-
Notifications
You must be signed in to change notification settings - Fork 0
Home
The code in this repository can be used to migrate knowledge about biological processes from various sources into the Gene Ontology's Causal Activity Model (GO-CAM) framework. GO-CAMs attempt to capture the linked network of molecular functions, enabled and controlled by gene products, that combine to carry out a biological process. They are biological pathway models implemented according to the philosophy of and using the core ontologies of the OBO Foundry - primarily the Gene Ontology and the Relation ontology. The current collection can be accessed for viewing/editing via the Noctua Web application (see also the development server). 'Production' stage models can be queried via rdf.geneontology.org.
Formally, a GO-CAM is an OWL ontology composed of OWL Individuals defined with Classes from the OBO collection and Relations from the Relation Ontology (see the owl-model spec). One of the motivations of the GO-CAM design and OWL implementation is to take advantage of automatic inferences enabled by OWL description logic reasoning. A simple example would be to compute that if A has_part B then B part_of A based on axioms that describe the meaning of has_part and part_of. See an introduction to reasoning on GO-CAMs for more information.
There is already a vast amount of information expressed in biological pathway databases. The code linked here provides ways to convert that knowledge into GO-CAMs. These conversions directly expand the content of the GO-CAM knowledge base and can be used to provide GO-CAM curators with 'seeds' from which new models can grow.
Biopax2GO converts pathways expressed using the BioPAX standard, such as Reactome, to GO-CAMs.
- Java
- PaxTools for parsing BioPAX files
- The OWL-API for generating the GO-CAM models
- Mapping documentation in progress.
Convert gene ontology annotations into GO-CAMs. pombase2go
Convert SynGO models to GO-CAMs (scala). syngo2lego