environments2wikidata

tools and results for mining connections between wikidata entries and ENVO or GAZ.

The resulting mappings can connect GAZ to ENVO, as per the following schema:

                      (wd curated)
   wikidata:<Place> --[rdf:type]-->   wikidata:<PlaceType>
         |                              |
         |                              |
      skos:match                      skos:match
         |                              |
         |                              |
   GAZ:<GAZ_ID>    ---[rdf:type]-->   ENVO:<ENVO_ID>
                      (inferred)

For more details and contex, see the following tickets:

• envo#833 ENVO to Wikidata mappings
• gaz#3 Upload all of GAZ to wikidata
• gaz#20 convert GAZ to instance-based

Results

• curated-high-confidence-envo.tsv (~1k)
• align-high-confidence-gaz.tsv (~167k)
• gaz-to-envo.tsv (~26k)

Note that intermediate results of first pass search of GAZ is store on OSF:

• All triples are stored on OSF (>100M): https://osf.io/unga9/

Methods

Scan and extract of wikidata

wikidata_ontomatcher is used to do a first pass search of wikidata using all classes in an ontology.

The results are an intermediate ttl file containing skos mapping triples, plus triples about the matched entities in wikidata. This may have many false positives due to homonyms.

Alignment

The above is used to do a more fine grained alignment using rdf_matcher using the exact command.

These are then filtered to obtain only high-quality mappings

GAZ to ENVO

This is simply a join between the rdf:types asserted in Wikidata and the matches.

Due to the conservative nature of both mappings we only get a fraction of GAZ entities with a type as this time (5%)

Future

We plan to use the conservative mappings to further boost results using kBOOM.

We also want to upload mappings to wikidata and have the community help extend mappings.

Also: GAZ to geonames.