Tag: genome annotation terms, ontologies and nomenclature

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

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 ...

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plant ...

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) re ...

A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for ...

Wiki database of biological databases

Gene Ontology-based functional similarity values for proteins and protein families

Domain-centric GO provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, on ...

Repository of protein names and naming rules

Gene annotation portal and a resource on gene and protein function

Network Extracted gene Ontology database

Gene Ontology Normal Usage Tracking System

Human Cell Lines Identification Resources

Disease and Gene Annotations database

The MIRIAM Registry provides a set of services for the generation of unique and perennial identifiers, in the form of URIs. The core of the Registry is a catalogue of data collections (corresponding to controlled vocabularies, databases, etc.)

The IUPAC Nomenclature database is mainly concerned with biochemical and organic chemical nomenclature. It includes most nomenclature recommendations prepared by the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature and the IUPAC Commission on ...

The IUBMB Nomenclature database is composed of Enzyme Nomenclature, with a classified list of characterised enzymes, and the full text of all nomenclature recommendations prepared by the Nomenclature Committee of IUBMB. For additional recommendations ...

BioThesaurus is a web-based system that maps a comprehensive collection of protein and gene names to protein entries in the UniProt Knowledgebase (UniProtKB). Currently covering more than two million protein sequences, BioThesaurus consists of over 2 ...