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Ontology Tools and Resources |
- OBO Foundry
- BioPortal: has over 700 biomedical ontologies, including the OBO Foundry ontologies. Users can search for terms or browse individual ontologies. BioPortal also provides tools to aid in increasing ontology interoperability.
- Ontology Lookup Service (OLS): lets users search for terms across all ontologies, or individual ontologies, as well as view term hierarchies. OLS also has an API so that ontologies can be browsed programmatically.
- Ontobee: Part of the Onto-Animal tool collection. Users can search all available ontologies and browse detailed descriptions of individiual terms. OntoBee is the default server for most OBO Foundry ontology IRIs.
- AberOWL: A repository of biological ontologies and access to reasoned versions of those ontologies. Ontolgies can be browsed by term labels or queried by Manchester OWL syntax statements.
- QuickGO
- AmiGO
- Linked Open Vocabularies
- OBO Ontology Training: lessons and tutorials aimed at database curators, ontology curators, ontology engineers/developers, and (semantic) software engineers. Includes the OBOOK, a collection of open documentation for biomedical ontology engineering.
- Introduction to Ontologies: slides from Cold Spring Harbor workshop, October 2018, by Nicole Vasilevsky.
- Ontology 101 Tutorial: from International Conference on Biological Ontology (ICBO) 2018
- Ontology 101 Open Educational Resource: Funded by NIH BD2K Initiative.
- Cell Ontology Tutorial: Led by David Osumi-Sutherland, Alex Diehl, Nico Matentzoglu and Nicole Vasilevsky
- ROBOT tutorial by James Overton
- OBO Academy: A YouTube channel with presentations and tutorials relevant to the OBO Foundry
- Pizza Tutorial for Protégé 5 by Michael DeBellis. More info.
- Introduction to Biomedical Ontologies: A training course in eight lectures by Barry Smith
- Building Ontologies with Basic Formal Ontology: By Robert Arp, Barry Smith, and Andrew Spear
- Ontology Development Kit (ODK): A toolkit for initializing a new ontology repository. The template includes a structured directory, a Makefile with automated release workflows, continuous integration testing, and full documentation.
- ROBOT: A command line tool to automate ontology workflows. It includes commands that can be used manually or integrated in automated processes to develop and release ontologies.
- Protégé: An ontology editing environment for OWL ontologies. It allows developers to visualize the ontology hierarchy, add and edit ontology terms, reason over the ontology, and more.
- Onto-Animals: Tools to extract external ontology terms, compare ontologies, edit ontology terms, query and visualize ontologies, and more.
- VOCOL: An integrated environment for collaborative vocabulary development
- Karma Data Integration: A data integration tool
- Ontofox: An ontology term and relation extraction and reuse tool
- Ubergraph: A sparql endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized
- OBO Dashboard: An assesment of OBO Foundry ontologies' conformance to OBO Foundry principles
- OBO Community Health Report: A self-updating assessment of the quality of metadata, responsiveness of the maintainers, and the overall community engagement for each OBO Foundry ontology.
- Ontology Quality Assessment: A self-updating assesment of the semantic quality of OBO Foundry ontologies and beyond (using known prefixes, using standard identifiers, etc.)
- Current Ontology Versions: A daily refreshed list of OBO ontology versions and their compatibility with OBO Foundry Identifier Policy.
- OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies (2021). Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith, Christian J Stoeckert Jr., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters. Database, Volume 2021, baab069, https://doi.org/10.1093/database/baab069
- The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration (Smith et al., 2007). Nat Biotechnol 2007 Nov;25(11):1251–1255. http://dx.doi.org/10.1038/nbt1346
- MIRO: guidelines for minimum information for the reporting of an ontology (2018). Nicolas Matentzoglu, James Malone, Chris Mungall and Robert Stevens, Journal of Biomedical Semantics 2018 9:6, https://doi.org/10.1186/s13326-017-0172-7
- Monkeying around with OWL: a technical blog on ontologies and ontology engineering by Chris Mungall.
- Feed your head: a technical blog on ontologies and ontology engineering by Robert Stevens.
- Biomedical ontologies, data integration and annotation, British sense of humour: a technical blog on ontologies and ontology engineering by James Malone.
- What are Ontologies?
- Semantic Web for the Working Ontologist, Second Edition by Dean Allemang and James Hendler
- Linked Data Patterns: A pattern catalogue for modelling, publishing, and consuming Linked Data by Leigh Dodds and Ian Davis
- Learning SPARQL by Bob DuCharme
- Guidelines for writing definitions in ontologies by Selja Seppälä, Alan Ruttenberg and Barry Smith