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{{Paper
|id=Vol-3603/Poster3
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|title=The Interplay of Wikidata and the Cell Ontology
|pdfUrl=https://ceur-ws.org/Vol-3603/Poster3.pdf
|volume=Vol-3603
|authors=Tiago Lubiana
|dblpUrl=https://dblp.org/rec/conf/icbo/Lubiana23
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==The Interplay of Wikidata and the Cell Ontology==
https://ceur-ws.org/Vol-3603/Poster3.pdf
The Interplay of Wikidata and the Cell Ontology
Tiago Lubiana 1
1
University of São Paulo, R. Cidade Universitária, 374 - Butantã, São Paulo, SP, Brazil
Abstract
This poster presentation centers on the potential of Wikidata, a comprehensive and
collaborative knowledge base, to advance biomedical ontologies, particularly the Open
Biological and Biomedical Ontologies (OBO) Foundry ontologies. The spotlight is on the
integration of Wikidata with the ontology landscape, showcasing its integration with the Cell
Ontology (CL).The CL, established around 2005, has been expanding to currently include over
2,600 cell classes, with technical enhancements and the addition of novel cell types over the
years. Despite these advancements, contributing to it can be daunting, and its coverage of cell
types is yet far from complete.Ontologies, though highly effective, require substantial technical
expertise and specific software installations, restricting potential contributors with limited
access or skills.In contrast, Wikidata promotes communal contribution and is welcoming for
users of varying technical proficiency. Its strength stems from a vast community of active
contributors, with broad coverage of diverse concepts. The speed, breadth, and accessibility of
Wikidata, along with its CC0 public domainlicense, render it an inviting platform for
widespread use and contribution.Our work exemplifies the advantages arising from the
integration of Wikidata with OBO Foundry ontologies. For instance, Wikidata's multilingual
capability promotes inclusivity in stark contrast to the predominantly anglocentric ontologies
and, its direct linkages to Wikipedia facilitate access to textual descriptions often lacking in
ontology development. Finally, Wikidata's connections to Wikipedia and other controlled
vocabularies can support ontologies in validating information.To map concepts in Wikidata to
the Cell Ontology, we developed a streamlined workflow combining ROBOT and a custom
Python package for real-time natural language term curation in Wikidata, resulting in over
2,600 cross-references from Wikidata to the Cell Ontology. These curation efforts have
revealed several cell types listed on Wikipedia but absent from CL, providing a unique
opportunity for expansion and enhancement of CL's scope, as well as opening a gateway for
multilingualism in applications that use CL identifiers.To sum up, the integration of Wikidata
and ontologies can significantly benefit the ontology ecosystem, enriching the value of
ontologies and fostering broader collaboration. Our work with the Cell Ontology suggests its
connection other ontologies is a promising work direction for the future.
Keywords 1
Wikidata, Cell Ontology, cell types, knowledge graph.
1. Acknowledgements
This work was funded by FAPESP grant #19/26284-1.
Proceedings of the International Conference on Biomedical Ontologies 2023, August 28th-September 1st, 2023, Brasilia, Brazil
EMAIL: tiago.lubiana.alves@usp.br (A. 1)
ORCID: : 0000-0003-2473-2313 (A. 1)
©️ 2023 Copyright for this paper by its authors.
Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
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