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[bioontology-support] obsolete properties (was: Combine search and property_search endpoints)

John Graybeal jgraybeal at stanford.edu
Fri Jul 5 17:05:21 PDT 2019


John,

I've created a new thread about your obsolete properties question.

I'm not sure exactly what you're asking (Is an obsolete property possible? Does an instance of an obsolete property exist in BioPortal? Does BioPortal contain code that handles obsolete properties?)  I find the various interpretation of 'property' in this context doesn't help us talk clearly about it either!

I have no idea if any of the ontologies in BioPortal contain obsolete properties; I know some do contain obsolete classes. Our interface allows specification of "obsolete status for ontology classes", as shown below (hope that can be displayed for you, or that you can get the idea), whenever a user creates a new submission (in the Advanced OWL section, under Identify Obsolete Classes). I am 98% sure these settings work for classes.

Obsolete propertyOptionally enter a property ID that indicates obsolete status for ontology classes (the property value must be set to "true"). Note that by default, BioPortal checks for existence of the owl:deprecated property.
Obsolete branch rootOptionally enter a class ID for the root of an obsolete branch. All classes in the branch will be marked as obsolete, with the exception of the root class.
It so happens that the OWL 2 technique for specifying an obsolete property is the same as for specifying an obsolete class, namely, an annotation for the property that owl:deprecated is "true". I can't tell you today if BioPortal actually makes use of that information for properties (not sure we've had the question come up before, certainly not since my arrival in 2015).

Can you clarify what you'd like to know?  If it's about BioPortal's handling of properties that have been made obsolete, most likely we'll have to review the code and/or write some tests to determine the answer. You're welcome to tell us anything you learn in that regard!

John


On Jul 5, 2019, at 11:58 AM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

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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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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