From support at bioontology.org  Tue Jun  4 07:16:49 2019
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 04 Jun 2019 07:16:49 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Craig DuTremble
Message-ID: <5cf67d51aa42_16c92b13df5ac6e8613c7@ncbo-prd-app-08.stanford.edu.mail>

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From walsbr at ohsu.edu  Tue Jun  4 10:30:52 2019
From: walsbr at ohsu.edu (Brian Walsh)
Date: Tue, 4 Jun 2019 17:30:52 +0000
Subject: [bioontology-support] MONDO ontology submission 39 empty on
 bioontology? (http://data.bioontology.org/ontologies/MONDO/classes)
Message-ID: <E7A763C6-99A5-4ADB-85F1-67BE27470C47@ohsu.edu>


Receiving 404 errors attempting to look up a MONDO class by id

curl http://data.bioontology.org/ontologies/MONDO/classes/MONDO:0004992/ancestors?apikey=XXXXXXXXX
{"errors":["Resource 'MONDO:0004992' not found in ontology MONDO submission 39"],"status":404}

When I examine

http://data.bioontology.org/ontologies/MONDO/classes

It looks like all pages are empty?


Thanks very much,

-Brian


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From c.cruschi at elif.it  Tue Jun  4 09:31:22 2019
From: c.cruschi at elif.it (Claudio Cruschi)
Date: Tue, 4 Jun 2019 18:31:22 +0200
Subject: [bioontology-support] Help for Bioportal
Message-ID: <9bfb7c45-b398-33ab-35d7-c7b121c8a93d@elif.it>

Hi

I have some problems with configuration of email for "reset password" 
functionality. In ontologies_api project, I modified the smtp 
configuration (config\environments\appliance.rb) as below:

config.enable_notifications =true
config.email_sender ="myemail at mydomain.eu"# Default sender for emails
config.email_override ="myemail at mydomain.eu"# all email gets sent here. 
Disable with email_override_disable.
config.email_disable_override =true
config.smtp_host ="my_smtp_server"
config.smtp_port =465
config.smtp_auth_type =:login# :none, :plain, :login, :cram_md5
config.smtp_domain ="mydomain.eu"
config.smtp_user ="myusername"
config.smtp_password ="mypassword"

but when I try to deploy it on virtual appliance (I copied new project 
folder in ontologies_api/releases and I created the current s-link to 
this one) and run bprestart command something goes wrong; in particular 
unicorn does not start. Additionally, the server returns an error 500 
due to a request timeout.

I tried rebooting the virtual appliance; after that, the unicorn runs, 
but the server still returns an error 500.

Could you help me please?

Regards

Claudio



---
Questa e-mail ? stata controllata per individuare virus con Avast antivirus.
https://www.avast.com/antivirus
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From vendetti at stanford.edu  Tue Jun  4 13:20:22 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 4 Jun 2019 20:20:22 +0000
Subject: [bioontology-support] MONDO ontology submission 39 empty on
 bioontology? (http://data.bioontology.org/ontologies/MONDO/classes)
In-Reply-To: <E7A763C6-99A5-4ADB-85F1-67BE27470C47@ohsu.edu>
References: <E7A763C6-99A5-4ADB-85F1-67BE27470C47@ohsu.edu>
Message-ID: <3999F6B7-0B6C-4A2B-B115-6C96E2032384@stanford.edu>

Hello Brian,

Thanks for reporting that. I?ve entered an issue in our tracker so that we can have a look: https://github.com/ncbo/bioportal-project/issues/125.

Apologies for the inconvenience.

Jennifer


On Jun 4, 2019, at 10:30 AM, Brian Walsh <walsbr at ohsu.edu<mailto:walsbr at ohsu.edu>> wrote:


Receiving 404 errors attempting to look up a MONDO class by id

curl http://data.bioontology.org/ontologies/MONDO/classes/MONDO:0004992/ancestors?apikey=XXXXXXXXX
{"errors":["Resource 'MONDO:0004992' not found in ontology MONDO submission 39"],"status":404}

When I examine

http://data.bioontology.org/ontologies/MONDO/classes

It looks like all pages are empty?


Thanks very much,

-Brian


_______________________________________________
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

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From vendetti at stanford.edu  Tue Jun  4 14:50:17 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 4 Jun 2019 21:50:17 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Fred Trotter
In-Reply-To: <5cf0815ec1778_49622b0491c0c9b460481@ncbo-prd-app-08.stanford.edu.mail>
References: <5cf0815ec1778_49622b0491c0c9b460481@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <DEC816B2-5356-4936-BBE3-8AE5602567E0@stanford.edu>

Hi Fred,

I?m not sure I understand what you?re asking. I navigated to the CMT release page to read about these release files: https://www.nlm.nih.gov/research/umls/Snomed/cmt.html. In particular, I downloaded the Vascular Procedures List, which is described as a ?collection of concepts? from Kaiser Permanente?s electronic medical record system. The concepts are stored in Excel format. BioPortal is able to handle ontology submissions in OWL, OBO, and/or SKOS. Were you asking us to convert the spread sheet content to one of these formats?

I also looked at the vocabulary documentation for the latest UMLS Metathesaurus release: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html. It doesn?t appear that they offer CMT as a distinct vocabulary.

Wondering if you might be able to offer a little more detail on what you?d like to see in BioPortal?

Kind regards,
Jennifer



On May 30, 2019, at 6:20 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Fred Trotter

Email: fred.trotter at gmail.com<mailto:fred.trotter at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fsearch%3Fopt%3Dadvanced

Feedback:

any chance you could import and link the Convergent Medical Terminology (CMT) Release Files from Snowmed CT as an ontology?

They are not often updated but it is useful to have mappings to everyday languages..

https://www.nlm.nih.gov/healthit/snomedct/archive.html

Thanks for the amazing app.
-Fred Trotter

_______________________________________________
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From support at bioontology.org  Wed Jun  5 06:44:29 2019
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 05 Jun 2019 06:44:29 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Claudia Pulgarin
Message-ID: <5cf7c73d2f29e_76782ae8f97837fc61364@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Wed Jun  5 16:44:59 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 5 Jun 2019 23:44:59 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Craig DuTremble
In-Reply-To: <5cf67d51aa42_16c92b13df5ac6e8613c7@ncbo-prd-app-08.stanford.edu.mail>
References: <5cf67d51aa42_16c92b13df5ac6e8613c7@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <78E15F41-F1C6-4058-87F2-5CCDA3B54867@stanford.edu>

Hi Craig,

Thank you for reporting that issue, which I?ve entered into our issue tracker:

https://github.com/ncbo/bioportal_web_ui/issues/95

I?m afraid the only workaround for viewing those classes in the BioPortal UI is to navigate to them directly using the tree control, until such time as we?re able to fix this and do a new release.

3342F: Category || Codes -> Diagnostic/Screening Processes or Results -> Mammogram assessment category of "benign," documented (RAD)
3341F: Category || Codes -> Diagnostic/Screening Processes or Results -> Mammogram assessment category of "negative," documented (RAD)

Apologies for the inconvenience.

Kind regards,
Jennifer



On Jun 4, 2019, at 7:16 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Craig DuTremble

Email: cdutremble at partnersbhm.org<mailto:cdutremble at partnersbhm.org>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

Your CPT search seems to be encountering an undefined error when attempting to retrieve codes 3342F and 3341F. I suspect the SQL back-end is having trouble with the apostrophes/glitches in the names of these mammogram services.

_______________________________________________
bioontology-support mailing list
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From fred.trotter at gmail.com  Wed Jun  5 17:31:38 2019
From: fred.trotter at gmail.com (fred trotter)
Date: Wed, 5 Jun 2019 20:31:38 -0400
Subject: [bioontology-support] [BioPortal] Feedback from Fred Trotter
In-Reply-To: <DEC816B2-5356-4936-BBE3-8AE5602567E0@stanford.edu>
References: <5cf0815ec1778_49622b0491c0c9b460481@ncbo-prd-app-08.stanford.edu.mail>
 <DEC816B2-5356-4936-BBE3-8AE5602567E0@stanford.edu>
Message-ID: <CACmAiqaoAk-2iD2DXquPxZesci0gux7uthu+ub0dpkayTpCPkQ@mail.gmail.com>

On Tue, Jun 4, 2019 at 5:50 PM Jennifer Leigh Vendetti
<vendetti at stanford.edu> wrote:
>
> Hi Fred,
>
> I?m not sure I understand what you?re asking. I navigated to the CMT release page to read about these release files: https://www.nlm.nih.gov/research/umls/Snomed/cmt.html. In particular, I downloaded the Vascular Procedures List, which is described as a ?collection of concepts? from Kaiser Permanente?s electronic medical record system. The concepts are stored in Excel format. BioPortal is able to handle ontology submissions in OWL, OBO, and/or SKOS. Were you asking us to convert the spread sheet content to one of these formats?

That would be best for me, as apparently someone has to do it.
Kaiser Permenente supplies the updates to the CMT file to the NIH as a
donated ontology, and perhaps they have the data available in a better
format.
I think I might be able to arrange an introduction, but you are
physically closer to them than me and I suspect you might have better
connections with them than I do.
If you don't have the bandwitdth and we cannot get it by asking KP
nicely, I am willing to (evventually) take this on and write and
release a conversion tool that you might be able to use.

> I also looked at the vocabulary documentation for the latest UMLS Metathesaurus release: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html. It doesn?t appear that they offer CMT as a distinct vocabulary.

Because its job is to link an existing vocabulary to natural language.
I believe that the right way to think about it is that your Snomed CT
work is incomplete because it is not properly decorated with CMT. (75%
sure of this)

>
> Wondering if you might be able to offer a little more detail on what you?d like to see in BioPortal?

There are two killer features here. The first is to see natural
language descriptions of all of the conditions on snomed through
bioportal (I am 95% sure that CMT links to snomed)

The second is to enable your general search functionality to "find"
snomed  codes (and by proxy the other resources that you have embedded
into bioportal) by searching for natural language terms, like "heart
attack" rather than "cardio something blah blah"

Thank you for giving this such careful consideration. No matter what
you decide to do, I very much appreciate the attention.

Regards,
-FT

From vendetti at stanford.edu  Thu Jun  6 15:19:45 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Jun 2019 22:19:45 +0000
Subject: [bioontology-support] MONDO ontology submission 39 empty on
 bioontology? (http://data.bioontology.org/ontologies/MONDO/classes)
In-Reply-To: <3999F6B7-0B6C-4A2B-B115-6C96E2032384@stanford.edu>
References: <E7A763C6-99A5-4ADB-85F1-67BE27470C47@ohsu.edu>
 <3999F6B7-0B6C-4A2B-B115-6C96E2032384@stanford.edu>
Message-ID: <9139C2B6-2451-4C37-B5EA-369192FCE3FC@stanford.edu>

Hi again Brian,

After some initial investigation, it?s apparent that our system is struggling to handle mondo.owl, and diagnosing / fixing the issue isn?t altogether trivial. I?ve uploaded the OBO version of MONDO (mondo.obo) until such time that we?re able to have a more in depth look at the issue. BioPortal processes mondo.obo w/out issue, so the classes are fully available from the UI and/or the REST endpoint, e.g.:

https://bioportal.bioontology.org/ontologies/MONDO?p=classes

http://data.bioontology.org/ontologies/MONDO/classes/

http://data.bioontology.org/ontologies/MONDO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0004992/ancestors<http://data.bioontology.org/ontologies/MONDO/classes/http://purl.obolibrary.org/obo/MONDO_0004992/ancestors>

Jennifer



On Jun 4, 2019, at 1:20 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Brian,

Thanks for reporting that. I?ve entered an issue in our tracker so that we can have a look: https://github.com/ncbo/bioportal-project/issues/125.

Apologies for the inconvenience.

Jennifer


On Jun 4, 2019, at 10:30 AM, Brian Walsh <walsbr at ohsu.edu<mailto:walsbr at ohsu.edu>> wrote:


Receiving 404 errors attempting to look up a MONDO class by id

curl http://data.bioontology.org/ontologies/MONDO/classes/MONDO:0004992/ancestors?apikey=XXXXXXXXX
{"errors":["Resource 'MONDO:0004992' not found in ontology MONDO submission 39"],"status":404}

When I examine

http://data.bioontology.org/ontologies/MONDO/classes

It looks like all pages are empty?


Thanks very much,

-Brian


_______________________________________________
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

_______________________________________________
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

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From vendetti at stanford.edu  Thu Jun  6 15:29:40 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Jun 2019 22:29:40 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Claudia Pulgarin
In-Reply-To: <5cf7c73d2f29e_76782ae8f97837fc61364@ncbo-prd-app-09.stanford.edu.mail>
References: <5cf7c73d2f29e_76782ae8f97837fc61364@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <FB428367-034E-4CC7-AB84-F76D7E1D7A5E@stanford.edu>

Hi Claudia,


On Jun 5, 2019, at 6:44 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Claudia Pulgarin

Email: Claudia.Pulgarin at nyulangone.org<mailto:Claudia.Pulgarin at nyulangone.org>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FRXNORM%3Fp%3Dclasses%26conceptid%3D2582

Feedback:

Hi,
I don't think that a couple of RXNorm CUIs are correct
995226
995230
995940
http://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=2582

You mentioned that you think ?a couple? of the CUIs are incorrect. Are you referring to all four CUI values that you listed above? Or, are there two out of those four that you don?t think belong?

Also, is it possible for you to let us know what resource you?re checking against? If it?s publicly available, it would be helpful if we could have a look.

Thank you,
Jennifer


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From Claudia.Pulgarin at nyulangone.org  Thu Jun  6 15:41:38 2019
From: Claudia.Pulgarin at nyulangone.org (Pulgarin, Claudia)
Date: Thu, 6 Jun 2019 22:41:38 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Claudia Pulgarin
In-Reply-To: <FB428367-034E-4CC7-AB84-F76D7E1D7A5E@stanford.edu>
References: <5cf7c73d2f29e_76782ae8f97837fc61364@ncbo-prd-app-09.stanford.edu.mail>
 <FB428367-034E-4CC7-AB84-F76D7E1D7A5E@stanford.edu>
Message-ID: <cc445e981d884d869f0430b3da489fad@nyulangone.org>

Hi,

Just the ones below.
My resource is private, but you can just google these.

995226
995230
995940

Clauduia

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: June 6, 2019 6:30 PM
To: support at bioontology.org
Cc: Pulgarin, Claudia <Claudia.Pulgarin at nyulangone.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Claudia Pulgarin

Hi Claudia,



On Jun 5, 2019, at 6:44 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Claudia Pulgarin
Email: Claudia.Pulgarin at nyulangone.org<mailto:Claudia.Pulgarin at nyulangone.org>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=9P7wT5Nb_a0pfciVyzD2YQneRcr9ETDaIxUMfDu-QKk&m=9_8AqDCtih3vcRj4ziQyP5-_RFcwJS3nc20UF-b-pKU&s=b4aQm7oy8rqoc00Bo-jYcf9IaQHPHlX20le6yJHVMDE&e=>%2Fontologies%2FRXNORM%3Fp%3Dclasses%26conceptid%3D2582

Feedback:
Hi,
I don't think that a couple of RXNorm CUIs are correct
995226
995230
995940
http://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=2582<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_RXNORM-3Fp-3Dclasses-26conceptid-3D2582&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=9P7wT5Nb_a0pfciVyzD2YQneRcr9ETDaIxUMfDu-QKk&m=9_8AqDCtih3vcRj4ziQyP5-_RFcwJS3nc20UF-b-pKU&s=5wh3ri48CTty7Fv-cCNbH4I142QaJbLhNuFFd3StdkY&e=>

You mentioned that you think ?a couple? of the CUIs are incorrect. Are you referring to all four CUI values that you listed above? Or, are there two out of those four that you don?t think belong?

Also, is it possible for you to let us know what resource you?re checking against? If it?s publicly available, it would be helpful if we could have a look.

Thank you,
Jennifer


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From vendetti at stanford.edu  Thu Jun  6 15:55:13 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Jun 2019 22:55:13 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Claudia Pulgarin
In-Reply-To: <cc445e981d884d869f0430b3da489fad@nyulangone.org>
References: <5cf7c73d2f29e_76782ae8f97837fc61364@ncbo-prd-app-09.stanford.edu.mail>
 <FB428367-034E-4CC7-AB84-F76D7E1D7A5E@stanford.edu>
 <cc445e981d884d869f0430b3da489fad@nyulangone.org>
Message-ID: <916DFC29-53AF-423E-81C9-B16972529E39@stanford.edu>

OK, thank you for the reply. I?ve entered an issue in our tracker: https://github.com/ncbo/umls2rdf/issues/30.

Jennifer


On Jun 6, 2019, at 3:41 PM, Pulgarin, Claudia <Claudia.Pulgarin at nyulangone.org<mailto:Claudia.Pulgarin at nyulangone.org>> wrote:

Hi,

Just the ones below.
My resource is private, but you can just google these.

995226
995230
995940

Clauduia

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: June 6, 2019 6:30 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Pulgarin, Claudia <Claudia.Pulgarin at nyulangone.org<mailto:Claudia.Pulgarin at nyulangone.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Claudia Pulgarin

Hi Claudia,



On Jun 5, 2019, at 6:44 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Claudia Pulgarin
Email: Claudia.Pulgarin at nyulangone.org<mailto:Claudia.Pulgarin at nyulangone.org>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=9P7wT5Nb_a0pfciVyzD2YQneRcr9ETDaIxUMfDu-QKk&m=9_8AqDCtih3vcRj4ziQyP5-_RFcwJS3nc20UF-b-pKU&s=b4aQm7oy8rqoc00Bo-jYcf9IaQHPHlX20le6yJHVMDE&e=>%2Fontologies%2FRXNORM%3Fp%3Dclasses%26conceptid%3D2582

Feedback:
Hi,
I don't think that a couple of RXNorm CUIs are correct
995226
995230
995940
http://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=2582<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_RXNORM-3Fp-3Dclasses-26conceptid-3D2582&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=9P7wT5Nb_a0pfciVyzD2YQneRcr9ETDaIxUMfDu-QKk&m=9_8AqDCtih3vcRj4ziQyP5-_RFcwJS3nc20UF-b-pKU&s=5wh3ri48CTty7Fv-cCNbH4I142QaJbLhNuFFd3StdkY&e=>

You mentioned that you think ?a couple? of the CUIs are incorrect. Are you referring to all four CUI values that you listed above? Or, are there two out of those four that you don?t think belong?

Also, is it possible for you to let us know what resource you?re checking against? If it?s publicly available, it would be helpful if we could have a look.

Thank you,
Jennifer

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From cjmungall at lbl.gov  Thu Jun  6 17:21:52 2019
From: cjmungall at lbl.gov (Chris Mungall)
Date: Thu, 6 Jun 2019 17:21:52 -0700
Subject: [bioontology-support] MONDO ontology submission 39 empty on
 bioontology? (http://data.bioontology.org/ontologies/MONDO/classes)
In-Reply-To: <9139C2B6-2451-4C37-B5EA-369192FCE3FC@stanford.edu>
References: <E7A763C6-99A5-4ADB-85F1-67BE27470C47@ohsu.edu>
 <3999F6B7-0B6C-4A2B-B115-6C96E2032384@stanford.edu>
 <9139C2B6-2451-4C37-B5EA-369192FCE3FC@stanford.edu>
Message-ID: <CAN9AiftRZq7mbERTr+MeARqjmwYyZcx76GkcMArxOa1A6DJo=A@mail.gmail.com>

Simon does the same for OLS, I expect it's the equivalence axioms

On Thu, Jun 6, 2019 at 3:20 PM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi again Brian,
>
> After some initial investigation, it?s apparent that our system is
> struggling to handle mondo.owl, and diagnosing / fixing the issue isn?t
> altogether trivial. I?ve uploaded the OBO version of MONDO (mondo.obo)
> until such time that we?re able to have a more in depth look at the issue.
> BioPortal processes mondo.obo w/out issue, so the classes are fully
> available from the UI and/or the REST endpoint, e.g.:
>
> *https://bioportal.bioontology.org/ontologies/MONDO?p=classes
> <https://bioportal.bioontology.org/ontologies/MONDO?p=classes>*
>
> http://data.bioontology.org/ontologies/MONDO/classes/
>
>
> http://data.bioontology.org/ontologies/MONDO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0004992/ancestors
> <http://data.bioontology.org/ontologies/MONDO/classes/http://purl.obolibrary.org/obo/MONDO_0004992/ancestors>
>
> Jennifer
>
>
>
> On Jun 4, 2019, at 1:20 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu>
> wrote:
>
> Hello Brian,
>
> Thanks for reporting that. I?ve entered an issue in our tracker so that we
> can have a look: https://github.com/ncbo/bioportal-project/issues/125.
>
> Apologies for the inconvenience.
>
> Jennifer
>
>
> On Jun 4, 2019, at 10:30 AM, Brian Walsh <walsbr at ohsu.edu> wrote:
>
>
> Receiving 404 errors attempting to look up a MONDO class by id
>
> curl
> http://data.bioontology.org/ontologies/MONDO/classes/MONDO:0004992/ancestors?apikey=XXXXXXXXX
> {"errors":["Resource 'MONDO:0004992' not found in ontology MONDO
> submission 39"],"status":404}
>
> When I examine
>
> http://data.bioontology.org/ontologies/MONDO/classes
>
> It looks like all pages are empty?
>
>
> Thanks very much,
>
> -Brian
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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From support at bioontology.org  Fri Jun  7 07:27:44 2019
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 07 Jun 2019 07:27:44 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Anneli Karlsson
Message-ID: <5cfa746089ffb_59392af251a0ae2487746@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Jun  7 11:19:12 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 7 Jun 2019 18:19:12 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Anneli Karlsson
In-Reply-To: <5cfa746089ffb_59392af251a0ae2487746@ncbo-prd-app-08.stanford.edu.mail>
References: <5cfa746089ffb_59392af251a0ae2487746@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <1872FF1D-199B-4998-8E36-AD583AB524EE@stanford.edu>

Hi Anneli,

I looked at the log files on our production server and it appears that was an error in the backend on the first attempt to process this new version. I kicked off a reprocessing, which has successfully completed. You should be able to download the CSV representation now.

Kind regards,
Jennifer


On Jun 7, 2019, at 7:27 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Anneli Karlsson

Email: anneli at scibite.com<mailto:anneli at scibite.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FORDO

Feedback:

Hello. I was wondering if you will be providing a csv file for downloading the newest ORDO update soon?
Kind regards
Anneli

_______________________________________________
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

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From joseph.padfield at ng-london.org.uk  Mon Jun 10 06:11:50 2019
From: joseph.padfield at ng-london.org.uk (Joseph Padfield)
Date: Mon, 10 Jun 2019 14:11:50 +0100
Subject: [bioontology-support] Ontoportal Virtual Appliance
Message-ID: <e61031f9-32c0-8998-0c55-8ddadd30868d@ng-london.org.uk>

Hi,

I recently saw a presentation of the BioPortal system, by John Graybeal, 
as part of a Linked Conservation Data meeting in Stanford 
(https://www.ligatus.org.uk/lcd/meeting/terminology).

As part of the meeting we discussed the potential of gathering together 
Ontologies, Vocabularies and Thesauri, related to conservation to form a 
Conservation/Heritage Science portal.

As part of this I would be interested to learn how one might be able to 
get hold of a copy of the VMWare Virtual Appliance for local testing?

I have not had a chance to explore the actual BioPortal too much yet, so 
I will try to do that in the next few weeks, but I did not know how long 
it might take to organise setting up a local copy so I thought I would 
try to initiate this right away.

Thanks

Joe Padfield

-- 
*Joseph Padfield*
Conservation Scientist
Scientific Department
The National Gallery
Trafalgar Square
London WC2N 5DN
+44 (0)20 7747 2553
http://research.ng-london.org.uk
http://www.twitter.com/JoePadfield
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From arkinrd2 at illinois.edu  Mon Jun 10 07:00:16 2019
From: arkinrd2 at illinois.edu (Arkin Dharawat)
Date: Mon, 10 Jun 2019 14:00:16 +0000
Subject: [bioontology-support] Questions about API Rate Limit
Message-ID: <d48c1930-da2f-6a4c-5c29-483281a43652@mixmax.com>

Hi,
I am an Undergraduate Senior at the University of Illinois at Urbana-Champaign.
I am working on a project that involves annotation for medical text and for this
I am using the bio-ontology API.
However, there are a lot of entries and I have to put a timed-wait so I don't
get a time-out. Is there any way you can help me by extending the rate-limit on
my API key? or any other that's possible too.
Best,Arkin DharawatUniversity of Illinois at Urbana-ChampaignMathematics and
Computer Science | Class of 2019
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From jgraybeal at stanford.edu  Mon Jun 10 13:31:11 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 10 Jun 2019 20:31:11 +0000
Subject: [bioontology-support] Questions about API Rate Limit
In-Reply-To: <d48c1930-da2f-6a4c-5c29-483281a43652@mixmax.com>
References: <d48c1930-da2f-6a4c-5c29-483281a43652@mixmax.com>
Message-ID: <76398F43-8327-4968-A67C-D648AEDA0A0E@stanford.edu>

Hi Arkin,


It isn't clear how big an annotation request you have, or how you are structuring your queries right now, so the best I can do is offering a few simple tips.

You can control the ontologies for which the annotations are requested, which should speed up the responses quite a bit.

If you aren't doing it already, you can implement a queuing system, which would keep track of how many submissions have been submitted each second, and also (our request) allow time between the completion of one submission, and the beginning of the next set. It is possible to bring the system down by repeatedly sending 10-15 submissions every second (on top of everything else Bioportal is doing), so we ask heavy users to give the BioPortal system time to respond to other API requests.

Unfortunately, annotations are a somewhat demanding request, so we can't really open up the API to making more requests per second than the existing limit. We generally recommend to people who are doing a lot of API submissions that they request and install the Virtual Appliance, so they can meet their API needs locally.

John


On Jun 10, 2019, at 7:00 AM, Arkin Dharawat <arkinrd2 at illinois.edu<mailto:arkinrd2 at illinois.edu>> wrote:

Hi,

I am an Undergraduate Senior at the University of Illinois at Urbana-Champaign. I am working on a project that involves annotation for medical text and for this I am using the bio-ontology API.

However, there are a lot of entries and I have to put a timed-wait so I don't get a time-out. Is there any way you can help me by extending the rate-limit on my API key? or any other that's possible too.

Best,
Arkin Dharawat
University of Illinois at Urbana-Champaign
Mathematics and Computer Science | Class of 2019

_______________________________________________
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


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From support at bioontology.org  Fri Jun 14 04:08:58 2019
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 14 Jun 2019 04:08:58 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Solene Grosdidier
Message-ID: <5d03804aa9a55_cab2aba8834e91085965@ncbo-prd-app-08.stanford.edu.mail>

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From mdorf at stanford.edu  Fri Jun 14 15:15:38 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 14 Jun 2019 22:15:38 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Solene
	Grosdidier
In-Reply-To: <5d03804aa9a55_cab2aba8834e91085965@ncbo-prd-app-08.stanford.edu.mail>
References: <5d03804aa9a55_cab2aba8834e91085965@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <8C53A84B-F735-4DD6-B864-1C51D26F6E8E@stanford.edu>

Hi Solene,

What you?re describing is a known issue: https://github.com/ncbo/ontologies_linked_data/issues/88.

Background: At some point in the past, we?ve implemented a system that prevents expensive COUNT queries going live against our 4store backend. These queries used to really bog down our servers, often resulting in downtime. The COUNT queries used to be executed on paged REST services, like the one that retrieves all mappings for a given ontology.  So, in order to determine the correct number of pages for a given call, our system used to first execute a COUNT query, storing the result in the output. The new system would pre-cache these counts, so when a paged service call is made, the count would be retrieved from a static repository. Unfortunately, there appears to be a bug in this process that triggers the behavior you are seeing.

For your specific example, it?s best to simply use an iterator to go through ALL pages of available mappings until you hit an empty collection instead of relying on the reported totalCount.

Thanks again for your report. Hope this works as a workaround for what you are trying to accomplish.

Michael


On Jun 14, 2019, at 4:08 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Solene Grosdidier

Email: s.grosdidier at erasmusmc.nl<mailto:s.grosdidier at erasmusmc.nl>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fmappings

Feedback:

Dear Bioportal team,

I am trying to retrieve all the mappings available in Bioportal between SNOMEDCT and NCIT through the API. Unfortunately, after the 321st page, I do get empty json for the following pages (reproducible on 2 different computers). Below is a copy-paste of my script.

#---------------------------------------------------------------------------------------------------------

#!/usr/bin/python3

import urllib.request, urllib.error, urllib.parse
import simplejson as json
import requests
REST_URL = "http://data.bioontology.org"
API_KEY = "2c84c2c2-3510-46fa-b7af-732659784401"

def get_json(url):
opener = urllib.request.build_opener()
opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
return json.loads(opener.open(url).read())
#print(REST_URL + "/mappings?ontologies=MEDDRA,SNOMEDCT")
mapping = get_json(REST_URL+"/mappings?ontologies=NCIT,SNOMEDCT")
#print(json.dumps(mapping,indent=4))

pages = mapping["pageCount"]

print(str(pages))
for i in range (1,pages+1):
print("page: " + str(i))
mapping2 = get_json(REST_URL+"/mappings?ontologies=NCIT%2CSNOMEDCT&page=" + str(i))
#print(json.dumps(mapping2,indent=4))
try:
for element in mapping2["collection"]:
print(element["source"] + "\t" + element["classes"][0]["@id"]+ "\t" + element["classes"][1]["@id"])
except:
print("NO COLLECTION")
#-------------------------------------------------------------------------------------------------------------

Can you help me understanding what is happening?
Thank you very much for your help. I am looking forward to hearing from you.

Best,
Solene Grosdidier

_______________________________________________
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

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From s.grosdidier at erasmusmc.nl  Sun Jun 16 22:54:56 2019
From: s.grosdidier at erasmusmc.nl (S. Grosdidier)
Date: Mon, 17 Jun 2019 05:54:56 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Solene
 Grosdidier
In-Reply-To: <8C53A84B-F735-4DD6-B864-1C51D26F6E8E@stanford.edu>
References: <5d03804aa9a55_cab2aba8834e91085965@ncbo-prd-app-08.stanford.edu.mail>,
 <8C53A84B-F735-4DD6-B864-1C51D26F6E8E@stanford.edu>
Message-ID: <4996CAEF09713448B1483DE5C9D9B7DDFD2933F8@EXCH-HE03.erasmusmc.nl>

Hi Michael,

Thank you very much for your answer.
I am not sure I understand: I already use an iterator to go through all pages of available mappings. 1st empty collection occurs for page number 362. If I cannot rely on the reported totalCount, I should still retrieve those 48243 mappings available between NCIT and SNOMEDCT as indicated in the json response in agreement with the bioportal web browser (https://bioportal.bioontology.org/ontologies/NCIT?p=mappings). Unfortunately, after 361 pages, I get only a subset of the whole information (15953 pairs of NCIT-SNOMEDCT code). Considering the number of pairs I get back per pages, for 48243, number of pages should indeed be 965 (as indicated in the json response).

I had to do the exact same request for mappings between SNOMEDCT and MedDRA on month ago and it unexpectedly worked after several days: my last email to support stayed unanswered and I did believe that somebody did fix that bug at the time.

I understand that this query is heavy and slowing down your servers. The system even seems down this morning (I hope not because of me). Would it be possible to get these mappings in a compressed file temporarily available somewhere for me? I only need the NCIT-SNOMEDCT pair of codes.


I am looking forward to hearing from you.
Best,
Solene




Sol?ne Grosdidier
Scientific Researcher
Department of Medical Informatics

Email:    s.grosdidier at erasmusmc.nl<mailto:s.grosdidier at erasmusmc.nl>
Phone:    +31 (0) 10 704 4879

Mailing address:   P.O.Box 2040 ? 3000 CA
Visiting address:  Wytemaweg 80 ? 3015 CN | Room Na-2609
                          Rotterdam, The Netherlands



________________________________
From: Michael Dorf [mdorf at stanford.edu]
Sent: Saturday, June 15, 2019 12:15 AM
To: support at bioontology.org
Cc: S. Grosdidier
Subject: Re: [bioontology-support] [BioPortal] Feedback from Solene Grosdidier

Hi Solene,

What you?re describing is a known issue: https://github.com/ncbo/ontologies_linked_data/issues/88<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fontologies_linked_data%2Fissues%2F88&data=02%7C01%7Cs.grosdidier%40erasmusmc.nl%7C6696e303c938429907e308d6f115d8e3%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C636961473483005610&sdata=IfJJERKbo7rMyfPoTidwMvnJYAE8q51Cotm2Tio9Kzs%3D&reserved=0>.

Background: At some point in the past, we?ve implemented a system that prevents expensive COUNT queries going live against our 4store backend. These queries used to really bog down our servers, often resulting in downtime. The COUNT queries used to be executed on paged REST services, like the one that retrieves all mappings for a given ontology.  So, in order to determine the correct number of pages for a given call, our system used to first execute a COUNT query, storing the result in the output. The new system would pre-cache these counts, so when a paged service call is made, the count would be retrieved from a static repository. Unfortunately, there appears to be a bug in this process that triggers the behavior you are seeing.

For your specific example, it?s best to simply use an iterator to go through ALL pages of available mappings until you hit an empty collection instead of relying on the reported totalCount.

Thanks again for your report. Hope this works as a workaround for what you are trying to accomplish.

Michael


On Jun 14, 2019, at 4:08 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Solene Grosdidier

Email: s.grosdidier at erasmusmc.nl<mailto:s.grosdidier at erasmusmc.nl>

Location: https%3A%2F%2Fbioportal.bioontology.org<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2F2Fbioportal.bioontology.org&data=02%7C01%7Cs.grosdidier%40erasmusmc.nl%7C6696e303c938429907e308d6f115d8e3%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C636961473483005610&sdata=0G%2FhHL3HvwbbJvOVehaigEt3CO7cxxZhNG96V0Nlsx0%3D&reserved=0>%2Fmappings

Feedback:

Dear Bioportal team,

I am trying to retrieve all the mappings available in Bioportal between SNOMEDCT and NCIT through the API. Unfortunately, after the 321st page, I do get empty json for the following pages (reproducible on 2 different computers). Below is a copy-paste of my script.

#---------------------------------------------------------------------------------------------------------

#!/usr/bin/python3

import urllib.request, urllib.error, urllib.parse
import simplejson as json
import requests
REST_URL = "http://data.bioontology.org<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org&data=02%7C01%7Cs.grosdidier%40erasmusmc.nl%7C6696e303c938429907e308d6f115d8e3%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C636961473483015623&sdata=3SN9OguSrjv0jboRHfC3jvg3ODpNUaSIpH7Mq1AQ0JI%3D&reserved=0>"
API_KEY = "2c84c2c2-3510-46fa-b7af-732659784401"

def get_json(url):
opener = urllib.request.build_opener()
opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
return json.loads(opener.open(url).read())
#print(REST_URL + "/mappings?ontologies=MEDDRA,SNOMEDCT")
mapping = get_json(REST_URL+"/mappings?ontologies=NCIT,SNOMEDCT")
#print(json.dumps(mapping,indent=4))

pages = mapping["pageCount"]

print(str(pages))
for i in range (1,pages+1):
print("page: " + str(i))
mapping2 = get_json(REST_URL+"/mappings?ontologies=NCIT%2CSNOMEDCT&page=" + str(i))
#print(json.dumps(mapping2,indent=4))
try:
for element in mapping2["collection"]:
print(element["source"] + "\t" + element["classes"][0]["@id"]+ "\t" + element["classes"][1]["@id"])
except:
print("NO COLLECTION")
#-------------------------------------------------------------------------------------------------------------

Can you help me understanding what is happening?
Thank you very much for your help. I am looking forward to hearing from you.

Best,
Solene Grosdidier

_______________________________________________
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

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From maleeha18112 at iiitd.ac.in  Sun Jun 16 08:13:49 2019
From: maleeha18112 at iiitd.ac.in (Maleeha Arif Yasvi)
Date: Sun, 16 Jun 2019 20:43:49 +0530
Subject: [bioontology-support] Bulk Downloading Ontologies
Message-ID: <CAJEA6r_2E5LDwvTGmWegw52Lk+Gn9+=qyG2BLR_Mrppuv4-FEg@mail.gmail.com>

Respected Sir/Ma'am,
I am currently doing masters thesis and my topic is related to ontologies.
Is it possible to bulk download the ontologies (downloading all the
ontologies in one go ) from this site?

Eagerly waiting for your reply.

Thank You and Regards
Maleeha Arif Yasvi
Mtech-IIITD
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From jgraybeal at stanford.edu  Mon Jun 17 18:34:53 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 18 Jun 2019 01:34:53 +0000
Subject: [bioontology-support] Bulk Downloading Ontologies
In-Reply-To: <CAJEA6r_2E5LDwvTGmWegw52Lk+Gn9+=qyG2BLR_Mrppuv4-FEg@mail.gmail.com>
References: <CAJEA6r_2E5LDwvTGmWegw52Lk+Gn9+=qyG2BLR_Mrppuv4-FEg@mail.gmail.com>
Message-ID: <8F10446F-77F5-4E21-8164-A31D6D68E9DB@stanford.edu>

Hello Maleeha,

It is possible to download some of the ontologies, namely those that are publicly available for download.

You can download the source file for a given ontology via our REST endpoint, e.g.:

  http://data.bioontology.org/ontologies/BRO/download

Our REST API is documented here:

  http://data.bioontology.org/documentation

To download multiple source files, you can programmatically loop through the ontology objects and download the source file for each.

We provide sample code in multiple languages for using our REST API  in this GitHub repository:

  https://github.com/ncbo/ncbo_rest_sample_code

There is also a Ruby script (referenced in the Virtual Appliance FAQ at https://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_migrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_into_a_new_Appliance.3F) that was built for downloading ontologies into a Bioportal repository.  Even if you don't code in Ruby, it illustrates the API method got get all the ontology information, including the pull location.

  https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb, 

If you want to download the UMLS content, which makes up most of the ontologies that are *not* available for download, you'll have to transform the original content into ontologies yourself using the UMLS2RDF software (https://github.com/ncbo/umls2rdf), using a UMLS key obtained from National Libraries of Medicine (see https://www.nlm.nih.gov/research/umls/). We can not promise this will always work, as sometimes updating the script for the latest UMLS changes may be required. 

John



> On Jun 16, 2019, at 8:13 AM, Maleeha Arif Yasvi <maleeha18112 at iiitd.ac.in> wrote:
> 
> Respected Sir/Ma'am,
> I am currently doing masters thesis and my topic is related to ontologies. Is it possible to bulk download the ontologies (downloading all the ontologies in one go ) from this site?
> 
> Eagerly waiting for your reply.
> 
> Thank You and Regards
> Maleeha Arif Yasvi
> Mtech-IIITD
> 
> _______________________________________________
> bioontology-support mailing list
> 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




From mdorf at stanford.edu  Tue Jun 18 10:45:18 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 18 Jun 2019 17:45:18 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Solene
	Grosdidier
In-Reply-To: <4996CAEF09713448B1483DE5C9D9B7DDFD2933F8@EXCH-HE03.erasmusmc.nl>
References: <5d03804aa9a55_cab2aba8834e91085965@ncbo-prd-app-08.stanford.edu.mail>
 <8C53A84B-F735-4DD6-B864-1C51D26F6E8E@stanford.edu>
 <4996CAEF09713448B1483DE5C9D9B7DDFD2933F8@EXCH-HE03.erasmusmc.nl>
Message-ID: <67ABAD08-32D1-45E3-B0C5-D2F47DF3EDF8@stanford.edu>

Hi Solene,

To clarify, please ignore the pageCount value in your code. Instead, iterate over all the pages for a specific set of ontology mappings. Stop when you encounter an empty page. That simply means there are no more mappings remaining. Example:

http://data.bioontology.org/mappings?ontologies=NCIT%2CSNOMEDCT&page=319<http://data.bioontology.org/mappings?ontologies=NCIT,SNOMEDCT&page=319> - This is the last full page containing the default number of 50 records inside the ?collection? array.
http://data.bioontology.org/mappings?ontologies=NCIT%2CSNOMEDCT&page=320<http://data.bioontology.org/mappings?ontologies=NCIT,SNOMEDCT&page=320> - This page contains only two remaining records inside the ?collection? array.
http://data.bioontology.org/mappings?ontologies=NCIT%2CSNOMEDCT&page=321<http://data.bioontology.org/mappings?ontologies=NCIT,SNOMEDCT&page=321> - The first empty page.

As far as downloading mappings as a file, unfortunately, this isn?t an option at this point. We've had similar requests in the past and have an existing open ticket in Github that tracks this issue:

https://github.com/ncbo/bioportal-project/issues/84

We are a small team, and our development schedule is highly selective. Unfortunately, this issue hasn't yet made it to the top of our priority list.

Thanks,

Michael


On Jun 16, 2019, at 10:54 PM, S. Grosdidier <s.grosdidier at erasmusmc.nl<mailto:s.grosdidier at erasmusmc.nl>> wrote:

Hi Michael,

Thank you very much for your answer.
I am not sure I understand: I already use an iterator to go through all pages of available mappings. 1st empty collection occurs for page number 362. If I cannot rely on the reported totalCount, I should still retrieve those 48243 mappings available between NCIT and SNOMEDCT as indicated in the json response in agreement with the bioportal web browser (https://bioportal.bioontology.org/ontologies/NCIT?p=mappings). Unfortunately, after 361 pages, I get only a subset of the whole information (15953 pairs of NCIT-SNOMEDCT code). Considering the number of pairs I get back per pages, for 48243, number of pages should indeed be 965 (as indicated in the json response).

I had to do the exact same request for mappings between SNOMEDCT and MedDRA on month ago and it unexpectedly worked after several days: my last email to support stayed unanswered and I did believe that somebody did fix that bug at the time.

I understand that this query is heavy and slowing down your servers. The system even seems down this morning (I hope not because of me). Would it be possible to get these mappings in a compressed file temporarily available somewhere for me? I only need the NCIT-SNOMEDCT pair of codes.


I am looking forward to hearing from you.
Best,
Solene




Sol?ne Grosdidier
Scientific Researcher
Department of Medical Informatics
Email:    s.grosdidier at erasmusmc.nl<mailto:s.grosdidier at erasmusmc.nl>
Phone:    +31 (0) 10 704 4879
Mailing address:   P.O.Box 2040 ? 3000 CA
Visiting address:  Wytemaweg 80 ? 3015 CN | Room Na-2609
                          Rotterdam, The Netherlands


________________________________
From: Michael Dorf [mdorf at stanford.edu<mailto:mdorf at stanford.edu>]
Sent: Saturday, June 15, 2019 12:15 AM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: S. Grosdidier
Subject: Re: [bioontology-support] [BioPortal] Feedback from Solene Grosdidier

Hi Solene,

What you?re describing is a known issue: https://github.com/ncbo/ontologies_linked_data/issues/88<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fontologies_linked_data%2Fissues%2F88&data=02%7C01%7Cs.grosdidier%40erasmusmc.nl%7C6696e303c938429907e308d6f115d8e3%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C636961473483005610&sdata=IfJJERKbo7rMyfPoTidwMvnJYAE8q51Cotm2Tio9Kzs%3D&reserved=0>.

Background: At some point in the past, we?ve implemented a system that prevents expensive COUNT queries going live against our 4store backend. These queries used to really bog down our servers, often resulting in downtime. The COUNT queries used to be executed on paged REST services, like the one that retrieves all mappings for a given ontology.  So, in order to determine the correct number of pages for a given call, our system used to first execute a COUNT query, storing the result in the output. The new system would pre-cache these counts, so when a paged service call is made, the count would be retrieved from a static repository. Unfortunately, there appears to be a bug in this process that triggers the behavior you are seeing.

For your specific example, it?s best to simply use an iterator to go through ALL pages of available mappings until you hit an empty collection instead of relying on the reported totalCount.

Thanks again for your report. Hope this works as a workaround for what you are trying to accomplish.

Michael


On Jun 14, 2019, at 4:08 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Solene Grosdidier
Email: s.grosdidier at erasmusmc.nl<mailto:s.grosdidier at erasmusmc.nl>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2F2Fbioportal.bioontology.org&data=02%7C01%7Cs.grosdidier%40erasmusmc.nl%7C6696e303c938429907e308d6f115d8e3%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C636961473483005610&sdata=0G%2FhHL3HvwbbJvOVehaigEt3CO7cxxZhNG96V0Nlsx0%3D&reserved=0>%2Fmappings

Feedback:
Dear Bioportal team,
I am trying to retrieve all the mappings available in Bioportal between SNOMEDCT and NCIT through the API. Unfortunately, after the 321st page, I do get empty json for the following pages (reproducible on 2 different computers). Below is a copy-paste of my script.
#---------------------------------------------------------------------------------------------------------
#!/usr/bin/python3
import urllib.request, urllib.error, urllib.parse
import simplejson as json
import requests
REST_URL = "http://data.bioontology.org<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org&data=02%7C01%7Cs.grosdidier%40erasmusmc.nl%7C6696e303c938429907e308d6f115d8e3%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C636961473483015623&sdata=3SN9OguSrjv0jboRHfC3jvg3ODpNUaSIpH7Mq1AQ0JI%3D&reserved=0>"
API_KEY = "2c84c2c2-3510-46fa-b7af-732659784401"
def get_json(url):
opener = urllib.request.build_opener()
opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
return json.loads(opener.open(url).read())
#print(REST_URL + "/mappings?ontologies=MEDDRA,SNOMEDCT")
mapping = get_json(REST_URL+"/mappings?ontologies=NCIT,SNOMEDCT")
#print(json.dumps(mapping,indent=4))
pages = mapping["pageCount"]
print(str(pages))
for i in range (1,pages+1):
print("page: " + str(i))
mapping2 = get_json(REST_URL+"/mappings?ontologies=NCIT%2CSNOMEDCT&page=" + str(i))
#print(json.dumps(mapping2,indent=4))
try:
for element in mapping2["collection"]:
print(element["source"] + "\t" + element["classes"][0]["@id"]+ "\t" + element["classes"][1]["@id"])
except:
print("NO COLLECTION")
#-------------------------------------------------------------------------------------------------------------
Can you help me understanding what is happening?
Thank you very much for your help. I am looking forward to hearing from you.
Best,
Solene Grosdidier

_______________________________________________
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

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From support at bioontology.org  Tue Jun 18 06:42:55 2019
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 18 Jun 2019 06:42:55 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Pranita Mahajan
Message-ID: <5d08ea5f78a01_70262adb56eea8c05454@ncbo-prd-app-08.stanford.edu.mail>

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From mdorf at stanford.edu  Tue Jun 18 11:06:15 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 18 Jun 2019 18:06:15 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Pranita Mahajan
In-Reply-To: <5d08ea5f78a01_70262adb56eea8c05454@ncbo-prd-app-08.stanford.edu.mail>
References: <5d08ea5f78a01_70262adb56eea8c05454@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <93045965-416C-4AA4-A9AB-B5D5621CCC1F@stanford.edu>

Hi Pranita,

Thank you for contacting us. I don?t know what your planned algorithm is for finding a connection between a symptom and disease, but here are a few BioPortal REST services that may be of help:

All classes of SYMP ontology
?????????????
The default page size is 50. You can iterate over all the pages, processing each symptom individually:
http://data.bioontology.org/ontologies/SYMP/classes

All mappings of SYMP ontology
??????????????
This service may give you possible connections between various symptoms and terms from other ontologies.
http://data.bioontology.org/ontologies/SYMP/mappings

Mappings between two ontologies
???????????????
This particular one is all the mappings between the Symptom and Disease ontologies. It may provide some idea on how these two related
http://data.bioontology.org/mappings?ontologies=SYMP,DOID

You may find some other services that may be of use as well. Here is the link to our REST services documentation:
http://data.bioontology.org/documentation

Unfortunately, we don?t have any resident Python experts on our team, so I can?t provide you with the exact sample code that you require. We do have some examples of Python code that may be of help:
https://github.com/ncbo/ncbo_rest_sample_code/tree/master/python

While they don?t offer the exact scenario you are looking for, they give you an idea on how to connect to our services and use them to extract data you are interested in.

Hope this helps!

Michael



On Jun 18, 2019, at 6:42 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Pranita Mahajan

Email: pranita.mahajan at gmail.com<mailto:pranita.mahajan at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSYMP%3Fp%3Dsummary

Feedback:

I want to read symptom ontology in python and query it to find relation between symptom and disease, for example something like, cold and fever may lead to flu. Will it be possible to do so using available symptom ontology and Python? It will be great help if you can provide resources or related links.

_______________________________________________
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

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From r.ansari at se17.qmul.ac.uk  Thu Jun 20 01:16:03 2019
From: r.ansari at se17.qmul.ac.uk (Rayyan Aziz Ansari)
Date: Thu, 20 Jun 2019 08:16:03 +0000
Subject: [bioontology-support] Annotator plus API compatibility
Message-ID: <VI1PR0702MB3757C4FD4B237156E317F94587E40@VI1PR0702MB3757.eurprd07.prod.outlook.com>

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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From andon.tchechmedjiev at lirmm.fr  Thu Jun 20 02:28:21 2019
From: andon.tchechmedjiev at lirmm.fr (Andon Tchechmedjiev)
Date: Thu, 20 Jun 2019 11:28:21 +0200
Subject: [bioontology-support] Annotator plus API compatibility
In-Reply-To: <VI1PR0702MB3757C4FD4B237156E317F94587E40@VI1PR0702MB3757.eurprd07.prod.outlook.com>
References: <VI1PR0702MB3757C4FD4B237156E317F94587E40@VI1PR0702MB3757.eurprd07.prod.outlook.com>
Message-ID: <f49d9735-ad2b-14c9-7b8c-82643425c15e@lirmm.fr>

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
> bioontology-support at lists.stanford.edu
> 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'Al?s-LGI2P, Site Croupillac, 7 rue Jules Renard, Al?s - 30319 Cedex FRANCE | andon.tchechmedjiev.eu

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From jgraybeal at stanford.edu  Thu Jun 20 18:57:37 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 21 Jun 2019 01:57:37 +0000
Subject: [bioontology-support] Annotator plus API compatibility
In-Reply-To: <f49d9735-ad2b-14c9-7b8c-82643425c15e@lirmm.fr>
References: <VI1PR0702MB3757C4FD4B237156E317F94587E40@VI1PR0702MB3757.eurprd07.prod.outlook.com>
 <f49d9735-ad2b-14c9-7b8c-82643425c15e@lirmm.fr>
Message-ID: <132FB52E-07D2-458F-961E-D8EDF3C1F01E@stanford.edu>

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.:
  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 <andon.tchechmedjiev at lirmm.fr<mailto:andon.tchechmedjiev at lirmm.fr>> wrote:

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
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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'Al?s-LGI2P, Site Croupillac, 7 rue Jules Renard, Al?s - 30319 Cedex FRANCE | andon.tchechmedjiev.eu<http://andon.tchechmedjiev.eu/>

_______________________________________________
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


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From jgraybeal at stanford.edu  Thu Jun 20 19:17:19 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 21 Jun 2019 02:17:19 +0000
Subject: [bioontology-support] Annotator plus API compatibility
In-Reply-To: <132FB52E-07D2-458F-961E-D8EDF3C1F01E@stanford.edu>
References: <VI1PR0702MB3757C4FD4B237156E317F94587E40@VI1PR0702MB3757.eurprd07.prod.outlook.com>
 <f49d9735-ad2b-14c9-7b8c-82643425c15e@lirmm.fr>
 <132FB52E-07D2-458F-961E-D8EDF3C1F01E@stanford.edu>
Message-ID: <F1C8BC65-B00D-4427-9974-FA561A822388@stanford.edu>

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).

<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>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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> 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.:
  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 <andon.tchechmedjiev at lirmm.fr<mailto:andon.tchechmedjiev at lirmm.fr>> wrote:

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
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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'Al?s-LGI2P, Site Croupillac, 7 rue Jules Renard, Al?s - 30319 Cedex FRANCE | andon.tchechmedjiev.eu<http://andon.tchechmedjiev.eu/>

_______________________________________________
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


_______________________________________________
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


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From support at bioontology.org  Sat Jun 22 16:29:53 2019
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 22 Jun 2019 16:29:53 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel
Message-ID: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Sun Jun 23 17:39:27 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 24 Jun 2019 00:39:27 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel
In-Reply-To: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail>
References: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu>

Hi Melissa,

Can you help us with more precise details about your concern?

Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies). These statistics change monthly based on Google metrics for page visits.

The Recommender (https://bioportal.bioontology.org/recommender) makes recommendations based on a number of factors, one of which is the visit-based popularity.

Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric?  I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages.

John

On Jun 22, 2019, at 4:29 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Melissa Haendel

Email: melissa at tislab.org<mailto:melissa at tislab.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies

Feedback:

popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much?

_______________________________________________
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


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From r.ansari at se17.qmul.ac.uk  Mon Jun 24 02:27:58 2019
From: r.ansari at se17.qmul.ac.uk (Rayyan Aziz Ansari)
Date: Mon, 24 Jun 2019 09:27:58 +0000
Subject: [bioontology-support] Commercial License for Annotations needed or
	not
Message-ID: <AM0PR0702MB37462D4FE29BC829EFEF672287E00@AM0PR0702MB3746.eurprd07.prod.outlook.com>

Hi,
I plan to use the Annotator plus to get clinical annotations on doctors notes. I plan to filter/tag using UMLS semantic groups. If i am using this commercially, I am confused about licensing.
Do I have to get a license for ALL possible ontologies that might show up?! that would be unlikely since there are so many.
P.S. I just plan on getting annotations / clinical term recognition and that's all.
Thanks for the information,
Rayyan
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From support at bioontology.org  Mon Jun 24 00:55:35 2019
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 24 Jun 2019 00:55:35 -0700
Subject: [bioontology-support] [BioPortal] Feedback from PARROT
Message-ID: <5d1081f7ae003_19ac2b0141d8cef45765f@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Jun 24 08:02:26 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 24 Jun 2019 15:02:26 +0000
Subject: [bioontology-support] [BioPortal] Feedback from PARROT
In-Reply-To: <5d1081f7ae003_19ac2b0141d8cef45765f@ncbo-prd-app-09.stanford.edu.mail>
References: <5d1081f7ae003_19ac2b0141d8cef45765f@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <85ECDE5F-5C8F-40A4-B5E9-A7C67DFF5B60@stanford.edu>

Hello Adrien,

Thank you for reporting that issue, which I was able to reproduce on our end. The PURL service has been restored, and you should be able to access that URL now.

Apologies for the inconvenience.

Kind regards,
Jennifer


On Jun 24, 2019, at 12:55 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: PARROT

Email: adrien.parrot at caramail.fr<mailto:adrien.parrot at caramail.fr>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSNMI%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FSNMI%252FL-56800

Feedback:

Are you currently experiencing difficulties with the following domain: http://purl.bioontology.org/ontology

I was attempting to access http://purl.bioontology.org/ontology/SURGICAL and received the following error messages:
Proxy Error

The proxy server received an invalid response from an upstream server.
"The proxy server could not handle the request GET /ontology/SURGICAL.

Reason: Error reading from remote server"

I was accessing these resources from https://bioportal.bioontology.org/ontologies/SURGICAL.

_______________________________________________
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

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From jgraybeal at stanford.edu  Mon Jun 24 08:56:04 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 24 Jun 2019 15:56:04 +0000
Subject: [bioontology-support] Commercial License for Annotations needed
 or	not
In-Reply-To: <AM0PR0702MB37462D4FE29BC829EFEF672287E00@AM0PR0702MB3746.eurprd07.prod.outlook.com>
References: <AM0PR0702MB37462D4FE29BC829EFEF672287E00@AM0PR0702MB3746.eurprd07.prod.outlook.com>
Message-ID: <E9277537-AA6C-4C05-A490-2C93B4D68732@stanford.edu>

Rayyan,

Several things must be considered in determining whether you can use BioPortal and its ontologies. The existing BioPortal Terms of Use are at https://ncbo.bioontology.org/terms; if you haven't read them already, please do so. We are about to update these Terms of Use, so members of the community are encouraged to contact us with any requests and concerns.

First, the existing BioPortal Terms of Use do not permit commercial or clinical use of the service. There are several reasons for this:
 1) Our service at Stanford University is not capable of sustaining the level of requests required to satisfy regular commercial users.
 2) It is expensive for us to provide this service, and we can not afford to make it freely available to all those who might want to use it in their commercial pipelines.
 3) We have neither governmental approval in the US, nor the necessary investment in the software and its operations, to make it appropriate to use in clinical settings.

If you have a use case which is commercial but not clinical (in the US regulatory sense of 'clinical'), we encourage you to contact us directly about service licensing terms that we can offer, whether for a service we operate, or for downloading and using our Virtual Appliance.

Note that if you download the Virtual Appliance that addresses issue (1) above, but not issues (2) and (3). It would also give you a way to easily manage which ontologies are used in your service, so you could exclude ones for which you don't have licenses (or don't have a need).

Regarding ontologies, additional information about their use can be read in the Terms of Use agreement. To summarize the key point, if there is no "License Information" field in the Summary page of the ontology, or the License Information field is empty, the ontology is made freely available to the public, and you do not have to worry about 'getting a license'. If there is licensing information provided, you have to look up and follow the terms of that are described or referenced. (Most of the terms refer to the UMLS licensing agreement, which is extremely difficult to parse, but we can't give you advice about that.

Finally, I can not offer legal advice anyway, but I note the interpretation of these terms for users who are not in the United States may require special knowledge. (For one example, the SNOMED licensing is country-based.) So you may want to contact a lawyer to discuss your specific situation.

I am sorry that this is so complicated; I hope that some of it may become less complicated with our new Terms of Use. But for commercial use in a clinical setting, I imagine this will always be complicated (at best), at least in the United States.

John



On Jun 24, 2019, at 2:27 AM, Rayyan Aziz Ansari <r.ansari at se17.qmul.ac.uk<mailto:r.ansari at se17.qmul.ac.uk>> wrote:

Hi,
I plan to use the Annotator plus to get clinical annotations on doctors notes. I plan to filter/tag using UMLS semantic groups. If i am using this commercially, I am confused about licensing.
Do I have to get a license for ALL possible ontologies that might show up?! that would be unlikely since there are so many.
P.S. I just plan on getting annotations / clinical term recognition and that's all.
Thanks for the information,
Rayyan
_______________________________________________
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


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From melissa at tislab.org  Mon Jun 24 19:09:57 2019
From: melissa at tislab.org (Melissa Haendel)
Date: Mon, 24 Jun 2019 19:09:57 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel
In-Reply-To: <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu>
References: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail>
 <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu>
Message-ID: <D832D655-E0CF-4065-B171-5B3AEA776F52@tislab.org>

Hi John,

Nice to see you in my inbox.

We are seeing a lot of variability in the rankings. Also there are some outdated or never-used ontologies on the list higher than some we know are more widely used. Is it simply because of people landing there from Google? 

This is an interesting question- how to monitor usage. I wonder what a longer period might look like, and/or by ontologies for which someone actually opens the graph or downloads the file? 

For openly available ontologies, its a nice metric for popularity that we can use in our grants, but not if the ranking changes frequently and by a lot. 

Anyway, there may well be nothing wrong, its just less useful for this purpose then?

Let me know if you want to brainstorm. 

Cheers,
Melissa 

> On Jun 23, 2019, at 5:39 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
> Hi Melissa,
> 
> Can you help us with more precise details about your concern?
> 
> Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies <https://bioportal.bioontology.org/ontologies>). These statistics change monthly based on Google metrics for page visits.
> 
> The Recommender (https://bioportal.bioontology.org/recommender <https://bioportal.bioontology.org/recommender>) makes recommendations based on a number of factors, one of which is the visit-based popularity. 
> 
> Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric?  I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages.
> 
> John
> 
>> On Jun 22, 2019, at 4:29 PM, support at bioontology.org <mailto:support at bioontology.org> wrote:
>> 
>> Name: Melissa Haendel
>> 
>> Email: melissa at tislab.org <mailto:melissa at tislab.org>
>> Location: https%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fontologies
>> 
>> 
>> Feedback:
>> 
>> popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much?
>> 
>> 
>> _______________________________________________
>> 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
> 
> 

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From jgraybeal at stanford.edu  Mon Jun 24 19:32:57 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 25 Jun 2019 02:32:57 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel
In-Reply-To: <D832D655-E0CF-4065-B171-5B3AEA776F52@tislab.org>
References: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail>
 <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu>
 <D832D655-E0CF-4065-B171-5B3AEA776F52@tislab.org>
Message-ID: <A9BFC16A-70DE-4492-8119-21D9CC48CF6B@stanford.edu>

Hi Melissa,

Concrete examples will be helpful for me to appreciate your perspective. (For example, sometimes outdated ontologies actually get heavy usage for particular reasons, depending on the ontology. But the never-used case seems very strange.)

Yes, I think these rankings are significantly driven by people landing from Google. We have thought about other ways to monitor traffic/value, like downloads, time-on-page, tree view clicks, API calls (weighted for ontology size, since we require people to page through an entire ontology it makes for more calls), and so on.  I think it would be a really interesting exercise to brainstorm all the options with you, and perhaps others to review as well.

We may have historical statistics, I will see what we can put together. I'd like to get a better idea what causes the variation if we can. Possibly we can change the algorithm to use a longer period of time, but no point if the variability has a long cycle.

We'll see if anyone else chimes in on the list on this topic, and I'll let you know offline if/when I get more data.

I should say, we are likely stretched too thin to make any immediate changes unless they are super-easy. But maybe we can get some data you can use for your purposes.

John



On Jun 24, 2019, at 7:09 PM, Melissa Haendel <melissa at tislab.org<mailto:melissa at tislab.org>> wrote:

Hi John,

Nice to see you in my inbox.

We are seeing a lot of variability in the rankings. Also there are some outdated or never-used ontologies on the list higher than some we know are more widely used. Is it simply because of people landing there from Google?

This is an interesting question- how to monitor usage. I wonder what a longer period might look like, and/or by ontologies for which someone actually opens the graph or downloads the file?

For openly available ontologies, its a nice metric for popularity that we can use in our grants, but not if the ranking changes frequently and by a lot.

Anyway, there may well be nothing wrong, its just less useful for this purpose then?

Let me know if you want to brainstorm.

Cheers,
Melissa

On Jun 23, 2019, at 5:39 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hi Melissa,

Can you help us with more precise details about your concern?

Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies). These statistics change monthly based on Google metrics for page visits.

The Recommender (https://bioportal.bioontology.org/recommender) makes recommendations based on a number of factors, one of which is the visit-based popularity.

Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric?  I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages.

John

On Jun 22, 2019, at 4:29 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Melissa Haendel

Email: melissa at tislab.org<mailto:melissa at tislab.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies

Feedback:

popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much?

_______________________________________________
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




========================
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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From melissa at tislab.org  Mon Jun 24 19:42:06 2019
From: melissa at tislab.org (Melissa Haendel)
Date: Mon, 24 Jun 2019 19:42:06 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel
In-Reply-To: <A9BFC16A-70DE-4492-8119-21D9CC48CF6B@stanford.edu>
References: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail>
 <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu>
 <D832D655-E0CF-4065-B171-5B3AEA776F52@tislab.org>
 <A9BFC16A-70DE-4492-8119-21D9CC48CF6B@stanford.edu>
Message-ID: <C9AFD13C-9E2F-498B-8FFA-9891BA89500F@tislab.org>

Hi John,
Well check on the following ones, just for grins and giggles:

HPO (the popular one we care about)
Mondo (the new not so popular one we care about)

Some examples of surprising results:
"Body in numbers project terminology? and ?growth medium ontology? are higher on the list than EFO or Uberon or GO

FoodOn is pretty low down, lower than OGMS (which as far as I know, no one actually uses). FoodOn is quite popular in agriculture and diet domains these days.

I know that ?use? is different than ?visited? or ?searched on Google and found? but I wonder if there is not some combined measure that would actually help understand usage? 

Another example is the Symptom ontology- no one uses this except the Disease ontology developers, but its a common search string. 

Do you see what I mean? Mind you I am not complaining whatsoever, this is just a really hard problem! 
Its more of a philosophical request than an actual one ;-)






> On Jun 24, 2019, at 7:32 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
> Hi Melissa,
> 
> Concrete examples will be helpful for me to appreciate your perspective. (For example, sometimes outdated ontologies actually get heavy usage for particular reasons, depending on the ontology. But the never-used case seems very strange.)
> 
> Yes, I think these rankings are significantly driven by people landing from Google. We have thought about other ways to monitor traffic/value, like downloads, time-on-page, tree view clicks, API calls (weighted for ontology size, since we require people to page through an entire ontology it makes for more calls), and so on.  I think it would be a really interesting exercise to brainstorm all the options with you, and perhaps others to review as well.
> 
> We may have historical statistics, I will see what we can put together. I'd like to get a better idea what causes the variation if we can. Possibly we can change the algorithm to use a longer period of time, but no point if the variability has a long cycle.
> 
> We'll see if anyone else chimes in on the list on this topic, and I'll let you know offline if/when I get more data. 
> 
> I should say, we are likely stretched too thin to make any immediate changes unless they are super-easy. But maybe we can get some data you can use for your purposes. 
> 
> John
> 
> 
> 
>> On Jun 24, 2019, at 7:09 PM, Melissa Haendel <melissa at tislab.org <mailto:melissa at tislab.org>> wrote:
>> 
>> Hi John,
>> 
>> Nice to see you in my inbox.
>> 
>> We are seeing a lot of variability in the rankings. Also there are some outdated or never-used ontologies on the list higher than some we know are more widely used. Is it simply because of people landing there from Google? 
>> 
>> This is an interesting question- how to monitor usage. I wonder what a longer period might look like, and/or by ontologies for which someone actually opens the graph or downloads the file? 
>> 
>> For openly available ontologies, its a nice metric for popularity that we can use in our grants, but not if the ranking changes frequently and by a lot. 
>> 
>> Anyway, there may well be nothing wrong, its just less useful for this purpose then?
>> 
>> Let me know if you want to brainstorm. 
>> 
>> Cheers,
>> Melissa 
>> 
>>> On Jun 23, 2019, at 5:39 PM, John Graybeal <jgraybeal at stanford.edu <mailto:jgraybeal at stanford.edu>> wrote:
>>> 
>>> Hi Melissa,
>>> 
>>> Can you help us with more precise details about your concern?
>>> 
>>> Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies <https://bioportal.bioontology.org/ontologies>). These statistics change monthly based on Google metrics for page visits.
>>> 
>>> The Recommender (https://bioportal.bioontology.org/recommender <https://bioportal.bioontology.org/recommender>) makes recommendations based on a number of factors, one of which is the visit-based popularity. 
>>> 
>>> Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric?  I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages.
>>> 
>>> John
>>> 
>>>> On Jun 22, 2019, at 4:29 PM, support at bioontology.org <mailto:support at bioontology.org> wrote:
>>>> 
>>>> Name: Melissa Haendel
>>>> 
>>>> Email: melissa at tislab.org <mailto:melissa at tislab.org>
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fontologies
>>>> 
>>>> 
>>>> Feedback:
>>>> 
>>>> popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much?
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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 <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
>>> 
>>> 
>> 
> 
> ========================
> 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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From swt at stanford.edu  Mon Jun 24 22:35:49 2019
From: swt at stanford.edu (Samson Tu)
Date: Tue, 25 Jun 2019 05:35:49 +0000
Subject: [bioontology-support] MED-RT
Message-ID: <FC420A10-B099-4C14-A11F-65FC10C74E1B@stanford.edu>

Hi,

MED-RT in UMLS is supposed to be a replacement and successor to NDF-RT. Since I use NDF-RT a lot, I am quite pleased that Bioportal finally includes MED-RT. However, instead of a full-featured drug knowledge base/ontology of drug information, MED-RT contains only 127 skeletal classes. What went wrong?

With best regards,
Samson

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From vendetti at stanford.edu  Tue Jun 25 14:01:11 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 25 Jun 2019 21:01:11 +0000
Subject: [bioontology-support] MED-RT
In-Reply-To: <FC420A10-B099-4C14-A11F-65FC10C74E1B@stanford.edu>
References: <FC420A10-B099-4C14-A11F-65FC10C74E1B@stanford.edu>
Message-ID: <D3C06640-52A6-4EC1-9B05-E6E43A8B84D7@stanford.edu>

Hi Samson,

Our Python script that converts UMLS to TTL files didn?t handle MED-RT very well. There?s a ticket GitHub with more details:

https://github.com/ncbo/umls2rdf/issues/27

Unfortunately we haven?t had the bandwidth to investigate this yet. Apologies that we don?t have a better answer for you.

Jennifer



On Jun 24, 2019, at 10:35 PM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

MED-RT in UMLS is supposed to be a replacement and successor to NDF-RT. Since I use NDF-RT a lot, I am quite pleased that Bioportal finally includes MED-RT. However, instead of a full-featured drug knowledge base/ontology of drug information, MED-RT contains only 127 skeletal classes. What went wrong?

With best regards,
Samson

_______________________________________________
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

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From dolzodmaa at gmail.com  Wed Jun 26 09:30:29 2019
From: dolzodmaa at gmail.com (Dolzodmaa Davaasuren)
Date: Wed, 26 Jun 2019 12:30:29 -0400
Subject: [bioontology-support] MedDRA API
Message-ID: <CAJrqdhd5EPKGKusqA90t0Zd8xtCVwenv6RDD_7+3MG=g1fEUgA@mail.gmail.com>

Hi,

I was wondering if BioPortal API support MedDRA term search as it was not
documented in the API Documentation page. If so, can you help me with that?

Thank you,
Dolzodmaa
The Pennsylvania State University
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From vendetti at stanford.edu  Wed Jun 26 11:12:43 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 26 Jun 2019 18:12:43 +0000
Subject: [bioontology-support] MedDRA API
In-Reply-To: <CAJrqdhd5EPKGKusqA90t0Zd8xtCVwenv6RDD_7+3MG=g1fEUgA@mail.gmail.com>
References: <CAJrqdhd5EPKGKusqA90t0Zd8xtCVwenv6RDD_7+3MG=g1fEUgA@mail.gmail.com>
Message-ID: <297A6E30-5DE0-4A07-ADDC-FF47E1DA85D1@stanford.edu>

Hello Dolzodmaa,

Yes, you can use the /search endpoint to search for terms in the MEDDRA ontology. The endpoint accepts an ?ontologies? parameter that allows you to narrow the search results to particular ontologies. To follow is an example API call to search for the term ?cardiac? in MEDDRA:

http://data.bioontology.org/search?q=cardiac&ontologies=MEDDRA

The search endpoint is documented here:

http://data.bioontology.org/documentation#nav_search

? along with the various parameters you can pass.

Kind regards,
Jennifer



On Jun 26, 2019, at 9:30 AM, Dolzodmaa Davaasuren <dolzodmaa at gmail.com<mailto:dolzodmaa at gmail.com>> wrote:

Hi,

I was wondering if BioPortal API support MedDRA term search as it was not documented in the API Documentation page. If so, can you help me with that?

Thank you,
Dolzodmaa
The Pennsylvania State University
_______________________________________________
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

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From vendetti at stanford.edu  Wed Jun 26 14:29:33 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 26 Jun 2019 21:29:33 +0000
Subject: [bioontology-support] MedDRA API
In-Reply-To: <CAJrqdhd=bEq-3oq1W2p+3=tuOynxQGaE3F5tGo9TYTfn0yeGGQ@mail.gmail.com>
References: <CAJrqdhd5EPKGKusqA90t0Zd8xtCVwenv6RDD_7+3MG=g1fEUgA@mail.gmail.com>
 <297A6E30-5DE0-4A07-ADDC-FF47E1DA85D1@stanford.edu>
 <CAJrqdhd=bEq-3oq1W2p+3=tuOynxQGaE3F5tGo9TYTfn0yeGGQ@mail.gmail.com>
Message-ID: <92F9465D-9832-4888-B978-AC82FE6BA121@stanford.edu>

Hello Dolzodmaa,

There are instructions for getting an API key on our wiki:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

Kind regards,
Jennifer


On Jun 26, 2019, at 12:11 PM, Dolzodmaa Davaasuren <dolzodmaa at gmail.com<mailto:dolzodmaa at gmail.com>> wrote:

Dear Jennifer,

Thank you for your reply. It's asking me to provide API key. I have my institutional access to MedDRA but I don't have any API key. How do I request an API key?

Best,
Dolzodmaa

On Wed, Jun 26, 2019 at 2:12 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Dolzodmaa,

Yes, you can use the /search endpoint to search for terms in the MEDDRA ontology. The endpoint accepts an ?ontologies? parameter that allows you to narrow the search results to particular ontologies. To follow is an example API call to search for the term ?cardiac? in MEDDRA:

http://data.bioontology.org/search?q=cardiac&ontologies=MEDDRA

The search endpoint is documented here:

http://data.bioontology.org/documentation#nav_search

? along with the various parameters you can pass.

Kind regards,
Jennifer



On Jun 26, 2019, at 9:30 AM, Dolzodmaa Davaasuren <dolzodmaa at gmail.com<mailto:dolzodmaa at gmail.com>> wrote:

Hi,

I was wondering if BioPortal API support MedDRA term search as it was not documented in the API Documentation page. If so, can you help me with that?

Thank you,
Dolzodmaa
The Pennsylvania State University
_______________________________________________
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


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From alexgarciac at gmail.com  Thu Jun 27 00:55:50 2019
From: alexgarciac at gmail.com (Alexander Garcia Castro)
Date: Thu, 27 Jun 2019 09:55:50 +0200
Subject: [bioontology-support] bioportal and 30gigs ontology
Message-ID: <CALAe=OLK3sx0kJN78A10Dq8kYTomwGsGWoCfGX0hrBnA8HTCEg@mail.gmail.com>

Hi, I would like to run my own installation of bioportal but I have one
ontology that is 30 gigas in size. is this loadable? I cant open it in
protege and if the ontology is parsed on a line by line basis chances are
it wont work. how big can the ontologies in bioportal be? can it load a 30
gigas ontology?

-- 
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
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From support at bioontology.org  Thu Jun 27 05:58:57 2019
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 27 Jun 2019 05:58:57 -0700
Subject: [bioontology-support] [BioPortal] Feedback from ShebaRedCap
Message-ID: <5d14bd91285ba_451b2ad44474681c15d5@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Thu Jun 27 10:31:49 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 27 Jun 2019 17:31:49 +0000
Subject: [bioontology-support] bioportal and 30gigs ontology
In-Reply-To: <CALAe=OLK3sx0kJN78A10Dq8kYTomwGsGWoCfGX0hrBnA8HTCEg@mail.gmail.com>
References: <CALAe=OLK3sx0kJN78A10Dq8kYTomwGsGWoCfGX0hrBnA8HTCEg@mail.gmail.com>
Message-ID: <B93D46A9-7B65-4258-B319-4979701BF5DF@stanford.edu>

Hi Alexander,

We have not successfully loaded a document of that size. I do not believe our current limitation is due to any inherent limitation in BioPortal's software, but has to do with communication limits between BioPortal's modules. Unfortunately we haven't had time to investigate this in detail yet.

However, if you are unable to load the ontology in Protege, it is possible there is a size limitation in the parsing process. I assume you have tried massively increasing the memory allocated to Protege (I think its ontology parsing is heavily dependent on available memory). Have you discussed the Protege loading issue on the Protege mailing list?

If the ontology can be parsed by Protege, I expect we could help you find a workaround that would enable you to upload it into BioPortal's triple store, but it would be a stress test for the entire system that we have not tried yet.

Please contact me offline if you would like to discuss options further, I could provide more technical details if that is of interest.

John



On Jun 27, 2019, at 12:55 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

Hi, I would like to run my own installation of bioportal but I have one ontology that is 30 gigas in size. is this loadable? I cant open it in protege and if the ontology is parsed on a line by line basis chances are it wont work. how big can the ontologies in bioportal be? can it load a 30 gigas ontology?

--
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

_______________________________________________
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


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From vendetti at stanford.edu  Thu Jun 27 13:14:00 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 27 Jun 2019 20:14:00 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ShebaRedCap
In-Reply-To: <5d14bd91285ba_451b2ad44474681c15d5@ncbo-prd-app-08.stanford.edu.mail>
References: <5d14bd91285ba_451b2ad44474681c15d5@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <F6B5D7E6-D032-47DE-8400-35D588F98888@stanford.edu>

Hello Yaron,

There are instructions for getting a BioPortal API key on our wiki:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

Kind regards,
Jennifer



On Jun 27, 2019, at 5:58 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: ShebaRedCap

Email: RedCap.Administrator at sheba.health.gov.il<mailto:RedCap.Administrator at sheba.health.gov.il>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

Hi,
We have Redcap server installed in our organization.
We want to enable searching within a biomedical ontology.
We need to enter API token provide by your site.
Can you send me my API token?

Regards,
Yaron
Sheba Medical Center

_______________________________________________
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

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From alexgarciac at gmail.com  Fri Jun 28 04:41:46 2019
From: alexgarciac at gmail.com (Alexander Garcia Castro)
Date: Fri, 28 Jun 2019 13:41:46 +0200
Subject: [bioontology-support] bioportal and 30gigs ontology
In-Reply-To: <B93D46A9-7B65-4258-B319-4979701BF5DF@stanford.edu>
References: <CALAe=OLK3sx0kJN78A10Dq8kYTomwGsGWoCfGX0hrBnA8HTCEg@mail.gmail.com>
 <B93D46A9-7B65-4258-B319-4979701BF5DF@stanford.edu>
Message-ID: <CALAe=OKVu9ntjKuwn88Gy+m_hUiHN2cOsrC-GaC=pouhiamgmw@mail.gmail.com>

I will start with a test, trying to load a simpler one. Geonames whic is in
RDF and has mostly individuals. Can Bioprotal deal with individuals?

On Thu, Jun 27, 2019 at 7:31 PM John Graybeal <jgraybeal at stanford.edu>
wrote:

> Hi Alexander,
>
> We have not successfully loaded a document of that size. I do not believe
> our current limitation is due to any inherent limitation in BioPortal's
> software, but has to do with communication limits between BioPortal's
> modules. Unfortunately we haven't had time to investigate this in detail
> yet.
>
> However, if you are unable to load the ontology in Protege, it is possible
> there is a size limitation in the parsing process. I assume you have tried
> massively increasing the memory allocated to Protege (I think its ontology
> parsing is heavily dependent on available memory). Have you discussed the
> Protege loading issue on the Protege mailing list?
>
> If the ontology can be parsed by Protege, I expect we could help you find
> a workaround that would enable you to upload it into BioPortal's triple
> store, but it would be a stress test for the entire system that we have not
> tried yet.
>
> Please contact me offline if you would like to discuss options further, I
> could provide more technical details if that is of interest.
>
> John
>
>
>
> On Jun 27, 2019, at 12:55 AM, Alexander Garcia Castro <
> alexgarciac at gmail.com> wrote:
>
> Hi, I would like to run my own installation of bioportal but I have one
> ontology that is 30 gigas in size. is this loadable? I cant open it in
> protege and if the ontology is parsed on a line by line basis chances are
> it wont work. how big can the ontologies in bioportal be? can it load a 30
> gigas ontology?
>
> --
> Alexander Garcia
> https://www.researchgate.net/profile/Alexander_Garcia
> http://www.usefilm.com/photographer/75943.html
> http://www.linkedin.com/in/alexgarciac
>
> _______________________________________________
> bioontology-support mailing list
> 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
>
>
>

-- 
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
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From support at bioontology.org  Fri Jun 28 21:50:28 2019
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 28 Jun 2019 21:50:28 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Lynne Sopchak
Message-ID: <5d16ee14f01d2_70f22b14010992c49878@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Sat Jun 29 10:10:19 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 29 Jun 2019 17:10:19 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Lynne Sopchak
In-Reply-To: <5d16ee14f01d2_70f22b14010992c49878@ncbo-prd-app-08.stanford.edu.mail>
References: <5d16ee14f01d2_70f22b14010992c49878@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <66CD0DE4-7196-483D-99CA-CCCB2375B66B@stanford.edu>

Hello Lynne,

I queried our system for an account associated with your Gmail address, and didn?t get any results. Would you have perhaps registered with a different email address?

I was able to reproduce the error you mention below with new account creation. I will enter a ticket in our issue tracker and we will start looking into this now.

Apologies for the inconvenience.

Kind regards,
Jennifer


On Jun 28, 2019, at 9:50 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Lynne Sopchak

Email: lynne.sopchak at gmail.com<mailto:lynne.sopchak at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500

Feedback:

I am having a difficult time creating an account or signing in to one I thought I created in the past.

I get the following message--
We're sorry but something has gone wrong. We have been notified of this error.

If I created an account please email me my user name and password. If there is a glitch on your end that would be helpful to know also.

Thank you

_______________________________________________
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

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From support at bioontology.org  Sat Jun 29 21:44:07 2019
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 29 Jun 2019 21:44:07 -0700
Subject: [bioontology-support] [SPAM:#] [SPAM:#] [BioPortal] Feedback from
	Margarito Koontz
Message-ID: <5d183e173d374_b3f2b2139b73b647366e@ncbo-prd-app-08.stanford.edu.mail>

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From RedCap.Administrator at sheba.health.gov.il  Sun Jun 30 05:32:58 2019
From: RedCap.Administrator at sheba.health.gov.il (RedCap.Administrator at sheba.health.gov.il)
Date: Sun, 30 Jun 2019 12:32:58 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ShebaRedCap
In-Reply-To: <F6B5D7E6-D032-47DE-8400-35D588F98888@stanford.edu>
References: <5d14bd91285ba_451b2ad44474681c15d5@ncbo-prd-app-08.stanford.edu.mail>
 <F6B5D7E6-D032-47DE-8400-35D588F98888@stanford.edu>
Message-ID: <37E609F3B74B4E498366A599649D7C9601F8F3D5F0@SBWNEX02D.sheba.gov.il>

Hi Jennifer.
I tried to insert the key and got an error message:

[cid:image001.jpg at 01D52F59.17B12DA0]


Regards,
Yaron

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Thursday, June 27, 2019 11:14 PM
To: support at bioontology.org
Cc: RedCap Administrator <RedCap.Administrator at sheba.health.gov.il>
Subject: Re: [bioontology-support] [BioPortal] Feedback from ShebaRedCap

Hello Yaron,

There are instructions for getting a BioPortal API key on our wiki:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

Kind regards,
Jennifer




On Jun 27, 2019, at 5:58 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: ShebaRedCap
Email: RedCap.Administrator at sheba.health.gov.il<mailto:RedCap.Administrator at sheba.health.gov.il>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:
Hi,
We have Redcap server installed in our organization.
We want to enable searching within a biomedical ontology.
We need to enter API token provide by your site.
Can you send me my API token?
Regards,
Yaron
Sheba Medical Center

_______________________________________________
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

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From vendetti at stanford.edu  Sun Jun 30 07:12:27 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sun, 30 Jun 2019 14:12:27 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ShebaRedCap
In-Reply-To: <37E609F3B74B4E498366A599649D7C9601F8F3D5F0@SBWNEX02D.sheba.gov.il>
References: <5d14bd91285ba_451b2ad44474681c15d5@ncbo-prd-app-08.stanford.edu.mail>
 <F6B5D7E6-D032-47DE-8400-35D588F98888@stanford.edu>
 <37E609F3B74B4E498366A599649D7C9601F8F3D5F0@SBWNEX02D.sheba.gov.il>
Message-ID: <9C0BD1D2-0091-4CA0-BFAB-7EF9BE4811A8@stanford.edu>

Hello Yaron,

I assume you are using the account with username ?ShebaRedCap?? I looked up this account and associated API key in our system. I issued a CURL command to our REST API to retrieve data for a particular ontology using your API key, e.g.:

curl -H "Authorization: apikey token=your_api_key_here" http://data.bioontology.org/ontologies/BRO

(I removed your API key from the example call above for security purposes). The call returned data for me with no issues. I am not seeing a problem on our end with your API key.

One thing you could do on your end to test your API key would be to open a browser window and try using your API key to retrieve data for an ontology. For example, you could enter the following REST call in your browser?s address bar:

http://data.bioontology.org/ontologies/SNOMEDCT?apikey=

You would need to enter your API key at the end of that URL.

Kind regards,
Jennifer



On Jun 30, 2019, at 5:32 AM, RedCap.Administrator at sheba.health.gov.il<mailto:RedCap.Administrator at sheba.health.gov.il> wrote:

Hi Jennifer.
I tried to insert the key and got an error message:

<image001.jpg>


Regards,
Yaron

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Thursday, June 27, 2019 11:14 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: RedCap Administrator <RedCap.Administrator at sheba.health.gov.il<mailto:RedCap.Administrator at sheba.health.gov.il>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from ShebaRedCap

Hello Yaron,

There are instructions for getting a BioPortal API key on our wiki:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

Kind regards,
Jennifer




On Jun 27, 2019, at 5:58 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: ShebaRedCap
Email: RedCap.Administrator at sheba.health.gov.il<mailto:RedCap.Administrator at sheba.health.gov.il>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2F

Feedback:
Hi,
We have Redcap server installed in our organization.
We want to enable searching within a biomedical ontology.
We need to enter API token provide by your site.
Can you send me my API token?
Regards,
Yaron
Sheba Medical Center

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