Release 1.1.4

Full Changelog: v1.1.3...v1.1.4

Release 1.1.3

v1.1.3

Release 1.1.3.

Release 1.1.2

v1.1.2

Release 1.1.2.

Pathways2GO v1.1.0

This release adds the ability to convert biopax models without pre-building an entity ontology. It was specifically designed to work with YeastCyc models like https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?object=THRESYN-PWY .

The key changes to the command line operations are the addition of two parameters, -e and -sssom
-e YeastCyc
will result in conversions using the YeastCyc (non-reacto) pattern. Use -e REACTO for the entity ontology pattern. The YeastCyc pattern makes direct references to terms in the neo and go-lego ontology collections when they are found in the biopax content. When they are missing, an appropriate upper level class such as chebi:chemical or go:protein-containing complex is used instead.
-sssom ./obomatch-go-yeastpathway.sssom.tsv.txt
sssom is a standard for representing ontology mappings https://github.com/OBOFoundry/SSSOM/blob/master/SSSOM.md . If an sssom file is provided, the converter will add the best match it can find for activity instances and biological process instances missing GO annotations in the input biopax.

Pathways2GO Version 1

This release provides the ability to convert the Reactome knowledge base into a collection of GO-CAM RDF models. The Reactome content must be accessed in BioPAX Level 3 format. For example, downloaded from https://reactome.org/download/current/biopax.zip.

The jar file provides command line access to generate an ontology of all physical entities in Reactome as well as generating the GO-CAMs for each (non-disease) pathway. The models are dependent on importing the physical entity ontology as well as the ontologies imported by go-lego.owl (as with any other GO-CAM).

This code may work on other BioPAX level 3 inputs but has only been tested thoroughly with Reactome.