Ontologies

Phenotype and Trait Ontology (PATO)

An ontology of phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.

Gene Ontology (GO)

The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. There are three distinct ontologies developed by GO: molecular function, biological process, and cellular component.

Ontologies for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and medical experiments and investigations. This ontology will support the consistent annotation of biomedical investigations, regardless of the particular field of study.

Resources

OBO Foundry

The OBO Foundry is an open, inclusive, and collaborative core of interoperable ontologies developed by the research community. The goal is to facilitate the creation of consistent, compatible, and unambiguous ontologies thereby supporting the biomedical research community. The contributors are those biological researchers and ontology developers who have agreed to work together on an evolving set of design principles that can foster interoperability of ontologies, and ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.

Generic Model Organism Databases

The Generic Model Organism Project (GMOD) is a joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology.

Institute for Formal Ontology and Medical Information Science (IFOMIS)

The Institute for Formal Ontology and Medical Information Science (IFOMIS) comprehends an interdisciplinary research group with members from Philosophy, Computer and Information Science, Logic, Medicine, and Medical Informatics, focusing on theoretically grounded research in both formal and applied ontology.

MGED

The Microarray Gene Expression Data (MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.

Ontology Lookup Service

The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.

Plant Ontology Consortium

The Plant Ontology Consortium (POC) aims to develop, curate and share structured controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages. Through this effort, the project aims to facilitate cross database querying by fostering consistent use of these vocabularies in the annotation of tissue and/or growth stage specific expression of genes, proteins and phenotypes.

Proteomics Standards Initiative

Is also interested in guidelines for the development of Controlled Vocabularies.