[bioontology-support] Annotator plus API compatibility

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[bioontology-support] Annotator plus API compatibility

Rayyan Aziz Ansari
Hi everyone, can the new Bio Annotator plus platform be called from a Python API as was the case previously?
I just checked the Api documentation, and it does not seem to be updated to reflect the new query parameters like
"UMLS semantic groups" or negation etc. Could you please let me know if there is a timeline
for when I could use an api for these new features?
Thanks you for your time,
Rayyan


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Re: [bioontology-support] Annotator plus API compatibility

tchechmedj

Dear Rayyan,


Having developed much of the current Annotator+ extension, I also have a simple python package to query the extended API.

You may find it here: https://github.com/twktheainur/python_ncbo_annotator_client


An usage example is given in the README. Although you can't install it with pip yet, you can copy the "client" directory into your project to use the package.


Please don't hesitate if you have further interrogations.


Best Regards,

Andon Tchechmedjiev




On 20/06/2019 10:16, Rayyan Aziz Ansari wrote:
Hi everyone, can the new Bio Annotator plus platform be called from a Python API as was the case previously?
I just checked the Api documentation, and it does not seem to be updated to reflect the new query parameters like
"UMLS semantic groups" or negation etc. Could you please let me know if there is a timeline
for when I could use an api for these new features?
Thanks you for your time,
Rayyan


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
-- 
Andon Tchechmedjiev, PhD. Associate Professor in NLP, Comp. Ling and Biomedical Informatics
at Ecole des Mines d'Alès-LGI2P, Site Croupillac, 7 rue Jules Renard, Alès - 30319 Cedex FRANCE | andon.tchechmedjiev.eu 

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Re: [bioontology-support] Annotator plus API compatibility

John Graybeal-2
Rayyan,

There is more detailed documentation in the PDF at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972606/bin/bty009_supplement_bioinf-2017-1427.r2-3.pdf  which is pointed to by the main paper about this capability at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972606/.

I just tried the API on BioPortal using this string, which corresponds to the one in the first PDF.:
  <a href="http://data.bioontology.org/annotator?text=The&#43;patient&#43;has&#43;no&#43;sign&#43;of&#43;melanoma,&#43;but&#43;his&#43;father&#43;had&#43;history&#43;of&#43;skin&#43;cancer.&amp;ontologies=MESH&amp;longest_only=true&amp;exclude_numbers=false&amp;whole_word_only=true&amp;exclude_synonyms=false&amp;expand_mappings=false&amp;negation=true&amp;experiencer=true&amp;temporality=true&amp;lemmatize=false&amp;score=cvalue&amp;semantic_groups=DISO&amp;display_links=false&amp;display_context=false&amp;apikey=4a5011ea-75fa-4be6-8e89-f45c8c84844e" class="">http://data.bioontology.org/annotator?text=The+patient+has+no+sign+of+melanoma,+but+his+father+had+history+of+skin+cancer.&ontologies=MESH&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=false&negation=true&experiencer=true&temporality=true&lemmatize=false&score=cvalue&semantic_groups=DISO&display_links=false&display_context=false&apikey=4a5011ea-75fa-4be6-8e89-f45c8c84844e

This did not produce the expected results—my construction may be wrong—so we'll have to see what's happening at the moment. Sorry for the inconvenience!

John


On Jun 20, 2019, at 2:28 AM, Andon Tchechmedjiev <[hidden email]> wrote:

Dear Rayyan, 

Having developed much of the current Annotator+ extension, I also have a simple python package to query the extended API. 

An usage example is given in the README. Although you can't install it with pip yet, you can copy the "client" directory into your project to use the package. 

Please don't hesitate if you have further interrogations.

Best Regards, 
Andon Tchechmedjiev



On 20/06/2019 10:16, Rayyan Aziz Ansari wrote:
Hi everyone, can the new Bio Annotator plus platform be called from a Python API as was the case previously?
I just checked the Api documentation, and it does not seem to be updated to reflect the new query parameters like 
"UMLS semantic groups" or negation etc. Could you please let me know if there is a timeline
for when I could use an api for these new features?
Thanks you for your time,
Rayyan


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
-- 
Andon Tchechmedjiev, PhD. Associate Professor in NLP, Comp. Ling and Biomedical Informatics
at Ecole des Mines d'Alès-LGI2P, Site Croupillac, 7 rue Jules Renard, Alès - 30319 Cedex FRANCE | andon.tchechmedjiev.eu 
_______________________________________________
bioontology-support mailing list
[hidden email]
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



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Re: [bioontology-support] Annotator plus API compatibility

John Graybeal-2
Rayyan,

Sorry, I sent that too soon. The correct API calling sequence for BIoPortal's AnnotatorPlus is as follows (you'll need your own apikey).

<a href="http://services.data.bioontology.org/annotatorplus/?text=The&#43;patient&#43;has&#43;no&#43;sign&#43;of&#43;melanoma,&#43;but&#43;his&#43;father&#43;had&#43;history&#43;of&#43;skin&#43;cancer.&amp;ontologies=MESH&amp;longest_only=true&amp;exclude_numbers=false&amp;whole_word_only=true&amp;exclude_synonyms=false&amp;expand_mappings=false&amp;negation=true&amp;experiencer=true&amp;temporality=true&amp;lemmatize=false&amp;score=cvalue&amp;semantic_groups=DISO&amp;display_links=false&amp;display_context=false&amp;apikey=44444444-4444-4444-4444-44444444" class=""><a href="http://services.data.bioontology.org/annotatorplus/?text=The&#43;patient&#43;has&#43;no&#43;sign&#43;of&#43;melanoma,&#43;but&#43;his&#43;father&#43;had&#43;history&#43;of&#43;skin&#43;cancer.&amp;ontologies=MESH&amp;longest_only=true&amp;exclude_numbers=false&amp;whole_word_only=true&amp;exclude_synonyms=false&amp;expand_mappings=false&amp;negation=true&amp;experiencer=true&amp;temporality=true&amp;lemmatize=false&amp;score=cvalue&amp;semantic_groups=DISO&amp;display_links=false&amp;display_context=false&amp;apikey=44444444-4444-4444-4444-4" class="">http://services.data.bioontology.org/annotatorplus/?text=The+patient+has+no+sign+of+melanoma,+but+his+father+had+history+of+skin+cancer.&ontologies=MESH&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=false&negation=true&experiencer=true&temporality=true&lemmatize=false&score=cvalue&semantic_groups=DISO&display_links=false&display_context=false&apikey=44444444-4444-4444-4444-44444444 

With the information in the previously referenced documentation (see below), you should be all set.

John

On Jun 20, 2019, at 6:57 PM, John Graybeal <[hidden email]> wrote:

Rayyan,

There is more detailed documentation in the PDF at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972606/bin/bty009_supplement_bioinf-2017-1427.r2-3.pdf  which is pointed to by the main paper about this capability at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972606/.

I just tried the API on BioPortal using this string, which corresponds to the one in the first PDF.:
  <a href="http://data.bioontology.org/annotator?text=The&#43;patient&#43;has&#43;no&#43;sign&#43;of&#43;melanoma,&#43;but&#43;his&#43;father&#43;had&#43;history&#43;of&#43;skin&#43;cancer.&amp;ontologies=MESH&amp;longest_only=true&amp;exclude_numbers=false&amp;whole_word_only=true&amp;exclude_synonyms=false&amp;expand_mappings=false&amp;negation=true&amp;experiencer=true&amp;temporality=true&amp;lemmatize=false&amp;score=cvalue&amp;semantic_groups=DISO&amp;display_links=false&amp;display_context=false&amp;apikey=4a5011ea-75fa-4be6-8e89-f45c8c84844e" class="">http://data.bioontology.org/annotator?text=The+patient+has+no+sign+of+melanoma,+but+his+father+had+history+of+skin+cancer.&ontologies=MESH&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=false&negation=true&experiencer=true&temporality=true&lemmatize=false&score=cvalue&semantic_groups=DISO&display_links=false&display_context=false&apikey=4a5011ea-75fa-4be6-8e89-f45c8c84844e

This did not produce the expected results—my construction may be wrong—so we'll have to see what's happening at the moment. Sorry for the inconvenience!

John


On Jun 20, 2019, at 2:28 AM, Andon Tchechmedjiev <[hidden email]> wrote:

Dear Rayyan, 

Having developed much of the current Annotator+ extension, I also have a simple python package to query the extended API. 

An usage example is given in the README. Although you can't install it with pip yet, you can copy the "client" directory into your project to use the package. 

Please don't hesitate if you have further interrogations.

Best Regards, 
Andon Tchechmedjiev



On 20/06/2019 10:16, Rayyan Aziz Ansari wrote:
Hi everyone, can the new Bio Annotator plus platform be called from a Python API as was the case previously?
I just checked the Api documentation, and it does not seem to be updated to reflect the new query parameters like 
"UMLS semantic groups" or negation etc. Could you please let me know if there is a timeline
for when I could use an api for these new features?
Thanks you for your time,
Rayyan


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
-- 
Andon Tchechmedjiev, PhD. Associate Professor in NLP, Comp. Ling and Biomedical Informatics
at Ecole des Mines d'Alès-LGI2P, Site Croupillac, 7 rue Jules Renard, Alès - 30319 Cedex FRANCE | andon.tchechmedjiev.eu 
_______________________________________________
bioontology-support mailing list
[hidden email]
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


_______________________________________________
bioontology-support mailing list
[hidden email]
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



_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support