Open cthoyt opened 4 years ago
For PC7_2008
, here's what I found from https://neo4j.het.io/:
MATCH (n:Pathway)
WHERE n.identifier = 'PC7_2008'
RETURN n
<id>:37740
identifier:PC7_2008
license:CC BY 4.0
name:BMAL1:CLOCK,NPAS2 activates circadian gene expression
source:Reactome via Pathway Commons
Pathway resources were combined in this notebook.
The Pathway Commons raw data we used is Pathway Commons.7.All.GSEA.hgnc.gmt
, which includes the line:
9606: BMAL1:CLOCK,NPAS2 activates circadian gene expression datasource: reactome; organism: 9606; id type: hgnc symbol NAMPT PPARA CCRN4L HELZ2 RORA NR3C1 CHD9 NPAS2 CRY2 NR1D1 SMARCD3 SERPINE1 PER2 PER1 ARNTL2 BHLHE40 TGS1 BHLHE41 CRY1 TBL1XR1 AVP RXRA CREBBP ARNTL F7 PPARGC1A NCOA1 HDAC3 EP300 NCOA2 DBP NCOA6 TBL1X CARM1 NCOR1 CLOCK MED1
So it looks like this file lacked actual pathway identifiers so I assigned identifiers as incrementing integers prepended with PC7. Definitely not a good system! Not sure if Pathways Commons now provides pathway IDs for the source database in their data exports.
It's nice to have the exact revision
_r71358
, but this isn't what's necessary to resolve this pathway and merge with other resources.
Agree this would be best as a separate revision
property rather than as part of the node identifier.
I'm also not sure what the actionable item is for this. I don't think you would update the source data, would you? Are there plans for a Hetionet v2.0 that will include some of the other new updates?
I'm not currently working on Hetionet v2.0. If someone wants to take the lead, I'd be happy to advise and support. There's lot's of low hanging fruit like updating resources and adding more properties (like CURIEs and URLs where missing).
I think one actionable item from your comment is that it would be nice to have a mapping for each Hetionet v.1.0 node to a CURIE for that node. Nodes would have an extra curie
property, so it would be very backwards compatible. In the case of the Pathway Commons nodes, this might actually be a bit annoying to generate.
After a closer look, I'm having issues with the data source used for pathways.
Should correspond to the reactome pathway, https://reactome.org/content/detail/R-HSA-1368108, but it's not clear what this identifier is. I might guess "Pathway Commons 7"
Later, wikipathways identifiers (plus revisions) are used for other pathways
It's nice to have the exact revision
_r71358
, but this isn't what's necessary to resolve this pathway and merge with other resources.I'm also not sure what the actionable item is for this. I don't think you would update the source data, would you? Are there plans for a Hetionet v2.0 that will include some of the other new updates?