September 28, 2006
INOH BioPAX Level2 release update
INOH BioPAX Level2 release has been updated and is available here.
The update includes data error correction and new XREFs to various resources such as UniProt, IPR, KEGG, Reactome, GO, ChEBI.
1. (2006/09/28) For each Interaction instance that has LEFT and RIGHT property referring to the same instance, postfix "_act" was added to the RIGHT instance.
2. (2006/09/15) data error correction
In diagram file "GPCR_signaling-pertussis_toxin-.inoh", the following value of protein node "G alpha i_ADP" (GID:ll0000056 LID:id1339337698 MatID:MI0007292) was corrected.
"MoleculeRoleOntorogy" value was changed from "IMR_0000313:adenylate cyclase" to "IMR_0000319:G-alpha-i".
3. (2006/09/15) added more unificationXrefs and relationshipXrefs (UniProt, IPR, KEGG, Reactome, GO, ChEBI)
4. (2006/09/15) wrong unificationXref in several pathway/interaction instances
5. (2006/09/15) Strange use of unificationXref
Changed to the following scheme.
1 : http://www.biocarta.com/pathfiles/h_egfPathway.asp
2 : http://www.biocarta.com/pathfiles/h_metPathway.asp
3 : http://www.biocarta.com/pathfiles/h_ngfPathway.asp
4 : http://www.biocarta.com/pathfiles/h_pdgfPathway.asp
5 : http://www.stanford.edu/~rnusse/wntwindow.html
6. (2006/09/06) Added UniProt unificationXref inscances to protein
7. (2006/09/06) Deleted ORGANISM property from smallMolecule
8. (2006/09/06) smallMolecule instances, changed from sequenceParticipant to physicalEntityParticipant
9. (2006/09/06) relationshipXref, empty DB/ ID
10. (2006/09/06) Multiple instances with the same name "IC"
There was a file in which openControlledVocabulary instances and evidence instances had the same name "IC" (IC is an INOH evidence code that stands for Inferred by Curator).
Evidence instance name was generated automatically as EVIDENCE-CODE + "_" + XREF and instances without any XREF had only EVIDENCE-CODE for their names (for example IC)
The rule was changed to the following.Evidence instance without EVIDENCE-CODE has the name NOEVIDENCE-CODE + "_" +XREF?Evidence instance with empty XREF has the name EVIDENCE-CODE + "_" + "NOXREF". Now an instance evidence with evidence code IC and a blank XREF will have the name IC_NOXREF.
Posted by KenFukuda : September 28, 2006 10:02 PM
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