INOH Pathway Database

MoleculeRole Ontology Release Notes
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Version: 2.23 (Apr 28, 2010)

Molecule Role is a hierarchical ontology which contains the molecular functional group names, the abstract molecule names and the concrete molecule names collected from literature manually. This classification is based on a conceptual classification of molecular roles in protein interaction and signal transduction.

Changes from version 2.1x
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KEGG metabolic pathway related molecules (500~ chemicals and 300~ proteins) were added.

Changes from version 2.0x
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Over 13,000 synonyms were added from EntrezGene, HGNC, FlyBase, OMIM, MGI and RGD database in an automatic way, using UniProt ACs manually collected in Molecule Role.

Changes from version 1.xx
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The ontologies and definitions are provided together in a single OBO format flat file. This data is NOT also available in the GO flat file format as an ontology file and a definitions file.

Protein sequences (=UniProt ACs) in the DbXrefs of protein leaf-class entries have been separated as new protein leaf-class entries. The parents-children relationship type is "sequence_of". The relationships of "Concrete-Names (e.g. ERK1)" and protein sequences (e.g. P27361) have been defined explicitly.

More information about MoleculeRole Ontology
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Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi, Ken Ichiro Fukuda. The Molecule Role Ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. Comparative and Functional Genomics 2004 Volume 5, Issue 6-7, p 528-536. (http://www3.interscience.wiley.com/cgi-bin/fulltext/109860932/HTMLSTART)

Statistics
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All entries 9132
Chemicals 593
Proteins 8538
Definition 250

UniProt ACs 5823
GO IDs 347
InterPro ACs 32
KEGG COMPOUND IDs 588
PubMed IDs 160