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[bioontology-support] [BioPortal] Feedback from Lynn Schriml

Schriml, Lynn lschriml at som.umaryland.edu
Wed Nov 18 11:36:36 PST 2020


Thank you Michael !!


________________________________
From: Michael Dorf <mdorf at stanford.edu>
Sent: Wednesday, November 18, 2020 1:05 PM
To: Schriml, Lynn <lschriml at som.umaryland.edu>
Cc: John Graybeal <jgraybeal at stanford.edu>; NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Lynn Schriml

Hi Lynn,

We have a few ideas in the works on how to improve our tree display, but at the moment we’re short staffed and tightly financed. At this point, "what you see is what you get” is the best I can offer, sorry. We’ll keep you posted on any new features that affect the tree display in the future.

Thank you again for your input!

Michael

On Nov 18, 2020, at 6:51 AM, Schriml, Lynn <lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>> wrote:

Thank you Michael,
Makes sense.

Can you display the Protege inferred view ?

Cheers,
Lynn
________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Tuesday, November 17, 2020 5:02 PM
To: Schriml, Lynn <lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Lynn Schriml

Hi Lynn,

We use OWL API to process ontologies into our system, and our tree display is generally consistent with that of the Protege class hierarchy browser, so I’m afraid the answer in this case would be NO.

<Screen Shot 2020-11-17 at 1.52.44 PM.png>

Your own DOID browser possibly uses an algorithm to filter out all specific terms from the tree display. Unfortunately, ours has to be generic enough to handle multiple ontologies and terminologies, so it wouldn’t be straightforward on our end to filter out the same classes for DOID only.

Please keep us posted if you run into any other issues with BioPortal.

Thank you,

----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------


On Nov 17, 2020, at 6:15 AM, Schriml, Lynn <lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>> wrote:

Hello John,
  When we open the doid.owl file in our browser,
the upper level DO terms are displayed (see attachment).

Is it possible to show this same view in the BioPortal ?

Cheers,
Lynn

________________________________
From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Tuesday, November 17, 2020 2:45 AM
To: Schriml, Lynn <lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Lynn Schriml

Lynn,

It looks like the new ontology is parsed, has the new metrics, and produces the new values.

Can you have a look and let me know if anything seems amiss?

Also, if you can drop me a line when the next update happens, or just check BioPortal the next day and see if it has updated correctly, I'd appreciate it.

Thanks for checking up on BioPortal, appreciate it!

John

On Nov 16, 2020, at 12:12 PM, Schriml, Lynn <lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>> wrote:

Hello John,
Either is fine with me.

Much appreciated !!
Cheers,
Lynn
________________________________
From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Monday, November 16, 2020 1:39 PM
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Schriml, Lynn <lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Lynn Schriml

Lynn,

can you give us the IRI that you want us to use?  I would expect it's either of these:
- https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/main/src/ontology/doid.owl<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FDiseaseOntology%2FHumanDiseaseOntology%2Fmain%2Fsrc%2Fontology%2Fdoid.owl&data=04%7C01%7Clschriml%40som.umaryland.edu%7C0dfca6d8d0e64a8c7ca008d88bec8de4%7C717009a620de461a88940312a395cac9%7C0%7C1%7C637413196208670244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=hK6T5IbQ4viEN0KgjCW7sA3GGcp3LoMeKdzA0W74oPw%3D&reserved=0>
- http://purl.obolibrary.org/obo/doid.owl<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdoid.owl&data=04%7C01%7Clschriml%40som.umaryland.edu%7C0dfca6d8d0e64a8c7ca008d88bec8de4%7C717009a620de461a88940312a395cac9%7C0%7C1%7C637413196208670244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=e0%2F%2B4RI4jDW%2BkWXnNuzM3P8mPezYEZRwNuV%2BvgnAwcM%3D&reserved=0>

It appears we may have been configured to use the first one, but with 'master' in the IRI instead of 'main'.

I'm also taking the liberty of updating the Homepage and Documentation metadata.

John

On Nov 13, 2020, at 3:22 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Lynn Schriml
Email: lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=04%7C01%7Clschriml%40som.umaryland.edu%7C0dfca6d8d0e64a8c7ca008d88bec8de4%7C717009a620de461a88940312a395cac9%7C0%7C1%7C637413196208680243%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=sFy8vcMFtBC6Rv22gnSMbttXU56ZonEWn1NESCdSKy8%3D&reserved=0>%2Fontologies%2FDOID

Feedback:
Hello, I noticed that the Human Disease Ontology has not been updated in the Bioportal since 2018. We update the DO’s GitHub releases at least once a month.
Is there a problem with the ontology file ?
Thank you,
Lynn Schriml
lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>
PI Human Disease Ontology

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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

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