These identifier mapping databases contain mappings for metabolites extracted from HMDB, ChEBI and Wikidata.

• Webpage: https://github.com/egonw/create-bridgedb-hmdb/blob/master/README.md
• Authors: Egon Willighagen (Orcid), Denise Slenter (Orcid)
• License: CCZero
• Mapping Sources: HMDB (version 20180929), ChEBI 168, Wikidata (2018-10-05)
• Source code: https://github.com/egonw/create-bridgedb-hmdb
• Issues: https://github.com/egonw/create-bridgedb-hmdb/issues

Releases

• 2018-10-05: metabolites_20181005.bridge (QC_report)
  • Mapping sources: HMDB 4.0 (version 20180929), ChEBI 168, Wikidata (2018-10-05)
  • Please cite using https://doi.org/10.6084/m9.figshare.7177097.v1
  • This work was funded by ELIXIR, the research infrastructure for life-science data.
• 2018-08-09: metabolites_20180809.bridge (QC_report)
  • Compared to 2018-07-05, almost 500 new mappings originating from Wikidata.
  • Mapping sources: HMDB 4.0 (version 20180708), ChEBI 166, Wikidata (2018-08-09)
  • Please cite using https://doi.org/10.6084/m9.figshare.6953144
• 2018-07-05: metabolites_20180705.bridge (QC_report)
  • Compared to 2018-05-11, about 120% more mappings to LIPID MAPS IDs from 2018-06-30 data release.
  • Changed mapping between old (secondary) and new(primary) HMDB ID structure.
  • Mapping sources: HMDB 4.0 (version 20180618), ChEBI 165, Wikidata (2018-07-05)
  • Please cite using doi.org/10.6084/m9.figshare.6741491.v1
• 2018-05-11: metabolites_20180508.bridge (QC report)
  • Please cite using 10.6084/m9.figshare.6260003.v1
• 2018-03-18: metabolites_20180318.bridge (QC report)
  • Mapping sources: HMDB 4.0 (version 20180318), ChEBI 161, Wikidata (2018-03-04)
  • Please cite using 10.6084/m9.figshare.10847750
• 2018-02-01: metabolites_20180201.bridge (QC report)
  • Mapping sources: HMDB 4.0, ChEBI 160, Wikidata (2018-02-01)
  • Compatible with old and new HMDB identifier structure!
  • Please cite using 10.6084/m9.figshare.5845134.v1
• 2018-01-11: metabolites_20180111.bridge (QC report)
  • Mapping sources: HMDB 4.0, ChEBI 159, Wikidata (2018-01-11)
  • Compatible with latest Pathvisio version (3.3.0)
  • Compared to 2017-08-26, about 20% more mappings, resulting from HMDB 4.0 release
  • Compared to 2017-12-03 (available via Figshare), similar amount of mappings
  • Please cite using 10.6084/m9.figshare.5809491
• 2017-08-26: metabolites_20170809.bridge (QC report)
  • mapping sources: HMDB 3.6, ChEBI 154, Wikidata (2017-08-26)
  • About 20% more mappings, resulting from a newer HMDB 3.6 release
  • please cite using 10.6084/m9.figshare.5349967.v1
• 2017-07-09: metabolites_20170809.bridge (QC report)
  • mapping sources: HMDB 3.6, ChEBI 153, Wikidata (2017-07-09)
  • please cite using 10.6084/m9.figshare.5135035.v1
• 2017-06-21: metabolites_20170621.bridge (QC report)
  • mapping sources: HMDB 3.6, ChEBI 152, Wikidata (2017-06-21)
  • please cite using 10.6084/m9.figshare.5135035.v2
• 2016-10-12: metabolites_20161012.bridge.gz (QC report)
  • mapping sources: HMDB 3.6, ChEBI 144, Wikidata (2016-10-12)
  • About 80% more mappings, thanks to the work by Sebastian Burgstaller
  • please cite using 10.6084/m9.figshare.4010787.v1
• 2016-09-10: metabolites_20160910.bridge.gz (QC report)
  • mapping sources: HMDB 3.6, ChEBI 142, Wikidata (2016-09-07)
  • now includes metabolites names from ChEBI
  • please cite using 10.6084/m9.figshare.3817386.v1
• 2016-06-05: metabolites_20160605.bridge.zip (QC report)
  • mapping sources: HMDB 3.6, ChEBI 140, Wikidata (2016-06-04)
  • now includes metabolites names from Wikidata
  • adds numeric ChEBI IDs from the ChEBI source
  • please cite using 10.6084/m9.figshare.3413668.v1
• 2016-04-17: metabolites_20160412.bridge.zip (QC report)
  • mapping sources: HMDB 3.6, ChEBI 138, Wikidata (2016-04-11)
  • please cite using 10.6084/m9.figshare.3169147.v1
• 2016-01-17: metabolites_20160113.bridge.gz (QC report)
  • mapping sources: HMDB 3.6, ChEBI 135, Wikidata (2016-01-13)
  • adds LIPID Maps and KNApSAcK as data sources with mappings
  • please cite using 10.6084/m9.figshare.3083842.v1
• 2015-07-17: metabolites_20150717.bridge.gz (QC report)
  • mapping sources: HMDB 3.6, ChEBI 125, Wikidata
  • adds InChIKey, Wikidata, KEGG Drug as data sources with mappings
  • more mappings for PubChem and Chemspider
  • please cite using 10.6084/m9.figshare.1487696.v2
• 2014-05-16: metabolites_20140516.bridge.zip (QC report)
  • mapping sources: HMDB 3.5, ChEBI