standards > terminology artifact > DOI:10.25504/FAIRsharing.4ndncv

ready PRotein Ontology

Abbreviation: PRO

General Information
Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).


Developed in United States

Created in 2006

Taxonomic range

Knowledge Domains 


How to cite this record PRO; PRotein Ontology; DOI:; Last edited: March 12, 2019, 1:31 p.m.; Last accessed: Apr 21 2019 5:17 a.m.

Publication for citation  Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Natale DA,Arighi CN,Blake JA,Bona J,Chen C,Chen SC,Christie KR,Cowart J,D'Eustachio P,Diehl AD,Drabkin HJ,Duncan WD,Huang H,Ren J,Ross K,Ruttenberg A,Shamovsky V,Smith B,Wang Q,Zhang J,El-Sayed A,Wu CH; Nucleic Acids Res ; 2016; 10.1093/nar/gkw1075;

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Record updated: March 12, 2019, 1:29 p.m. by The FAIRsharing Team.

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Protein Ontology: a controlled structured network of protein entities.

Natale DA,Arighi CN,Blake JA,Bult CJ,Christie KR,Cowart J,D'Eustachio P,Diehl AD,Drabkin HJ,Helfer O,Huang H,Masci AM,Ren J,Roberts NV,Ross K,Ruttenberg A,Shamovsky V,Smith B,Yerramalla MS,Zhang J,AlJanahi A,Celen I,Gan C,Lv M,Schuster-Lezell E,Wu CH
Nucleic Acids Res 2014

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The Protein Ontology: a structured representation of protein forms and complexes.

Natale DA,Arighi CN,Barker WC,Blake JA,Bult CJ,Caudy M,Drabkin HJ,D'Eustachio P,Evsikov AV,Huang H,Nchoutmboube J,Roberts NV,Smith B,Zhang J,Wu CH
Nucleic Acids Res 2011

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Framework for a protein ontology.

Natale DA,Arighi CN,Barker WC,Blake J,Chang TC,Hu Z,Liu H,Smith B,Wu CH
BMC Bioinformatics 2007

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The representation of protein complexes in the Protein Ontology (PRO).

Bult CJ,Drabkin HJ,Evsikov A,Natale D,Arighi C,Roberts N,Ruttenberg A,D'Eustachio P,Smith B,Blake JA,Wu C
BMC Bioinformatics 2011

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Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Natale DA,Arighi CN,Blake JA,Bona J,Chen C,Chen SC,Christie KR,Cowart J,D'Eustachio P,Diehl AD,Drabkin HJ,Duncan WD,Huang H,Ren J,Ross K,Ruttenberg A,Shamovsky V,Smith B,Wang Q,Zhang J,El-Sayed A,Wu CH
Nucleic Acids Res 2016

View Paper (PubMed) View Publication

PR Ontology Display

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Implementing Databases (4)
UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

Immunology Database and Analysis Portal
The ImmPort system serves as a long-term, sustainable archive of immunology research data generated by investigators mainly funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data and clinical trial data. The analytical tools created and integrated as part of the ImmPort system are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided mainly by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time. ImmPort, is the data submission portal where researchers upload, QC, and curate their data prior to sharing in OpenImmPort.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Complex Portal
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download.

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  • This record is maintained by dnatale



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