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[bioontology-support] NCBO Annotator VM Question

John Graybeal jgraybeal at stanford.edu
Tue Apr 14 17:03:12 PDT 2020


Megan,

Please send me your exact API request that you are sending, so we can attempt to duplicate the issue here. Thank you.

John

On Apr 14, 2020, at 2:28 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Thanks John,

It’s true that adding “&exclude_synonyms=true" to the API string removes synonyms from the BioPortal mappings (despite the curious fact that I had been including that parameter setting in the data POSTed already).  We would actually like for the synonyms to be included in the response from our VM, however.  I tried adding “&exclude_synonyms=false" to the API string we send to our VM and synonyms are still not included.

Best,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Wednesday, April 8, 2020 at 11:17 AM
To: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Thanks Megan.

I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing.

The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent.

When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings.

If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included.

John




On Apr 8, 2020, at 7:16 AM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Forwarding this message to the support channel, as I realize I forgot to include it in my reply.

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Date: Friday, April 3, 2020 at 2:04 PM
To: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Hi John,

Thanks for your help.  As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request:

http://data.bioontology.org/annotator?text=surrounding+end+of+life+care

with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"}

The annotations we get back that come from NCIT are:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

I will attach full responses from each, as well.  Let me know if there’s more info I can provide.

Thanks,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Friday, April 3, 2020 at 11:32 AM
To: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Megan,

Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal—nothing mentioned Annotator since 2.5 release of the Virtual Appliance—and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.

John




On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Hello BioPortal Support,

I’m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


_______________________________________________
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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  | ORCID  0000-0001-6875-5360



<local_response.json><bioportal_response.json>_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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