@inbook{
 type = {inbook},
 year = {2022},
 keywords = {data integration,linkset,ontology design,semantic web ontology,semantic web vocabulary},
 pages = {81-96},
 volume = {13514 LNAI},
 websites = {https://link.springer.com/10.1007/978-3-031-17105-5_6},
 id = {748d85e4-f239-330b-942c-c9cd047df172},
 created = {2022-09-24T06:07:44.948Z},
 accessed = {2022-09-24},
 file_attached = {true},
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 last_modified = {2024-04-24T10:17:29.056Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Idrissou2022},
 private_publication = {false},
 abstract = {Data integration is an essential task in the open world of the Semantic Web. Many approaches have been proposed that achieve such integration by linking related entities across data providers, but they lack the support for in-depth documentation of the involved processes such as the creation, manipulation and evaluation of links. As a consequence, detailed documentation that eases the understanding and reproducibility of underlying processes is needed for a reliable reuse of graphs of identity available in the Semantic Web. We present here an approach to document such links and their processes, building upon a representation we call VoID+. It enables link-publishers to provide data-users with information that better support them in accessing and using links. We show that our approach with the proposed VoID+ ontology allows us to address the relevant competency questions around the reuse of integrated Semantic Web data. We also demonstrate how our approach has been successfully implemented in the Lenticular Lens, a user interface tool that annotates links it discovers, manipulates or validates under user’s guidance. Based on a real-life humanities case study, we can show that the ontology amply annotates links in its life-cycle for reliable decision making by data-users.},
 bibtype = {inbook},
 author = {Idrissou, Al and Zamborlini, Veruska and Kuhn, Tobias},
 doi = {10.1007/978-3-031-17105-5_6},
 chapter = {Documenting the Creation, Manipulation and Evaluation of Links for Reuse and Reproducibility},
 title = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}
}

Data integration is an essential task in the open world of the Semantic Web. Many approaches have been proposed that achieve such integration by linking related entities across data providers, but they lack the support for in-depth documentation of the involved processes such as the creation, manipulation and evaluation of links. As a consequence, detailed documentation that eases the understanding and reproducibility of underlying processes is needed for a reliable reuse of graphs of identity available in the Semantic Web. We present here an approach to document such links and their processes, building upon a representation we call VoID+. It enables link-publishers to provide data-users with information that better support them in accessing and using links. We show that our approach with the proposed VoID+ ontology allows us to address the relevant competency questions around the reuse of integrated Semantic Web data. We also demonstrate how our approach has been successfully implemented in the Lenticular Lens, a user interface tool that annotates links it discovers, manipulates or validates under user’s guidance. Based on a real-life humanities case study, we can show that the ontology amply annotates links in its life-cycle for reliable decision making by data-users.

@inbook{
 type = {inbook},
 year = {2021},
 pages = {99-141},
 websites = {https://www.nomos-elibrary.de/index.php?doi=10.5771/9783956506611-99},
 publisher = {Ergon – ein Verlag in der Nomos Verlagsgesellschaft},
 city = {Baden-Baden},
 edition = {1},
 id = {97b8cf1f-2758-3b3d-9a6d-fe47675035e9},
 created = {2021-10-18T20:12:39.061Z},
 file_attached = {true},
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 last_modified = {2024-04-24T10:17:38.199Z},
 read = {true},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {VandenHeuvel2021},
 source_type = {CHAP},
 language = {en},
 private_publication = {false},
 bibtype = {inbook},
 author = {van den Heuvel, Charles and Zamborlini, Veruska},
 editor = {Smiraglia, Richard P and Scharnhorst, Andrea},
 doi = {10.5771/9783956506611-99},
 chapter = {Modeling and Visualizing Storylines of Historical Interactions. Kubler’s Shape of Time and Rembrandt’s Night Watch},
 title = {Linking Knowledge}
}

@misc{
 title = {Toward an ontology for archival resources. Modelling persons, objects and places in the Golden Agents research infrastructure},
 type = {misc},
 year = {2021},
 websites = {https://dhistory.hypotheses.org/361},
 month = {1},
 publisher = {Data for History Lecture 2021: Modelling Time, Places, Agents},
 id = {f399af2a-640f-3839-927b-d33fc32eabc3},
 created = {2023-05-22T10:54:47.401Z},
 file_attached = {false},
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 last_modified = {2023-05-22T10:54:47.401Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {vanwissenetal2021dataforhistory},
 source_type = {misc},
 notes = {Data for History Lecture 2021: Modelling Time, Places, Agents, Online},
 private_publication = {false},
 bibtype = {misc},
 author = {van Wissen, Leon and Zamborlini, Veruska and van den Heuvel, Charles}
}

@inproceedings{
 title = {Contextual entity disambiguation in domains with weak identity criteria: Disambiguating golden age amsterdamers},
 type = {inproceedings},
 year = {2019},
 keywords = {Data integration,Entity disambiguation,Entity reconciliation,Entity resolution,Linked data},
 pages = {259-262},
 websites = {https://dl.acm.org/doi/10.1145/3360901.3364440},
 month = {9},
 publisher = {ACM},
 day = {23},
 city = {New York, NY, USA},
 id = {8e38b77a-977c-37eb-b97d-630e6ab40758},
 created = {2020-03-15T13:38:17.054Z},
 accessed = {2020-03-15},
 file_attached = {true},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2024-03-08T14:29:53.978Z},
 read = {false},
 starred = {true},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Idrissou2019},
 private_publication = {false},
 abstract = {Entity disambiguation is a widely investigated topic, and many matching algorithms have been proposed. However, this task has not yet been satisfactorily addressed when the domain of interest provides poor or incomplete data with little discriminating power. In these cases, the use of content fields such as name and date is not enough and the simple use of relations with other entities is not of much help when these related entities also need disambiguation before they can be used. Therefore, we propose an approach for the disambiguation of clustered resources using context (related entities that are also clustered) as evidence for reconciling matched entities. We test the proposed method on datasets of historical records from Amsterdam in the 17th century for which context is available, and we compare the results of the proposed approach to a gold standard generated by three experts, which we make available online. The results show that the proposed approach manages to meaningfully use context for isolating identity sub-clusters with higher quality by eliminating potentially false positive matches.},
 bibtype = {inproceedings},
 author = {Idrissou, Al and Zamborlini, Veruska and Van Harmelen, Frank and Latronico, Chiara},
 doi = {10.1145/3360901.3364440},
 booktitle = {K-CAP 2019 - Proceedings of the 10th International Conference on Knowledge Capture}
}

Entity disambiguation is a widely investigated topic, and many matching algorithms have been proposed. However, this task has not yet been satisfactorily addressed when the domain of interest provides poor or incomplete data with little discriminating power. In these cases, the use of content fields such as name and date is not enough and the simple use of relations with other entities is not of much help when these related entities also need disambiguation before they can be used. Therefore, we propose an approach for the disambiguation of clustered resources using context (related entities that are also clustered) as evidence for reconciling matched entities. We test the proposed method on datasets of historical records from Amsterdam in the 17th century for which context is available, and we compare the results of the proposed approach to a gold standard generated by three experts, which we make available online. The results show that the proposed approach manages to meaningfully use context for isolating identity sub-clusters with higher quality by eliminating potentially false positive matches.

@inproceedings{
 title = {The Shape of Time and Storifying Data Modeling Historical Processes and their Temporal Dimension in Knowledge Graphs [Abstract]},
 type = {inproceedings},
 year = {2018},
 websites = {http://dataforhistory.org/sites/default/files/eadh2018_heuvel_zamborlini_abstract.pdf},
 city = {Galway},
 id = {7f5cb59a-5e7f-335a-ad0d-858628b0acc2},
 created = {2019-04-16T08:28:15.174Z},
 file_attached = {false},
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 last_modified = {2019-04-16T08:28:15.174Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Heuvel2018},
 source_type = {abstract},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {van den Heuvel, Charles and Zamborlini, Veruska},
 booktitle = {in the European Association for Digital Humanities (EADH 2018) Conference}
}

@inproceedings{
 title = {Filtering clinical guideline interactions with pre-conditions: A case study on diabetes guideline},
 type = {inproceedings},
 year = {2018},
 volume = {2237},
 websites = {https://www.semanticscholar.org/paper/Filtering-Clinical-Guideline-Interactions-with-A-on-Zamborlini-Heijden/3b20166445617c7414f62536551e4758a84a4219},
 id = {c408ab5a-01fd-39e0-ad1c-41c3303319bf},
 created = {2019-04-26T20:15:15.557Z},
 accessed = {2019-04-26},
 file_attached = {true},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2021-11-08T19:45:16.417Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Clinical Guidelines are meant to support healthcare providers to offer a better service via evidence-based recommendations that apply according to certain circumstances given a certain disease or condition. However, the high number of recommendations in a single guideline makes it humanly impossible to verify for all possible interactions. The goal of this work is twofold: (i) to analyse pros and cons of formalising a real guideline using the TMR model and then (ii) to infer interaction among (some of) the recommendations from the the Scottish Guideline on Diabetes. To this end we extend the TMR Model to formalize the pre-conditions that define in which circumstances a recommendations may apply and we implemented the reasoning in SWI-Prolog. The results show that (i) properly formalising the diabetes guideline is a cross-disciplinary task that requires both the formalisation know-how and the medical background; and (ii) indeed the diabetes guideline presents conflicting recommendations which can be automatically detected provided the suitable modeling and background knowledge. It is reasonable to conclude that these conclusions hold for other guidelines too.},
 bibtype = {inproceedings},
 author = {Zamborlini, Veruska and van der Heijden, Roelof and ten Teije, Annette},
 booktitle = {CEUR Workshop Proceedings}
}

Clinical Guidelines are meant to support healthcare providers to offer a better service via evidence-based recommendations that apply according to certain circumstances given a certain disease or condition. However, the high number of recommendations in a single guideline makes it humanly impossible to verify for all possible interactions. The goal of this work is twofold: (i) to analyse pros and cons of formalising a real guideline using the TMR model and then (ii) to infer interaction among (some of) the recommendations from the the Scottish Guideline on Diabetes. To this end we extend the TMR Model to formalize the pre-conditions that define in which circumstances a recommendations may apply and we implemented the reasoning in SWI-Prolog. The results show that (i) properly formalising the diabetes guideline is a cross-disciplinary task that requires both the formalisation know-how and the medical background; and (ii) indeed the diabetes guideline presents conflicting recommendations which can be automatically detected provided the suitable modeling and background knowledge. It is reasonable to conclude that these conclusions hold for other guidelines too.

@inproceedings{
 title = {Amsterdamers from the Golden Age to the Information Age via Lenticular Lenses},
 type = {inproceedings},
 year = {2018},
 websites = {http://hdl.handle.net/20.500.11755/ceb0401d-7ef5-45fb-9c2e-905c1d8e3a62},
 city = {Amsterdam},
 id = {9a8e832a-94f7-3f23-8a1c-9ed8fb5942c5},
 created = {2020-03-15T13:58:31.108Z},
 accessed = {2020-03-15},
 file_attached = {true},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2024-04-24T10:17:29.062Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Idrissou, Al and Zamborlini, Veruska and Latronico, Chiara and Van Harmelen, Frank and Van Den Heuvel, Charles},
 booktitle = {in Digital Humanities Benelux 2018 Conference}
}

@article{
 title = {Analyzing interactions on combining multiple clinical guidelines},
 type = {article},
 year = {2017},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0933365717301501},
 month = {4},
 id = {2923b469-88c7-3d01-98a9-48f08f4a7eb4},
 created = {2016-11-18T09:55:00.000Z},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2022-02-08T00:37:44.073Z},
 read = {false},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {ZamborliniAIIM2017},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Zamborlini, Veruska and da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and Geleijn, Edwin and van der Leeden, Marike and Stuiver, Martijn and van Harmelen, Frank},
 doi = {10.1016/j.artmed.2017.03.012},
 journal = {Artificial Intelligence in Medicine}
}

@inbook{
 type = {inbook},
 year = {2017},
 pages = {360-386},
 websites = {http://link.springer.com/10.1007/978-3-319-54717-6_20},
 publisher = {Springer International Publishing},
 id = {b3a56032-6f5a-3b32-b8d1-ac89882aa230},
 created = {2017-04-14T08:26:00.552Z},
 accessed = {2017-04-14},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2018-09-26T11:23:55.180Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zamborlini2017},
 private_publication = {false},
 bibtype = {inbook},
 author = {Zamborlini, Veruska and Hoekstra, Rinke and da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and van Harmelen, Frank},
 doi = {10.1007/978-3-319-54717-6_20},
 chapter = {Generalizing the Detection of Clinical Guideline Interactions Enhanced with LOD},
 title = {Biomedical Engineering Systems and Technologies}
}

@inbook{
 type = {inbook},
 year = {2017},
 pages = {71-89},
 websites = {http://link.springer.com/10.1007/978-3-319-55014-5_5},
 publisher = {Springer, Cham},
 id = {cad1a3d5-688f-35cd-b33c-afb782238479},
 created = {2017-04-14T08:27:36.017Z},
 accessed = {2017-04-14},
 file_attached = {true},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2019-04-16T08:28:15.301Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zamborlini2017},
 private_publication = {false},
 bibtype = {inbook},
 author = {Zamborlini, Veruska and Hu, Qing and Huang, Zhisheng and da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and van Harmelen, Frank},
 editor = {Riaño, David and Lenz, Richard and Reichert, Manfred},
 doi = {10.1007/978-3-319-55014-5_5},
 chapter = {Knowledge-Driven Paper Retrieval to Support Updating of Clinical Guidelines: A case study on PubMed},
 title = {Knowledge Representation for Health Care. KR4HC 2016, ProHealth 2016. Lecture Notes in Computer Science vol 10096}
}

@inproceedings{
 title = {Toward a Core Conceptual Model for (Im)material Cultural Heritage in the Golden Agents project: Storifying data},
 type = {inproceedings},
 year = {2017},
 keywords = {Cultural Heritage,Events,Golden Agents,Ontology,Storytelling},
 volume = {2063},
 websites = {http://nbn-resolving.de/urn:nbn:de:0074-2063-4},
 city = {Amsterdam},
 id = {63b44136-21c7-32c0-ae07-131171595717},
 created = {2018-04-06T14:51:49.632Z},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2022-02-08T00:40:13.495Z},
 read = {false},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zamborlini2017},
 private_publication = {false},
 abstract = {© 2017 Copyright held by the author/owners. This paper reports on the initial idea of a core conceptual model for the Golden Agents Project, which aims to integrate several heterogeneous datasets about cultural heritage of the Dutch Golden Age.We hypothesize that the combination of event and storytelling modeling would provide us a common infrastructure to represent and retrieve some core information regardless to its specific nature: Painting, book, notary act or theatre performance. The proposed model was developed based on (i) several discussions conducted with humanities experts and (ii) foundational ontology for grounding the modeling decisions. It is assessed through a case study about Vermeer, the painting 'Girl with a Pearl Earring' and a novel written about the production of the painting. We conclude that the model satisfactorily addresses the case study, and we discuss some next steps to further assess and extend the model, as well as implementing and testing it in practice.},
 bibtype = {inproceedings},
 author = {Zamborlini, V. and Betti, A. and Van Den Heuvel, C.},
 editor = {Fensel, Anna and Daniele, Laura and Aroyo, Lora and de Boer, Victor and Inel, Oana and Kuys, Gerard and Petram, Lodewijk},
 booktitle = {Joint Proceedings of SEMANTiCS 2017 Workshops co-located with the 13th International Conference on Semantic Systems (SEMANTiCS 2017)}
}

© 2017 Copyright held by the author/owners. This paper reports on the initial idea of a core conceptual model for the Golden Agents Project, which aims to integrate several heterogeneous datasets about cultural heritage of the Dutch Golden Age.We hypothesize that the combination of event and storytelling modeling would provide us a common infrastructure to represent and retrieve some core information regardless to its specific nature: Painting, book, notary act or theatre performance. The proposed model was developed based on (i) several discussions conducted with humanities experts and (ii) foundational ontology for grounding the modeling decisions. It is assessed through a case study about Vermeer, the painting 'Girl with a Pearl Earring' and a novel written about the production of the painting. We conclude that the model satisfactorily addresses the case study, and we discuss some next steps to further assess and extend the model, as well as implementing and testing it in practice.

@inproceedings{
 title = {Empirically evaluating three proposals for representing changes in OWL2},
 type = {inproceedings},
 year = {2017},
 keywords = {Empirical assessment of ontology codification alte,Formal ontology,OWL,Perdurantist representation,Temporally changing information},
 volume = {2050},
 id = {fbbb56a3-f880-3ba7-9f24-a47980f18ef6},
 created = {2018-04-26T10:51:36.088Z},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2021-11-08T19:45:16.337Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {In almost all domains in practice, it is fundamental to properly represent entities amenable to changes. For instance, in business analytics, we must be able to reason with large amounts of time-changing KPI (key performance indicators) data. For this reason, general-purpose practical knowledge representation frameworks must be able to support the representation of temporally changing information and in a way that affords decidable automated reasoning. In this paper, we address the issue of representing entities amenable to intrinsic or extrinsic changes in OWL2. These sources of change are illustrated in a simplified model of the scholar domain. We then propose three strategies to represent entities amenable to changes as well as their changes. In particular, we do that by employing strategies that are based on a philosophical stance called perdurantism, which sees all individuals as 4D entities, i.e., as individuals that unfold in time as well as in space. Finally, we compare these three alternatives by generating synthetic instances and performing an empirical evaluation of reasoning tasks.},
 bibtype = {inproceedings},
 author = {Bourguet, J. R. and Guizzardi, G. and Benevides, A. Botti and Zamborlini, V.},
 booktitle = {CEUR Workshop Proceedings}
}

In almost all domains in practice, it is fundamental to properly represent entities amenable to changes. For instance, in business analytics, we must be able to reason with large amounts of time-changing KPI (key performance indicators) data. For this reason, general-purpose practical knowledge representation frameworks must be able to support the representation of temporally changing information and in a way that affords decidable automated reasoning. In this paper, we address the issue of representing entities amenable to intrinsic or extrinsic changes in OWL2. These sources of change are illustrated in a simplified model of the scholar domain. We then propose three strategies to represent entities amenable to changes as well as their changes. In particular, we do that by employing strategies that are based on a philosophical stance called perdurantism, which sees all individuals as 4D entities, i.e., as individuals that unfold in time as well as in space. Finally, we compare these three alternatives by generating synthetic instances and performing an empirical evaluation of reasoning tasks.

@phdthesis{
 title = {Knowledge Representation for Clinical Guidelines - with applications to Multimorbidity Analysis and Literature Search},
 type = {phdthesis},
 year = {2017},
 keywords = {Clinical Guidelines,Comorbidity,Guideline Update,Knowledge Representation,Multimorbidity,Semantic Web},
 websites = {https://research.vu.nl/en/publications/knowledge-representation-for-clinical-guidelines-with-application},
 id = {2be2a8bc-fa0f-3513-b4d9-ffed5b22dd35},
 created = {2019-04-26T20:19:48.928Z},
 accessed = {2019-04-26},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2022-02-08T00:35:58.958Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Enormous efforts are being invested in producing clinical knowledge and making it available in practice via the clinical guidelines (CG). However, the increasing amount of knowledge and its complexity make it difficult to efficiently apply it to the benefit of the patient. The research question that arises is: which clinical knowledge is needed to support clinical guideline (CG) tasks while fostering knowledge reuse across them? We propose a model called TMR (Transition-based Medical Recom- mendation) that has as core elements actions and transitions, where the actions can be both believed to cause a transition with some fre- quency and be recommended to be pursued or avoided for that rea- son. The applicability of the TMR is assessed for two GC-tasks: mul- timorbidity analysis and literature search. The multimorbidity analy- sis is necessary to support the treatment of patients that suffer from more than one disease at the same time. In this case, the medical best-practices, mostly established for addressing a single disease at a time, can interact in several ways, e.g. contradicting or repeating treatments. The more diseases involved, the more difficult it gets to identify all possible interactions. As a secondary task, literature search is necessary to gather the publications that serve as scientific evidence for the recommended actions to be performed or avoided. As new evidence is produced daily on a large scale, literature search is often necessary to keep the clinical guidelines up-to-date. Those tasks as well as other CG-tasks are called knowledge intensive tasks as they require large amounts of information to be processed. By relying on the TMR model we provide (i) a fixed number of generic rules for detecting several types of interactions among sev- eral recommendations; (ii) generic reuse of medical data from hetero- geneous medical datasets; and (iii) a flexible method to compose a search-query for medical literature that takes into account the seman- tic role of the medical terms and possible alternative descriptions. We have successfully applied this approach to case studies taken from the medical informatics literature as well as a case study developed in cooperation with healthcare-professionals. The case studies are (i) combining three (parts of) guidelines for Osteoarthritis, Diabetes and Hypertension; (ii) combining (parts of) guidelines for exercise therapy for Breast Cancer Patients combined with Osteoarthritis, Hyper- tension and Congestive Heart Failure; and finally (iii) searching for literature to update the Dutch Breast Cancer Guideline of 2004. This work is a step in the direction of investigating the knowledge underlying CGs that is necessary to address several tasks. The pro- posed approach is designed to be both task- and technology- independent, though the evaluation is performed through specific CG-tasks and technology. The Semantic Web provide a suitable en- vironment for the implementation by allowing the reuse of large datasets as Linked Open Data, besides the provision of reusable knowl- edge. The evaluation for multimorbidity analysis and literature search show relevant contributions with respect to the state of the art.},
 bibtype = {phdthesis},
 author = {Zamborlini, Veruska}
}

Enormous efforts are being invested in producing clinical knowledge and making it available in practice via the clinical guidelines (CG). However, the increasing amount of knowledge and its complexity make it difficult to efficiently apply it to the benefit of the patient. The research question that arises is: which clinical knowledge is needed to support clinical guideline (CG) tasks while fostering knowledge reuse across them? We propose a model called TMR (Transition-based Medical Recom- mendation) that has as core elements actions and transitions, where the actions can be both believed to cause a transition with some fre- quency and be recommended to be pursued or avoided for that rea- son. The applicability of the TMR is assessed for two GC-tasks: mul- timorbidity analysis and literature search. The multimorbidity analy- sis is necessary to support the treatment of patients that suffer from more than one disease at the same time. In this case, the medical best-practices, mostly established for addressing a single disease at a time, can interact in several ways, e.g. contradicting or repeating treatments. The more diseases involved, the more difficult it gets to identify all possible interactions. As a secondary task, literature search is necessary to gather the publications that serve as scientific evidence for the recommended actions to be performed or avoided. As new evidence is produced daily on a large scale, literature search is often necessary to keep the clinical guidelines up-to-date. Those tasks as well as other CG-tasks are called knowledge intensive tasks as they require large amounts of information to be processed. By relying on the TMR model we provide (i) a fixed number of generic rules for detecting several types of interactions among sev- eral recommendations; (ii) generic reuse of medical data from hetero- geneous medical datasets; and (iii) a flexible method to compose a search-query for medical literature that takes into account the seman- tic role of the medical terms and possible alternative descriptions. We have successfully applied this approach to case studies taken from the medical informatics literature as well as a case study developed in cooperation with healthcare-professionals. The case studies are (i) combining three (parts of) guidelines for Osteoarthritis, Diabetes and Hypertension; (ii) combining (parts of) guidelines for exercise therapy for Breast Cancer Patients combined with Osteoarthritis, Hyper- tension and Congestive Heart Failure; and finally (iii) searching for literature to update the Dutch Breast Cancer Guideline of 2004. This work is a step in the direction of investigating the knowledge underlying CGs that is necessary to address several tasks. The pro- posed approach is designed to be both task- and technology- independent, though the evaluation is performed through specific CG-tasks and technology. The Semantic Web provide a suitable en- vironment for the implementation by allowing the reuse of large datasets as Linked Open Data, besides the provision of reusable knowl- edge. The evaluation for multimorbidity analysis and literature search show relevant contributions with respect to the state of the art.

@inproceedings{
 title = {Generalizing the Detection of Internal and External Interactions in Clinical Guidelines},
 type = {inproceedings},
 year = {2016},
 websites = {http://www.cs.vu.nl/~annette/papers-pdf/2016HealthInf-Zamborlini.pdf},
 city = {Rome, Italy},
 id = {75b02b37-fc80-3c5a-8504-250161dcd5ff},
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 author = {Zamborlini, Veruska and Hoekstra, Rinke and Silveira, Marcos and Pruski, Cedric and Teije, Annette},
 booktitle = {Proceedings of the 9th International Conference on Health Informatics (HEALTHINF2016)}
}

@article{
 title = {Inferring recommendation interactions in clinical guidelines1},
 type = {article},
 year = {2016},
 keywords = {Clinical knowledge representation,OWL,SPARQL,SWRL,combining medical guidelines,multimorbidity,reasoning,rules},
 pages = {421-446},
 volume = {7},
 websites = {http://www.medra.org/servlet/aliasResolver?alias=iospress&doi=10.3233/SW-150212},
 month = {5},
 day = {27},
 id = {705a8c2b-ffda-3eb5-895b-6eef2a7b08e9},
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 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2022-02-08T00:37:46.849Z},
 read = {false},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zamborlini2016},
 private_publication = {false},
 abstract = {The formal representation of clinical knowledge is still an open research topic. Classical representation languages for clinical guidelines are used to produce diagnostic and treatment plans. However, they have important limitations, e.g. when looking for ways to re-use, combine, and reason over existing clinical knowledge. These limitations are especially problematic in the context of multimorbidity; patients that suffer from multiple diseases. To overcome these limitations, this paper proposes a model for clinical guidelines (TMR4I) that allows the re-use and combination of knowledge from multiple guidelines. Semantic Web technology is applied to implement the model, allowing us to automatically infer interactions between recommendations, such as recommending the same drug more than once. It relies on an existing Linked Data set, DrugBank, for identifying drug-drug interactions. We evaluate the model by applying it to two realistic case studies on multimorbidity that combine guidelines for two (Duodenal Ulcer and Transient Ischemic Attack) and three diseases (Osteoarthritis, Hypertension and Diabetes) and compare the results with existing methods.},
 bibtype = {article},
 author = {Zamborlini, Veruska and Hoekstra, Rinke and Da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and van Harmelen, Frank},
 editor = {Schlobach, Stefan and Janowicz, Krzysztof and Schlobach, Stefan and Janowicz, Krzysztof},
 doi = {10.3233/SW-150212},
 journal = {Semantic Web},
 number = {4}
}

The formal representation of clinical knowledge is still an open research topic. Classical representation languages for clinical guidelines are used to produce diagnostic and treatment plans. However, they have important limitations, e.g. when looking for ways to re-use, combine, and reason over existing clinical knowledge. These limitations are especially problematic in the context of multimorbidity; patients that suffer from multiple diseases. To overcome these limitations, this paper proposes a model for clinical guidelines (TMR4I) that allows the re-use and combination of knowledge from multiple guidelines. Semantic Web technology is applied to implement the model, allowing us to automatically infer interactions between recommendations, such as recommending the same drug more than once. It relies on an existing Linked Data set, DrugBank, for identifying drug-drug interactions. We evaluate the model by applying it to two realistic case studies on multimorbidity that combine guidelines for two (Duodenal Ulcer and Transient Ischemic Attack) and three diseases (Osteoarthritis, Hypertension and Diabetes) and compare the results with existing methods.

@inproceedings{
 title = {Knowledge-driven Paper Retrieval to support updating of Clinical Guidelines: A case study on PubMed},
 type = {inproceedings},
 year = {2016},
 id = {cbe8320b-3a0e-3200-aa9a-676399330ea0},
 created = {2016-11-18T09:55:00.000Z},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {ZamborliniKR4HC2016},
 source_type = {proceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Zamborlini, Veruska and Hu, Qing and Huang, Zhisheng and da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and van Harmelen, Frank},
 booktitle = {Knowledge Representation for Health-Care (KR4HC 2016)}
}

@inproceedings{
 title = {Generalizing the detection of internal and external interactions in clinical guidelines},
 type = {inproceedings},
 year = {2016},
 keywords = {Clinical guidelines,Knowledge representation,Ontologies,Semantic web},
 id = {723ae285-5ef1-3310-9577-cc44eea09aa7},
 created = {2017-05-19T11:32:51.422Z},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2018-09-01T18:34:21.528Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Copyright © 2016 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved.This paper presents a method for formally representing Computer-Interpretable Guidelines to deal with multimorbidity. Although some approaches for merging guidelines exist, improvements are still required for combining several sources of information and coping with possibly conflicting pieces of evidence coming from clinical studies. Our main contribution is twofold: (i) we provide general models and rules for representing guidelines that expresses evidence as causation beliefs; (ii) we introduce a mechanism to exploit external medical knowledge acquired from Linked Open Data (Drugbank, Sider, DIKB) to detect potential interactions between recommendations. We apply this framework to merge three guidelines (Osteoarthritis, Diabetes, and Hypertension) in order to illustrate the capability of this approach for detecting potential conflicts between guidelines and eventually propose alternatives.},
 bibtype = {inproceedings},
 author = {Zamborlini, V. and Hoekstra, Rinke and Da Silveira, M. and Pruski, C. and Ten Teije, A. and Van Harmelen, F.},
 booktitle = {HEALTHINF 2016 - 9th International Conference on Health Informatics, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016}
}

Copyright © 2016 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved.This paper presents a method for formally representing Computer-Interpretable Guidelines to deal with multimorbidity. Although some approaches for merging guidelines exist, improvements are still required for combining several sources of information and coping with possibly conflicting pieces of evidence coming from clinical studies. Our main contribution is twofold: (i) we provide general models and rules for representing guidelines that expresses evidence as causation beliefs; (ii) we introduce a mechanism to exploit external medical knowledge acquired from Linked Open Data (Drugbank, Sider, DIKB) to detect potential interactions between recommendations. We apply this framework to merge three guidelines (Osteoarthritis, Diabetes, and Hypertension) in order to illustrate the capability of this approach for detecting potential conflicts between guidelines and eventually propose alternatives.

@inproceedings{
 title = {SWISH for prototyping Clinical Guideline Interactions Theory},
 type = {inproceedings},
 year = {2016},
 keywords = {Clinical guideline interactions,Multimorbidity,Prolog,RDF,SWISH},
 volume = {1795},
 series = {CEUR Workshop Proceedings},
 id = {d3c024c7-ee4a-3617-93cd-1388a669d18a},
 created = {2017-06-06T19:11:32.242Z},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2017-06-06T19:11:32.242Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {ZamborliniSWAT4LS2016},
 source_type = {proceedings},
 private_publication = {false},
 abstract = {SWISH provides a general purpose collaborative infrastructure for applying Prolog reasoning over an RDF dataset together with features that facilitates prototyping Semantic Web applications. In this paper we report on the use of SWISH for efficiently developing a prototype for detection of clinical guideline interactions. These guidelines are a set of medical recommendations meant for supporting doctors on tackling a single disease. However, often guidelines need to be combined for treating patients that suffer from multiple diseases, and then a number of interactions can occur. The generic interaction rules are implemented in SWI-Prolog and the guideline RDF-data is enriched with clinical Linked Open Data (LOD) (e.g. Drugbank, Sider). We show the implementation of the proposed theory about interaction detection in a case-study on combining three guidelines. The experiment is interactively described using a SWISH notebook and the results are graphical visualised empowered by graphviz.},
 bibtype = {inproceedings},
 author = {Zamborlini, Veruska and Wielemaker, Jan and da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and van Harmelen, Frank},
 booktitle = {Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, Amsterdam, Netherlands}
}

SWISH provides a general purpose collaborative infrastructure for applying Prolog reasoning over an RDF dataset together with features that facilitates prototyping Semantic Web applications. In this paper we report on the use of SWISH for efficiently developing a prototype for detection of clinical guideline interactions. These guidelines are a set of medical recommendations meant for supporting doctors on tackling a single disease. However, often guidelines need to be combined for treating patients that suffer from multiple diseases, and then a number of interactions can occur. The generic interaction rules are implemented in SWI-Prolog and the guideline RDF-data is enriched with clinical Linked Open Data (LOD) (e.g. Drugbank, Sider). We show the implementation of the proposed theory about interaction detection in a case-study on combining three guidelines. The experiment is interactively described using a SWISH notebook and the results are graphical visualised empowered by graphviz.

@inbook{
 type = {inbook},
 year = {2015},
 keywords = {Clinical knowledge representation,Combining medical guide-lines,Multimorbidity},
 pages = {317-326},
 websites = {http://link.springer.com/10.1007/978-3-319-19551-3_40},
 id = {dc63743e-a612-322d-a6fb-32fa83daf94b},
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 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zamborlini2015},
 private_publication = {false},
 abstract = {Accounting for patients with multiple health conditions is a complex task that requires analysing potential interactions among recom-mendations meant to address each condition. Although some approaches have been proposed to address this issue, important features still require more investigation, such as (re)usability and scalability. To this end, this paper presents an approach that relies on reusable rules for detecting interactions among recommendations coming from various guidelines. It extends previously proposed models by introducing the notions of action type hierarchy and causation beliefs, and provides a systematic analy-sis of relevant interactions in the context of multimorbidity. Finally, the approach is assessed based on a case-study taken from the literature to highlight the added value of the approach.},
 bibtype = {inbook},
 author = {Zamborlini, Veruska and da Silveira, Marcos and Pruski, Cedric and ten Teije, Annette and van Harmelen, Frank},
 doi = {10.1007/978-3-319-19551-3_40},
 chapter = {Analyzing Recommendations Interactions in Clinical Guidelines: Impact of action type hierarchies and causation beliefs},
 title = {Artificial Intelligence in Medicine AIME}
}

Accounting for patients with multiple health conditions is a complex task that requires analysing potential interactions among recom-mendations meant to address each condition. Although some approaches have been proposed to address this issue, important features still require more investigation, such as (re)usability and scalability. To this end, this paper presents an approach that relies on reusable rules for detecting interactions among recommendations coming from various guidelines. It extends previously proposed models by introducing the notions of action type hierarchy and causation beliefs, and provides a systematic analy-sis of relevant interactions in the context of multimorbidity. Finally, the approach is assessed based on a case-study taken from the literature to highlight the added value of the approach.

@article{
 title = {Using a trope-based foundational ontology for bridging different areas of concern in ontology-driven conceptual modeling},
 type = {article},
 year = {2014},
 keywords = {Conceptual domain modeling,Foundational ontology,Ontological foundations for conceptual modeling,Temporal reification,Trope theory},
 pages = {417-443},
 volume = {96},
 websites = {http://www.sciencedirect.com/science/article/pii/S0167642314000896,http://linkinghub.elsevier.com/retrieve/pii/S0167642314000896},
 month = {12},
 id = {0d892aed-9570-3bc4-8424-032c3b7f9bf4},
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 accessed = {2014-05-15},
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 last_modified = {2022-02-08T00:37:58.982Z},
 read = {true},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Guizzardi2014},
 private_publication = {false},
 abstract = {In recent years, ontology-driven reference models have gained much attention in the literature due to their potential key role in activities such as complex information modeling and semantic interoperability. The engineering process of these conceptual models should account for different phases addressing different areas of concern. In an initial phase of conceptual domain modeling, the target modeling artifacts should be constructed with the goal of maximizing quality attributes such as expressivity and truthfulness to the represented domain in reality. In a subsequent development phase, the resulting domain models can be used to guide the design decisions in the construction of different implementation artifacts addressing different computational concerns. In this paper, we present a philosophically sound, cognitively-oriented and formally characterized foundational theory of objects and tropes (property-instances). Moreover, we use this theory to bring about engineering contributions to both the aforementioned phases of ontology-driven conceptual modeling. Firstly, we show how this theory has been used to (re)design a system of modeling primitives underlying the conceptual domain modeling language OntoUML. Furthermore, we provide precise directives on how to map conceptual domain models in this language to their implementation in less-expressive computationally-oriented codification languages. In particular, we address here a mapping strategy to OWL (Web Ontology Language) that partially preserves the modal-temporal semantics of OntoUML. Finally, we discuss computational support for the proposed approach in terms of conceptual model construction, automatic transformation and temporal querying.},
 bibtype = {article},
 author = {Guizzardi, Giancarlo and Zamborlini, Veruska},
 doi = {10.1016/j.scico.2014.02.022},
 journal = {Science of Computer Programming}
}

In recent years, ontology-driven reference models have gained much attention in the literature due to their potential key role in activities such as complex information modeling and semantic interoperability. The engineering process of these conceptual models should account for different phases addressing different areas of concern. In an initial phase of conceptual domain modeling, the target modeling artifacts should be constructed with the goal of maximizing quality attributes such as expressivity and truthfulness to the represented domain in reality. In a subsequent development phase, the resulting domain models can be used to guide the design decisions in the construction of different implementation artifacts addressing different computational concerns. In this paper, we present a philosophically sound, cognitively-oriented and formally characterized foundational theory of objects and tropes (property-instances). Moreover, we use this theory to bring about engineering contributions to both the aforementioned phases of ontology-driven conceptual modeling. Firstly, we show how this theory has been used to (re)design a system of modeling primitives underlying the conceptual domain modeling language OntoUML. Furthermore, we provide precise directives on how to map conceptual domain models in this language to their implementation in less-expressive computationally-oriented codification languages. In particular, we address here a mapping strategy to OWL (Web Ontology Language) that partially preserves the modal-temporal semantics of OntoUML. Finally, we discuss computational support for the proposed approach in terms of conceptual model construction, automatic transformation and temporal querying.

@inbook{
 type = {inbook},
 year = {2014},
 pages = {29-44},
 volume = {8903},
 publisher = {Springer Berlin Heidelberg},
 city = {Vienna, Austria},
 series = {Lecture Notes in Computer Science},
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 citation_key = {ZamborliniKR4HC2014},
 source_type = {inproceedings},
 folder_uuids = {59af0a17-112b-407c-843e-b9a79697297f},
 private_publication = {false},
 abstract = {Computer-Interpretable Guidelines (CIGs) are representations of Clinical Guidelines (CGs) in computer interpretable languages. CIGs have been pointed as an alternative to deal with the various limitations of paper based CGs to support healthcare activities. Although the improvements offered by existing CIG languages, the complexity of the medical domain requires advanced features in order to reuse, share, update, combine or personalize their contents. We propose a conceptual model for representing the content of CGs as a result from an iterative approach that take into account the content of real CGs, CIGs languages and foundational ontologies in order to enhance the reasoning capabilities required to address CIG use-cases. In particular, we apply our approach to the comorbidity use-case and illustrate the model with a realistic case study (Duodenal Ulcer and Transient Ischemic Attack) and compare the results against an existing approach.},
 bibtype = {inbook},
 author = {Zamborlini, Veruska and da Silveira, Marcos and Pruski, Cédric and ten Teije, Annette and van Harmelen, Frank},
 doi = {10.1007/978-3-319-13281-5_3},
 chapter = {Towards a Conceptual Model for Enhancing Reasoning about Clinical Guidelines: A case-study on Comorbidity},
 title = {Knowledge Representation for Health Care (KR4HC 2014). Lecture Notes in Computer Science}
}

Computer-Interpretable Guidelines (CIGs) are representations of Clinical Guidelines (CGs) in computer interpretable languages. CIGs have been pointed as an alternative to deal with the various limitations of paper based CGs to support healthcare activities. Although the improvements offered by existing CIG languages, the complexity of the medical domain requires advanced features in order to reuse, share, update, combine or personalize their contents. We propose a conceptual model for representing the content of CGs as a result from an iterative approach that take into account the content of real CGs, CIGs languages and foundational ontologies in order to enhance the reasoning capabilities required to address CIG use-cases. In particular, we apply our approach to the comorbidity use-case and illustrate the model with a realistic case study (Duodenal Ulcer and Transient Ischemic Attack) and compare the results against an existing approach.

@inbook{
 type = {inbook},
 year = {2014},
 keywords = {Clinical knowledge representation,Combining medical guidelines,Multimorbidity,Reasoning},
 pages = {591-606},
 volume = {8876},
 websites = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84914126892&partnerID=tZOtx3y1},
 publisher = {Springer},
 city = {Linkoping, Sweden},
 series = {Lecture Notes in Computer Science},
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 citation_key = {ZamborliniEKAW2014},
 source_type = {inproceedings},
 folder_uuids = {59af0a17-112b-407c-843e-b9a79697297f},
 private_publication = {false},
 abstract = {Representation of clinical knowledge is still an open research topic. In particular, classical languages designed for representing clinical guidelines, which were meant for producing diagnostic and treatment plans, present limitations such as for re-using, combining, and reasoning over existing knowledge. In this paper, we address such limitations by proposing an extension of the TMR conceptual model to represent clinical guidelines that allows re-using and combining knowledge from several guidelines to be applied to patients with multimorbidities. We provide means to (semi)automatically detect interactions among recommendations that require some attention from experts, such as recommending more than once the same drug. We evaluate the model by applying it to a realistic case study involving 3 diseases (Osteoarthritis, Hypertension and Diabetes) and compare the results with two other existing methods.},
 bibtype = {inbook},
 author = {Zamborlini, Veruska and Hoekstra, Rinke and da Silveira, Marcos and Pruski, Cédric and ten Teije, Annette and van Harmelen, Frank},
 doi = {10.1007/978-3-319-13704-9_44},
 chapter = {A conceptual model for detecting interactions among medical recommendations in clinical guidelines: A case-study on multimorbidity},
 title = {Knowledge Engineering and Knowledge Management (EKAW). Lecture Notes in Computer Science, vol. 8876}
}

Representation of clinical knowledge is still an open research topic. In particular, classical languages designed for representing clinical guidelines, which were meant for producing diagnostic and treatment plans, present limitations such as for re-using, combining, and reasoning over existing knowledge. In this paper, we address such limitations by proposing an extension of the TMR conceptual model to represent clinical guidelines that allows re-using and combining knowledge from several guidelines to be applied to patients with multimorbidities. We provide means to (semi)automatically detect interactions among recommendations that require some attention from experts, such as recommending more than once the same drug. We evaluate the model by applying it to a realistic case study involving 3 diseases (Osteoarthritis, Hypertension and Diabetes) and compare the results with two other existing methods.

@inproceedings{
 title = {A common foundational theory for bridging two levels in ontology-driven conceptual modeling},
 type = {inproceedings},
 year = {2013},
 keywords = {Conceptual Domain Modeling,OWL,OntoUML,Ontological Foundations,Temporally Changing Information,UFO},
 pages = {286-310},
 volume = {7745 LNCS},
 websites = {http://link.springer.com/chapter/10.1007/978-3-642-36089-3_17},
 publisher = {Springer},
 series = {Lecture Notes in Computer Science},
 id = {0eb2bf8a-ca6d-3502-9cda-7b2d5d6cada0},
 created = {2013-04-02T13:45:50.000Z},
 accessed = {2013-06-08},
 file_attached = {false},
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 last_modified = {2017-03-15T11:42:28.317Z},
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 confirmed = {true},
 hidden = {false},
 citation_key = {DBLP:conf/sle/GuizzardiZ12},
 source_type = {inproceedings},
 folder_uuids = {1afa96aa-ed3c-4d3a-8085-025458a3fcc2},
 private_publication = {false},
 abstract = {In recent years, there has been a growing interest in the use of Foundational Ontologies, i.e., ontological theories in the philosophical sense to provide real-world semantics and principled modeling guidelines for conceptual domain modeling languages. In this paper, we demonstrate how a philosophically sound and cognitively-oriented ontological theory of objects and moments (property-instances) has been used to: (i) (re)design a system of modeling primitives underlying the conceptual domain modeling language OntoUML; (ii) derive supporting technology for mapping these conceptual domain models to less-expressive computationally-oriented codification languages. In particular, we address here a mapping strategy to OWL (Web Ontology Language) which addresses the issue of temporally changing information.},
 bibtype = {inproceedings},
 author = {Guizzardi, Giancarlo and Zamborlini, Veruska},
 editor = {Czarnecki, Krzysztof and Hedin, Görel},
 doi = {10.1007/978-3-642-36089-3_17},
 booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}
}

In recent years, there has been a growing interest in the use of Foundational Ontologies, i.e., ontological theories in the philosophical sense to provide real-world semantics and principled modeling guidelines for conceptual domain modeling languages. In this paper, we demonstrate how a philosophically sound and cognitively-oriented ontological theory of objects and moments (property-instances) has been used to: (i) (re)design a system of modeling primitives underlying the conceptual domain modeling language OntoUML; (ii) derive supporting technology for mapping these conceptual domain models to less-expressive computationally-oriented codification languages. In particular, we address here a mapping strategy to OWL (Web Ontology Language) which addresses the issue of temporally changing information.

@inproceedings{
 title = {An Ontologically-Founded Reification Approach for Representing Temporally Changing Information in OWL},
 type = {inproceedings},
 year = {2013},
 websites = {http://www.commonsense2013.cs.ucy.ac.cy/docs/commonsense2013_submission_23.pdf},
 id = {5c2548bc-7083-3bf2-aefa-f8ea46f894e7},
 created = {2016-11-18T09:54:59.000Z},
 file_attached = {false},
 profile_id = {aebd07e2-f364-3186-a6b6-baa8ed624f46},
 last_modified = {2017-03-15T11:42:28.317Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zamborlini2013},
 private_publication = {false},
 abstract = {In this paper we present an approach for representing temporally changing information in OWL. This approach is based on a reification strategy founded on results from the philosophical discipline of Formal Ontology. These results grant ontological meaning to the reified individuals (intrinsic and relational properties) and provide an ontological semantics to the resulting specification. We also propose here some methodological guidelines for guiding the use of the proposed framework in supporting modeling decisions in OWL. By using the proposed framework, one can represent domain information regarding sources of temporal change such as the distinction between necessary versus contingent properties, or mutable versus immutable ones. Finally, we compare the proposed approach with another commonly used strategy for circumventing OWL´s limitation w.r.t. temporally changing information.},
 bibtype = {inproceedings},
 author = {Zamborlini, Veruska Carretta and Guizzardi, Giancarlo},
 booktitle = {11th International Symposium on Logical Formalizations of Commonsense Reasoning (COMMONSENSE 2013)}
}

In this paper we present an approach for representing temporally changing information in OWL. This approach is based on a reification strategy founded on results from the philosophical discipline of Formal Ontology. These results grant ontological meaning to the reified individuals (intrinsic and relational properties) and provide an ontological semantics to the resulting specification. We also propose here some methodological guidelines for guiding the use of the proposed framework in supporting modeling decisions in OWL. By using the proposed framework, one can represent domain information regarding sources of temporal change such as the distinction between necessary versus contingent properties, or mutable versus immutable ones. Finally, we compare the proposed approach with another commonly used strategy for circumventing OWL´s limitation w.r.t. temporally changing information.

@inproceedings{
 title = {An approach for managing and semantically enriching the publication of Linked Open Governmental Data},
 type = {inproceedings},
 year = {2011},
 pages = {82-95},
 websites = {http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:An+approach+for+managing+and+semantically+enriching+the+publication+of+Linked+Open+Governmental+Data#0},
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 bibtype = {inproceedings},
 author = {Cordeiro, Kelli De Faria and Faria, Fabrício Firmino and Pereira, Bianca and Freitas, André and Ribeiro, Expedito and Freitas, João Vitor and Zamborlini, Veruska and Guizzardi, Giancarlo and Campos, M L M},
 booktitle = {Workshop de Computação Aplicada em Governo Eletrônico do Simpósio Brasileiro de Banco de Dados}
}

With the growth of e-government programs, the available data to citizens is growing in volume every day. However, to make these data a useful source of information, to be referenced and integrated more easily by different applications, they should be published according to the best practices of Linked Open Data, using standards for description (RDF) and identification (URI) of data resources on the web. The main goal of this work is to propose a platform and approach to support the exposure, sharing and association of data resources in the form of Linked Open Data, offering a user-friendly environment to stimulate the publication of data and their association to other existing data. Central functionalities to be included are data cleaning, transformation, linking, annotation and referencing to terminology mechanisms.

@techreport{
 title = {Estudo de Alternativas de Mapeamento de Ontologias da Linguagem OntoUML Para OWL: Abordagens Para Representação de Informação Temporal},
 type = {techreport},
 year = {2011},
 source = {Federal University of Espírito Santo. Master Thesis. Available only in Portuguese},
 keywords = {Codificação de Ontologias,Mapeamento,Ontologia,Representação de Informação Temporal em OWL.},
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 abstract = {computação, especialmente no contexto da Web Semântica. Entretanto, observa-se uma forte tendência em priorizar a eficiência computacional em detrimento da qualidade da representação, deixando de lado importantes características do domínio, como aspectos temporais. De fato, a linguagem OWL, padrão adotado na Web Semântica, não permite, em princípio, a representação de informação temporal. As principais estratégias propostas na literatura para resolver este problema, as abordagens Perdurantista 4D e de Reificação Temporal, não provêem suporte para apoiar as decisões do modelagem, deixando a responsabilidade nas mãos do usuário. Neste contexto, este trabalho objetiva, através da aplicação de resultados vindos da disciplina filosófica de Ontologia Formal, fundamentar tais abordagens para representação de informação temporal em OWL, provendo uma estrutura-base ontologicamente fundamentada e diretrizes para guiar sua utilização, avaliando e comparando as alternativas propostas. Ademais, uma vez que não é tarefa trivial a aplicação direta das noções ontológicas, observa-se que, utilizando-se uma linguagem de modelagem que as incorpore, é possível definir mapeamentos sistemáticos a partir desta linguagem para OWL de tal forma que se permita a geração automática de modelos num processo de Engenharia de Ontologias. Assim, outro objetivo deste trabalho é propor alternativas de mapeamentos entre a linguagem nível ontológico OntoUML e a linguagem de nível epistemológico OWL. Realiza-se ainda um estudo de caso no domínio de Eletrocardiografia, aplicando-se uma das alternativas para codificar automaticamente uma ontologia de referência de ECG, seguindo-se um processo de Engenharia de Ontologias, permitindo representar a informação temporal. Por fim, os resultados obtidos neste trabalho são relevantes no contexto de Engenharia de Ontologias por prover mapeamentos sistemáticos que, uma vez implementados, permitem que a codificação da ontologia de referência seja realizada de forma automatizada e eficiente, preservando a qualidade do modelo de referência e evitando erros decorrentes do processo de codificação manual; e, além disso, permitem contornar a limitação da linguagem OWL quanto à representação da informação temporal.},
 bibtype = {techreport},
 author = {Zamborlini, Veruska}
}

computação, especialmente no contexto da Web Semântica. Entretanto, observa-se uma forte tendência em priorizar a eficiência computacional em detrimento da qualidade da representação, deixando de lado importantes características do domínio, como aspectos temporais. De fato, a linguagem OWL, padrão adotado na Web Semântica, não permite, em princípio, a representação de informação temporal. As principais estratégias propostas na literatura para resolver este problema, as abordagens Perdurantista 4D e de Reificação Temporal, não provêem suporte para apoiar as decisões do modelagem, deixando a responsabilidade nas mãos do usuário. Neste contexto, este trabalho objetiva, através da aplicação de resultados vindos da disciplina filosófica de Ontologia Formal, fundamentar tais abordagens para representação de informação temporal em OWL, provendo uma estrutura-base ontologicamente fundamentada e diretrizes para guiar sua utilização, avaliando e comparando as alternativas propostas. Ademais, uma vez que não é tarefa trivial a aplicação direta das noções ontológicas, observa-se que, utilizando-se uma linguagem de modelagem que as incorpore, é possível definir mapeamentos sistemáticos a partir desta linguagem para OWL de tal forma que se permita a geração automática de modelos num processo de Engenharia de Ontologias. Assim, outro objetivo deste trabalho é propor alternativas de mapeamentos entre a linguagem nível ontológico OntoUML e a linguagem de nível epistemológico OWL. Realiza-se ainda um estudo de caso no domínio de Eletrocardiografia, aplicando-se uma das alternativas para codificar automaticamente uma ontologia de referência de ECG, seguindo-se um processo de Engenharia de Ontologias, permitindo representar a informação temporal. Por fim, os resultados obtidos neste trabalho são relevantes no contexto de Engenharia de Ontologias por prover mapeamentos sistemáticos que, uma vez implementados, permitem que a codificação da ontologia de referência seja realizada de forma automatizada e eficiente, preservando a qualidade do modelo de referência e evitando erros decorrentes do processo de codificação manual; e, além disso, permitem contornar a limitação da linguagem OWL quanto à representação da informação temporal.

@inproceedings{
 title = {On the Representation of Temporally Changing Information in OWL},
 type = {inproceedings},
 year = {2010},
 keywords = {description logics,formal ontology,knowledge representation,owl,temporally changing information},
 pages = {283-292},
 websites = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5629069},
 month = {10},
 publisher = {IEEE},
 id = {69be6135-a757-39d0-8434-40828f851245},
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 abstract = {An important challenge in the Knowledge Representation area is on representing and reasoning over temporally changing information. Particularly, a number of authors have been investigating approaches to extend the expressivity beyond what is currently supported by the DL (Description Logics) based languages in order to address this issue, while maintaining compatibility with subclasses of DLs adopted in the Semantic Web. This is mainly due to the increasing popularity of the Semantic Web initiative as well as the role played by DL in that context. In this paper we defend the need of a higher-level foundational framework based on results coming from the discipline of Formal Ontology. We present two complementary proposals for modeling temporally changing information in OWL, based on the most discussed strategy in the literature to address this problem, namely, the use of a perdurantist (or 4D) view of domain entities. Moreover we compare the results with some related work and discuss its limitations and further improvements.},
 bibtype = {inproceedings},
 author = {Zamborlini, Veruska and Guizzardi, Giancarlo},
 doi = {10.1109/EDOCW.2010.50},
 booktitle = {2010 14th IEEE International Enterprise Distributed Object Computing Conference Workshops}
}

An important challenge in the Knowledge Representation area is on representing and reasoning over temporally changing information. Particularly, a number of authors have been investigating approaches to extend the expressivity beyond what is currently supported by the DL (Description Logics) based languages in order to address this issue, while maintaining compatibility with subclasses of DLs adopted in the Semantic Web. This is mainly due to the increasing popularity of the Semantic Web initiative as well as the role played by DL in that context. In this paper we defend the need of a higher-level foundational framework based on results coming from the discipline of Formal Ontology. We present two complementary proposals for modeling temporally changing information in OWL, based on the most discussed strategy in the literature to address this problem, namely, the use of a perdurantist (or 4D) view of domain entities. Moreover we compare the results with some related work and discuss its limitations and further improvements.

@inproceedings{
 title = {An Ontology-based Application in Heart Electrophysiology : Representation , Reasoning and Visualization on the Web},
 type = {inproceedings},
 year = {2009},
 pages = {816–820},
 websites = {http://portal.acm.org/citation.cfm?id=1529282.1529456&coll=portal&dl=GUIDE&type=series&idx=SERIES179&part=series&WantType=Proceedings&title=SAC},
 publisher = {ACM},
 id = {e98e5179-feb7-3a01-9990-088c3da14e49},
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 abstract = {Computational technologies have been increasingly explored to make biomedical knowledge and data more accessible for human understanding, comparison, analysis and communication. In this context, ontology has been recognized in the bioinformatics literature as a suitable technique for advancing knowledge and data representations in Biomedicine. Moreover, automated reasoning and visualization mechanisms can favor in providing support for human comprehensibility as well as in dealing with the complexity inherent to this domain. This paper elaborates on the application of ontology for heart electrophysiology representation, reasoning and visualization on the web. The ontology-based application we propose can be used to offer support for interactive learning in heart electrophysiology.},
 bibtype = {inproceedings},
 author = {Gonçalves, Bernardo and Zamborlini, Veruska and Guizzardi, Giancarlo and Pereira Filho, José Gonçalves},
 doi = {10.1145/1529282.1529456},
 booktitle = {Expert Systems}
}

Computational technologies have been increasingly explored to make biomedical knowledge and data more accessible for human understanding, comparison, analysis and communication. In this context, ontology has been recognized in the bioinformatics literature as a suitable technique for advancing knowledge and data representations in Biomedicine. Moreover, automated reasoning and visualization mechanisms can favor in providing support for human comprehensibility as well as in dealing with the complexity inherent to this domain. This paper elaborates on the application of ontology for heart electrophysiology representation, reasoning and visualization on the web. The ontology-based application we propose can be used to offer support for interactive learning in heart electrophysiology.

@misc{
 title = {An ontological analysis of the electrocardiogram},
 type = {misc},
 year = {2009},
 source = {RECIIS},
 keywords = {biomedical ontology,electrocardiogram,heart electrophysiology},
 pages = {1-26},
 volume = {3},
 issue = {1},
 websites = {http://www.reciis.cict.fiocruz.br/index.php/reciis/article/view/242/255,http://www.revista.icict.fiocruz.br/index.php/reciis/article/viewArticle/242},
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 bibtype = {misc},
 author = {Gonçalves, Bernardo and Zamborlini, Veruska and Guizzardi, Giancarlo},
 doi = {10.3395/reciis.v3i1.242en}
}

Bioinformatics has been a fertile field for the application of the discipline of formal ontology. The principled representation of biomedical entities has increasingly supported biological research, with direct benefits ranging from the reformulation of medical terminologies to the introduction of new perspectives for enhanced models of Electronic Health Records (EHR). This paper introduces an application-independent ontological analysis of the electrocardiogram (ECG) grounded in the Unified Foundational Ontology. With the objective of investigating the phenomena underlying this cardiological exam, we deal with the sub-domains of human heart electrophysiology and anatomy. We then outline an ECG Ontology built upon the OBO Relation Ontology. In addition, the domain ontology sketched here takes inspiration both in the Foundational Model of Anatomy and in the Ontology of Functions proposed under the auspices of the General Formal Ontology (GFO) research program.

@article{
 title = {Uma análise ontológica do eletrocardiograma},
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@inproceedings{
 title = {Codification and Application of a Well-Founded Heart-ECG Ontology},
 type = {inproceedings},
 year = {2008},
 city = {Campinas, Brazil},
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 booktitle = {3rd Workshop on Ontologies and Metamodels in Software and Data Engineering},
 keywords = {biomedical ontology,heart electrophysiology and ecg,medical education,owl dl + swrl,web animations}
}

@inproceedings{
 title = {Using a lightweight ontology of heart electrophysiology in an interactive web application},
 type = {inproceedings},
 year = {2008},
 pages = {77},
 websites = {http://portal.acm.org/citation.cfm?doid=1809980.1810001},
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 doi = {10.1145/1809980.1810001},
 booktitle = {Companion Proceedings of the XIV Brazilian Symposium on Multimedia and the Web - WebMedia '08},
 keywords = {biomedical ontology,heart electrophysiology and ecg,medical education,owl dl + swrl,web animations}
}