Obsolete terms have URL to Github issues that are not IRI

[aleixpuigb]

When a term is obsoleted, the standard is to include a term_tracker_item with the URL to the Github issue as IRI. This ticket is to track and edit those that do not follow the standard:

• obsolete barrier epithelial cell
• obsolete seminal fluid secreting cell
• obsolete primary pigment cell
• obsolete secondary pigment cell
• obsolete tertiary pigment cell

[shawntanzk]

Was a bit sick of my work so was finding something to do that was more fun so here I am, hi :D

Here's a sparql query I ran to detect all with the above issue:

prefix owl: <http://www.w3.org/2002/07/owl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT *
WHERE {

  ?term ?predicate ?iri .
  FILTER EXISTS { ?term owl:deprecated true }
  FILTER (STRSTARTS(str(?iri), "https://github.com/"))
  FILTER (?predicate != <http://purl.obolibrary.org/obo/IAO_0000233>)
}

Came up with the following results:

term	predicate	iri
http://purl.obolibrary.org/obo/CL_0000665	http://www.w3.org/2000/01/rdf-schema#comment	#726
http://purl.obolibrary.org/obo/CL_0002371	http://www.w3.org/2000/01/rdf-schema#comment	#1150
http://purl.obolibrary.org/obo/CL_0017501	http://www.w3.org/2000/01/rdf-schema#seeAlso	#734
http://purl.obolibrary.org/obo/CL_4023073	http://www.w3.org/2000/01/rdf-schema#comment	#2043
http://purl.obolibrary.org/obo/CL_0000073	http://www.w3.org/2000/01/rdf-schema#comment	#1149
http://purl.obolibrary.org/obo/CL_0000161	http://www.w3.org/2000/01/rdf-schema#comment	#427
http://purl.obolibrary.org/obo/CL_0000124	http://www.w3.org/2000/01/rdf-schema#seeAlso	#715
http://purl.obolibrary.org/obo/CL_0000426	http://www.w3.org/2000/01/rdf-schema#seeAlso	#708
http://purl.obolibrary.org/obo/CL_0000181	http://www.w3.org/2000/01/rdf-schema#seeAlso	#720
http://purl.obolibrary.org/obo/CL_0000321	http://www.w3.org/2000/01/rdf-schema#comment	#1149
http://purl.obolibrary.org/obo/CL_0000243	http://www.w3.org/2000/01/rdf-schema#seeAlso	#715
http://purl.obolibrary.org/obo/CL_1001566	http://www.w3.org/2000/01/rdf-schema#seeAlso	#1443
http://purl.obolibrary.org/obo/CL_0000003	http://www.w3.org/2000/01/rdf-schema#comment	#2124
http://purl.obolibrary.org/obo/CL_0000663	http://www.w3.org/2000/01/rdf-schema#comment	#726
http://purl.obolibrary.org/obo/CL_0000548	http://www.w3.org/2000/01/rdf-schema#comment	#2124
http://purl.obolibrary.org/obo/CL_0000664	http://www.w3.org/2000/01/rdf-schema#comment	#726
http://purl.obolibrary.org/obo/CL_0000381	http://www.w3.org/2000/01/rdf-schema#comment	#1784 'neuroendocrine cell' (which has exact synonym "neurosecretory cell") and 'neurosecretory neuron' may all refer to the same cell type.

Personally I would manually edit http://purl.obolibrary.org/obo/CL_0000381 to not have extra text, then run the following sparql query to replace

prefix owl: <http://www.w3.org/2002/07/owl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

DELETE{
  ?term ?predicate ?iri .
}
INSERT{
  ?term <http://purl.obolibrary.org/obo/IAO_0000233> ?iri .
}
WHERE {

  ?term ?predicate ?iri .
  FILTER EXISTS { ?term owl:deprecated true }
  FILTER (STRSTARTS(str(?iri), "https://github.com/"))
  FILTER (?predicate != <http://purl.obolibrary.org/obo/IAO_0000233>)
}

Hope that helps :)
Ok back to less fun work lol

[aleixpuigb]

Thank you very much Shawn, that helps a lot!