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[bioontology-support] NCBO Virtual Appliance configuration with RadLex

Kulkarni, Rushikesh RushikeshKulkarni at mednet.ucla.edu
Thu Nov 5 11:49:58 PST 2020


Hi Clement,

Thanks for all the information! I tried few failing negation scenarios and it seems to work perfectly with new changes.
Do you know how soon new version of VA along with LIRMM sync will be available?

Meanwhile, I will go through annotator project as well as  web_ui project and try to integrate into our locally running VA.
If I understood correctly, I need to integrate following two projects into currently running VA.

1.       Annotators- https://github.com/ontoportal-lirmm/annotators

2.       Web UI- https://github.com/ontoportal-lirmm/bioportal_web_ui
Right?

Once again, Thanks for all your help!

Regards,
Rushi

From: Clement Jonquet <jonquet at lirmm.fr>
Sent: Thursday, November 5, 2020 9:20 AM
To: Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu>
Cc: Michael Dorf <mdorf at stanford.edu>; John Graybeal <jgraybeal at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex


CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
Hi Rushi,

I am responding as this is related to the AnnotatorPlus.

First, I need to inform you that we have done significant change on this component on our installation of BioPortal at LIRMM.
Basically we updated the code to the latest version of NegEx called FastContext.
 https://github.com/jianlins/FastContext<https://urldefense.com/v3/__https:/github.com/jianlins/FastContext__;!!F9wkZZsI-LA!QPd7hCvlFsyKgmTMFEFg8VPaJapaKEoFtZUtVlMK97NaHjpuLF1WF7p3NV5vXCQgkvetlqS7V5To$>

The new code seems to fixe the issue you encounter.
You can test it here :
http://bioportal.lirmm.fr/ncbo_annotatorplus<https://urldefense.com/v3/__http:/bioportal.lirmm.fr/ncbo_annotatorplus__;!!F9wkZZsI-LA!QPd7hCvlFsyKgmTMFEFg8VPaJapaKEoFtZUtVlMK97NaHjpuLF1WF7p3NV5vXCQgkvetlsj6mvZ1$>
:
[cid:image001.png at 01D6B364.9A127250]

 Is there any way I can make changes to negation pipeline (NegEx)? Or integrate different negation pipeline?
The code is here: https://github.com/ontoportal-lirmm/annotators<https://urldefense.com/v3/__https:/github.com/ontoportal-lirmm/annotators__;!!F9wkZZsI-LA!QPd7hCvlFsyKgmTMFEFg8VPaJapaKEoFtZUtVlMK97NaHjpuLF1WF7p3NV5vXCQgkvetlmTR7paP$>
You can easily change it and customize the trigger term list… see explanation for French here :
https://github.com/practikpharma/FrenchFastContext<https://urldefense.com/v3/__https:/github.com/practikpharma/FrenchFastContext__;!!F9wkZZsI-LA!QPd7hCvlFsyKgmTMFEFg8VPaJapaKEoFtZUtVlMK97NaHjpuLF1WF7p3NV5vXCQgkvetljzXRFZ4$>
Actually customizing the trigger list is mandatory of you really want to have good result with the Context algorithm

HOWEVER
The latest version of the « annotators » project is not the one integrated in the NCBO BioPortal nor in the latest VA that you are using with RadLex.
We have not done the migration with Stanford to the latest code.

So if you really need this now in your own appliance:
- check out our annotators project
- you might also need to check out the corresponding UI page in the web_ui project in the same repo as the UI page goes of course with what the API is doing.

Or, you wait a bit longer for us to sync the code with Stanford and then include this in next version of the VA.
In the meantime you can use our box at LIRMM.

Am I clear ?
Sorry if not. I do it again ;)

Bye
Clement

-------------------------------------------------------------------------------------------
Dr. Clement JONQUET  –  PhD in Informatics
Associate Research Scientist – INRAE (MISTEA)
Associate Professor – University of Montpellier (LIRMM)
-------------------------------------------------------------------------------------------




Le 4 nov. 2020 à 20:59, Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>> a écrit :

Hi Michael,

I hope you are doing well!
I am currently trying to integrate AnnotatorPlus API into one of our application and wanted to check with you about AnnotatorPlus Negation. Is there any way I can make changes to negation pipeline (NegEx)? Or integrate different negation pipeline?
The negation detector is working perfectly for most of the time, but I came across certain scenarios where it did not give expected results.
For example, ‘No evidence of neoplasm’ actually returned ‘Affirmed Neoplasm’. (Attached annotations screenshot for reference.)

Thanks in advance!

Regards,
Rushi

From: Kulkarni, Rushikesh
Sent: Monday, October 12, 2020 2:08 PM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: RE: [bioontology-support] NCBO Virtual Appliance configuration with RadLex

Thanks Michael! It worked.

Regards,
Rushi

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Monday, October 12, 2020 10:02 AM
To: Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex

CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
Hi Rushi,

This is what we have set in our own version of NCIT:

Preferred Name:
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P108<https://urldefense.com/v3/__http:/ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl*P108__;Iw!!F9wkZZsI-LA!XEDmE5Zy4WUVnrJ1jCxtA0sx5i3G7s_S4og7T36_c56gLc0z0IcwwXDVU0zPRJJyieFVuNap-cgp$>

Synonym:
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90<https://urldefense.com/v3/__http:/ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl*P90__;Iw!!F9wkZZsI-LA!XEDmE5Zy4WUVnrJ1jCxtA0sx5i3G7s_S4og7T36_c56gLc0z0IcwwXDVU0zPRJJyieFVuPTgVq39$>

Definition:
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97<https://urldefense.com/v3/__http:/ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl*P97__;Iw!!F9wkZZsI-LA!XEDmE5Zy4WUVnrJ1jCxtA0sx5i3G7s_S4og7T36_c56gLc0z0IcwwXDVU0zPRJJyieFVuPNg0pJb$>

Let us know if that works.

Thanks!

Michael

<image001.png>

On Oct 9, 2020, at 12:07 PM, Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>> wrote:

Hi Michael,

I hope you are doing well! I am trying to configure NCIT (National Cancer Institute Thesaurus) into locally running bioportal. Do I have to setup any ‘advanced OWL options’ to configure Synonyms?
So far I have imported latest NCIT OWL and successfully parsed/indexed. There is ‘FULL_SYN’ property in class structure which represents synonyms. But, I don’t see actual ‘Synonyms’ property.

Thanks in advance!

Regards,
Rushi Kulkarni
UCLA Health

From: Kulkarni, Rushikesh
Sent: Thursday, October 1, 2020 2:55 PM
To: 'Michael Dorf' <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: RE: [bioontology-support] NCBO Virtual Appliance configuration with RadLex

Thanks Michael for all you help! I was able to login with admin credentials.

Regards,
Rushi

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, September 30, 2020 4:57 PM
To: Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex

CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
Hi Rushi,

Please see my responses embedded below.

Thanks,

Michael


On Sep 30, 2020, at 3:07 PM, Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>> wrote:

Hi Michael,

Thank you for your prompt reply! I followed your steps and able to set RadLex’s preferred name and other properties.

I am fairly new to NCBO virtual appliance and have some questions regarding appliance ID and its registration. Would you be able to answer it?
Here are my questions,
1.       How do I get the appliance ID required to register appliance? I tried http://{my-appliance-hostname}/admin#licensing<https://urldefense.proofpoint.com/v2/url?u=http-3A__-257Bmy-2Dappliance-2Dhostname-257D_admin-23licensing&d=DwQGaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=-JCQVo9x1iKRAvSAaweeL1Cw_XQukHx2zK2mrM1Q6HrkKy0K6qFLZA-6m2aPkjMk&m=cwA3tU8Mnb3onzvyyMk4JVD9GGoh8IQl3dwtKmNOzdo&s=sztMOWPWNrpGkLuZTEnb5TQd9nkW7Dfr-xW4zXYaOFs&e=> but, it took me to login page.

That’s the correct URL. Just login with your default admin credentials and you should see your Appliance ID there:


  *   Username: admin
  *   Password: changemeNOW
I encourage you to review our Virtual Appliance documentation. All of these answers can be found there:

https://ontoportal.github.io/administration/steps/initial_installation/<https://urldefense.proofpoint.com/v2/url?u=https-3A__ontoportal.github.io_administration_steps_initial-5Finstallation_&d=DwMGaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=-JCQVo9x1iKRAvSAaweeL1Cw_XQukHx2zK2mrM1Q6HrkKy0K6qFLZA-6m2aPkjMk&m=cwA3tU8Mnb3onzvyyMk4JVD9GGoh8IQl3dwtKmNOzdo&s=qcX1H9HXmdLuP7ukjF6jBYJpVYy8qmrF7RB0QSYfN7U&e=>
https://ontoportal.github.io/administration/steps/registration/<https://urldefense.proofpoint.com/v2/url?u=https-3A__ontoportal.github.io_administration_steps_registration_&d=DwMGaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=-JCQVo9x1iKRAvSAaweeL1Cw_XQukHx2zK2mrM1Q6HrkKy0K6qFLZA-6m2aPkjMk&m=cwA3tU8Mnb3onzvyyMk4JVD9GGoh8IQl3dwtKmNOzdo&s=sokayeEm6obk3cN1TgOGX2dtZCoYkuALoGbO2fglXNI&e=>

2.       Is there any default admin credential which gets created during virtual appliance setup? Or How do I create admin account?

Answered above



Once again, Thank you for all you help.

Regards,
Rushi

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, September 30, 2020 1:29 PM
To: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Cc: Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex

CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
Hi Rushi,

Try setting the Preferred Name, Synonym, and Definition properties under “advanced OWL options” via the “Edit Submission Information” page to these:

<image002.png>

Once you hit “Save Submission”, your ontology should re-process automatically within 15 minutes or so and your tree should appear correctly. If it still doesn’t try re-processing the ontology manually after you’ve set the advanced OWL options.

Let me know if this helps.

Thank you,

Michael




On Sep 30, 2020, at 1:18 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Rushi,

Thanks for the great problem report, I'm sorry for your trouble. We'll look into this right away.

John



On Sep 30, 2020, at 10:32 AM, Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu<mailto:RushikeshKulkarni at mednet.ucla.edu>> wrote:

Hello,

I am trying to integrate Radiology Lexicon ontology with locally running NCBO Virtual appliance. I was able to import RadLax 4.0 OWL using 'Submit Ontology' functionality from Ontoportal UI.
But, somehow class names are not configured correctly. RID0, RID1, RID3 .. etc. are showing up under preferred name and as well as under class tree structure. (attached screenshot for reference)
For example, RID3 is showing under class structure and for Preferred Name field, instead of 'anatomical entity'.
Can you please help me with this issue?

I tried following things to debug the issue,

  1.  Tried to integrate RadLex using Ontoportal UI as well as with bioportal_ontologies_import.rb script.
  2.  Checked parsed ontology status using Rest service and it has following status "submissionStatus": ["RDF","OBSOLETE","INDEXED_PROPERTIES","METRICS","RDF_LABELS","UPLOADED","ANNOTATOR","INDEXED"]
  3.  Imported another ontology (Cell Ontology CL) and it has been set up correctly with no issue. This is just to test my local virtual machine.
Thanks in advance.

Regards,
Rushi Kulkarni
UCLA Health


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