Category Archives: BridgeDb

EW8: replacing CAS registry numbers with free ChEBI identifiers

Hypothesis: CAS registry numbers can be replaced with free ChEBI identifiers.

Start date: 2014-12-07 End date: YYYY-MM-DD

casInWP

Description: CAS registry numbers are non-free identifiers for chemical substances. BridgeDb does not have identifier mappings for them, as it is legally not allowed to create such (large) mapping databases (without explicit, non-transferable approval). Because of the lack of these databases, PathVisio cannot map experimental data to <gpml:DataNode>s in WikiPathways with such identifiers.

The goal of this experiment is to replace CAS registry numbers with ChEBI identifiers for which many more mappings are available in BridgeDb-provided identifier mapping files.

Methods

  • generate a list of <gpml:DataNode>s with CAS registry data sources on WikiPathways
  • for each, verify the chemical identity with the CAS reference database common-chemistry.org
  • based on this chemical identity look up the matching ChEBI entry
  • replace the identifier in the WikiPathways (e.g. via GPML editing)

Report 

$DETAILS OF ACTUALLY PERFORMING THINGS

Conclusion: $CONCLUSIONS