Open Biomedical Ontologies

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Open Biomedical Ontologies (formerly Open Biological Ontologies) is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S. National Center for Biomedical Ontology, where it will form a central element of the NCBO's BioPortal.

OBO Foundry

The OBO Ontology library forms the basis of the OBO Foundry, a collaborative experiment involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to 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.

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.

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.

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.

OBO and Semantic Web

OBO2OWL - Layer Cakes and Roundtrip Transformations

As a migration path for biomedical ontologies, this is a solution for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL. Contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack. Project Page Morphster Project

External links

• Open Biomedical Ontologies (OBO)
• The OBO Foundry
• Morphster ATOL Project at The University of Texas at Austin
• Ontology browser for most of the Open Biological Ontologies at BRENDA website
• OBO Relation Ontology