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[bioontology-support] RXNORM Properties

Michael Dorf mdorf at stanford.edu
Fri Jun 26 11:23:10 PDT 2020


Hi David,

We’re replaced some of the original parameter names with more descriptive counterparts, but the documentation still shows the original names in some places. The old names have been preserved for backwards compatibility. In this case “display” is equivalent to “include”, which still works and is documented:

https://data.bioontology.org/search?q=Acetaminophen&ontologies=RXNORM&page=1&pagesize=2&roots_only=true&include=prefLabel,synonym,definition,notation,cui,semanticType,properties

It does look like “properties” isn’t on that list, however. I’ll make sure to have this updated in our next release. Thank you for bringing this to our attention!

Michael



On Jun 26, 2020, at 10:38 AM, David Saylor <david.saylor at beyondlucid.com<mailto:david.saylor at beyondlucid.com>> wrote:

Yes, I think that's just what we need!  I don't see the display parameter in the documentation.  Is that intentional?

We'll continue on our side.

Thank you!

Best regards,
David

David Saylor, Chief Engineer
Beyond Lucid Technologies, Inc.
(650) 648-ePCR office
(818) 660-5726 direct


On Wed, Jun 24, 2020 at 6:52 PM Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi David,

Thanks for contacting us. All of the attributes of a calls are stored in the “properties” collection. You should be able to get those by using the “display” query parameter:

https://data.bioontology.org/search?q=Acetaminophen&ontologies=RXNORM&page=1&pagesize=2&roots_only=true&display=prefLabel,synonym,definition,notation,cui,semanticType,properties

Let me know if this works.

Thanks!

Michael

On Jun 24, 2020, at 8:52 AM, David Saylor <david.saylor at beyondlucid.com<mailto:david.saylor at beyondlucid.com>> wrote:

Hello, we are trying to use the BioPortal API to look up RXNORM codes.
We are able to do the search via a query like below.  What we really want to know is the more detailed properties of a particular

Here is the page for Acetaminophen (link<https://bioportal.bioontology.org/ontologies/RXNORM/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161&jump_to_nav=true#details>).  We would really like to get the additional RXNORM properties from a page like, such as Has ingredient or Has ingredients.

Could you let me know the best way to pull out those properties?

Thanks and best regards,
David

Query
https://data.bioontology.org/search?q=Acetaminophen&ontologies=RXNORM&page=1&pagesize=2&roots_only=True


First Result
{
  "page": 1,
  "pageCount": 883,
  "totalCount": 1766,
  "prevPage": null,
  "nextPage": 2,
  "links": {
    "nextPage": "http://data.bioontology.org/search?q=Acetaminophen&ontologies=RXNORM&page=2&pagesize=2&roots_only=True",
    "prevPage": null
  },
  "collection": [
    {
      "prefLabel": "Acetaminophen",
      "cui": [
        "C0000970"
      ],
      "semanticType": [
        "T109",
        "T121"
      ],
      "obsolete": false,
      "matchType": "prefLabel",
      "ontologyType": "ONTOLOGY",
      "provisional": false,
      "@id": "http://purl.bioontology.org/ontology/RXNORM/161",
      "@type": "http://www.w3.org/2002/07/owl#Class",
      "links": {
        "self": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161",
        "ontology": "http://data.bioontology.org/ontologies/RXNORM",
        "children": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/children",
        "parents": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/parents",
        "descendants": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/descendants",
        "ancestors": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/ancestors",
        "instances": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/instances",
        "tree": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/tree",
        "notes": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/notes",
        "mappings": "http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161/mappings",
        "ui": "http://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F161",
        "@context": {
          "self": "http://www.w3.org/2002/07/owl#Class",
          "ontology": "http://data.bioontology.org/metadata/Ontology",
          "children": "http://www.w3.org/2002/07/owl#Class",
          "parents": "http://www.w3.org/2002/07/owl#Class",
          "descendants": "http://www.w3.org/2002/07/owl#Class",
          "ancestors": "http://www.w3.org/2002/07/owl#Class",
          "instances": "http://data.bioontology.org/metadata/Instance",
          "tree": "http://www.w3.org/2002/07/owl#Class",
          "notes": "http://data.bioontology.org/metadata/Note",
          "mappings": "http://data.bioontology.org/metadata/Mapping",
          "ui": "http://www.w3.org/2002/07/owl#Class"
        }
      },
      "@context": {
        "@vocab": "http://data.bioontology.org/metadata/",
        "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel",
        "obsolete": "http://data.bioontology.org/metadata/owlobsolete",
        "semanticType": "http://data.bioontology.org/metadata/umlssemanticType",
        "cui": "http://data.bioontology.org/metadata/umlscui"
      }
    }
  ]
}


David Saylor, Chief Engineer
Beyond Lucid Technologies, Inc.
(650) 648-ePCR office
(818) 660-5726 direct
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