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[bioontology-support] search by id in a subtree

Madani, Sina Sina.Madani at vumc.org
Fri Sep 1 10:29:42 PDT 2017


Hi Michael,

Thank you so much for the info. I have a couple of follow up questions:


  1.  I tried to load SNOMED.ttl into our local instance of bioportal appliance (RC2) but after a minute I got "Incomplete response received from application” in my browser. Which log file I need to look at to see what went wrong. The SNOMED.ttl file was provided to me previously and I believe it’s a product of UMLS2RDF script
  2.  When tried to add a new ontology to the appliance, in the drop down format, I saw UMLS. How does it work? Does it transform UMLS RRF files directly into the bioportal appliance? My understanding is that we need to use UMLS2RDF script externally and load the result file into the bioportal appliance.
  3.  Is there anyway to included obsolete/retired concepts in the output ttl file when using UMLS2RDF script?  If I look for SNOMED concept Dermoid Cyst of Ovary “119424003”, even when obsolete option is checked in NCBO bioportal, no concept is returned. It would be great if we can find out the status of a SNOEMD concept (active versus inactive). It would be even better to see the additional metadata for this retired concept from ref sets like “Possibly equivalent to” “Benign teratoma of Ovary”.
  4.  Could you please show how to use an apikey in one of your examples below? It seems the syntax has been changed since few years ago.


Thanks !

Sina

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Thursday, August 31, 2017 at 5:38 PM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] search by id in a subtree

Hi Sina,

I am not sure which one of the two interpretations you are asking about:

1. Determine whether a term with a given id is located within a specific subtree. If that’s the case, yes, you should be able to do this. Here is an example that searches for the term "Uncomplicated moderate persistent asthma”, id = http://purl.bioontology.org/ontology/SNOMEDCT/707512002<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=Djid4IeYolSffvWdNQN0t3ArG2gyknqpLr1mJ%2FZ%2B%2B0Y%3D&reserved=0> in a subtree of the term “Asthma”, id = http://purl.bioontology.org/ontology/SNOMEDCT/195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=1v21JOokiz1RqMv8T%2F8c%2ByvSiVUtinbCyQ9Sqp8YqjE%3D&reserved=0>:

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fq%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002%26ontology%3DSNOMEDCT%26subtree_root_id%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=4%2BdwosGLQUm2EtM6y3hgEngHrF4iW6EqwyZwxDDO%2BdM%3D&reserved=0>

OR

2. Get ALL the descendants (direct/indirect) of a given term (“Asthma”). In this case, the call would be:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/tree<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMEDCT%2Fclasses%2Fhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001%2Ftree&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=5egh6wZ81Ymp7SHFkAflQCM%2B0HoEsEm7rt0Q4pcV%2BJg%3D&reserved=0>

Let me know if this helps.

Thank you for keeping in touch with us!

Michael


On Aug 29, 2017, at 12:26 PM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi,

Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children?

Thanks!
Sina
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