Publications Related to the OBO Foundry

Operations Committee

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• Mailing Lists
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Editorial Working Group

• Review Process
• Review Criteria

Technical Working Group

• PURL Requests
• OBO PURL Configuration
• Ontology tools and resources

Outreach Working Group

Papers about the OBO Foundry

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

Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis

Nature Biotechnology 25, 1251 - 1255 (2007)

Google Scholar list of papers citing The OBO Foundry.

Some Ontology Project Publications (not a complete list)

• Agronomy Ontology (agro): Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.
• BRENDA tissue / enzyme source (bto): The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
• Biological Spatial Ontology (bspo): Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
• C. elegans Gross Anatomy Ontology (wbbt): Building a cell and anatomy ontology of Caenorhabditis elegans
• C. elegans development ontology (wbls): WormBase: a modern Model Organism Information Resource
• C. elegans phenotype (wbphenotype): Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
• Cell Ontology (cl): The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
• Chemical Entities of Biological Interest (chebi): ChEBI in 2016: Improved services and an expanding collection of metabolites.
• Clinical measurement ontology (cmo): Three ontologies to define phenotype measurement data.
• Drosophila Phenotype Ontology (dpo): The Drosophila phenotype ontology.
• Drosophila gross anatomy (fbbt): [The Drosophila anatomy ontology. Journal of Biomedical Semantics
• Environment Ontology (envo): The environment ontology: contextualising biological and biomedical entities
• Evidence ontology (eco): ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
• Experimental condition ontology (xco): Three ontologies to define phenotype measurement data.
• Fission Yeast Phenotype Ontology (fypo): FYPO: The Fission Yeast Phenotype Ontology.
• Foundational Model of Anatomy Ontology (subset) (fma): Translating the Foundational Model of Anatomy into OWL
• Human Disease Ontology (doid): Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
• Human Phenotype Ontology (hp): The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.
• Human developmental anatomy, abstract (ehdaa2): A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).
• Mass spectrometry ontology (ms): The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
• Measurement method ontology (mmo): Three ontologies to define phenotype measurement data.
• PRotein Ontology (PRO) (pr): Publications & Dissemination
• Pathway ontology (pw): The Rat Genome Database pathway portal.
• Plant Environment Ontology (eo): Ontologies as integrative tools for plant science.
• Plant Experimental Conditions Ontology (peco): The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
• Plant Ontology (po): The plant ontology as a tool for comparative plant anatomy and genomic analyses.
• Plant Trait Ontology (to): The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
• Porifera Ontology (poro): The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology
• Protein modification (mod): The PSI-MOD community standard for representation of protein modification data
• Rat Strain Ontology (rs): Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
• Sequence types and features ontology (so): The Sequence Ontology: a tool for the unification of genome annotations.
• Teleost Anatomy Ontology (tao): The teleost anatomy ontology: anatomical representation for the genomics age
• The Drug-Drug Interactions Ontology (dinto): DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.
• Uberon multi-species anatomy ontology (uberon): Uberon, an integrative multi-species anatomy ontology
• Unipathway (upa): UniPathway: a resource for the exploration and annotation of metabolic pathways
• Xenopus Anatomy Ontology (xao): An ontology for Xenopus anatomy and development.
• Zebrafish anatomy and development ontology (zfa): The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.