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).



How to cite this record FAIRsharing.org: PRO; PRotein Ontology; DOI: https://doi.org/10.25504/FAIRsharing.4ndncv; Last edited: April 29, 2019, 11:02 a.m.; Last accessed: May 21 2019 4:36 p.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;


This record is maintained by dnatale

Record updated: April 28, 2019, 11:44 p.m. by The FAIRsharing Team.

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Publications

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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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 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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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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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 (8)
ChEMBL
ChEMBL is an open large-scale bioactivity database containing information largely manually extracted from the medicinal chemistry literature. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.

Reactome - a curated knowledgebase of biological pathways
The cornerstone of Reactome is a freely available, open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. Inferred orthologous reactions are available for 17 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, and Arabidopsis.

Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.

Neuroscience Information Framework (NIF)
NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web.

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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Grant Number(s)

  • 1UL1TR001412 (National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA)

  • DBI-1062520 (National Science Foundation (NSF), USA)

  • HHSN272201200028C (National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA)

  • R01GM080646 (National Institutes of Health (NIH), Bethesda, MD, USA)