From Purdue Genomics Database Facility

Contents 1 Ontologies 1.1 NCBO - National Center for Biological Ontologies 1.2 OBO Foundry - Open Biomedical Ontologies 1.3 Metabolic pathways 1.3.1 BioPax - Biological pathways Exchange 1.3.2 Pathway Commons 1.4 Sequences 1.4.1 Sequence Ontology

Ontologies

NCBO - National Center for Biological Ontologies

• website
• bioportal (repository)
• educational materials
• tools

OBO Foundry - Open Biomedical Ontologies

• OBO Foundry

Metabolic pathways

BioPax - Biological pathways Exchange

• Website
• BioPax Wiki
• BioPax level 1
• BioPax level 2
• BioPax level 3

Pathway Commons

• Pathway Commons
• Web services
  • search
    webservice.do?version=2.0&q=BRCA2&output=xml&cmd=search
  • get_pathways
    webservice.do?cmd=get_pathways&version=2.0&q=O14763&input_id_type=UNIPROT
  • get_neighbors
    webservice.do?cmd=get_pathways&version=2.0&q=O14763&input_id_type=UNIPROT
  • get_parents
    webservice.do?version=2.0&q=45202&output=xml&cmd=get_parents
  • get_record_by_cpath_id
    webservice.do?cmd=get_record_by_cpath_id&version=2.0&q=1&output=biopax

Sequences

Sequence Ontology

The four major aspects of the complete Sequence Ontology are:

• Sequence Ontology website

• located sequence features for objects that can be located on sequence in coordinates,
• sequence attributes for describing the properties of features,
• consequences of mutation for the annotation of the effects of a mutation
• chromosome variation to describe large scale variations.

A "lite" version of SO is also available called SOFA (Sequence Ontology Feature Annotation) which includes only locatable sequence features and is designed for use in such outputs as GFF3. It is for this reason that all SO terms are "unix friendly" (i.e. contain no white space, never begin with an integer and do not include characters such as "'" or hypens). SOFA is a subset of SO and all terms in SOFA that are also in SO are marked in SO with the category tag "SOFA". SOFA will be more stable than the full version of SO.

Currently three versions of the Sequence Ontology exist:

• The full version - called SO, contains several hundred terms and is intended to be used in concert with a heavily curated genome annotation project.
• The SOFA version - which stands for 'Sequence Ontology Feature Annotation', has terms that can be directly located to biological sequence. These terms are most likely to be used in a concert with a partially or fully automated annotation effort.
• The cross-product version - which contains all of the cross-product terms.