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[bioontology-support] Need help for CPT Ontology

Michael Dorf mdorf at stanford.edu
Mon Sep 23 15:06:31 PDT 2019


Hi Vinod,

Thank you for contacting us. Please see my answers inline below:


On Sep 23, 2019, at 1:49 PM, Vinod Himatsinghani <vh at jade-biz.com<mailto:vh at jade-biz.com>> wrote:

Hello,

I wanted help on the following items. A quick response would be appreciated:

1. I found following API to get the data specific to CPT ontology class information.

http://data.bioontology.org/ontologies/CPT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F59850
http://purl.bioontology.org/ontology/CPT/59850

              Here 59950 is the CPT code (or "notation" as shown in the data)

              When I use header "Accept" as application/json I do not see the data that we see in Bioportal.
              When I use remove the header "Accept, I get the data in HTML form that has all data shown in Bioportal.

              Is there any other API to get the complete information in JSON form? Am I missing anything? How can I get the data in following form?

Trying using the parameter “display=all” in your API call. You should be able to see the full term info:

http://data.bioontology.org/ontologies/CPT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F59850?display=all<http://data.bioontology.org/ontologies/CPT/classes/http://purl.bioontology.org/ontology/CPT/59850?display=all>

2. I am accessing CPT ontology, for different codes the data I get has different number of fields. In some cases some fields are missing. Is there a way to find the superset of the possible fields for the CPT ontology.

You should be able to get that info using the Properties service. This will give you a list of all possible properties that the ontology contains. Some terms, as you noticed, have don’t have ALL properties populated:

http://data.bioontology.org/ontologies/CPT/properties?display=all


3. Is there a way to know the cardinality of specific field. for example "CUI", "Inverse of SIB" fields may have multiple items. Though the JSON example shown has "Citation" field with one item, for some other CPT code "Citation" field may have more items, etc, Is there any documentation that has information on the info structure?

The short answer is: it’s safe to assume that all these fields are arrays. They may contain a single or multiple values depending on the term, but the cardinality is always >= 1.

A bit longer answer is BioPortal accepts ontologies in multiple different formats including OBO, OWL, and SKOS. When the system consumes an ontology, we have a set of eight “BioPortal standard properties" that we attempt to populate for each class, regardless of ontology format. The set of standard properties are:

ID
Preferred Name
Synonyms
Definitions
CUI
Semantic Types
Obsolete
Parents

Some of these, like ID,  Preferred Name and Obsolete have a single value. All others are multiples. So are the individual properties defined within the ontology.

Hope this helps!

Michael



----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------



Thanks
Vinod Himatsinghani
(848) 250-9195

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