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Saturday, May 18, 2019

LIPID MAPS: mass spectra and species annotation from Wikidata

Part of the LIPID MAPS classification
scheme in Wikidata (try it).
A bit over a week I attended LIPID MAPS Working Group meeting in Cambridge, as I have become member of the Working Group 2: Tools and Technical Committee in autumn. That followed a fruitful effort by Eoin Fahy to make several LIPID MAPS pathways available in WikiPathways (see this Lipids Portal), e.g. the Omega-3/Omega-6 FA synthesis pathway. It was a great pleasure to attend the meeting, meet everyone, and I learned a lot about the internals of the LIPID MAPS project.

I showed them how we contribute to WikiPathways, particularly in the area of lipids. Denise Slenter and I have been working on having more identifier mappings in Wikidata, among which the lipids. Some results of that work was part of this presentation. One of the nice things about Wikidata is that you can make live Venn diagrams, e.g. compounds in LIPID MAPS for which Wikidata also has a statement about which species it is found in (try it):

SELECT ?lipid ?lipidLabel ?lmid ?species ?speciesLabel
            ?source ?sourceLabel ?doi
WHERE {
  ?lipid wdt:P2063 ?lmid ;
         p:P703 ?speciesStatement .
  OPTIONAL {
    ?speciesStatement prov:wasDerivedFrom/pr:P248 ?source ;
                      ps:P703 ?species .
    OPTIONAL { ?source wdt:P356 ?doi }
  }
  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
  }
}

A second query searches lipids for which also mass spectra are found in MassBank (try it):

SELECT
  ?lipid ?lipidLabel ?lmid
  (GROUP_CONCAT(DISTINCT ?massbanks) as ?massbank)
WHERE {
  ?lipid wdt:P2063 ?lmid ;
         wdt:P6689 ?massbanks .
  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
  }
} GROUP BY ?lipid ?lipidLabel ?lmid

Enjoy!

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