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Build project for all CEDAR Java repositories
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can't see Value Sets or their terms #1146

Open graybeal opened 3 years ago

graybeal commented 3 years ago

In the template editor, a search term of T0 yields only classes (394 of them). But if we take the search string that CEDAR is making and run it, we see many values from the CEDAR-VS value set.

https://terminology.metadatacenter.org/bioportal/search?q=t0&scope=classes,values&page=1&page_size=500

And CEDAR can't even see the CEDAR-VS value set (or NLMVW) when I try to enter it as an ontology to search on or for.

Screen Shot 2021-08-07 at 4.16.30 PM.png

graybeal commented 3 years ago

As I've been troubleshooting I have been creating Q&A about value sets in https://docs.google.com/document/d/10KJsxHZfHb-ZD-xPJN5-HD2sJplLHGodHVVIdqqGT5k/edit#. So far I have the following, bold items are relevant to this issue.

  1. How does BioPortal know the difference between an ontology and a Value Set? a. ontologyType attribute is set to https://data.bioontology.org/ontology_types/VALUE_SET_COLLECTION instead of https://data.bioontology.org/ontology_types/ONTOLOGY
  2. How can you see the difference between an ontology and a VS in BioPortal? a. via API, the ontology metadata b. via UI—?
  3. Does BioPortal do anything different with Value Sets than it does with Ontologies? (List)
  4. Why is the CADSR-VS value set shown as Obsolete in the BioPortal Admin page, even though it is the one we are updating nightly? a. Is it used by CEDAR? >> It should be—values from it are in the response to the call above that CEDAR makes when search for concepts/values
  5. Why is CADSRVS not shown as obsolete (or deleted), even though it hasn't been updated since 2015? a. Is it used by CEDAR? b. note it is not a Value Set
  6. Is CDESVS used by CEDAR, even though it hasn't been updated since 2018? a. note it is not a value set
  7. Is CEDARVS used by CEDAR, even though it hasn't been updated since 2015?
  8. Are the following things that look like value sets (per the description) actually value sets (whatever that means to BioPortal)? >> Only 3 value sets in BioPortal: CEDARVS, CADSR-VS, and NLMVS are value seta; CADSRVS, CDESVS, and the TM- ones are not. a. Traditional Medicine Other Factors Value Set (TM-OTHER-FACTORS) b. Traditional Medicine Signs and Symptoms Value Set (TM-SIGNS-AND-SYMPTS) c. NIH NLM Value Sets (NLMVS) d. Traditional Medicine Constitution Value Set (TM-CONST) e. Traditional Medicine Meridian Value Sets (TM-MER)
graybeal commented 3 years ago

There are only 3 value sets in BioPortal per above, CEDARVS, CADSR-VS, and NLMVS. CEDAR can't identify any of them, either as auto-complete in the 'search within ontologies' field (but I think that option only looks for ontologies) nor when using the find value sets button. (So it isn't just the parsing or Obsolete issues with CADSR-VS causing this. In fact I can search for 'delivery' in the same string as above and it returns NLMVS values too, but CEDAR can't see those either.

It appears the "search for value sets" command does not work as expected, at least at the moment. The call that generates (if I captured it correctly) looks like https://terminology.metadatacenter.org/bioportal/search?q=Delivery%20Procedures&scope=value_sets&page=1&page_size=500 but it returns matching terms (and the value sets that contain them), not actual value set name matches. Maybe that's by design but the UI doesn't suggest it works that way. And of course, none of that gets reported back to the user anyway. Report this as a separate bug?