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Introduction

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 via the Noctua Web application (see also the development server).

Formally, a GO-CAM is an OWL ontology composed at the level 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 from 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.

Translation services

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.

Biopax2GO-CAM

Convert pathways expressed using the BioPAX standard, such as Reactome, to GO-CAMs (Java). Biopax2GO

GO2GO-CAM

Convert gene ontology annotations into GO-CAMs (python). pombase2go

SynGO

Convert SynGO models to GO-CAMs (scala). syngo2lego