Pathway Commons v6 is now available.

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Igor Rodchenkov

Dec 9, 2014, 9:31:24 AM12/9/14

Pathway Commons is a collection of publicly available pathways, currently containing 12 pathway and interaction databases, focused on human. These are: Reactome, NCI Pathway Interaction Database, PhosphoSitePlus, HumanCyc, HPRD, PANTHER, DIP, BioGRID, IntAct, IntAct complexes, BIND and CORUM. We will continue to add more databases in the future.

This release fixes some data issues and adds minor features compared to our recent v5 release.

  • Data

  • For software developers using the web service

    • updated the ‘search’ XML schema (backward compatible): added <size> element (the number of child processes) for pathway and interaction hits;

    • updated the full-text search/index using the latest Lucene API: improves reporting of matching text fragments (excerpts) and also, e.g., makes  such queries as /search?q=*&type=provenance&datasource=IntAct,  /search?q=*&type=biosource&organism=9606 now return hits; now wildcard queries that begin with “*” are allowed (e.g., /search?q=*ulin*&type=pathway); search returns up to 100 hits per page (was 500).

    • also updated and endpoints.

  • Core software

    • PC2 v6 is powered by cPath2 v6 (6.0.0-SNAPSHOT) that uses a new, easy to support and update BioPAX full-text search implementation and the latest Paxtools and BioPAX Validator core libraries.

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