User:ProteinBoxBot/2016 WikiPathways sprint

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Overall summary[edit]

Participants[edit]

Gameplan[edit]

  1. (In)Form pathway community
  2. identify pathways used on Wikipedia (Q52) using the WikiPathways (Q7999828) widget
    1. decide if the new entries need new WD entries or can be part of existing entries
  3. Prepare Wikidata (Q2013) data model to capture pathways content
    1. identify pathway entities (DataNode's) that have a type (instance of (P31)) in Wikidata
    2. determine type of new Wikidata pages (instance of (P31))
    3. determine property that links the new pathway entries with metabolite/gene/etc
      1. from pathway to gene/metabolite ?
      2. from gene/metabolite to pathway ?
    4. found in taxon (P703) ?
  4. Import all PubMed (Q180686) citations in WikiPathways
  5. Manually populate the Wikidata entries for the selected examples
  6. Write a bot
  7. Run bot on 2 pathways
  8. Run bot on 10 pathways
  9. Run bot on all pathways

Template cases[edit]

tricarboxylic acid cycle[edit]

Wikipathways =[edit]

Reactome (homo sapiens)[edit]

Wikidata model[edit]

Wikipedia -> Wikidata[edit]

Property Reference properties Qualifier properties
instance of (P31) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
described by source (P1343) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

WikiPathways[edit]

Property Reference properties Qualifier properties
instance of (P31) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
WikiPathways ID (P2410) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
found in taxon (P703) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
cites (P2860) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
has part (P527) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
connects with (P2789) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

Reactome[edit]

Property Reference properties Qualifier properties comments
instance of (P31)+ stated in (P248)+, retrieved (P813)+, reference URL (P854)+
catalog code (P528)+ stated in (P248)+, retrieved (P813)+, reference URL (P854)+ catalog (P972)+ A property for reactome ID is needed instead to be able to reference a Reactome record
found in taxon (P703) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
cites (P2860) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
has part (P527) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
part of (P361) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
connects with (P2789) stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

Links[edit]