Indexing the scholarly literature around RNA-Seq & cell types in Wikidata

[Daniel-Mietchen]

Wikidata is a multilingual database that anyone can edit. It covers a wide range of topics, including human genes (example: ND1) mouse genes (example: ND1), cell lines (example: 3T3), and scholarly publications (example: Massively parallel single-nucleus RNA-seq with DroNc-seq).

To get an overview of the Wikidata-indexed literature on any of these topics, use https://tools.wmflabs.org/scholia/topic , e.g. https://tools.wmflabs.org/scholia/topic/Q2542347 for RNA-Seq.

[Daniel-Mietchen]

Here's a SPARQL query for cell lines and their Cellosaurus ID:

# Cell lines and their Cellosaurus ID
SELECT ?item ?itemLabel ?CellosaurusID WHERE {
  ?item wdt:P31 wd:Q21014462 .
  OPTIONAL { ?item wdt:P3289 ?CellosaurusID }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

[Daniel-Mietchen]

Here is a SPARQL query for scientific papers on RNA-Seq whose Wikidata items have been modified during the course of the hackathon:

SELECT ?q { ?q wdt:P31 wd:Q13442814 ; wdt:P921 wd:Q2542347 }

between

2017110705

and

2017110905

Results:

Total number of items : 6124 6123 items have changed between 2017-11-07 05:00:00 and 2017-11-09 05:00:00