Open Biomedical Ontologies - Related Projects

Related Projects

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.

Gene Ontology Consortium

The goal of the Gene ontology (GO) consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes.

Sequence Ontology

The Sequence Ontology (SO) is a part of the Gene Ontology project and the aim is to develop an ontology suitable for describing biological sequences. It is a joint effort by genome annotation centres, including WormBase, the Berkeley Drosophila Genome Project, FlyBase, the Mouse Genome Informatics group, and the Sanger Institute.

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.

Standards and Ontologies for Functional Genomics

SOFG is both a meeting and a website; it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments.

FGED

The Functional Genomics Data (FGED) 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 experiments.

Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an open access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL).

Plant ontology

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.

Phenoscape

Phenoscape is a project to develop a database of phenotype data for species across the Osteriophysi, a large group of Teleost fish. The data is captured using annotations that combine terms from an Anatomy Ontology, an accompanying Taxonomic Ontology, and quality terms from the PATO ontology of phenotype qualities. Several other OBO ontologies are also used. The anatomy ontology was developed from the zebrafish anatomy ontology developed by the Zebrafish Information Network.