No result in IndexFungorum using wikidata-web

[nleguillarme]

Hi @jhpoelen

Looking for taxid IF:7106 using wikidata-web gets me no result. Looking for the same taxon using its NCBI id NCBI:128151 gets me some results, but none in the IndexFungorum taxo, although the info is in wikidata : https://www.wikidata.org/wiki/Q133266

Does the wikidata-web matcher apply some filter to discard results in "unwanted" taxonomies ?

[jhpoelen]

Hey @nleguillarme thanks for sharing that you expected:

$ echo -e "IF:7106" | nomer wikidata-web 

to resolve some fungus taxon known to index fungorum , but instead got something like:

IF:7106 NONE    IF:7106                         http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=7106

as a result.

I checked the implementation and found that the WikiData's support for the Index Fungorum taxon identification scheme was not yet known (i.e. mapped) to Nomer.

I've added the mapping and extra tests. The functionality should be available in the next Nomer release.

Please let me know if this is urgent, or whether you are ok waiting a couple of weeks.

-jorrit

about the missing mapping between index fungorum and their associated Wikidata property id.

[jhpoelen]

Note that the upcoming Nomer version is producing results like:

$ echo -e "IF:7106" | nomer append wikidata-web 
IF:7106 SAME_AS WD:Q133266  Alternaria          Alternaria  https://www.wikidata.org/wiki/Q133266   
IF:7106 SAME_AS NCBI:5598   Alternaria          Alternaria  https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5598    
IF:7106 SAME_AS ITIS:14134  Alternaria          Alternaria  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=14134 
IF:7106 SAME_AS EOL:16498   Alternaria          Alternaria  http://eol.org/pages/16498  
IF:7106 SAME_AS GBIF:2616104    Alternaria          Alternaria  http://www.gbif.org/species/2616104 
IF:7106 SAME_AS WORMS:100208    Alternaria          Alternaria  https://www.marinespecies.org/aphia.php?p=taxdetails&id=100208  
IF:7106 SAME_AS IF:7106 Alternaria          Alternaria      http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=7106    
IF:7106 SAME_AS INAT_TAXON:327996   Alternaria          Alternaria          https://inaturalist.org/taxa/327996 
IF:7106 SAME_AS NBN:NHMSYS0001474393    Alternaria          Alternaria          https://data.nbn.org.uk/Taxa/NHMSYS0001474393   
IF:7106 SAME_AS IRMNG:1312559   Alternaria          Alternaria  https://www.irmng.org/aphia.php?p=taxdetails&id=1312559 
IF:7106 SAME_AS OTT:464790  Alternaria          Alternaria  https://tree.opentreeoflife.org/opentree/ottol@464790   

Please let me know the above result is as expected.

[nleguillarme]

Hi @jhpoelen , that's it, thank you ! Fast as lightning as always. This can wait a few weeks until you're ready to release a new version.

[jhpoelen]

@nleguillarme happy to help and thanks for confirming. Also, I am able to work quickly because of the immense amount of work our open source/data colleagues have already done/do around the world.