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[bioontology-support] BioPortal: Questions

John Graybeal jgraybeal at stanford.edu
Wed Jul 11 14:00:45 PDT 2018


Thanks very much for this followup Samson. The only 'documentation' of which I am aware is the repository itself for the conversion software (https://github.com/ncbo/umls2rdf). I'm not seeing any documentation there; https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py is the relevant code I believe.

Your research suggests we need to take a closer look at this (while recognizing it was written by others, who have since left the team), though to be honest we will be constrained by resources for at least a while. We will welcome any further input you or Simon care to offer to improve our understanding.

John


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

When I searched NLM’s Metathesaurus browser for “Antibiotic” with ATC as the source terminology, I didn't get STY’s Antibiotic in the results. In that respect Bioportal’s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal’s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?

With best regards,
Samson


On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson’s suggestion is a good one.

I understand your frustration about what is and isn’t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited—but with opposing intentions—by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

•         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for “Event” in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



•         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
<image001.png>

o   Logged in
<image004.png>

•         Regarding the missing classes in ICD10, I don’t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact “whoever maintains UMLS to explain or correct these missing concepts”.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term “Event” and Logged in: error message “We're sorry but something has gone wrong. We have been notified of this error.”

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

•         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using “Jump To” in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

•         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term “Event”<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message “We're sorry but something has gone wrong. We have been notified of this error.”

•         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
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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


========================
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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