Table 1 Biological ontologies used to generate CeN–CAM models
From: Semantic representation of neural circuit knowledge in Caenorhabditis elegans
GO–CAM element | Ontology | Example |
|---|---|---|
Molecular activity | GO Molecular Function | serotonin receptor activity (GO: 0099589) |
Biological process | GO Biological Process | membrane depolarization (GO: 0051899) |
Location | GO Cellular Component | cytosol (GO: 0005829) |
Cell | WormBase Anatomy Ontology | HSN (WBbt: 0006830) |
Active entity (gene/gene product) | WormBase | tph-1 (WBGene00006600) |
Chemical inputs | Chemical Entities of Biological Interest (ChEBI) | dioxygen (CHEBI: 15379) |
Relations arrows | Relations Ontology (RO), Basic Formal Ontology (BFO) | occurs in (RO_0002479) |
Evidence codes | Evidence and Conclusions Ontology (ECO) | optogenetic evidence used in manual assertion (ECO: 0006033) |
Environmental conditions | Phenotype and Trait Ontology (PATO) Environmental Conditions, Treatments and Exposure Ontology (ECTO) | increased duration (PATO_0000498) |