User:ProteinBoxBot/2016 WikiPathways sprint

Participants

• Andra Waagmeester
• Egon Willighagen
• Alex Pico
• Eric Prud'hommeaux

Gameplan

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

tricarboxylic acid cycle

• Wikipedia (en) Wikidata SQUID

Wikipathways =

• Wikidata SQUID (homo sapiens)
• Wikidata SQUID (mus musculus)

Reactome (homo sapiens)

• Wikidata SQUID

Wikidata model

Wikipedia -> Wikidata

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

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 work (P2860)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
has part(s) (P527)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
connects with (P2789)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

Reactome

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 work (P2860)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
has part(s) (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

• All WikiPathways templates used in articles. Can find all article currently using each template by using the 'What links here' tool.
• Google doc on datamodel [1]