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thechiselgroup / biomixer

BioMixer
http://bio-mixer.appspot.com/
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Invalid Concept Ids #509

Closed everbeek closed 9 years ago

everbeek commented 9 years ago

Ids that do not refer to entities available in Bioportal have been showing up, in UBERON for example.

One of the subClassOf values for a sample concept is an invalid id with respect to Bioportal. This means that I cannot create a node from it, because it will only have the id and nothing else. Bioportal will return a 404 error in this case. I need to see why I do not catch this already, and decide if I should conserve the node with that id, or if I should forget about such nodes.

See: http://127.0.0.1:8888/conceptPathToRoot.html?initial_vis=paths_to_root&ontology_acronym=UBERON&full_concept_id=http://purl.obolibrary.org/obo/UBERON_0006590

http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0006591?include=properties&apikey=efcfb6e1-bcf8-4a5d-a46a-3ae8867241a1

http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fbioportal.bioontology.org%2F.well-known%2Fgenid%2Fbb5e53d4-94e8-453f-be79-03a81ddf214a%2F2b061000000000b/children?&page=1&apikey=efcfb6e1-bcf8-4a5d-a46a-3ae8867241a1

everbeek commented 9 years ago

It appears that I should check for prefLabel, and if it is not present, then to ignore the node. This might be touchy to implement in the places where node parsing is called for, but hopefully not.

everbeek commented 9 years ago

Fixed, but if I get different understanding of this later, I might roll back this change.

everbeek commented 9 years ago

I pushed on this further, and these ids that do not resolve to a useful page appear to be blank nodes or skolemizations, or concepts that are unnamed and without fixed identity. These are valid, but are considered harmful. I believe I should be rendering them, with some name in the rectangle designating them as unnamed ( perhaps?). I am going to seek some advice on this.

everbeek commented 9 years ago

I added as the label for these nodes, but the REST calls I was using just stopped returning this data.