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[bioontology-support] search by id in a subtree

Michael Dorf mdorf at stanford.edu
Fri Sep 1 11:54:52 PDT 2017


Please see answers inline.

Thanks!

Michael


On Sep 1, 2017, at 10:29 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

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

The parsing log file should be located in the repository directory for that ontology/submission number. Usually, that structure is:

/srv/ncbo/repository/SNOMEDCT/5/parsing.log

If the submission itself has not made it through, you can check the REST server log, located in:

/srv/ncbo/ontologies_api/shared/log

My sysadmin tells me that by default that log is not enabled. You need to edit this file:

/srv/ncbo/ontologies_api/current/config/unicorn.rb

And uncomment these lines:

#stderr_path 'log/unicorn.stderr.log'
#stdout_path 'log/unicorn.stdout.log'

  1.  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.

As far as I am aware, ALL UMLS ontologies in our repository are imported directly from the source in a bulk job that we run periodically via the UMLS2RDF script. I am not sure whether the appliance would be able to handle the RRF files via a straight submission.

  1.  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”.

Another developer on the team who is no longer with us had written the original UMLS2RDF script. Sorry I can’t offer much assistance with this question. If I were dealing with the same issue, I’d probably try to find the relevant lines in the python script and modify them to see if they produce the effect you are seeking:

https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py

  1.  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.

You can pass the API key either via the ?apikey=<yourapikey> request parameter or via the Authorization var in the headers:

Key: Authorization
Value: apikey token=<yourapikey>

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&apikey=yourapikey<http://data.bioontology.org/search?q=http://purl.bioontology.org/ontology/SNOMEDCT/707512002&ontology=SNOMEDCT&subtree_root_id=http://purl.bioontology.org/ontology/SNOMEDCT/195967001&apikey=yourapikey>


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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