ArticleNucleic acids research2017
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- GlyGen: a knowledgebase linking glycan data with protein and gene data to reveal novel biological connections.Research square · 2026Article
- Immune biomarkers, profiles, and responses: a vaccine ontology perspective.Journal of biomedical semantics · 2026Article
- PomBase in 2026: expanding knowledge, modeling connections.Genetics · 2026Review
- SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis.Scientific data · 2026Article
- The DO-KB knowledgebase 2026 update: expanding programmatic and language access.Nucleic acids research · 2026Article
- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- Harnessing Nanobodies for Precision Targeting of Proteoforms: Opportunities and Challenges in Therapeutics and Diagnostics.ACS chemical biology · 2025Review
- MedKG: enabling drug discovery through a unified biomedical knowledge graph.Molecular diversity · 2025Article
- Automated descriptive cell type naming in flow and mass cytometry with CytoPheno.Scientific reports · 2025Article
- A fourfold pathogen reference ontology suite.Journal of biomedical semantics · 2025Article
- A Fourfold Pathogen Reference Ontology Suite.ArXiv · 2025Article
- The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity.Nucleic acids research · 2025Article
- Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0.Current protocols · 2024Article
- The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity.bioRxiv : the preprint server for biology · 2024Article
- Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature.Scientific data · 2024Article
- Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis.Journal of biomedical semantics · 2024Article
- Survey on large language model annotation of cellular senescence from figures in review articles.Genomics & informatics · 2024Article
- Homeostasis imbalance process ontology: a study on COVID-19 infectious processes.BMC medical informatics and decision making · 2024Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
Abstract
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.