User:ProteinBoxBot/2017 CIViC sprint

Overall summary

This sprint is continuation of the efforts started at the CIViC hackathon, which was held at the NKI in Amsterdam Dec 1st & 2nd, 2016. There an initial data model was reviewed. The purpose of this sprint it to (1) mature the data model prepared for and discussed during the hackathon, (2) implement this data model in Wikidata, (3) do a full import of CIViC into Wikidata, (4) define a sustainability model, (5) apply the data model on other related resource, and (6) define example queries on Wikidata, using CIViC data in combination with other Wikidata data.

Participants

• Andra Waagmeester
• Ben Ainscough
• Elvira Mitraka
• Núria Queralt Rosinach
• Sebastian Burgstaller
• Eric Prud'hommeaux

Gameplan

1. (In)Form the community
2. Review the current data model
3. Extent the datamodel

Showcase variants

• V600E: Wikidata Wikipedia CIViC
• Rs1801133 |Wikidata Wikipedia dbSNP

Current data model

Property	Reference properties	Qualifier properties
part of (P361)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
genomic start (P644)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	genomic assembly (P659)+
genomic end (P645)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	genomic assembly (P659)+
chromosome (P1057)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	genomic assembly (P659)+
instance of (P31)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
described at URL (P973)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
positive therapeutic predictor for (P3354)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	medical condition treated (P2175)+, statement disputed by (P1310)*
negative therapeutic predictor for (P3355)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	medical condition treated (P2175)+, statement disputed by (P1310)*
positive diagnostic predictor for (P3356)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	statement disputed by (P1310)*
negative diagnostic predictor for (P3357)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	statement disputed by (P1310)*
positive prognostic predictor for (P3358)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	statement disputed by (P1310)*
negative prognostic predictor for (P3359)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+	statement disputed by (P1310)*
CIViC variant ID (P3329)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
described at URL (P973)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
Ensembl transcript ID (P704)	stated in (P248)+, retrieved (P813)+, reference URL (P854)+
+ = required * = optional

Data model extentions

Property needed	Property request	Comments
Biological variant of	Wikidata:Property_proposal/Natural_science#biological_variant_of
CIViC rating score	tbd	This property might be covered by review score. A linkable score is preferred, since different star rating systems exist.
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