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[bioontology-support] Combine search and property_search endpoints

Michael Dorf mdorf at stanford.edu
Fri Jul 5 11:58:42 PDT 2019


Hi John,

I am not an ontology building expert, so can’t really speak with authority on whether there exists such a thing as an obsolete property. What I can tell for sure is that we don’t track that information in our system. There is no “obsolete” attribute defined on the properties model classes:

https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/properties/object_property.rb

Michael


On Jul 4, 2019, at 6:48 AM, John Zobolas <john.zobolas at ntnu.no<mailto:john.zobolas at ntnu.no>> wrote:

​One more question: Are there any obsolete properties? (I don't see any obsolete property defined in the returned JSON when using the `property_search` endpoint)​
________________________________
From: John Zobolas
Sent: Thursday, July 4, 2019 3:37 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Subject: Combine search and property_search endpoints

​Hi,

The story:

I was using the `search` endpoint to request for a term in an ontology, but some people (while doing a free text search) wanted to get back the properties of the ontologies returned as terms - for example these ones: https://bioportal.bioontology.org/ontologies/OBOREL/?p=properties. So, asking for `causally related to` in the OBOREL ontology using the `search` endpoint returned nothing. I saw that you have a endpoint the `property_search` for that, which means that I will have to duplicate every search query that the users make. But then, when I request for IDs internally in my application, I ask queries like this one:
http://data.bioontology.org/search?q=http%3A%2F%2Fwww.semanticweb.org%2Fpallabi.d%2Fontologies%2F2014%2F2%2Funtitled-ontology-11%23CXorf36-Glu142%2A&ontologies=&require_exact_match=true&also_search_obsolete=true&display_context=false,<http://data.bioontology.org/search?q=http%3A%2F%2Fwww.semanticweb.org%2Fpallabi.d%2Fontologies%2F2014%2F2%2Funtitled-ontology-11%23CXorf36-Glu142%2A&ontologies=&require_exact_match=true&also_search_obsolete=true&display_context=false> and if it is an ID of a property, you have to ask also the `property_search` endpoint or otherwise you will never get it. So I have to duplicate the `getID` related-queries as well. For example, asking for this ID does not return anything: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002410&exact_match=true&page=1&pagesize=130&display_context=false, but changing to the `property_search` endpoint you find all the ontologies that have this ID and refers to the `causally related to` term/label)

The Questions:

  *   Why have two different endpoints for searching? Is it possible to provide a single endpoint that combines both?
  *   I had been given a hacked kind of query to ask for all IDs within all ontologies in BioPortal (paginated): http://data.bioontology.org/search?ontologies=&ontology_types=ONTOLOGY&page=1&display_context=false. Do you know if the above will include the property terms? (I guess not because some of the properties of the returned JSON objects are different between the `search` and `property_search` endpoints)

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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