Notes and Sources¶

For early work on the Organization Ontology and thoughts behind what might be needed and how things might be addressed, we relied on “Early Thoughts on Representing Organizations in VIVO” by the VIVO Ontology Interest Group [VOIG2019a]. While not everything there has been implemented here, and not everything here is implemented as described there, the general outline of representing organizations using Basic Formal Ontology (BFO) according to Open Biomedical Ontologies (OBO) Principles was first described there. A good reference for BFO is [Arp2015]. The VIVO Ontology Interest Group has been considering BFO/OBO ontologies for scholarship and related domains for some time. The first white paper [VOIG2019] led to papers on subsumption [VOIG2019b], domains [VOIG2019c], and use of other ontologies [VOIG2019d]. Ideas from each of these papers is reflected in the Organization Ontology.

For class expressions, reasoning, and DL queries, [Horridge2017] was a valuable resource.

We use [Wikipedia], [Wiktionary], and [Wikidata] often. Term definitions, references, fact-checking, and identifiers may come from these sources.

We use Ontobee [Ong2017] for looking up terms in OBO Foundry ontologies.

We use protege [Musen2015] for modeling org-header.ttl and the MIREOT plug-in for protege [Hannah2012] for adding terms from other ontologies to org-header.ttl We use robot [Jackson2019] for processing templates of properties, merging them and org-header.ttl together to produce org.ttl and then to run reports against org.ttl for validation.

We use WebVOWL [Lohmann2016] to visualize ontologies.

We have tried to represent organizations in a manner that is inclusive of ideas regarding organizations that have been represented elsewhere. The VIVO Ontology [vivo2013] provides organizational representation, but is not BFO or OBO conformant. We hope we have represented here what is represented in the VIVO Ontology. The W3C Organization Ontology [Reynolds2014] has been a second source for terms and concepts that might be included in a BFO/OBO conformant ontology.

We have used the [GRID], [ROR21], and [schema.org] data models as sources of concepts and properties that may need to be represented in the Organization Ontology. See Translating from VIVO to the Organization Ontology, Translating from ROR to the Organization Ontology, and Translating from schema.org to the Organization Ontology for details of how types and other properties are mapped from these sources to the Organization Ontology.

Regarding the W3C Organization Ontology¶

The W3C Organization Ontology (W3CO) provides a set of useful terms for representing organizations. Many terms there are represented in this work. Our work uses BFO as an upper level ontology – everything in the Organization Ontology fits in the BFO subsumption hierarchy. cross-walking the W3C Organization Ontology and the VIVO Organization Ontology (VORG) is straightforward. Below are comments related to mapping.

Purpose in W3CO is open-ended text. In VORG, purpose is represented by dispositions
Classification in W3CO are interests in VORG.
Identifiers in VORG are handled using IDO
Linked to in W3CO is replaced by semantic object properties indicating the relationship between organizations
Formal Organization in W3CO is any organization that is not an Informal Organization in VORG.
OrganizationUnit in W3CO is Organization Part in VORG.
Membership in VORG is modeled using standard BFO roles and occurent part representation
Posts in W3CO are modeled as positions in VORG in a manner analogous to memberships (same conceptual model, different roles and entities)
Reports to in W3CO is deconstructed. Personnel relationships are distinct from org relationships in VORG. Person to person relationships are out of scope for VORG.
Locations in VORG are modeled as BFO sites. See Locations <locations>
Addresses in VORG are modeled as IAO entities. See Addresses <addresses>
based at is a property of a person and is out of scope for VORG.
OrganizationCollaboration is a project and is modeled using standard BFO constructs. Organizations have participant in projects
Change event is a BFO process boundary

References¶

VOIG2019a: VIVO Ontology Interest Group (2021) Early Thoughts on the representation of organizations in VIVO. on-line. http://bit.ly/2EhMdPq
Arp2015: Arp, Smith, and Spear (2015) Building Ontologies with Basic Formal Ontology. MIT Press. ISBN 978-0262527811. 248 pages.
VOIG2019: VIVO Ontology Interest Group (January 2019) VIVO Ontology Version 2. on-line. http://bit.ly/2R8gYuI
VOIG2019b: VIVO Ontology Interest Group (February 2019) Early Thoughts on VIVO Subsumption Hierarchy. on-line. http://bit.ly/2Ekg7m6
VOIG2019c: VIVO Ontology Interest Group (February 2019) Early Thoughts on VIVO Related Domains. on-line. http://bit.ly/2Jn3MTV
VOIG2019d: VIVO Ontology Interest Group (March 2019) Early Thoughts on Ontologies Used in VIVO. on-line. https://bit.ly/3fWdL0K
Horridge2017: Horridge, M (March, 2017) Hands-On OWL: Language, Reasoning and Querying. Course notes, Stanford University. 126 pages.
Wikipedia: Wikipedia (2021) we site. http://wikipedia.org
Wiktionary: Wiktionary (2021) web site. http://wiktionary.org
Wikidata: Wikidata (2021) web site. http://wikidata.org
Ong2017: Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query, and integration. Nucleic Acid Research. 2017 Jan 4;45(D1):D347-D352. PMID: 27733503. PMCID: PMC5210626.
Musen2015: Musen, M.A. The Protégé project: A look back and a look forward. AI Matters. Association of Computing Machinery Specific Interest Group in Artificial Intelligence, 1(4), June 2015. https://doi.org/10.1145/2757001.2757003.
Hannah2012: Hannah, J, Chen, C, Crow, WA, et al. (2012) Simplifying MIREOT: A MIREOT Protege Plugin. International Semantic Web Conference, http://ceur-ws.org/Vol-914/paper_48.pdf
Jackson2019: Jackson, R.C., Balhoff, J.P., Douglass, E. et al. ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinformatics 20, 407 (2019). https://doi.org/10.1186/s12859-019-3002-3
Lohmann2016: Lohmann, S, Negru, S, Haag, F and Ertl, T (2016) Visualizing Ontologies with VOWL” Accessed June 9, 2021. DOI: 10.3233/SW-150200 https://content.iospress.com/articles/semantic-web/sw200.
vivo2013: Conlon, M. Mitchell, S. (2018) VIVO Ontology for Researcher Discovery. Ontology. https://bioportal.bioontology.org/ontologies/VIVO
Reynolds2014: Reynolds, Dave (ed) (2014) The Organization Ontology. Ontology. https://www.w3.org/TR/vocab-org/
GRID: Digital Science, (2021) GRID Global Research Identifier Database. https://grid.ac
ROR21: ROR Community (2021) Research Organization Registry. Database. https://ror.org
schema.org: W3C Schema.org Community Group (2021) Schema.org. Website. https://schema.org