inproceedings{gil2017towards2,
	title        = {Towards Continuous Scientific Data Analysis and Hypothesis Evolution.},
	author       = {Gil, Yolanda and Garijo, Daniel and Ratnakar, Varun and Mayani, Rajiv and Adusumilli, Ravali and Boyce, Hunter and Srivastava, Arunima and Mallick, Parag},
	year         = 2017,
	booktitle    = {Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence},
	pages        = {4406--4414},
	doi          = {10.1609/aaai.v31i1.11157},
	url          = {https://dgarijo.com/papers/aaai2017.pdf}
}

@article{garijo2017abstract,
	title        = {Abstract, link, publish, exploit: An end to end framework for workflow sharing},
	author       = {Garijo, Daniel and Gil, Yolanda and Corcho, Oscar},
	year         = 2017,
	journal      = {Future Generation Computer Systems},
	publisher    = {North-Holland},
	doi          = {10.1016/j.future.2017.01.008},
	url          = {https://dgarijo.com/papers/fgcs2017.pdf},
	funding      = {DARPA  W911NF-15-1-0555, USNSF ICER-1440323}
}

@inproceedings{gil2017towards,
	title        = {Towards Automating Data Narratives},
	author       = {Gil, Yolanda and Garijo, Daniel},
	year         = 2017,
	booktitle    = {Proceedings of the 22nd International Conference on Intelligent User Interfaces},
	pages        = {565--576},
	doi          = {10.1145/3025171.3025193},
	url          = {https://dgarijo.com/papers/iui2017.pdf},
	organization = {ACM},
	funding      = {DARPA W911NF-15-1-0555, NIH 1R01GM117097}
}

@article{garijo2017ai,
	title        = {AI buzzwords explained: scientific workflows},
	author       = {Garijo, Daniel},
	year         = 2017,
	journal      = {AI Matters},
	publisher    = {ACM},
	volume       = 3,
	number       = 1,
	pages        = {4--8},
	doi          = {10.1145/3054837.3054839},
	url          = {https://dgarijo.com/papers/aibuzzword2017.pdf}
}

@article{allen_et_al:DM:2017:7146,
	title        = {{Engineering Academic Software (Dagstuhl Perspectives Workshop 16252)}},
	author       = {Alice Allen and Cecilia Aragon and Christoph Becker and Jeffrey Carver and Andrei Chis and Benoit Combemale and Mike Croucher and Kevin Crowston and Daniel Garijo and Ashish Gehani and Carole Goble and Robert Haines and Robert Hirschfeld and James Howison and Kathryn Huff and Caroline Jay and Daniel S. Katz and Claude Kirchner and Katie Kuksenok and Ralf L{\"a}mmel and Oscar Nierstrasz and Matt Turk and Rob van Nieuwpoort and Matthew Vaughn and Jurgen J. Vinju},
	year         = 2017,
	journal      = {Dagstuhl Manifestos},
	publisher    = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
	address      = {Dagstuhl, Germany},
	volume       = 6,
	number       = 1,
	pages        = {1--20},
	doi          = {10.4230/DagMan.6.1.1},
	issn         = {2193-2433},
	url          = {https://dgarijo.com/papers/dagstuhl_2017.pdf},
	editor       = {Alice Allen et al.},
	urn          = {urn:nbn:de:0030-drops-71468},
	annote       = {Keywords: Academic software, Research software, Software citation, Software sustainability}
}

@inproceedings{gil2017controlled,
	title        = {A Controlled Crowdsourcing Approach for Practical Ontology Extensions and Metadata Annotations},
	author       = {Gil, Yolanda and Garijo, Daniel and Ratnakar, Varun and Khider, Deborah and Emile-Geay, Julien and McKay, Nicholas},
	year         = 2017,
	booktitle    = {d'Amato C. et al. (eds) The Semantic Web – ISWC 2017},
	volume       = 10588,
	pages        = {231--246},
	doi          = {10.1007/978-3-319-68204-4_24},
	url          = {https://dgarijo.com/papers/linkedEarth-iswc2017.pdf},
	funding      = {USNSF  IIS-1344272},
	organization = {Springer, Cham}
}

@inproceedings{garijo2017widoco,
	title        = {{WIDOCO}: a wizard for documenting ontologies},
	author       = {Garijo, Daniel},
	year         = 2017,
	booktitle    = {d'Amato C. et al. (eds) The Semantic Web – ISWC 2017},
	volume       = 10588,
	pages        = {94--102},
	doi          = {10.1007/978-3-319-68204-4_9},
	url          = {https://dgarijo.com/papers/widoco-iswc2017.pdf},
	organization = {Springer, Cham},
	funding      = {USNSF ICER-1541029, NIH 1R01GM117097-01}
}

@article{parkkila2017ontology,
	title        = {An ontology for videogame interoperability},
	author       = {Parkkila, Janne and Radulovic, Filip and Garijo, Daniel and Poveda-Villal{\'o}n, Mar{\'i}a and Ikonen, Jouni and Porras, Jari and G{\'o}mez-P{\'e}rez, Asunci{\'o}n},
	year         = 2016,
	journal      = {Multimedia Tools and Applications},
	publisher    = {Springer US},
	volume       = 76,
	number       = 4,
	pages        = {4981--5000},
	doi          = {10.1007/s11042-016-3552-6},
	url          = {https://dgarijo.com/papers/vgo.pdf},
	funding      = {FPU FPU2012/04084}
}

@inproceedings{gil2016automated,
	title        = {Automated Hypothesis Testing with Large Scientific Data Repositories},
	author       = {Gil, Yolanda and Garijo, Daniel and Ratnakar, Varun and Mayani, Rajiv and Adusumilli, Ravali and Boyce, Hunter and Mallick, Parag},
	year         = 2016,
	booktitle    = {Proceedings of the Fourth Annual Conference on Advances in Cognitive Systems (ACS)},
	url          = {https://dgarijo.com/papers/acs2016.pdf},
	funding      = {DARPA W911NF-15-1-0555, NIH 1U01CA196387}
}

@inproceedings{gil2016ontosoft,
	title        = {OntoSoft: A distributed semantic registry for scientific software},
	author       = {Gil, Yolanda and Garijo, Daniel and Mishra, Saurabh and Ratnakar, Varun},
	year         = 2016,
	booktitle    = {e-Science (e-Science), 2016 IEEE 12th International Conference on},
	pages        = {331--336},
	doi          = {10.1109/eScience.2016.7870916},
	url          = {https://dgarijo.com/papers/ontoSoft2016.pdf},
	organization = {IEEE}
}

@article{allen2016lightning,
	title        = {Lightning Talk:" I solemnly pledge": A Manifesto for Personal Responsibility in the Engineering of Academic Software},
	author       = {Allen, Alice and Aragon, Cecilia and Becker, Christoph and Carver, Jeffrey and Chis, Vasile-Andrei and Combemale, Benoit and Croucher, Mike and Crowston, Kevin and Garijo, Daniel and Gehani, Ashish and others},
	year         = 2016,
	publisher    = {CEUR},
	url          = {https://dgarijo.com/papers/WSSSPE4_paper_15.pdf}
}

@article{belhajjame2015using,
	title        = {Using a suite of ontologies for preserving workflow-centric research objects},
	author       = {Belhajjame, Khalid and Zhao, Jun and Garijo, Daniel and Gamble, Matthew and Hettne, Kristina and Palma, Raul and Mina, Eleni and Corcho, Oscar and G{\'o}mez-P{\'e}rez, Jos{\'e} Manuel and Bechhofer, Sean and others},
	year         = 2015,
	journal      = {Web Semantics: Science, Services and Agents on the World Wide Web},
	publisher    = {Elsevier},
	volume       = 32,
	pages        = {16--42},
	doi          = {10.1016/j.websem.2015.01.003},
	url          = {https://dgarijo.com/papers/ros.pdf}
}

@inproceedings{garijo2015ldp4ros,
	title        = {LDP4ROs: Managing Research Objects with the W3C Linked Data Platform},
	author       = {Garijo, Daniel and Mihindukulasooriya, Nandana and Corcho, Oscar},
	year         = 2015,
	booktitle    = {Proceedings of the 24th International Conference on World Wide Web},
	pages        = {1057--1058},
	doi          = {10.1145/2740908.2742016},
	url          = {https://dgarijo.com/papers/garijo-savesd2015.pdf},
	organization = {ACM}
}

@inproceedings{gil2015ontosoft,
	title        = {OntoSoft: Capturing scientific software metadata},
	author       = {Gil, Yolanda and Ratnakar, Varun and Garijo, Daniel},
	year         = 2015,
	booktitle    = {Proceedings of the 8th International Conference on Knowledge Capture},
	pages        = 32,
	doi          = {10.1145/2815833.2816955},
	url          = {https://dgarijo.com/papers/gil-etal-kcap2015.pdf},
	organization = {ACM},
	funding      = {USNSF ICER-1440323}
}

@inproceedings{alobaid2015ontoology,
	title        = {OnToology, a tool for collaborative development of ontologies.},
	author       = {Alobaid, Ahmad and Garijo, Daniel and Poveda-Villal{\'o}n, Mar{\'i}a and P{\'e}rez, Idafen Santana and Corcho, Oscar},
	year         = 2015,
	booktitle    = {ICBO},
	url          = {https://dgarijo.com/papers/ontoology.pdf}
}

@phdthesis{garijo2015mining,
	title        = {Mining Abstractions in Scientific Workows},
	author       = {Garijo Verdejo, Daniel},
	year         = 2015,
	url          = {https://dgarijo.com/papers/tesis.pdf},
	school       = {ETSI\_Informatica}
}

@article{garijo2014common,
	title        = {Common motifs in scientific workflows: An empirical analysis},
	author       = {Garijo, Daniel and Alper, Pinar and Belhajjame, Khalid and Corcho, Oscar and Gil, Yolanda and Goble, Carole},
	year         = 2014,
	journal      = {Future Generation Computer Systems},
	publisher    = {North-Holland},
	volume       = 36,
	pages        = {338--351},
	doi          = {10.1016/j.future.2013.09.018},
	url          = {https://dgarijo.com/papers/fgcs-paper-motifs.pdf},
	funding      = {USAFOSR FA9550-11-1-0104}
}

@article{DBLP:journals/corr/BelhajjameZGHPCGBKG14,
	title        = {The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web},
	author       = {Khalid Belhajjame and Jun Zhao and Daniel Garijo and Kristina M. Hettne and Ra{\'{u}}l Palma and {\'{O}}scar Corcho and Jos{\'{e}} Manu{\'{e}}l G{\'{o}}mez{-}P{\'{e}}rez and Sean Bechhofer and Graham Klyne and Carole A. Goble},
	year         = 2014,
	journal      = {CoRR},
	volume       = {abs/1401.4307},
	url          = {https://dgarijo.com/papers/ro.pdf}
}

@inproceedings{garijo2014workflow,
	title        = {Workflow reuse in practice: a study of neuroimaging pipeline users},
	author       = {Garijo, Daniel and Corcho, Oscar and Gil, Yolanda and Braskie, Meredith N and Hibar, Derrek and Hua, Xue and Jahanshad, Neda and Thompson, Paul and Toga, Arthur W},
	year         = 2014,
	booktitle    = {e-Science (e-Science), 2014 IEEE 10th International Conference on},
	volume       = 1,
	pages        = {239--246},
	doi          = {10.1109/eScience.2014.33},
	url          = {https://dgarijo.com/papers/usersurvey-escience14.pdf},
	organization = {IEEE},
	funding      = {USNSF IIS-1344272}
}

@inproceedings{garijo2014fragflow,
	title        = {Fragflow automated fragment detection in scientific workflows},
	author       = {Garijo, Daniel and Corcho, Oscar and Gil, Yolanda and Gutman, Boris A and Dinov, Ivo D and Thompson, Paul and Toga, Arthur W},
	year         = 2014,
	booktitle    = {e-Science (e-Science), 2014 IEEE 10th International Conference on},
	volume       = 1,
	pages        = {281--289},
	doi          = {10.1109/eScience.2014.32},
	url          = {https://dgarijo.com/papers/fragflow-escience14.pdf},
	organization = {IEEE},
	funding      = {USNSF IIS-1344272, NIH R01AG040060}
}

@inproceedings{garijo2014towards,
	title        = {Towards workflow ecosystems through semantic and standard representations},
	author       = {Garijo, Daniel and Gil, Yolanda and Corcho, Oscar},
	year         = 2014,
	booktitle    = {Proceedings of the 9th Workshop on Workflows in Support of Large-Scale Science},
	pages        = {94--104},
	doi          = {10.1109/WORKS.2014.13},
	url          = {https://dgarijo.com/papers/west-works14.pdf},
	organization = {IEEE Press}
}

@inproceedings{garijo2014challenges,
	title        = {Challenges for provenance analytics over geospatial data},
	author       = {Garijo, Daniel and Gil, Yolanda and Harth, Andreas},
	year         = 2014,
	booktitle    = {International Provenance and Annotation Workshop},
	pages        = {261--263},
	doi          = {10.1007/978-3-319-16462-5_28},
	url          = {https://dgarijo.com/papers/geo.pdf},
	organization = {Springer, Cham}
}

@article{atemezing2013transforming,
	title        = {Transforming meteorological data into linked data},
	author       = {Atemezing, Ghislain and Corcho, Oscar and Garijo, Daniel and Mora, Jos{\'e} and Poveda-Villal{\'o}n, Mar{\'i}a and Rozas, Pablo and Vila-Suero, Daniel and Villaz{\'o}n-Terrazas, Boris},
	year         = 2013,
	journal      = {Semantic Web},
	publisher    = {IOS Press},
	volume       = 4,
	number       = 3,
	pages        = {285--290},
	doi          = {10.3233/SW-120089},
	url          = {https://dgarijo.com/papers/meteo.pdf}
}

@inproceedings{belhajjame2013workflow,
	title        = {A workflow PROV-corpus based on taverna and wings},
	author       = {Belhajjame, Khalid and Zhao, Jun and Garijo, Daniel and Garrido, Aleix and Soiland-Reyes, Stian and Alper, Pinar and Corcho, Oscar},
	year         = 2013,
	booktitle    = {Proceedings of the Joint EDBT/ICDT 2013 Workshops},
	pages        = {331--332},
	doi          = {10.1145/2457317.2457376},
	url          = {https://dgarijo.com/papers/prov-bench-paper.pdf},
	organization = {ACM}
}

@techreport{lebo2013prov,
	title        = {{PROV-O}: The {PROV} ontology},
	author       = {Lebo, Timothy and Sahoo, Satya and McGuinness, Deborah and Belhajjame, Khalid and Cheney, James and Corsar, David and Garijo, Daniel and Soiland-Reyes, Stian and Zednik, Stephan and Zhao, Jun},
	year         = 2013,
	journal      = {W3C recommendation},
	publisher    = {W3C},
	volume       = 30,
	url          = {https://www.w3.org/TR/2013/REC-prov-o-20130430/}
}

@inproceedings{garijo2013detecting,
	title        = {Detecting common scientific workflow fragments using templates and execution provenance},
	author       = {Garijo, Daniel and Corcho, Oscar and Gil, Yolanda},
	year         = 2013,
	booktitle    = {Proceedings of the seventh international conference on Knowledge capture},
	pages        = {33--40},
	doi          = {10.1145/2479832.2479848},
	url          = {https://dgarijo.com/papers/paperKCAP2013.pdf},
	organization = {ACM},
	funding      = {USAFOSR FA9550-11-1-0104}
}

@inproceedings{holl2013specifying,
	title        = {On specifying and sharing scientific workflow optimization results using research objects},
	author       = {Holl, Sonja and Garijo, Daniel and Belhajjame, Khalid and Zimmermann, Olav and De Giovanni, Renato and Obst, Matthias and Goble, Carole},
	year         = 2013,
	booktitle    = {Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science},
	pages        = {28--37},
	doi          = {10.1145/2534248.2534251},
	url          = {https://dgarijo.com/papers/works13.pdf},
	organization = {ACM}
}

@article{garijo2013quantifying,
	title        = {Quantifying reproducibility in computational biology: the case of the tuberculosis drugome},
	author       = {Garijo, Daniel and Kinnings, Sarah and Xie, Li and Xie, Lei and Zhang, Yinliang and Bourne, Philip E and Gil, Yolanda},
	year         = 2013,
	journal      = {PloS one},
	publisher    = {Public Library of Science},
	volume       = 8,
	number       = 11,
	pages        = {e80278},
	doi          = {10.1371/journal.pone.0080278},
	url          = {https://dgarijo.com/papers/plos.pdf}
}

@techreport{dcprov,
	title        = {Dublin Core to {PROV} Mapping},
	author       = {Daniel Garijo and Kai Eckert},
	year         = 2013,
	month        = apr,
	url          = {http://www.w3.org/TR/2013/NOTE-prov-dc-20130430/},
	note         = {http://www.w3.org/TR/2013/NOTE-prov-dc-20130430/},
	type         = {{W3C} Note},
	institution  = {W3C}
}

@techreport{belhajjame2013wf4ever,
	title        = {Wf4Ever research object model},
	author       = {Belhajjame, K and Klyne, G and Garijo, D and Corcho, O and Garc{\'i}a-Cuesta, E and Palma, R},
	year         = 2013,
	url          = {http://wf4ever.github.io/ro}
}

@inproceedings{6404427,
	title        = {Common motifs in scientific workflows: An empirical analysis},
	author       = {D. Garijo and P. Alper and K. Belhajjame and O. Corcho and Y. Gil and C. Goble},
	year         = 2012,
	month        = oct,
	booktitle    = {2012 IEEE 8th International Conference on E-Science},
	pages        = {1--8},
	doi          = {10.1109/eScience.2012.6404427},
	url          = {https://dgarijo.com/papers/motifs2012.pdf},
	keywords     = {natural sciences computing;workflow management software;Taverna systems;Wings systems;common motifs;data adaptation steps;data oriented motifs;data preparation;empirical analysis;scientific workflows;understandability problem;workflow abstraction generation;workflow oriented motifs;Bioinformatics;Cleaning;Data visualization;Drugs;Genomics;Humans;Servers},
	funding      = {USAFOSR  FA9550-11-1-0104}
}

@article{belhajjame2012workflow,
	title        = {Workflow-Centric Research Objects: First Class Citizens in Scholarly Discourse},
	author       = {Belhajjame, Khalid and Corcho, Oscar and Garijo, Daniel and Zhao, Jun and Missier, Paolo and Newman, David and Palma, Ra{\'u}l and Bechhofer, Sean and Garc{\'i}a, Esteban and Cuesta, Jos{\'e} Manuel G{\'o}mez-P{\'e}rez and others},
	year         = 2012,
	doi          = {10.1.1.383.203},
	url          = {https://dgarijo.com/papers/sepublica2012.pdf}
}

@article{villazon2012publishing,
	title        = {Publishing Linked Data-There is no One-Size-Fits-All Formula},
	author       = {Villaz{\'o}n-Terrazas, Boris and Vila-Suero, Daniel and Garijo, Daniel and Vilches-Bl{\'a}zquez, Luis M and Poveda-Villal{\'o}n, Mar{\'i}a and Mora, Jos{\'e} and Corcho, Oscar and G{\'o}mez-P{\'e}rez, Asunci{\'o}n},
	year         = 2012,
	url          = {https://dgarijo.com/papers/poster5.pdf}
}

@inproceedings{garijo-gil-lisc12,
	title        = {Augmenting PROV with Plans in P-PLAN: Scientific Processes as Linked Data},
	author       = {Daniel Garijo and Yolanda Gil},
	year         = 2012,
	booktitle    = {Second International Workshop on Linked Science: Tackling Big Data (LISC), held in conjunction with the International Semantic Web Conference (ISWC)},
	address      = {Boston, MA},
	url          = {https://dgarijo.com/papers/p-plan-lisc2012.pdf}
}

@techreport{belhajjame2012prov,
	title        = {Prov model primer},
	author       = {Miles, Simon and Gil, Yolanda and Belhajjame, Khalid and Deus, Helena and Garijo, Daniel and Klyne, Graham and Missier, Paolo and Soiland-Reyes, Stian and Zednik, Stephen},
	year         = 2012,
	journal      = {W3C recommendation},
	publisher    = {W3C},
	url          = {http://www.w3.org/TR/provprimer}
}

@inproceedings{garijo2011new,
	title        = {A new approach for publishing workflows: abstractions, standards, and linked data},
	author       = {Garijo, Daniel and Gil, Yolanda},
	year         = 2011,
	booktitle    = {Proceedings of the 6th workshop on Workflows in support of large-scale science},
	pages        = {47--56},
	doi          = {10.1145/2110497.2110504},
	url          = {https://dgarijo.com/papers/works11.pdf},
	funding      = {USNSF CCF-0725332, AFOSR FA9550-11-1-0104},
	organization = {ACM}
}

@inproceedings{eckert2011metadata,
	title        = {Metadata provenance: dublin core on the next level},
	author       = {Eckert, Kai and Garijo, Daniel and Panzer, Michael and Per{\c{c}}in, {\"O}mer},
	year         = 2011,
	booktitle    = {Proceedings of the 2011 International Conference on Dublin Core and Metadata Applications},
	pages        = {192--193},
	url          = {http://dcpapers.dublincore.org/pubs/article/download/3646/1872},
	organization = {Dublin Core Metadata Initiative}
}

@inproceedings{eckert2011extending,
	title        = {Extending DCAM for metadata provenance},
	author       = {Eckert, Kai and Garijo, Daniel and Panzer, Michael},
	year         = 2011,
	booktitle    = {International Conference on Dublin Core and Metadata Applications},
	pages        = {12--25},
	url          = {https://dgarijo.com/papers/dc2011.pdf}
}

@mastersthesis{garijo2011provenance,
	title        = {A Provenance-Enabled Service for News and Blog Aggregation},
	author       = {Garijo Verdejo, Daniel},
	year         = 2011,
	url          = {http://oa.upm.es/6567/},
	school       = {Informatica}
}

@inproceedings{Garijo:2011:PLD:2063518.2063554,
	title        = {A Provenance-aware Linked Data Application for Trip Management and Organization},
	author       = {Garijo, Daniel and Villaz\'{o}n-Terrazas, Boris and Corcho, Oscar},
	year         = 2011,
	booktitle    = {Proceedings of the 7th International Conference on Semantic Systems},
	location     = {Graz, Austria},
	publisher    = {ACM},
	address      = {New York, NY, USA},
	series       = {I-Semantics '11},
	pages        = {224--226},
	doi          = {10.1145/2063518.2063554},
	isbn         = {978-1-4503-0621-8},
	url          = {https://dgarijo.com/papers/triplification.pdf},
	numpages     = 3,
	acmid        = 2063554,
	keywords     = {blog, linked data, news, provenance}
}

@techreport{gil2010provenance,
	title        = {Provenance xg final report},
	author       = {Gil, Yolanda and Cheney, James and Groth, PT and Hartig, Olaf and Miles, Simon and Moreau, Luc and Pinheiro da Silva, P},
	year         = 2010,
	journal      = {W3C Incubator Group Reports},
	publisher    = {W3C},
	url          = {https://www.w3.org/2005/Incubator/prov/XGR-prov-20101214/}
}