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[bioontology-support] Questions regarding the REST API

John Zobolas john.zobolas at ntnu.no
Fri Nov 9 05:57:21 PST 2018


Hi,


I am developing a module that's uses your API to get results back from different ontologies and I want to ask a few things:

  1.  ?I see that when I search for a string, in the results there is a property obsolete (e.g. http://data.bioontology.org/search?q=melanoma)<http://data.bioontology.org/search?q=melanoma> which almost always (as far as I can tell) is false. Can I ever find it to be true (meaning that that entry is not used any more so I will have to prune that result)? Or you automatically filter the results to show only obsolete:false ones?
  2.  Is the URL parameter no_contexts=true equal to display_context=false (I accidentally discovered that they work the same but the first one is not mentioned in the documentation, so I should probably use the later!)
  3.  I was looking at the documentation in the available media types section, and I was wondering that if I send an HTTP request with method DELETE to a URL like http://data.bioontology.org/groups/:acronym or http://data.bioontology.org/ontologies/:acronym,<http://data.bioontology.org/ontologies/:acronym> will I be actually deleting that specific group/ontology? I mean do I even have the privileges to do that or is something that only an `admin` could do (because in the documentation it is not specified who can do what for every HTTP verb and media type).
  4.  The format of error responses is always the same no matter what query I use in your provided REST service (an object with errors and status properties, the first having an array of Strings as a value and the second the status code/number as a value)??? E.g. what I will get when I hit: http://data.bioontology.org/ontologies/GOfr
  5.  If I have the acronym of an ontology, I can access (all) the classes: (e.g. http://data.bioontology.org/ontologies/MCCL/classes). The first result in the previous query has the prefLabel:FetalCellLine. So, if I query the: http://data.bioontology.org/search?q=FetalCellLine&ontologies=MCCL I get this one result and whatever property was empty in the 'classes query' result (e.g. definition:[ ]), it's not shown in the later query, right?
  6.  Is there a way to get all the results from an ontology (paginated of course) through a query different than the one like /ontologies/:acronym/classes and have the results pruned (no empty properties) as when you query by search string?
  7.  I have noticed that the @id in the results is not a unique id, right? For example, there are many results with this id: http://purl.obolibrary.org/obo/DOID_1909, belonging to different ontologies - and the difference between them is small, for example one result does not provide the definition while the other does.
  8.  Is there a way to get results by id? Something like: /searchByID/id=URLid  (according to (7) this could result in more than 1 result) or /searchByID/ids={URLid1,URLid2,URLid3,...}?
  9.  Is there a way to get results by a combination of id+ontology acronym? Something like /searchByIDAndOntology/id=URL&ontology=OntologyAcronym? Actually, if you merge the 2 last questions, what I am asking is this query: /searchByIDAndOntology/id=[list of URLids]&ontologies=[list of ontologies]? The nearest I found in the documentation was the query with the subtree_root_id which needs the search string (so I can't use it in my case). Also, this could cover the (6) if the list of ids is empty!

?BR, John.
?------------------
John Zobolas
PhD Student
Department of Biology, Faculty of Natural Sciences, NTNU
Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU

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