From shaker_elsapagh at yahoo.com  Mon Oct  1 05:32:38 2018
From: shaker_elsapagh at yahoo.com (Shaker El-Sappagh)
Date: Mon, 1 Oct 2018 12:32:38 +0000 (UTC)
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
 El-Sappagh
In-Reply-To: <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu>
References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>
 <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu>
 <2032047650.1906847.1537846277280@mail.yahoo.com>
 <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu>
Message-ID: <960254277.2690608.1538397158535@mail.yahoo.com>

Hello Dr. Jennifer,I hope that you are fine.Please, I have uploaded the ontology after handling the mentioned error. However, the ontology is still not working.Kindly, guide me until the ontology become properly work.
Best Regards.

..........................................................
Shaker El-Sappagh, PhD.
Post-Doctoral FellowUWB Wireless Communications Research Center,
Department of Information and Communication Engineering, 
Inha University, Incheon, South Korea.Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. 
 

    On Friday, September 28, 2018, 10:11:02 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:  
 
 Hello Dr. El-Sappagh,

The error that occurs in our log file is this:

"Illegal Element Name (Element Is Not A QName): http://www.co-ode.org/ontologies/ont.owl#DDO:0000002?

There are 3 occurrences in the FASTO.owl source file of the above URI, where the colon character isn?t allowed in the end fragment (DDO:0000002). The URI will need to be modified to remove the colon character, e.g., you could replace it with an underscore:

 http://www.co-ode.org/ontologies/ont.owl#DDO_0000002

After making this modification, I believe our system will be able to parse the ontology.

Kind regards,
Jennifer



> On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com> wrote:
> 
> Dear Dr. Jennifer,
> Thank you for your kind reply. 
> Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link:
> 
> http://bioportal.bioontology.org/ontologies/FASTO
> 
> Thank you for your support.
> 
> Best Regards. 
> 
> 
> ..........................................................
> Shaker El-Sappagh, PhD.
> Post-Doctoral Fellow
> UWB Wireless Communications Research Center,
> Department of Information and Communication Engineering, 
> Inha University, Incheon, South Korea.
> Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. 
> 
> 
> On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
> 
> 
> Hello Dr. El-Sappagh,
> 
> It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive:
> 
> http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html
> 
> Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system.
> 
> Kind regards,
> Jennifer
> 
> 
> 
>> On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote:
>> 
>> Name: Shaker El-Sappagh
>> 
>> Email: Shaker_elsapagh at yahoo.com
>> 
>> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO
>> 
>> 
>> Feedback:
>> 
>> Please, I have uploaded my FASTO ontology. It has not worked yet.
>> 
>> Best regards .
>> 
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

  
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From vendetti at stanford.edu  Mon Oct  1 08:00:51 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 1 Oct 2018 15:00:51 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
	El-Sappagh
In-Reply-To: <960254277.2690608.1538397158535@mail.yahoo.com>
References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>
 <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu>
 <2032047650.1906847.1537846277280@mail.yahoo.com>
 <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu>
 <960254277.2690608.1538397158535@mail.yahoo.com>
Message-ID: <974CC26B-740B-4A82-99E2-3BA2A99F95FD@stanford.edu>

Hello Dr. El-Sappagh,

Thank you for making the requested changes. The ontology parsing process proceeded further than last time, but there is a new error that I am currently investigating. Apologies that I don?t have it tracked down quite yet. I will update you with more information as soon as I?m able.

Kind regards,
Jennifer



On Oct 1, 2018, at 5:32 AM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com<mailto:shaker_elsapagh at yahoo.com>> wrote:

Hello Dr. Jennifer,
I hope that you are fine.
Please, I have uploaded the ontology after handling the mentioned error. However, the ontology is still not working.
Kindly, guide me until the ontology become properly work.

Best Regards.

..........................................................
Shaker El-Sappagh, PhD.
Post-Doctoral Fellow
UWB Wireless Communications Research Center,
Department of Information and Communication Engineering,
Inha University, Incheon, South Korea.
Email: Shaker_elsapagh at yahoo.com<http://us.mc1126.mail.yahoo.com/mc/compose?to=Shaker_elsapagh at yahoo.com>, sh.elsappagh at gmail.com.


On Friday, September 28, 2018, 10:11:02 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:


Hello Dr. El-Sappagh,

The error that occurs in our log file is this:

"Illegal Element Name (Element Is Not A QName): http://www.co-ode.org/ontologies/ont.owl#DDO:0000002?<http://www.co-ode.org/ontologies/ont.owl#DDO:0000002%E2%80%9D>

There are 3 occurrences in the FASTO.owl source file of the above URI, where the colon character isn?t allowed in the end fragment (DDO:0000002). The URI will need to be modified to remove the colon character, e.g., you could replace it with an underscore:

http://www.co-ode.org/ontologies/ont.owl#DDO_0000002

After making this modification, I believe our system will be able to parse the ontology.

Kind regards,
Jennifer



> On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com<mailto:shaker_elsapagh at yahoo.com>> wrote:
>
> Dear Dr. Jennifer,
> Thank you for your kind reply.
> Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link:
>
> http://bioportal.bioontology.org/ontologies/FASTO
>
> Thank you for your support.
>
> Best Regards.
>
>
> ..........................................................
> Shaker El-Sappagh, PhD.
> Post-Doctoral Fellow
> UWB Wireless Communications Research Center,
> Department of Information and Communication Engineering,
> Inha University, Incheon, South Korea.
> Email: Shaker_elsapagh at yahoo.com<mailto:Shaker_elsapagh at yahoo.com>, sh.elsappagh at gmail.com.<mailto:sh.elsappagh at gmail.com.>
>
>
> On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
>
>
> Hello Dr. El-Sappagh,
>
> It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive:
>
> http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html
>
> Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system.
>
> Kind regards,
> Jennifer
>
>
>
>> On Sep 24, 2018, at 8:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:
>>
>> Name: Shaker El-Sappagh
>>
>> Email: Shaker_elsapagh at yahoo.com<mailto:Shaker_elsapagh at yahoo.com>
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FFASTO
>>
>>
>> Feedback:
>>
>> Please, I have uploaded my FASTO ontology. It has not worked yet.
>>
>> Best regards .
>>
>>
>> _______________________________________________
>> 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  Wed Oct  3 01:54:41 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 03 Oct 2018 01:54:41 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5bb483d1e39b_49802b01733303ac57913@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Tue Oct  2 15:16:30 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 02 Oct 2018 15:16:30 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Cathy Bezek
Message-ID: <5bb3ee3e138e7_45782aada089ba0c647d3@ncbo-prd-app-09.stanford.edu.mail>

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From ritchiej at musc.edu  Tue Oct  2 08:20:48 2018
From: ritchiej at musc.edu (Ritchie, Jordon)
Date: Tue, 2 Oct 2018 15:20:48 +0000
Subject: [bioontology-support] API key
Message-ID: <SN6PR11MB2624ABA87C6C86600A04EFAEAAE80@SN6PR11MB2624.namprd11.prod.outlook.com>

Hi,


I am interested to investigate this  resource but I can't seem to find where to get an API key.


Can you help me?


Thanks,

Jordon




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From mdorf at stanford.edu  Wed Oct  3 14:42:04 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 3 Oct 2018 21:42:04 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5bb483d1e39b_49802b01733303ac57913@ncbo-prd-app-08.stanford.edu.mail>
References: <5bb483d1e39b_49802b01733303ac57913@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <04C133E5-5B7F-4C7B-93C1-D3764BA68D8A@stanford.edu>

Hi Chen,

I see your email from September 19th with three questions. To be honest, I?m not sure why it fell through our radar, but I?ll do my best to address it here. Please see my answers inline in BLUE:

1) I was going to get the permanent link of class "Case studies" in ONE, then I clicked the icon next to "class mappings"but get the ID of "Case studies": "http://purl.bioontology.org/ontology/ONE/standards#caseStudies". I cannot reach the class by the link. Could you please check?

The correct permanent link should be: http://purl.bioontology.org/ontology/ONE?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FONE%2Fstandards%23caseStudies<http://purl.bioontology.org/ontology/ONE?conceptid=http://purl.bioontology.org/ontology/ONE/standards#caseStudies>

It?s a bug in our system that results in a wrong link whenever the default classes view is loaded. Once you click on another class and come back to the original one, the permanent link will be correct. I?ve logged this behavior here:

https://github.com/ncbo/bioportal_web_ui/issues/84

2) But is it possible to set the ID as permanent link? For MeSH ontology, it works (e.g. "http://purl.bioontology.org/ontology/MESH/D000602" can be used to reach the class on BioPortal). The IDs of my Classes also start with "http://purl.bioontology.org/ontology/?.

MeSH is part of a group of UMLS ontologies that we import periodically into our system from a publicly available relational database. The import process generates our own permalinks and handles them accordingly for each ontology in this set. The rest of the ontologies use their original class IDs that are found in the ontology source file. Our uniform permalink structure for ALL ontologies is in the format:

http://purl.bioontology.org/ontology/<ONTOLOGY_ACRONYM>?conceptid=<URL_ENCODED_CONCEPT_ID>

3) For ONE, the mappings are still a problem. I reported it before. https://github.com/ncbo/ontologies_api/issues/50

This remains an open issue.  We?re a small team, so our development schedule is highly selective. Unfortunately, fixing this issue hasn?t hit the top of our priority list to date.

Thanks again for contacting us and sorry about the delay in responding.

Michael



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

On Oct 3, 2018, at 1:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

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

Feedback:

Dear,
I sent my questions 2 weeks ago (17 September, 2018). However, I have not got your answer yet.
Regards,
Chen

_______________________________________________
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 mdorf at stanford.edu  Wed Oct  3 15:18:23 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 3 Oct 2018 22:18:23 +0000
Subject: [bioontology-support] API key
In-Reply-To: <SN6PR11MB2624ABA87C6C86600A04EFAEAAE80@SN6PR11MB2624.namprd11.prod.outlook.com>
References: <SN6PR11MB2624ABA87C6C86600A04EFAEAAE80@SN6PR11MB2624.namprd11.prod.outlook.com>
Message-ID: <32A65A72-D3D3-495B-9FE0-C35D8EE2F8CE@stanford.edu>

Hi Jordon,

There are instructions on our wiki for this:

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

Thanks,

Michael


On Oct 2, 2018, at 8:20 AM, Ritchie, Jordon <ritchiej at musc.edu<mailto:ritchiej at musc.edu>> wrote:

This message was sent securely by MUSC<http://www.musc.edu/>

Hi,

I am interested to investigate this  resource but I can't seem to find where to get an API key.

Can you help me?

Thanks,
Jordon



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From vendetti at stanford.edu  Thu Oct  4 11:47:03 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 4 Oct 2018 18:47:03 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
	El-Sappagh
In-Reply-To: <960254277.2690608.1538397158535@mail.yahoo.com>
References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>
 <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu>
 <2032047650.1906847.1537846277280@mail.yahoo.com>
 <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu>
 <960254277.2690608.1538397158535@mail.yahoo.com>
Message-ID: <FD338285-9DCB-47B9-987B-6EC0E548CD60@stanford.edu>

Hello Dr. El-Sappagh,

I tracked down the issue that prevented our system from parsing your ontology. FASTO.owl has an import statement of:

<Import>http://www.owl-ontologies.com/OntoFood.owl</Import>

The above URL appears to have been hijacked by spammers, and results in a corrupt ontology import where an annotation property contains HTML tags. You can reproduce this behavior in the Protege ontology editor by opening FASTO.owl and using the drop down box at the top of the application to navigate to what should be the OntoFood import. What you see in the application is the failed / mostly empty import with a single annotation property with HTML tags as content:


[cid:2E73723B-4416-4AA4-A7F9-9E5D1EC0B749 at stanford.edu]
BioPortal is unable to load a corrupt import like this into our backend triplestore. As a test, I removed the OntoFood import statement and resubmitted your ontology, which then parsed successfully:

[cid:23F88B49-B3A1-4AC7-9208-A5208B868DC9 at stanford.edu]

I?m not sure if you are the maintainer of OntoFood. One suggestion I have would be to use Protege to change the ontology name (Refactor -> Change ontology IRI?). After doing this, you might also consider merging your ontologies into one OWL file (Refactor -> Merge ontologies?), and upload the resulting merged OWL file to BioPortal.

We've been keeping a detailed account of the parsing problems in our issue tracker:

https://github.com/ncbo/bioportal-project/issues/98

Kind regards,
Jennifer




On Oct 1, 2018, at 5:32 AM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com> wrote:

Hello Dr. Jennifer,
I hope that you are fine.
Please, I have uploaded the ontology after handling the mentioned error. However, the ontology is still not working.
Kindly, guide me until the ontology become properly work.

Best Regards.

..........................................................
Shaker El-Sappagh, PhD.
Post-Doctoral Fellow
UWB Wireless Communications Research Center,
Department of Information and Communication Engineering,
Inha University, Incheon, South Korea.
Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com.


On Friday, September 28, 2018, 10:11:02 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:


Hello Dr. El-Sappagh,

The error that occurs in our log file is this:

"Illegal Element Name (Element Is Not A QName): http://www.co-ode.org/ontologies/ont.owl#DDO:0000002?

There are 3 occurrences in the FASTO.owl source file of the above URI, where the colon character isn?t allowed in the end fragment (DDO:0000002). The URI will need to be modified to remove the colon character, e.g., you could replace it with an underscore:

http://www.co-ode.org/ontologies/ont.owl#DDO_0000002

After making this modification, I believe our system will be able to parse the ontology.

Kind regards,
Jennifer



> On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com> wrote:
>
> Dear Dr. Jennifer,
> Thank you for your kind reply.
> Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link:
>
> http://bioportal.bioontology.org/ontologies/FASTO
>
> Thank you for your support.
>
> Best Regards.
>
>
> ..........................................................
> Shaker El-Sappagh, PhD.
> Post-Doctoral Fellow
> UWB Wireless Communications Research Center,
> Department of Information and Communication Engineering,
> Inha University, Incheon, South Korea.
> Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com.
>
>
> On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
>
>
> Hello Dr. El-Sappagh,
>
> It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive:
>
> http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html
>
> Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system.
>
> Kind regards,
> Jennifer
>
>
>
>> On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote:
>>
>> Name: Shaker El-Sappagh
>>
>> Email: Shaker_elsapagh at yahoo.com
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO
>>
>>
>> Feedback:
>>
>> Please, I have uploaded my FASTO ontology. It has not worked yet.
>>
>> Best regards .
>>
>>
>> _______________________________________________
>> 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  Wed Oct  3 23:46:15 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 03 Oct 2018 23:46:15 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Bharat
Message-ID: <5bb5b73714a02_3efa2aca11cf97ec53632@ncbo-prd-app-09.stanford.edu.mail>

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From sarah.alghamdi.1 at kaust.edu.sa  Thu Oct  4 03:13:45 2018
From: sarah.alghamdi.1 at kaust.edu.sa (Sarah Alghamdi)
Date: Thu, 4 Oct 2018 13:13:45 +0300
Subject: [bioontology-support] Download Ontologies Mappings
Message-ID: <CACaLaUw1ReG2vDLDdBiSfB=d0-FgcWqnN4OdtZMiJNmc1TM3=Q@mail.gmail.com>

Dear team,
I hope this finds you very well,
For my research I want to acquire all the mappings available between pairs
of ontologies from the Bioportal, I'm currently using the REST API and
passing by all the pairs of ontologies, but this is taking me very long
time (might spend months).
would it be possible for you to provide all the mappings in a single
download link?

-- 
Best Regards,

Sarah M. Alghamdi
Computer Science PhD Student - KAUST

Bio-Ontology Research Group (BORG)
<https://borg.kaust.edu.sa/Pages/Home.aspx>

Computational Bioscience Research Center (CBRC)
<http://www.cbrc.kaust.edu.sa/>
Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE)
<https://cemse.kaust.edu.sa/Pages/Home.aspx>

-- 

This message and its contents, including attachments are intended solely 
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From mdorf at stanford.edu  Thu Oct  4 14:19:23 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 4 Oct 2018 21:19:23 +0000
Subject: [bioontology-support] Download Ontologies Mappings
In-Reply-To: <CACaLaUw1ReG2vDLDdBiSfB=d0-FgcWqnN4OdtZMiJNmc1TM3=Q@mail.gmail.com>
References: <CACaLaUw1ReG2vDLDdBiSfB=d0-FgcWqnN4OdtZMiJNmc1TM3=Q@mail.gmail.com>
Message-ID: <B15E99DC-2137-4FF8-AA72-FA3608B7CDE7@stanford.edu>

Hi Sarah,

Unfortunately, at this point, the answer is NO. 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.

Sorry, I couldn?t be of more help.

Michael


On Oct 4, 2018, at 3:13 AM, Sarah Alghamdi <sarah.alghamdi.1 at kaust.edu.sa<mailto:sarah.alghamdi.1 at kaust.edu.sa>> wrote:

Dear team,
I hope this finds you very well,
For my research I want to acquire all the mappings available between pairs of ontologies from the Bioportal, I'm currently using the REST API and passing by all the pairs of ontologies, but this is taking me very long time (might spend months).
would it be possible for you to provide all the mappings in a single download link?

--
Best Regards,

Sarah M. Alghamdi
Computer Science PhD Student - KAUST
Bio-Ontology Research Group (BORG)<https://borg.kaust.edu.sa/Pages/Home.aspx>
Computational Bioscience Research Center (CBRC)<http://www.cbrc.kaust.edu.sa/>
Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE)<https://cemse.kaust.edu.sa/Pages/Home.aspx>



________________________________
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________
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From mdorf at stanford.edu  Thu Oct  4 14:38:05 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 4 Oct 2018 21:38:05 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Bharat
In-Reply-To: <5bb5b73714a02_3efa2aca11cf97ec53632@ncbo-prd-app-09.stanford.edu.mail>
References: <5bb5b73714a02_3efa2aca11cf97ec53632@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <0B319C77-3881-4834-955D-C0F5405B50C8@stanford.edu>

Hi Bharat,

Thanks for contacting us. You don?t need to encapsulate your query in quotes. Any of these calls should work:

http://data.bioontology.org/search?q=blood+urea+nitrogen
http://data.bioontology.org/search?q=blood urea<http://data.bioontology.org/search?q=blood+urea> nitrogen<http://data.bioontology.org/search?q=blood+urea+nitrogen>
http://data.bioontology.org/search?q=blood%20urea%20nitrogen

I?m not a Python expert, but the pseudocode should be along the lines of:

bp_url = "http://data.bioontology.org/search?q=blood urea nitrogen"
response = RestClient.post(bp_url, {Authorization: "apiKey 11e3a33a-77b2-21b7-6a2a-232323bb1234", 'Content-Type': 'application/json'})

Hope this works for you.

Michael

On Oct 3, 2018, at 11:46 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Bharat

Email: bharat.shetty at gmail.com<mailto:bharat.shetty at gmail.com>

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

Feedback:

How to search multiple words for say "Blood Urea Nitrogen" ?

The REST API endpoint /search?q="blood urea nitrogen" doesnt seem to work from the python api call, but something like /search?q='BUN' or some single term search works. Please do point towards the appropriate REST api end point for a sentence text query.

Thanks,
Bharat

_______________________________________________
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From support at bioontology.org  Sat Oct  6 02:06:23 2018
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 06 Oct 2018 02:06:23 -0700
Subject: [bioontology-support] [BioPortal] Feedback from dr_jacoub
Message-ID: <5bb87b0f8beed_3b882ab9619b9930630d6@ncbo-prd-app-08.stanford.edu.mail>

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From l.andres.hernandez.18 at student.scu.edu.au  Sun Oct  7 18:16:21 2018
From: l.andres.hernandez.18 at student.scu.edu.au (Liliana Andres Hernandez)
Date: Mon, 8 Oct 2018 01:16:21 +0000
Subject: [bioontology-support] Personal or institutional account
Message-ID: <SY3PR01MB07802910AB9B6B8C7BCEF62399E60@SY3PR01MB0780.ausprd01.prod.outlook.com>

Dear BioPortal admistrator,

My name is Liliana Andres and I'm doing my PhD in Southern Cross University, Australia. In my project I'm working on the development of an ontology for nutritional composition in crops. I was wondering if instead of open a personal account, I can open an institutional account?

best regards,



Liliana Andres | PhD candidate
Southern Cross Plant Science| Southern Cross University | PO Box 157 | LISMORE  NSW  2480, AUSTRALIA
T: +61 416844027| E: l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au> W: http://www.scu.edu.au/scps/


[1506039948851_SCPS.jpg]
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From vendetti at stanford.edu  Mon Oct  8 15:09:28 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 8 Oct 2018 22:09:28 +0000
Subject: [bioontology-support] Personal or institutional account
In-Reply-To: <SY3PR01MB07802910AB9B6B8C7BCEF62399E60@SY3PR01MB0780.ausprd01.prod.outlook.com>
References: <SY3PR01MB07802910AB9B6B8C7BCEF62399E60@SY3PR01MB0780.ausprd01.prod.outlook.com>
Message-ID: <EFF9C76E-4118-4FED-B601-935479A42D13@stanford.edu>

Hello Liliana,

I?m not sure I understand what it is you want to do. We only have one type of user account for the BioPortal application. The account has an associated username, password, and API key. You?re free to create more than one account if you wish.

If you?d like for multiple people to have administrative access to a particular ontology, you can specify multiple user accounts on the edit ontology information page.

Kind regards,
Jennifer



On Oct 7, 2018, at 6:16 PM, Liliana Andres Hernandez <l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au>> wrote:


Dear BioPortal admistrator,

My name is Liliana Andres and I'm doing my PhD in Southern Cross University, Australia. In my project I'm working on the development of an ontology for nutritional composition in crops. I was wondering if instead of open a personal account, I can open an institutional account?

best regards,


Liliana Andres | PhD candidate
Southern Cross Plant Science| Southern Cross University | PO Box 157 | LISMORE  NSW  2480, AUSTRALIA
T: +61 416844027| E: l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au> W: http://www.scu.edu.au/scps/

<Outlook-1506039948.jpg>
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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From l.andres.hernandez.18 at student.scu.edu.au  Mon Oct  8 17:33:03 2018
From: l.andres.hernandez.18 at student.scu.edu.au (Liliana Andres Hernandez)
Date: Tue, 9 Oct 2018 00:33:03 +0000
Subject: [bioontology-support] Personal or institutional account
In-Reply-To: <EFF9C76E-4118-4FED-B601-935479A42D13@stanford.edu>
References: <SY3PR01MB07802910AB9B6B8C7BCEF62399E60@SY3PR01MB0780.ausprd01.prod.outlook.com>,
 <EFF9C76E-4118-4FED-B601-935479A42D13@stanford.edu>
Message-ID: <SY3PR01MB0780E598045342CC4053000C99E70@SY3PR01MB0780.ausprd01.prod.outlook.com>

Dear Jennifer,


Thanks, that helps.


best,


Liliana Andres | PhD candidate
Southern Cross Plant Science| Southern Cross University | PO Box 157 | LISMORE  NSW  2480, AUSTRALIA
T: +61 416844027| E: l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au> W: http://www.scu.edu.au/scps/


[1506039948851_SCPS.jpg]
________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Tuesday, October 9, 2018 9:09:28 AM
To: Liliana Andres Hernandez
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Personal or institutional account

Hello Liliana,

I?m not sure I understand what it is you want to do. We only have one type of user account for the BioPortal application. The account has an associated username, password, and API key. You?re free to create more than one account if you wish.

If you?d like for multiple people to have administrative access to a particular ontology, you can specify multiple user accounts on the edit ontology information page.

Kind regards,
Jennifer



On Oct 7, 2018, at 6:16 PM, Liliana Andres Hernandez <l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au>> wrote:


Dear BioPortal admistrator,

My name is Liliana Andres and I'm doing my PhD in Southern Cross University, Australia. In my project I'm working on the development of an ontology for nutritional composition in crops. I was wondering if instead of open a personal account, I can open an institutional account?

best regards,


Liliana Andres | PhD candidate
Southern Cross Plant Science| Southern Cross University | PO Box 157 | LISMORE  NSW  2480, AUSTRALIA
T: +61 416844027| E: l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au> W: http://www.scu.edu.au/scps/<http://www.scu.edu.au/scps/>

<Outlook-1506039948.jpg>
_______________________________________________
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>

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From support at bioontology.org  Thu Oct 11 10:11:08 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 11 Oct 2018 10:11:08 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Vijendra Ramlall
Message-ID: <5bbf842cd7c52_13942aef36f2209c44455@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Oct 11 12:48:19 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 11 Oct 2018 19:48:19 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Vijendra Ramlall
In-Reply-To: <5bbf842cd7c52_13942aef36f2209c44455@ncbo-prd-app-09.stanford.edu.mail>
References: <5bbf842cd7c52_13942aef36f2209c44455@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <E2148F0E-1218-452B-BADB-BFCB3D141489@stanford.edu>

Hello Vijendra,

Apologies - I?m not able to reproduce this behavior. Please try clearing your browser cache, then attempt your login again. If you let us know what browser you?re using, we can give you instructions for clearing the cache.

Kind regards,
Jennifer



On Oct 11, 2018, at 10:11 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Vijendra Ramlall

Email: vr2430 at cumc.columbia.edu<mailto:vr2430 at cumc.columbia.edu>

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

Feedback:

Hi,

I'm trying to login to my account. Once I put in my account name and password, I am redirected to a page says an error has occurred. When I try to go to the 'Annotator' pages, it say the same thing. When I sign out, I can go the Annotator page.

_______________________________________________
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From sarah.alghamdi.1 at kaust.edu.sa  Sat Oct 13 01:17:24 2018
From: sarah.alghamdi.1 at kaust.edu.sa (Sarah Alghamdi)
Date: Sat, 13 Oct 2018 11:17:24 +0300
Subject: [bioontology-support] Download Ontologies Mappings
In-Reply-To: <B15E99DC-2137-4FF8-AA72-FA3608B7CDE7@stanford.edu>
References: <CACaLaUw1ReG2vDLDdBiSfB=d0-FgcWqnN4OdtZMiJNmc1TM3=Q@mail.gmail.com>
 <B15E99DC-2137-4FF8-AA72-FA3608B7CDE7@stanford.edu>
Message-ID: <CACaLaUx_oTY0MBmXg+XTsELJn6tFPxJ=G9qAu5VB3wTEHQ22+Q@mail.gmail.com>

Thank you for your response.
I have a question, is the mappings directed?
while downloaded I had the assumption they are not, and I just want to make
sure before proceeding in my work,
in other words if I have mappings from ontology1 to ontology2 it is the
same as the mappings from ontology2 to ontology1



On Fri, Oct 5, 2018 at 12:19 AM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Sarah,
>
> Unfortunately, at this point, the answer is NO. 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.
>
> Sorry, I couldn?t be of more help.
>
> Michael
>
>
> On Oct 4, 2018, at 3:13 AM, Sarah Alghamdi <sarah.alghamdi.1 at kaust.edu.sa>
> wrote:
>
> Dear team,
> I hope this finds you very well,
> For my research I want to acquire all the mappings available between pairs
> of ontologies from the Bioportal, I'm currently using the REST API and
> passing by all the pairs of ontologies, but this is taking me very long
> time (might spend months).
> would it be possible for you to provide all the mappings in a single
> download link?
>
> --
> Best Regards,
>
> Sarah M. Alghamdi
> Computer Science PhD Student - KAUST
> Bio-Ontology Research Group (BORG)
> <https://borg.kaust.edu.sa/Pages/Home.aspx>
> Computational Bioscience Research Center (CBRC)
> <http://www.cbrc.kaust.edu.sa/>
> Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE)
> <https://cemse.kaust.edu.sa/Pages/Home.aspx>
>
>
>
> ------------------------------
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
> received this message in error, please notify me immediately and delete
> this message from your computer system. Any unauthorized use or
> distribution is prohibited. Please consider the environment before printing
> this email._______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>

-- 
Best Regards,

Sarah M. Alghamdi
Computer Science PhD Student - KAUST

Bio-Ontology Research Group (BORG)?
<https://borg.kaust.edu.sa/Pages/Home.aspx>

Computational Bioscience Research Center (CBRC)
<http://www.cbrc.kaust.edu.sa/>
Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE)?
<https://cemse.kaust.edu.sa/Pages/Home.aspx>

-- 

This message and its contents, including attachments are intended solely 
for the original recipient. If you are not the intended recipient or have 
received this message in error, please notify me immediately and delete 
this message from your computer system. Any unauthorized use or 
distribution is prohibited. Please consider the environment before printing 
this email.
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From support at bioontology.org  Mon Oct 15 01:51:11 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 15 Oct 2018 01:51:11 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Nicolas Joannin
Message-ID: <5bc454ffb0817_7832ab96945163425642@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Mon Oct 15 14:04:15 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 15 Oct 2018 14:04:15 -0700
Subject: [bioontology-support] [BioPortal] Feedback from jambrosiano
Message-ID: <5bc500cf7392a_9762ac67a915da068457@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Tue Oct 16 06:54:31 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 16 Oct 2018 06:54:31 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Rossella Troia
Message-ID: <5bc5ed97e17ec_2b582afeddaab958260bb@ncbo-prd-app-08.stanford.edu.mail>

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From john.zobolas at ntnu.no  Tue Oct 16 04:43:50 2018
From: john.zobolas at ntnu.no (John Zobolas)
Date: Tue, 16 Oct 2018 11:43:50 +0000
Subject: [bioontology-support] Server down?
Message-ID: <1539690230119.38604@ntnu.no>

Hi,


I noticed the web server was down (for requests through the REST API). Is this temporary or it happens frequently?


BR, John.?

------------------
John Zobolas
PhD Student
Department of Biology, Faculty of Natural Sciences, NTNU
Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU

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From redcap at uzgent.be  Wed Oct 17 00:16:56 2018
From: redcap at uzgent.be (redcap)
Date: Wed, 17 Oct 2018 07:16:56 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
Message-ID: <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>

Hi Jennifer,

My apologies for the delay in answering, I overlooked your emails (obviously).

I am able to issue a REST call successfully (see screenshot below).
[cid:image004.png at 01D465FA.25DAC270]

For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
[cid:image005.png at 01D465FA.25DAC270]

Thanks for your continued support!
Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: zaterdag 14 juli 2018 0:20
Aan: redcap <redcap at UZGENT.be>
CC: support at bioontology.org
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi again Simon,

There?s one other thing I?m wondering about. Are you able to issue a REST call in your browser for this term with our REST API? You would enter this URL in the browser:

http://data.bioontology.org/ontologies/ATC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051?apikey=your_api_key_here<http://data.bioontology.org/ontologies/ATC/classes/http:/purl.bioontology.org/ontology/STY/T051?apikey=your_api_key_here>

You need to enter your API key at the end of the URL, which you can access in the Account Settings section of the BioPortal UI. (After logging in, click on your account name to open the drop down menu and choose Account Settings). If the call is successful, you would see this in the way of a return result:



[cid:image003.png at 01D465F9.27CFAA10]

Kind regards,
Jennifer




On Jul 13, 2018, at 12:03 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Simon,



On Jul 12, 2018, at 11:48 PM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

I tried clearing the browser cache, but unfortunately the error persists. I did however notice that there is a JavaScript error in the console. Could this be related to the error message I am getting when logged in?<image001.png>


This JS error is reproducible on our end, but is unrelated and can be ignored.



Also, when I close and reopen the console, I am getting an additional error.
<image003.png>



Ok. I?m wondering if you could try something else for me? For the page that you see the 500 error:

1). Open the developer console.
2). Navigate to the Network tab.
3). Click the Clear icon in the top left of the developer console to clear any contents that might already be visible in the Network tab.
4). Tick the ?Disable cache? checkbox.
5). Refresh the page.

I?m interested to see what you get for results in the Network tab. For example, mine looks as such with a 200 response at the top for the API call to retrieve the Event concept:

<Screenshot 2018-07-13 11.46.07.png>

Another thing that would be helpful, is for you to let me know roughly the date and time that you perform the page refresh, as well as your BioPortal user account name that you are logged in with. I would like to try to grep the various production logs for this 500 error you?re seeing.

Apologies that you?re continuing to have difficulties.

Kind regards,
Jennifer



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From support at bioontology.org  Wed Oct 17 07:25:54 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 17 Oct 2018 07:25:54 -0700
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
Message-ID: <5bc74672c28e1_371f2b2a7a50e1d073881@ncbo-prd-app-08.stanford.edu.mail>

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From nicolas.matentzoglu at gmail.com  Wed Oct 17 07:04:28 2018
From: nicolas.matentzoglu at gmail.com (Nico Matentzoglu)
Date: Wed, 17 Oct 2018 15:04:28 +0100
Subject: [bioontology-support] License information when using the bioportal
	REST api
Message-ID: <CAMWhPOcZp_mxwJP5gPZ_uguA75AyWXdVyzwCKTxQOXE+fP_Nhg@mail.gmail.com>

Hello!

Navigating here: https://bioportal.bioontology.org/ontologies/CRISP
it is possible to see a field for License information.

Is it possible to access that field through the REST API?

Thank you very much!
Nicolas Matentzoglu
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From vendetti at stanford.edu  Wed Oct 17 09:35:17 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 17 Oct 2018 16:35:17 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
In-Reply-To: <5bc74672c28e1_371f2b2a7a50e1d073881@ncbo-prd-app-08.stanford.edu.mail>
References: <5bc74672c28e1_371f2b2a7a50e1d073881@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <C6C14C8E-E636-4621-8A4B-4464958AFA06@stanford.edu>

Hello Matus. If you refresh your browser now, I believe you?ll be able to see the latest alpha04 version of your ontology.

Jennifer


On Oct 17, 2018, at 7:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: mkalas

Email: matus.kalas at bccs.uib.no<mailto:matus.kalas at bccs.uib.no>

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

Feedback:

matus.kalas at uib.no<mailto:matus.kalas at uib.no>

The same problem as always when submitting a new version of an OWL ontology, unfortunately :-(

Submitted a new version an hour ago, and still not displayed in BioPortal.

https://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING shows alpha04 as Uploaded and still alpha03 as Parsed, Indexed, Metrics, Annotator

Clicking on the Classes tab leads to Problem retrieving classes in some browsers and to showing alpha03 in others (different cache).

Navigating to http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING/?p=classes&conceptid=root says We're sorry but something has gone wrong. We have been notified of this error or shows alpha03 if empty cache.

Searching for a new concept from alpha04 finds it correctly, but clicking on it returns The page you are looking for wasn't found. Please try again

Sorry for the stress, but it's quite urgent to get the new version up and running asap, we're sitting here in a workshop using it (#Hacktoberfest)

Million thanks for help,
Matus

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From mdorf at stanford.edu  Wed Oct 17 11:04:23 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 17 Oct 2018 18:04:23 +0000
Subject: [bioontology-support] License information when using the
 bioportal	REST api
In-Reply-To: <CAMWhPOcZp_mxwJP5gPZ_uguA75AyWXdVyzwCKTxQOXE+fP_Nhg@mail.gmail.com>
References: <CAMWhPOcZp_mxwJP5gPZ_uguA75AyWXdVyzwCKTxQOXE+fP_Nhg@mail.gmail.com>
Message-ID: <AD6772DC-8D61-4C06-8807-21B39D4C144D@stanford.edu>

Hi Nico,

Thanks for contacting us. Unfortunately, the answer is NO to both of your questions. We currently don?t store the UMLS license information for ontologies. The text you see in the UI is just a placeholder that gets displayed on our front end for the user to get info on how to obtain a UMLS license.

Michael


On Oct 17, 2018, at 7:04 AM, Nico Matentzoglu <nicolas.matentzoglu at gmail.com<mailto:nicolas.matentzoglu at gmail.com>> wrote:

Hello!

Navigating here: https://bioportal.bioontology.org/ontologies/CRISP
it is possible to see a field for License information.

Is it possible to access that field through the REST API?

Thank you very much!
Nicolas Matentzoglu
_______________________________________________
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 mdorf at stanford.edu  Wed Oct 17 11:20:21 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 17 Oct 2018 18:20:21 +0000
Subject: [bioontology-support] Download Ontologies Mappings
In-Reply-To: <CACaLaUx_oTY0MBmXg+XTsELJn6tFPxJ=G9qAu5VB3wTEHQ22+Q@mail.gmail.com>
References: <CACaLaUw1ReG2vDLDdBiSfB=d0-FgcWqnN4OdtZMiJNmc1TM3=Q@mail.gmail.com>
 <B15E99DC-2137-4FF8-AA72-FA3608B7CDE7@stanford.edu>
 <CACaLaUx_oTY0MBmXg+XTsELJn6tFPxJ=G9qAu5VB3wTEHQ22+Q@mail.gmail.com>
Message-ID: <A146D346-DBF7-49B4-83EE-889CD3157D38@stanford.edu>

Hi Sarah,

Mappings are NOT directed. Your assumption is correct about the mappings between ontology1 and ontology2.

Thanks,

Michael

On Oct 13, 2018, at 1:17 AM, Sarah Alghamdi <sarah.alghamdi.1 at kaust.edu.sa<mailto:sarah.alghamdi.1 at kaust.edu.sa>> wrote:

Thank you for your response.
I have a question, is the mappings directed?
while downloaded I had the assumption they are not, and I just want to make sure before proceeding in my work,
in other words if I have mappings from ontology1 to ontology2 it is the same as the mappings from ontology2 to ontology1



On Fri, Oct 5, 2018 at 12:19 AM Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Sarah,

Unfortunately, at this point, the answer is NO. 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.

Sorry, I couldn?t be of more help.

Michael


On Oct 4, 2018, at 3:13 AM, Sarah Alghamdi <sarah.alghamdi.1 at kaust.edu.sa<mailto:sarah.alghamdi.1 at kaust.edu.sa>> wrote:

Dear team,
I hope this finds you very well,
For my research I want to acquire all the mappings available between pairs of ontologies from the Bioportal, I'm currently using the REST API and passing by all the pairs of ontologies, but this is taking me very long time (might spend months).
would it be possible for you to provide all the mappings in a single download link?

--
Best Regards,

Sarah M. Alghamdi
Computer Science PhD Student - KAUST
Bio-Ontology Research Group (BORG)<https://borg.kaust.edu.sa/Pages/Home.aspx>
Computational Bioscience Research Center (CBRC)<http://www.cbrc.kaust.edu.sa/>
Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE)<https://cemse.kaust.edu.sa/Pages/Home.aspx>



________________________________
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________
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



--
Best Regards,

Sarah M. Alghamdi
Computer Science PhD Student - KAUST
Bio-Ontology Research Group (BORG)?<https://borg.kaust.edu.sa/Pages/Home.aspx>
Computational Bioscience Research Center (CBRC)<http://www.cbrc.kaust.edu.sa/>
Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE)?<https://cemse.kaust.edu.sa/Pages/Home.aspx>



________________________________
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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From mdorf at stanford.edu  Wed Oct 17 11:29:57 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 17 Oct 2018 18:29:57 +0000
Subject: [bioontology-support] [BioPortal] Feedback from jambrosiano
In-Reply-To: <5bc500cf7392a_9762ac67a915da068457@ncbo-prd-app-09.stanford.edu.mail>
References: <5bc500cf7392a_9762ac67a915da068457@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <D1C20753-09A7-4758-8EA3-9FB7CABD4B60@stanford.edu>

Hi John,

Thanks for getting in touch with us. Due to licensing restrictions, we?re unable to offer downloads of the ICD10 ontology source file from our public website. If you're a current UMLS license holder [1], please contact our technical program manager John Graybeal (cc'ed) offline for possible download options.

Alternatively, you can access ICD10 data via our REST API, which doesn't require a license. The API is documented here:

http://data.bioontology.org/documentation

If you decide to use the API, you'll need to get an API key:

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

Here's an example of a REST call that would retrieve the Neoplasms" class from ICD10:

http://data.bioontology.org/ontologies/ICD10/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FC00-D48.9?apikey=your_api_key_here<http://data.bioontology.org/ontologies/ICD10/classes/http://purl.bioontology.org/ontology/ICD10/C00-D48.9?apikey=your_api_key_here>

You can use the hypermedia links in the response to explore things like parents, children, descendants, etc.

Thanks,

Michael

[1] https://www.nlm.nih.gov/databases/umls.html#license_request



On Oct 15, 2018, at 2:04 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: jambrosiano

Email: ambro at lanl.gov<mailto:ambro at lanl.gov>

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

Feedback:

I want to download the latest version of the ICD-10 ontology in some suitable form. How do I do this? Thanks.

John Ambrosiano

Reply to ambro at lanl.gov<mailto:ambro at lanl.gov>

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From mdorf at stanford.edu  Wed Oct 17 11:44:33 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 17 Oct 2018 18:44:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Nicolas Joannin
In-Reply-To: <5bc454ffb0817_7832ab96945163425642@ncbo-prd-app-08.stanford.edu.mail>
References: <5bc454ffb0817_7832ab96945163425642@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <97E79A0D-04AF-494F-B76D-D746931126A5@stanford.edu>

Hi Nicolas,

Thank you for bringing this to our attention. We don?t offer actual download files for UMLS ontologies (unless you supply us your UMLS license, offline), but I definitely see what you mean when looking at the user interface that displays these terms:

http://bioportal.bioontology.org/ontologies/ICD9CM/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD9CM%2F386.00&jump_to_nav=true<http://bioportal.bioontology.org/ontologies/ICD9CM/?p=classes&conceptid=http://purl.bioontology.org/ontology/ICD9CM/386.00&jump_to_nav=true>

Roughly twice per year the UMLS [1] publishes a release of a group of ontologies, which we import into BioPortal.  ICD9CM and ICD10CM is one of the ontologies that?s pulled in when we do the UMLS imports.  At this point, I am not sure exactly where in the import process the wrong encoding gets introduced. I?ve logged this as an issue in our Github tracker:

https://github.com/ncbo/umls2rdf/issues/28

Thanks again for your report!

Michael

[1] https://www.nlm.nih.gov/research/umls/



On Oct 15, 2018, at 1:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Nicolas Joannin

Email: nicolas.joannin at linguamatics.com<mailto:nicolas.joannin at linguamatics.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FICD9CM

Feedback:

Encoding problems with your ICD9CM and ICD10CM TTL files:

Hello,

The files you provide for ICD9CM and ICD10CM have erroneous characters, e.g. "M??ni??re's disease" instead of "M?ni?re's disease".

This type of character replacement is typical when a UTF-8 encoded source file is read as a Windows-1252 encoded file (probably the default encoding of the machine used to process the data).

I would suggest that when next updating these files you consider updating your script to read the source data with the proper encoding.

Cheers,
Nicolas

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From vendetti at stanford.edu  Wed Oct 17 17:17:41 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 18 Oct 2018 00:17:41 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
 <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
Message-ID: <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>

Hi Simon,


On Oct 17, 2018, at 12:16 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

My apologies for the delay in answering, I overlooked your emails (obviously).


Not a problem.



I am able to issue a REST call successfully (see screenshot below).
<image004.png>


Ok - thanks for checking that. The fact that you?re able to retrieve data successfully for that class would indicate to us that the problem isn?t at the REST API level, or with our backend caching mechanism.



For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
<image005.png>


My colleague Michael and I spent some time looking at this today. We were unable to reproduce the 500 error in the BioPortal user interface, either logged in or out of the application. We're still leaning toward some kind of a local front-end caching issue. On that note, I?m wondering if you?d be willing to try opening a new incognito window in Chrome (File -> New Incognito Window), navigating to this class again [1], and letting us know if the error still occurs.

Kind regards,
Jennifer


[1] https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

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From redcap at uzgent.be  Thu Oct 18 00:24:06 2018
From: redcap at uzgent.be (redcap)
Date: Thu, 18 Oct 2018 07:24:06 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
 <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
 <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>
Message-ID: <b09d65e77c4e4f0bb00f706257126b42@UZGENT.be>

Hi Jennifer,

I tried navigating to the page in incognito mode, but the error persists.

Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: donderdag 18 oktober 2018 2:18
Aan: redcap <redcap at UZGENT.be>
CC: support at bioontology.org
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi Simon,



On Oct 17, 2018, at 12:16 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

My apologies for the delay in answering, I overlooked your emails (obviously).


Not a problem.




I am able to issue a REST call successfully (see screenshot below).
<image004.png>


Ok - thanks for checking that. The fact that you?re able to retrieve data successfully for that class would indicate to us that the problem isn?t at the REST API level, or with our backend caching mechanism.



For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
<image005.png>


My colleague Michael and I spent some time looking at this today. We were unable to reproduce the 500 error in the BioPortal user interface, either logged in or out of the application. We're still leaning toward some kind of a local front-end caching issue. On that note, I?m wondering if you?d be willing to try opening a new incognito window in Chrome (File -> New Incognito Window), navigating to this class again [1], and letting us know if the error still occurs.

Kind regards,
Jennifer


[1] https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

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From redcap at uzgent.be  Thu Oct 18 00:36:28 2018
From: redcap at uzgent.be (redcap)
Date: Thu, 18 Oct 2018 07:36:28 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <b09d65e77c4e4f0bb00f706257126b42@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
 <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
 <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>
 <b09d65e77c4e4f0bb00f706257126b42@UZGENT.be>
Message-ID: <4dc80d0106eb48d4a06dec0f4433e7a3@UZGENT.be>

Hi Jennifer,

  *   We're still leaning toward some kind of a local front-end caching issue.
As a backend developer I can confirm that a 500 HTTP error is always a backend issue. The error message can always be found in the server logs. If an incorrect argument is given a 4xx should be thrown. Not a 500 which means internal server error.
I can reproduce the problem as well, so it is not browser specific. Steps to reproduce are:

  1.  Login to bioportal. (This problem does not happen if you?re not logged in).
  2.  Browse to the https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true page.
  3.  Expected: The class shows
  4.  Actual: An error page is shown:
[cid:image001.png at 01D466C5.8C697920]
Hopefully this helps.

Kind regards,
Lieven


Van: Vanderschaeghe Simon Namens redcap
Verzonden: donderdag 18 oktober 2018 9:24
Aan: 'Jennifer Leigh Vendetti' <vendetti at stanford.edu>
CC: support at bioontology.org; redcap <redcap at UZGENT.be>
Onderwerp: RE: [bioontology-support] BioPortal: Questions

Hi Jennifer,

I tried navigating to the page in incognito mode, but the error persists.

Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: donderdag 18 oktober 2018 2:18
Aan: redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi Simon,


On Oct 17, 2018, at 12:16 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

My apologies for the delay in answering, I overlooked your emails (obviously).


Not a problem.



I am able to issue a REST call successfully (see screenshot below).
<image004.png>


Ok - thanks for checking that. The fact that you?re able to retrieve data successfully for that class would indicate to us that the problem isn?t at the REST API level, or with our backend caching mechanism.



For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
<image005.png>


My colleague Michael and I spent some time looking at this today. We were unable to reproduce the 500 error in the BioPortal user interface, either logged in or out of the application. We're still leaning toward some kind of a local front-end caching issue. On that note, I?m wondering if you?d be willing to try opening a new incognito window in Chrome (File -> New Incognito Window), navigating to this class again [1], and letting us know if the error still occurs.

Kind regards,
Jennifer


[1] https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

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From jgraybeal at stanford.edu  Thu Oct 18 10:35:38 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 18 Oct 2018 17:35:38 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <4dc80d0106eb48d4a06dec0f4433e7a3@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
 <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
 <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>
 <b09d65e77c4e4f0bb00f706257126b42@UZGENT.be>
 <4dc80d0106eb48d4a06dec0f4433e7a3@UZGENT.be>
Message-ID: <71866D50-046E-4D77-B9FE-0BF54B610BC6@stanford.edu>

Lieven, all,

Thanks very much for the additional input. I'm not on the developer side, but I'd like to offer additional information to the thread.

First, in case it's useful, I can not replicate the results by logging in to BioPortal in an incognito session. Of course, because I am an administrator of the ontology, it is conceivable there is a system interaction that is only visible to "people who are logged in but are not administrators of the ontology." That is something we could undertake to test on our end, especially since both of you (running different accounts I assume?) are seeing the issue on your end.

Some historical knowledge may be relevant. From experience, we know that people who are logged in can sometimes be exposed to faulty data that is not accessible to people who are not logged in (and therefore does not trigger the issue). So we understand how this problem may have initially occurred.

We also have had many occasions where either BioPortal's front-end cache, or a system that is local to the user, has cached the page reporting the error that resulted in this page being displayed. (In fact, one of us will often see this error in one or both of our local browsers, when our colleagues have seen the error is fixed in their browser.) In those situations, it seems pretty clear that while the error was originally in the back-end system, it is no longer there; and forcing a page reload or clearing the browser cache has fixed it. That pattern, when combined with our inability to duplicate the issue on our end, is why we will suggest caching issues as a possible scenario.

Again, thanks for your help on this, it is an unusually sticky issue and hopefully we can get to the bottom of it soon.

John

On Oct 18, 2018, at 12:36 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

Hi Jennifer,

  *   We're still leaning toward some kind of a local front-end caching issue.

As a backend developer I can confirm that a 500 HTTP error is always a backend issue. The error message can always be found in the server logs. If an incorrect argument is given a 4xx should be thrown. Not a 500 which means internal server error.
I can reproduce the problem as well, so it is not browser specific. Steps to reproduce are:

  1.  Login to bioportal. (This problem does not happen if you?re not logged in).
  2.  Browse to the https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true page.
  3.  Expected: The class shows
  4.  Actual: An error page is shown:

<image001.png>
Hopefully this helps.

Kind regards,
Lieven


Van: Vanderschaeghe Simon Namens redcap
Verzonden: donderdag 18 oktober 2018 9:24
Aan: 'Jennifer Leigh Vendetti' <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: RE: [bioontology-support] BioPortal: Questions

Hi Jennifer,

I tried navigating to the page in incognito mode, but the error persists.

Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: donderdag 18 oktober 2018 2:18
Aan: redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi Simon,


On Oct 17, 2018, at 12:16 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

My apologies for the delay in answering, I overlooked your emails (obviously).


Not a problem.



I am able to issue a REST call successfully (see screenshot below).
<image004.png>


Ok - thanks for checking that. The fact that you?re able to retrieve data successfully for that class would indicate to us that the problem isn?t at the REST API level, or with our backend caching mechanism.



For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
<image005.png>


My colleague Michael and I spent some time looking at this today. We were unable to reproduce the 500 error in the BioPortal user interface, either logged in or out of the application. We're still leaning toward some kind of a local front-end caching issue. On that note, I?m wondering if you?d be willing to try opening a new incognito window in Chrome (File -> New Incognito Window), navigating to this class again [1], and letting us know if the error still occurs.

Kind regards,
Jennifer


[1] https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

_______________________________________________
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 mdorf at stanford.edu  Thu Oct 18 10:50:15 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 18 Oct 2018 17:50:15 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <71866D50-046E-4D77-B9FE-0BF54B610BC6@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
 <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
 <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>
 <b09d65e77c4e4f0bb00f706257126b42@UZGENT.be>
 <4dc80d0106eb48d4a06dec0f4433e7a3@UZGENT.be>
 <71866D50-046E-4D77-B9FE-0BF54B610BC6@stanford.edu>
Message-ID: <9680BAB2-4E5E-4707-A3A7-C0F1A54B7CCD@stanford.edu>

Hi Lieven/Simon,

Just to add to John?s input, I have not been able to reproduce this error on any of non-Stanford wifi networks. I wanted to eliminate the possibility that our network is somehow ?shielding? us from seeing this behavior. I?ve tried your steps at home as well as a public wifi at a local Peet?s Coffee and was not able to reproduce the issue. On your side, can you please try reproducing the problem outside of your local network, just to exclude that factor as well?

Thanks!

Michael


On Oct 18, 2018, at 10:35 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Lieven, all,

Thanks very much for the additional input. I'm not on the developer side, but I'd like to offer additional information to the thread.

First, in case it's useful, I can not replicate the results by logging in to BioPortal in an incognito session. Of course, because I am an administrator of the ontology, it is conceivable there is a system interaction that is only visible to "people who are logged in but are not administrators of the ontology." That is something we could undertake to test on our end, especially since both of you (running different accounts I assume?) are seeing the issue on your end.

Some historical knowledge may be relevant. From experience, we know that people who are logged in can sometimes be exposed to faulty data that is not accessible to people who are not logged in (and therefore does not trigger the issue). So we understand how this problem may have initially occurred.

We also have had many occasions where either BioPortal's front-end cache, or a system that is local to the user, has cached the page reporting the error that resulted in this page being displayed. (In fact, one of us will often see this error in one or both of our local browsers, when our colleagues have seen the error is fixed in their browser.) In those situations, it seems pretty clear that while the error was originally in the back-end system, it is no longer there; and forcing a page reload or clearing the browser cache has fixed it. That pattern, when combined with our inability to duplicate the issue on our end, is why we will suggest caching issues as a possible scenario.

Again, thanks for your help on this, it is an unusually sticky issue and hopefully we can get to the bottom of it soon.

John

On Oct 18, 2018, at 12:36 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

Hi Jennifer,

  *   We're still leaning toward some kind of a local front-end caching issue.

As a backend developer I can confirm that a 500 HTTP error is always a backend issue. The error message can always be found in the server logs. If an incorrect argument is given a 4xx should be thrown. Not a 500 which means internal server error.
I can reproduce the problem as well, so it is not browser specific. Steps to reproduce are:

  1.  Login to bioportal. (This problem does not happen if you?re not logged in).
  2.  Browse to the https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true page.
  3.  Expected: The class shows
  4.  Actual: An error page is shown:

<image001.png>
Hopefully this helps.

Kind regards,
Lieven


Van: Vanderschaeghe Simon Namens redcap
Verzonden: donderdag 18 oktober 2018 9:24
Aan: 'Jennifer Leigh Vendetti' <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: RE: [bioontology-support] BioPortal: Questions

Hi Jennifer,

I tried navigating to the page in incognito mode, but the error persists.

Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: donderdag 18 oktober 2018 2:18
Aan: redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi Simon,


On Oct 17, 2018, at 12:16 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

My apologies for the delay in answering, I overlooked your emails (obviously).


Not a problem.



I am able to issue a REST call successfully (see screenshot below).
<image004.png>


Ok - thanks for checking that. The fact that you?re able to retrieve data successfully for that class would indicate to us that the problem isn?t at the REST API level, or with our backend caching mechanism.



For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
<image005.png>


My colleague Michael and I spent some time looking at this today. We were unable to reproduce the 500 error in the BioPortal user interface, either logged in or out of the application. We're still leaning toward some kind of a local front-end caching issue. On that note, I?m wondering if you?d be willing to try opening a new incognito window in Chrome (File -> New Incognito Window), navigating to this class again [1], and letting us know if the error still occurs.

Kind regards,
Jennifer


[1] https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

_______________________________________________
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

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From vendetti at stanford.edu  Thu Oct 18 18:27:41 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 19 Oct 2018 01:27:41 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <4dc80d0106eb48d4a06dec0f4433e7a3@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
 <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>
 <aa47725b509e413ab13ea750b5f49f96@UZGENT.be>
 <734D1612-E164-4691-B80D-8824A51189EF@stanford.edu>
 <b09d65e77c4e4f0bb00f706257126b42@UZGENT.be>
 <4dc80d0106eb48d4a06dec0f4433e7a3@UZGENT.be>
Message-ID: <FF3FE07E-8717-4ED9-BC4D-D26C579AACAA@stanford.edu>

Hi Lieven & Simon,

Since this issue is proving somewhat difficult for us to nail down / fix, I?ve started an issue in our GitHub repository where you can follow our progress:

https://github.com/ncbo/bioportal-project/issues/100


On Oct 18, 2018, at 12:36 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

Hi Jennifer,

  *   We're still leaning toward some kind of a local front-end caching issue.

As a backend developer I can confirm that a 500 HTTP error is always a backend issue.


Yes, I understand that. This is why I asked Simon in a previous correspondence to remove the BioPortal front-end from the equation altogether, and issue a call directly to our REST endpoint for the Event class in ATC. Simon reported that the call was successful, which I initially took as an indicator that the problem was originating from something else in the stack.

The request for Simon to access the Event class in an incognito window was essentially to allow us to be totally certain that the error page wasn?t cached.

Thanks for trying that out and letting us know the error still occurs.


The error message can always be found in the server logs. If an incorrect argument is given a 4xx should be thrown. Not a 500 which means internal server error.


I didn?t offer an update on the log files yesterday because I hadn?t yet finished my examination of them.

Our REST endpoint currently handles about 20 million requests per week. The UI traffic is load balanced across two servers and the REST API traffic is load balanced across three servers. We lack the resources to have any sort of log analysis software put into place. This means that tracking down particular errors is a manual process that requires us to sift through large files on multiple machines, and can take some time. In the end, I did locate a stack trace in one of our UI logs that allowed us to make some progress in understanding why the exception is occurring. Details were recorded in the GitHub issue I referenced above.


I can reproduce the problem as well, so it is not browser specific. Steps to reproduce are:

  1.  Login to bioportal. (This problem does not happen if you?re not logged in).
  2.  Browse to the https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true page.
  3.  Expected: The class shows
  4.  Actual: An error page is shown:

<image001.png>


Thanks for reiterating the set of steps. We did figure out today what we?d missed, which is that the error is only occurring for a particular type of account (non-administrative). Also, the error isn?t specific to ATC and the Event class, but rather is reproducible when searching for any of the UMLS Semantic Type classes while viewing any UMLS ontology. I recorded an updated set of steps to reproduce in the GitHub issue.

Kind regards,
Jennifer

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From markampa at pennmedicine.upenn.edu  Fri Oct 19 06:36:31 2018
From: markampa at pennmedicine.upenn.edu (Miller, Mark)
Date: Fri, 19 Oct 2018 13:36:31 +0000
Subject: [bioontology-support] are mapping counts accurate?
Message-ID: <BYAPR04MB4069C87A7BE4DED902B51328F7F90@BYAPR04MB4069.namprd04.prod.outlook.com>

I have been downloading your term mappings via the REST API.  Thanks.  I put an example of how I do it (in R) at the end of this message.

I noticed that the number of mappings I get rarely agrees with the counts I calculate form a page like http://bioportal.bioontology.org/ontologies/EXACT?p=mappings

Pasting that page into Excel and calculating the sum seems to say that there are 1110 BioPortal mappings from any EXACT term

But my code below retrieves 1894 mappings.  If I take out the match method and then make the results  non-redundant, I get 1893.  If I take out the match ontology column and make it unique (on just the source term and the match term), I get 674 mappings.

Another example: my mentod gets 10 mappings from EXACT to ICO, but the web pages says 9.  However, when I click on the ICO link on the EXACT mappings page (http://bioportal.bioontology.org/mappings/show/EXACT?target=http://data.bioontology.org/ontologies/ICO&height=600&width=800), I get 10 mappings!  (see immediately below.)


Thanks,
Mark



An ontology for experimental actions

Informed Consent Ontology

Source

information content entity<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000030>

IAO_0000030<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000030>

SAME_URI

one-dimensional temporal region<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000038>

BFO_0000038<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000038>

SAME_URI

object<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000030>

object<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23OWLClass_fede789e_08ff_4d4a_bf4a_cd6f393a670d>

LOOM

material entity<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000040>

BFO_0000040<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000040>

SAME_URI

role<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000023>

role<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23OWLClass_705c1d8b_d7b2_455e_9f80_d4bc62eb57b1>

LOOM

Version<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fusefulinc.com%2Fns%2Fdoap%23Version>

version<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23OWLClass_870d9f06_a65a_415d_b7cc_e1dbbbcc9b2c>

LOOM

centrifuge<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0400106>

centrifuge<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23Class_53>

LOOM

temporal region<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000008>

BFO_0000008<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000008>

SAME_URI

site<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000029>

BFO_0000029<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000029>

SAME_URI

textual entity<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000300>

IAO_0000300<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000300>

SAME_URI





library(jsonlite)
library(httr)

# assign api key here
API_KEY  <-  ""

PAGE_SIZE <- 500
REST_URL <- "http://data.bioontology.org"

sourceOntoAbbr  <-  "RXNORM"

# sourceOntoAbbr  <-  "EXACT"

next_page <-
  paste0(REST_URL,
         "/ontologies/",
         sourceOntoAbbr,
         "/mappings?pagesize=",
         PAGE_SIZE)

all.output.chunks <- list()

temp.rdf <- rrdf::new.rdf()

while (!is.null(next_page) > 0) {
  print(next_page)

  httpResponse <-
    GET(next_page,
        add_headers("Authorization" = paste0("apikey token=", API_KEY)),
        accept_json())

  page <-
    fromJSON(content(httpResponse, "text"), simplifyDataFrame = FALSE)

  next_page <- page$links$nextPage

  print(page$page)
  print(page$pageCount)

  one.output.chunk <-
    lapply(page$collection, function(current.collection) {


      matchMeth <- current.collection$source

      temp1 <- current.collection$classes[[1]]$links
      sourceOnt <- temp1$ontology
      inputTerm <- current.collection$classes[[1]]$`@id`

      temp2 <- current.collection$classes[[2]]$links
      matchOnt <- temp2$ontology
      matchTerm <- current.collection$classes[[2]]$`@id`

      return(
        list(
          "inputTerm" = inputTerm,
          "matchMeth" = matchMeth,
          "matchOnt" = matchOnt,
          "matchTerm" = matchTerm,
          "sourceOnt" = sourceOnt
        )
      )

    })
  one.output.chunk <- do.call(rbind.data.frame, one.output.chunk)

  all.output.chunks[[page$page]] <- one.output.chunk

}

all.output.chunks <- do.call(rbind.data.frame, all.output.chunks

write.table(all.output.chunks, sep = "\t", row.names = FALSE, file = paste0(sourceOntoAbbr, "_bioportal_mappings.tsv"))
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From support at bioontology.org  Fri Oct 19 05:22:12 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 19 Oct 2018 05:22:12 -0700
Subject: [bioontology-support] [BioPortal] Feedback from CS
Message-ID: <5bc9cc74306fd_1c6d2adaf943411820028@ncbo-prd-app-08.stanford.edu.mail>

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From mdorf at stanford.edu  Fri Oct 19 17:08:50 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Sat, 20 Oct 2018 00:08:50 +0000
Subject: [bioontology-support] are mapping counts accurate?
In-Reply-To: <BYAPR04MB4069C87A7BE4DED902B51328F7F90@BYAPR04MB4069.namprd04.prod.outlook.com>
References: <BYAPR04MB4069C87A7BE4DED902B51328F7F90@BYAPR04MB4069.namprd04.prod.outlook.com>
Message-ID: <96B5EE81-B686-4BEC-A552-407645C1AD19@stanford.edu>

Hi Mark,

Thanks for contacting us and bringing this issue to our attention.  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. I?ve created an issue in our Github repository to track our progress on fixing this problem:

https://github.com/ncbo/ontologies_linked_data/issues/88

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. For example:

http://data.bioontology.org/ontologies/EXACT/mappings?page=1&pagesize=500
vs
http://data.bioontology.org/ontologies/EXACT/mappings?page=50&pagesize=500

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

Michael


On Oct 19, 2018, at 6:36 AM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

I have been downloading your term mappings via the REST API.  Thanks.  I put an example of how I do it (in R) at the end of this message.

I noticed that the number of mappings I get rarely agrees with the counts I calculate form a page like http://bioportal.bioontology.org/ontologies/EXACT?p=mappings

Pasting that page into Excel and calculating the sum seems to say that there are 1110 BioPortal mappings from any EXACT term

But my code below retrieves 1894 mappings.  If I take out the match method and then make the results  non-redundant, I get 1893.  If I take out the match ontology column and make it unique (on just the source term and the match term), I get 674 mappings.

Another example: my mentod gets 10 mappings from EXACT to ICO, but the web pages says 9.  However, when I click on the ICO link on the EXACT mappings page (http://bioportal.bioontology.org/mappings/show/EXACT?target=http://data.bioontology.org/ontologies/ICO&height=600&width=800), I get 10 mappings!  (see immediately below.)


Thanks,
Mark



An ontology for experimental actions

Informed Consent Ontology

Source

information content entity<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000030>

IAO_0000030<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000030>

SAME_URI

one-dimensional temporal region<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000038>

BFO_0000038<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000038>

SAME_URI

object<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000030>

object<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23OWLClass_fede789e_08ff_4d4a_bf4a_cd6f393a670d>

LOOM

material entity<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000040>

BFO_0000040<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000040>

SAME_URI

role<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000023>

role<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23OWLClass_705c1d8b_d7b2_455e_9f80_d4bc62eb57b1>

LOOM

Version<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fusefulinc.com%2Fns%2Fdoap%23Version>

version<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23OWLClass_870d9f06_a65a_415d_b7cc_e1dbbbcc9b2c>

LOOM

centrifuge<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0400106>

centrifuge<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1184060740.owl%23Class_53>

LOOM

temporal region<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000008>

BFO_0000008<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000008>

SAME_URI

site<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000029>

BFO_0000029<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000029>

SAME_URI

textual entity<http://bioportal.bioontology.org/visualize/virtual/ICO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000300>

IAO_0000300<http://bioportal.bioontology.org/visualize/virtual/EXACT?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000300>

SAME_URI





library(jsonlite)
library(httr)

# assign api key here
API_KEY  <-  ""

PAGE_SIZE <- 500
REST_URL <- "http://data.bioontology.org<http://data.bioontology.org/>"

sourceOntoAbbr  <-  "RXNORM"

# sourceOntoAbbr  <-  "EXACT"

next_page <-
  paste0(REST_URL,
         "/ontologies/",
         sourceOntoAbbr,
         "/mappings?pagesize=",
         PAGE_SIZE)

all.output.chunks <- list()

temp.rdf <- rrdf::new.rdf()

while (!is.null(next_page) > 0) {
  print(next_page)

  httpResponse <-
    GET(next_page,
        add_headers("Authorization" = paste0("apikey token=", API_KEY)),
        accept_json())

  page <-
    fromJSON(content(httpResponse, "text"), simplifyDataFrame = FALSE)

  next_page <- page$links$nextPage

  print(page$page)
  print(page$pageCount)

  one.output.chunk <-
    lapply(page$collection, function(current.collection) {


      matchMeth <- current.collection$source

      temp1 <- current.collection$classes[[1]]$links
      sourceOnt <- temp1$ontology
      inputTerm <- current.collection$classes[[1]]$`@id`

      temp2 <- current.collection$classes[[2]]$links
      matchOnt <- temp2$ontology
      matchTerm <- current.collection$classes[[2]]$`@id`

      return(
        list(
          "inputTerm" = inputTerm,
          "matchMeth" = matchMeth,
          "matchOnt" = matchOnt,
          "matchTerm" = matchTerm,
          "sourceOnt" = sourceOnt
        )
      )

    })
  one.output.chunk <- do.call(rbind.data.frame, one.output.chunk)

  all.output.chunks[[page$page]] <- one.output.chunk

}

all.output.chunks <- do.call(rbind.data.frame, all.output.chunks

write.table(all.output.chunks, sep = "\t", row.names = FALSE, file = paste0(sourceOntoAbbr, "_bioportal_mappings.tsv"))
_______________________________________________
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 mdorf at stanford.edu  Fri Oct 19 17:21:58 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Sat, 20 Oct 2018 00:21:58 +0000
Subject: [bioontology-support] [BioPortal] Feedback from CS
In-Reply-To: <5bc9cc74306fd_1c6d2adaf943411820028@ncbo-prd-app-08.stanford.edu.mail>
References: <5bc9cc74306fd_1c6d2adaf943411820028@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <5B2E9A3C-1769-4BE3-9C20-895E811CAC18@stanford.edu>

Hi CS,

I?ve removed the empty ISO-FOOD ontology from our system. Thank you for getting in touch with us!

Michael

On Oct 19, 2018, at 5:22 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: CS

Email: cs at ijs.si<mailto:cs at ijs.si>

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

Feedback:

Dear,

could you please delete the ontology with the acronym ISO-FOOD because it is empty.

Kind regards,
CS

_______________________________________________
bioontology-support mailing list
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From amassengale at rsna.org  Mon Oct 22 06:07:45 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Mon, 22 Oct 2018 13:07:45 +0000
Subject: [bioontology-support] BioPortal API not working
Message-ID: <7E659177-EA82-4305-AE9E-0DC4BD11C0D3@hq.rsna.org>

Good morning.

We have been using the following API without problems until this morning:

https://data.bioontology.org/search?ontology=RADLEX&apikey=db7eeeef-59e7-448c-a98e-0cc7d4d2850d&q=whole+body&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000

However, we are now getting a net::ERR_CERT_DATE_INVALID error. It appears that your SSL certificate has expired for the data.bioontology.org domain. See screenshot below:

[cid:image001.png at 01D469DE.53FA3630]

Let me know if you need any more information.

Thanks,

Andrew M

Andrew Massengale
Team Lead | Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago
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From 15091519-002 at uog.edu.pk  Sat Oct 20 00:33:53 2018
From: 15091519-002 at uog.edu.pk (Umair Khawaja)
Date: Sat, 20 Oct 2018 12:33:53 +0500
Subject: [bioontology-support] Need Help
Message-ID: <CAKr0X_RowA6n1Mu_7C1dVY8GWKnwRL30=N1BTZE97aVbG5Gm9w@mail.gmail.com>

Dear,
How can I get API KEY to use the REST API?

-- 
Regards
*Khawaja Umair*
*BS-CS*
University of Gujrat, Hafiz Hayat Campus,
Gujrat, Punjab, Pakistan
e: 15091519-002 at uog.edu.pk
LinkedIn <https://www.linkedin.com/in/umair-khawaja-6926b4124/> | Facebook
<https://www.facebook.com/umair.b.zubair.03>
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From Algy.Taylor at mft.nhs.uk  Mon Oct 22 08:11:05 2018
From: Algy.Taylor at mft.nhs.uk (Taylor Algy (R0A) Manchester University NHS FT)
Date: Mon, 22 Oct 2018 15:11:05 +0000
Subject: [bioontology-support] SSL Certificate Problem
Message-ID: <2A255021E131BA46BA526810BCC716079EED7641@V-MBX-5A.xCMMC.nhs.uk>

Hi,

First, thanks for your amazing REST API service.  We've been using it here (Manchester Centre for Genomic Medicine, UK) for the last 2-3 years to improve the quality of our clinical data.

Anyway, I only write because I've noticed that I've been getting error messages from your search API:
[cid:image004.png at 01D46A21.D6101430]

Please let me know if I can provide any further help or details.


Best wishes,
Algy


--
Algy Taylor MBCS
Bioinformatics Developer
Manchester Centre for Genomic Medicine


[cid:image003.png at 01D46A21.B9530DC0]


Manchester Centre for Genomic Medicine
Manchester University NHS Foundation Trust
Saint Mary's Hospital
Oxford Road, Manchester, M13 9WL

T: 0161 276 8703
E: algy.taylor at mft.nhs.uk<mailto:algy.taylor at mft.nhs.uk>

www.mft.nhs.uk<http://www.mft.nhs.uk/>

Privacy and Confidentiality Notice: The information contained in this e-mail is intended for the named recipient(s) only. It may contain privileged and confidential information.  If you are not an intended recipient, you must not copy, distribute or take any action in reliance on it. If you have received this e-mail in error, we would be grateful if you would notify us immediately.  Thank you for your assistance.
 
Please note that e-mails sent or received by our staff may be disclosed under the Freedom of Information Act (unless exempt).
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From vendetti at stanford.edu  Mon Oct 22 10:27:58 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 22 Oct 2018 17:27:58 +0000
Subject: [bioontology-support] BioPortal API not working
In-Reply-To: <7E659177-EA82-4305-AE9E-0DC4BD11C0D3@hq.rsna.org>
References: <7E659177-EA82-4305-AE9E-0DC4BD11C0D3@hq.rsna.org>
Message-ID: <E37B1587-6ADC-4AE9-A733-BA10BCCE4EF4@stanford.edu>

Hi Andrew,


On Oct 22, 2018, at 6:07 AM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

We have been using the following API without problems until this morning:

https://data.bioontology.org/search?ontology=RADLEX&apikey=db7eeeef-59e7-448c-a98e-0cc7d4d2850d&q=whole+body&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000

However, we are now getting a net::ERR_CERT_DATE_INVALID error. It appears that your SSL certificate has expired for the data.bioontology.org<http://data.bioontology.org/> domain.


Sincere apologies for that. The certificate is renewed and you should be able to proceed without errors now.

Kind regards,
Jennifer


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From vendetti at stanford.edu  Mon Oct 22 10:29:17 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 22 Oct 2018 17:29:17 +0000
Subject: [bioontology-support] Need Help
In-Reply-To: <CAKr0X_RowA6n1Mu_7C1dVY8GWKnwRL30=N1BTZE97aVbG5Gm9w@mail.gmail.com>
References: <CAKr0X_RowA6n1Mu_7C1dVY8GWKnwRL30=N1BTZE97aVbG5Gm9w@mail.gmail.com>
Message-ID: <3C03D8D7-A9F9-44DA-BE76-E8BF5F0AAF1E@stanford.edu>

Hello Umair,

We have some instructions for this on our wiki:

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

Kind regards,
Jennifer



On Oct 20, 2018, at 12:33 AM, Umair Khawaja <15091519-002 at uog.edu.pk<mailto:15091519-002 at uog.edu.pk>> wrote:

Dear,
How can I get API KEY to use the REST API?

--
Regards
Khawaja Umair
BS-CS
University of Gujrat, Hafiz Hayat Campus,
Gujrat, Punjab, Pakistan
e: 15091519-002 at uog.edu.pk<mailto:15091519-002 at uog.edu.pk>
LinkedIn<https://www.linkedin.com/in/umair-khawaja-6926b4124/> | Facebook<https://www.facebook.com/umair.b.zubair.03>
_______________________________________________
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  Mon Oct 22 10:33:47 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 22 Oct 2018 17:33:47 +0000
Subject: [bioontology-support] SSL Certificate Problem
In-Reply-To: <2A255021E131BA46BA526810BCC716079EED7641@V-MBX-5A.xCMMC.nhs.uk>
References: <2A255021E131BA46BA526810BCC716079EED7641@V-MBX-5A.xCMMC.nhs.uk>
Message-ID: <103C8E7E-902F-4D4C-8A7D-437564CCB3DC@stanford.edu>

Hi Algy,

On Oct 22, 2018, at 8:11 AM, Taylor Algy (R0A) Manchester University NHS FT <Algy.Taylor at mft.nhs.uk<mailto:Algy.Taylor at mft.nhs.uk>> wrote:

First, thanks for your amazing REST API service.  We?ve been using it here (Manchester Centre for Genomic Medicine, UK) for the last 2-3 years to improve the quality of our clinical data.


We?re very glad to hear that the API has proved useful for your group.



Anyway, I only write because I?ve noticed that I?ve been getting error messages from your search API:


Sincere apologies for that. Our security certificate expired, which was the underlying cause of these errors. The certificate has been renewed and you should be able to proceed without errors now.

Kind regards,
Jennifer



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From amassengale at rsna.org  Mon Oct 22 11:24:25 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Mon, 22 Oct 2018 18:24:25 +0000
Subject: [bioontology-support] BioPortal API not working
In-Reply-To: <E37B1587-6ADC-4AE9-A733-BA10BCCE4EF4@stanford.edu>
References: <7E659177-EA82-4305-AE9E-0DC4BD11C0D3@hq.rsna.org>
 <E37B1587-6ADC-4AE9-A733-BA10BCCE4EF4@stanford.edu>
Message-ID: <BA9A66DD-8974-4776-BD30-3B4BCF0D2482@hq.rsna.org>

Confirmed. Thanks Jennifer!

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Monday, October 22, 2018 at 12:28 PM
To: Andrew Massengale <amassengale at rsna.org>
Cc: "support at bioontology.org" <support at bioontology.org>, Derrick Lottich <dlottich at rsna.org>
Subject: Re: [bioontology-support] BioPortal API not working

Hi Andrew,



On Oct 22, 2018, at 6:07 AM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

We have been using the following API without problems until this morning:

https://data.bioontology.org/search?ontology=RADLEX&apikey=db7eeeef-59e7-448c-a98e-0cc7d4d2850d&q=whole+body&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fontology%3DRADLEX%26apikey%3Ddb7eeeef-59e7-448c-a98e-0cc7d4d2850d%26q%3Dwhole%2Bbody%26format%3Djson%26subtree_root_id%3Dhttp%3A%252F%252Fwww.radlex.org%252FRID%252F%2523RID3%26roots_only%3Dtrue%26page%3D1%26pagesize%3D1000&data=02%7C01%7Camassengale%40rsna.org%7Ceac6508dd12e4347b85c08d63843bb66%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636758260900863578&sdata=Cj7ia1YqkNsoGf6eSTOfxYxhaBox5TMOtx0NF7b0yko%3D&reserved=0>

However, we are now getting a net::ERR_CERT_DATE_INVALID error. It appears that your SSL certificate has expired for the data.bioontology.org<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2F&data=02%7C01%7Camassengale%40rsna.org%7Ceac6508dd12e4347b85c08d63843bb66%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636758260900873590&sdata=T%2FKZqWyyyBv%2BtVeIR7Joyqwf1MfyZZuskNXKrtAPk98%3D&reserved=0> domain.


Sincere apologies for that. The certificate is renewed and you should be able to proceed without errors now.

Kind regards,
Jennifer


Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org>

Facebook<http://www.facebook.com/RSNAfans>
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From Ross.W.Filice at gunet.georgetown.edu  Tue Oct 23 08:32:48 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Tue, 23 Oct 2018 11:32:48 -0400
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu>
References: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <D9DB15C3-DDE1-4F3B-8496-70ED78987954@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B854F0DFF42@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <E4318C79-7578-4FE9-B31C-DC83A8914C42@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B854F0E00E6@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu>
Message-ID: <DAE74CB00EC3AD49975BE0428640870B855066425E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

Thanks very much Jennifer. I?m able to create mappings through the API for rdfs#sameAs which shows up as expected. However, for rdfs#subClassOf the ordering of things doesn?t appear to be respected.

For example, if I want to map something from our ontology (GAMUTS) which we consider to be a ?superclass? of an entity from another ontology. So, for example, I?m trying to make a mapping to state that the DOID entity 1003 (pelvic inflammatory disease) is a subClassOf GAMUTS entity ?abdominal_or_pelvic_inflammatory_disease?. If I submit the following JSON object:

{"creator":"rwfilice","relation":"http://www.w3.org/2002/07/rdfs#subClassOf","classes":{"http://purl.obolibrary.org/obo/DOID_1003":"DOID","http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease":"GAMUTS"}}

The API doesn?t appear to respect the order in which the classes are submitted ? which in some ways is understandable as the classes object is a hash which by definition does not have an order ? but is there any way to specify such an order? The same ordering problem occurs if you do what might be considered a more traditional mapping ? i.e. a GAMUTS class that is a subclass of some other ontology class.

In either case if you query the mappings for each entity you get the subclass relationship but they are in reverse order depending on which ontology you query. Below is the result of trying to do that superclass mapping I described above. The first class listed is just whatever ontology you query ? you don?t get an order that you can infer the subclass relationship from.

Thanks much,
Ross

GAMUTS query (first the GAMUTS entity, then the DOID entity):

{
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "source": "REST",
        "classes": [
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease",
                ?.
            },
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003",
                ?.
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
}

And the DOID query (first the DOID entity, then the GAMUTS entity):

    {
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "source": "REST",
        "classes": [
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003",
                ?.
            },
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease",
                ?.
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
        "@id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "@type": "http://data.bioontology.org/metadata/Mapping"
    },

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, September 25, 2018 8:16 PM
To: Filice, Ross W
Cc: bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] programmatic class mappings

** ATTENTION: This email originated from outside of the MedStar network.
** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.


Hi Ross,

My apologies that you?ve had to endure some back and forth with us. We?re a small team and I wasn?t able to look at this in some detail until today. The example code in our repository is outdated in more ways than I thought. I haven?t had time to modify the code, so instead I?ll add some information here about the JSON structure you need to use, along with some screenshots from testing in Postman.

This is the JSON structure that the mappings endpoint is expecting (which is simpler / has less nesting than the older version):

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":"SNOMEDCT"
  }
}

The ?classes? hash contains the data for the classes you want to create a mapping between, with the class ID on the left-hand side and the ontology acronym on the right-hand side.

You can also add the ?source", ?source_name", and ?comment" key value pairs as before, but they aren?t required. What I listed above is the minimum structure you need to create the mapping. Here is a another example with the additional pairs added:

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "source" : "vendetti",
  "source_name" : "Jennifer's Test Mapping Data",
  "comment" : "Creates a same as mapping between Melanoma (NCIT) and Malignant melanoma (SNOMEDCT)",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":?SNOMEDCT"
  }
}


If you want to test this in Postman, you?ll need header information like the following (please enter your API key where I?ve indicated):


[cid:image001.png at 01D46AC2.87DDB280]


? and here is the body text:


[cid:image002.png at 01D46AC2.87DDB280]


Clicking the Send button should result in a ?201 Created? status with a result that contains the mapping creation date, etc.:


[cid:image003.png at 01D46AC2.87DDB280]


? and here is what it looks like in BioPortal (you may have to refresh the SNOMEDCT page):


[cid:image004.png at 01D46AC2.87DDB280]


You can select the Malignant melanoma class in SNOMEDCT:

https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_SNOMEDCT_-3Fp-3Dclasses-26conceptid-3Dhttp-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=zHivVLJLDcMIQFj9sE8C_14WSL_Z9eUbxxMinrNUYvk&e=>

? and click the Class Mappings tab to view this in the production application. I created one of the mappings with a source_name, and one without. I?ll delete the test mappings in a day or two.

Let me know if you?re still having difficulties.

Kind regards,
Jennifer




On Sep 24, 2018, at 6:53 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks Jennifer. If I change to classes instead of terms as such:

{
 "creator" : "http://data.bioontology.org/user/rwfilice<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_rwfilice&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=9Kvl2F4iwxRotzPXcZeeuNimPXKgiegqHo8890U7kDU&e=>",
 "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
 "source" : "rwfilice",
 "source_name" : "rwfilice Mapping Data",
 "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",
 "classes" : [ {
   "ontology" : "NCIT",
   "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=KguElG_zro0KoJR-Tgb6CUu4Ty7E4Ozt68nY482TGE0&e=>" ]
 }, {
   "ontology" : "SNOMEDCT",
   "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=J5RkphjbVpl59HJk-oKWEHhgdo8lEq6ZBMvdlM8kk_w&e=>" ]
 } ]
}

I get an Internal Server Error (500)

Any further help would be much appreciated.
Thanks much,
Ross

-----Original Message-----
From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Monday, September 24, 2018 7:32 PM
To: Filice, Ross W
Cc: John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings


** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.

Hello Ross,



Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors.



Kind regards,

Jennifer






On Sep 24, 2018, at 10:37 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:





Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error:





{"errors":["Input does not contain classes"],"status":400}





I'm submitting the JSON object as provided by the github code:





{


"creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=",


"relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=",


"source" : "[USER]",


"source_name" : "[USER] Mapping Data",


"comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",


"terms" : [ {


  "ontology" : "NCIT",


  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ]


}, {


  "ontology" : "SNOMEDCT",


  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ]


} ]


}





Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings:





https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e=





It includes parameters "source" "id" "process" and "classes" without any other information.





Thanks much,


Ross





-----Original Message-----


From: John Graybeal [mailto:jgraybeal at stanford.edu]


Sent: Thursday, August 30, 2018 7:14 PM


To: Filice, Ross W


Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>


Subject: Re: [bioontology-support] programmatic class mappings








** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.





Hi Ross,











BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=.











Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept.  At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.)











But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=:











You can also manually create mappings using our REST API:











https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e=











We have example code for programmatically creating mappings in our GitHub sample code repository:











https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e=











I hope all this helps.











John

















On Aug 28, 2018, at 12:02 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:











Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other?











And similarly is there a way to map subclasses across ontologies?











Thanks much,





Ross











Ross W. Filice, M.D.





Associate Professor and Chief, Imaging Informatics





Department of Radiology, MedStar Georgetown University Hospital





Chief, Imaging Informatics





MedStar Medical Group Radiology





Clinical Informatics Scientist





National Center for Human Factors in Healthcare, MedStar Institute for Innovation











3800 Reservoir Road NW, CG 201





Washington DC, 20007





202-444-3450 PHONE





202-444-4899 FAX





ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>





https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e=











_______________________________________________





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https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e=











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





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


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https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=AF8-u_FYGJ9Bc9prtVxgWktndfWTn0vy_iu-5EXzp3o&e=

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From megapode32559 at gmail.com  Tue Oct 23 13:06:34 2018
From: megapode32559 at gmail.com (Michael Liu)
Date: Tue, 23 Oct 2018 15:06:34 -0500
Subject: [bioontology-support] How to always get the most up-to-date
	ontology file?
Message-ID: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>

Hi,

https://bioportal.bioontology.org/ontologies/BTO

I see the following URL on the above website. It is the currently most
updated ontology file. But it is associated with a specific
submission. It will outdated sooner or later.

http://data.bioontology.org/ontologies/BTO/submissions/33/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb

Is there a URL that always points to the latest version of the
ontology file? Thanks.

-- 
Best wishes,
Michael

From vendetti at stanford.edu  Tue Oct 23 16:54:06 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 23 Oct 2018 23:54:06 +0000
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <DAE74CB00EC3AD49975BE0428640870B855066425E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
References: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <D9DB15C3-DDE1-4F3B-8496-70ED78987954@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B854F0DFF42@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <E4318C79-7578-4FE9-B31C-DC83A8914C42@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B854F0E00E6@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B855066425E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
Message-ID: <9B53C4B3-0875-4674-97DF-B339BB74049B@stanford.edu>

Hi Ross,

Apologies that it?s likely not clear from any of our documentation that BioPortal only supports bidirectional mappings, e.g., owl:sameAs, skos:closeMatch, skos:exactMatch, etc.

I wasn?t on the team when the mapping functionality was designed and implemented, so unfortunately I can?t provide any historical perspective on why the system was designed in this manner. I?ll ping one of my predecessors and see if he?s able to offer any more detail.

Kind regards,
Jennifer


On Oct 23, 2018, at 8:32 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks very much Jennifer. I?m able to create mappings through the API for rdfs#sameAs which shows up as expected. However, for rdfs#subClassOf the ordering of things doesn?t appear to be respected.

For example, if I want to map something from our ontology (GAMUTS) which we consider to be a ?superclass? of an entity from another ontology. So, for example, I?m trying to make a mapping to state that the DOID entity 1003 (pelvic inflammatory disease) is a subClassOf GAMUTS entity ?abdominal_or_pelvic_inflammatory_disease?. If I submit the following JSON object:

{"creator":"rwfilice","relation":"http://www.w3.org/2002/07/rdfs#subClassOf","classes":{"http://purl.obolibrary.org/obo/DOID_1003":"DOID","http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease":"GAMUTS"}}

The API doesn?t appear to respect the order in which the classes are submitted ? which in some ways is understandable as the classes object is a hash which by definition does not have an order ? but is there any way to specify such an order? The same ordering problem occurs if you do what might be considered a more traditional mapping ? i.e. a GAMUTS class that is a subclass of some other ontology class.

In either case if you query the mappings for each entity you get the subclass relationship but they are in reverse order depending on which ontology you query. Below is the result of trying to do that superclass mapping I described above. The first class listed is just whatever ontology you query ? you don?t get an order that you can infer the subclass relationship from.

Thanks much,
Ross

GAMUTS query (first the GAMUTS entity, then the DOID entity):

{
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "source": "REST",
        "classes": [
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease",
                ?.
            },
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003",
                ?.
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
}

And the DOID query (first the DOID entity, then the GAMUTS entity):

    {
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "source": "REST",
        "classes": [
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003",
                ?.
            },
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease",
                ?.
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
        "@id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "@type": "http://data.bioontology.org/metadata/Mapping"
    },

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, September 25, 2018 8:16 PM
To: Filice, Ross W
Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings

** ATTENTION: This email originated from outside of the MedStar network.
** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.


Hi Ross,

My apologies that you?ve had to endure some back and forth with us. We?re a small team and I wasn?t able to look at this in some detail until today. The example code in our repository is outdated in more ways than I thought. I haven?t had time to modify the code, so instead I?ll add some information here about the JSON structure you need to use, along with some screenshots from testing in Postman.

This is the JSON structure that the mappings endpoint is expecting (which is simpler / has less nesting than the older version):

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":"SNOMEDCT"
  }
}

The ?classes? hash contains the data for the classes you want to create a mapping between, with the class ID on the left-hand side and the ontology acronym on the right-hand side.

You can also add the ?source", ?source_name", and ?comment" key value pairs as before, but they aren?t required. What I listed above is the minimum structure you need to create the mapping. Here is a another example with the additional pairs added:

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "source" : "vendetti",
  "source_name" : "Jennifer's Test Mapping Data",
  "comment" : "Creates a same as mapping between Melanoma (NCIT) and Malignant melanoma (SNOMEDCT)",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":?SNOMEDCT"
  }
}


If you want to test this in Postman, you?ll need header information like the following (please enter your API key where I?ve indicated):


<image001.png>


? and here is the body text:


<image002.png>


Clicking the Send button should result in a ?201 Created? status with a result that contains the mapping creation date, etc.:


<image003.png>


? and here is what it looks like in BioPortal (you may have to refresh the SNOMEDCT page):


<image004.png>


You can select the Malignant melanoma class in SNOMEDCT:

https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_SNOMEDCT_-3Fp-3Dclasses-26conceptid-3Dhttp-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=zHivVLJLDcMIQFj9sE8C_14WSL_Z9eUbxxMinrNUYvk&e=>

? and click the Class Mappings tab to view this in the production application. I created one of the mappings with a source_name, and one without. I?ll delete the test mappings in a day or two.

Let me know if you?re still having difficulties.

Kind regards,
Jennifer




On Sep 24, 2018, at 6:53 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks Jennifer. If I change to classes instead of terms as such:

{
 "creator" : "http://data.bioontology.org/user/rwfilice<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_rwfilice&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=9Kvl2F4iwxRotzPXcZeeuNimPXKgiegqHo8890U7kDU&e=>",
 "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
 "source" : "rwfilice",
 "source_name" : "rwfilice Mapping Data",
 "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",
 "classes" : [ {
   "ontology" : "NCIT",
   "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=KguElG_zro0KoJR-Tgb6CUu4Ty7E4Ozt68nY482TGE0&e=>" ]
 }, {
   "ontology" : "SNOMEDCT",
   "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=J5RkphjbVpl59HJk-oKWEHhgdo8lEq6ZBMvdlM8kk_w&e=>" ]
 } ]
}

I get an Internal Server Error (500)

Any further help would be much appreciated.
Thanks much,
Ross

-----Original Message-----
From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Monday, September 24, 2018 7:32 PM
To: Filice, Ross W
Cc: John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings


** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.

Hello Ross,



Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors.



Kind regards,

Jennifer






On Sep 24, 2018, at 10:37 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:





Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error:





{"errors":["Input does not contain classes"],"status":400}





I'm submitting the JSON object as provided by the github code:





{


"creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=",


"relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=",


"source" : "[USER]",


"source_name" : "[USER] Mapping Data",


"comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",


"terms" : [ {


  "ontology" : "NCIT",


  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ]


}, {


  "ontology" : "SNOMEDCT",


  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ]


} ]


}





Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings:





https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e=





It includes parameters "source" "id" "process" and "classes" without any other information.





Thanks much,


Ross





-----Original Message-----


From: John Graybeal [mailto:jgraybeal at stanford.edu]


Sent: Thursday, August 30, 2018 7:14 PM


To: Filice, Ross W


Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>


Subject: Re: [bioontology-support] programmatic class mappings








** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.





Hi Ross,











BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=.











Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept.  At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.)











But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=:











You can also manually create mappings using our REST API:











https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e=











We have example code for programmatically creating mappings in our GitHub sample code repository:











https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e=











I hope all this helps.











John

















On Aug 28, 2018, at 12:02 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:











Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other?











And similarly is there a way to map subclasses across ontologies?











Thanks much,





Ross











Ross W. Filice, M.D.





Associate Professor and Chief, Imaging Informatics





Department of Radiology, MedStar Georgetown University Hospital





Chief, Imaging Informatics





MedStar Medical Group Radiology





Clinical Informatics Scientist





National Center for Human Factors in Healthcare, MedStar Institute for Innovation











3800 Reservoir Road NW, CG 201





Washington DC, 20007





202-444-3450 PHONE





202-444-4899 FAX





ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>





https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e=











_______________________________________________





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https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e=











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





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


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https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=AF8-u_FYGJ9Bc9prtVxgWktndfWTn0vy_iu-5EXzp3o&e=

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From vendetti at stanford.edu  Tue Oct 23 17:00:30 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 24 Oct 2018 00:00:30 +0000
Subject: [bioontology-support] How to always get the most
	up-to-date	ontology file?
In-Reply-To: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
References: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
Message-ID: <B1FA66FE-CFAE-40EA-B8D6-E3EDFA9B75FC@stanford.edu>

Hi Michael,


On Oct 23, 2018, at 1:06 PM, Michael Liu <megapode32559 at gmail.com<mailto:megapode32559 at gmail.com>> wrote:

https://bioportal.bioontology.org/ontologies/BTO

I see the following URL on the above website. It is the currently most
updated ontology file. But it is associated with a specific
submission. It will outdated sooner or later.

http://data.bioontology.org/ontologies/BTO/submissions/33/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb

Is there a URL that always points to the latest version of the
ontology file? Thanks.


Yes - this REST API call:

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

? will always download the ontology source file associated with the most recent submission of the BTO ontology.

Kind regards,
Jennifer

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From Ross.W.Filice at gunet.georgetown.edu  Wed Oct 24 05:13:18 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Wed, 24 Oct 2018 08:13:18 -0400
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <9B53C4B3-0875-4674-97DF-B339BB74049B@stanford.edu>
References: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
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 <DAE74CB00EC3AD49975BE0428640870B854F0DFF42@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <E4318C79-7578-4FE9-B31C-DC83A8914C42@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B854F0E00E6@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu>
 <DAE74CB00EC3AD49975BE0428640870B855066425E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <9B53C4B3-0875-4674-97DF-B339BB74049B@stanford.edu>
Message-ID: <DAE74CB00EC3AD49975BE0428640870B85506645BE@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

No problem ? thanks for clarifying. If you find out any other information and can share of course that would be appreciated. And I guess you could consider this a feature request if it makes sense to your team.
Thanks again,
Ross

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, October 23, 2018 7:54 PM
To: Filice, Ross W
Cc: bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] programmatic class mappings

** ATTENTION: This email originated from outside of the MedStar network.
** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.


Hi Ross,

Apologies that it?s likely not clear from any of our documentation that BioPortal only supports bidirectional mappings, e.g., owl:sameAs, skos:closeMatch, skos:exactMatch, etc.

I wasn?t on the team when the mapping functionality was designed and implemented, so unfortunately I can?t provide any historical perspective on why the system was designed in this manner. I?ll ping one of my predecessors and see if he?s able to offer any more detail.

Kind regards,
Jennifer



On Oct 23, 2018, at 8:32 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks very much Jennifer. I?m able to create mappings through the API for rdfs#sameAs which shows up as expected. However, for rdfs#subClassOf the ordering of things doesn?t appear to be respected.

For example, if I want to map something from our ontology (GAMUTS) which we consider to be a ?superclass? of an entity from another ontology. So, for example, I?m trying to make a mapping to state that the DOID entity 1003 (pelvic inflammatory disease) is a subClassOf GAMUTS entity ?abdominal_or_pelvic_inflammatory_disease?. If I submit the following JSON object:

{"creator":"rwfilice","relation":"http://www.w3.org/2002/07/rdfs#subClassOf<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_rdfs-23subClassOf&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=9IJAWfwDA5zpgeTjultqHOa6LeIYW43u2eChFg8ss1c&e=>","classes":{"http://purl.obolibrary.org/obo/DOID_1003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_DOID-5F1003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=OZhp8d6j16e2MFdHiTQ-uv2W2nrNs_t0uF_RRr5atqc&e=>":"DOID","http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gamuts.net_entity-23abdominal-5For-5Fpelvic-5Finflammatory-5Fdisease&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=4ZcxeqAZRQgPyX8G58td8PUgTmUxMG_o9vWsANEU1UE&e=>":"GAMUTS"}}

The API doesn?t appear to respect the order in which the classes are submitted ? which in some ways is understandable as the classes object is a hash which by definition does not have an order ? but is there any way to specify such an order? The same ordering problem occurs if you do what might be considered a more traditional mapping ? i.e. a GAMUTS class that is a subclass of some other ontology class.

In either case if you query the mappings for each entity you get the subclass relationship but they are in reverse order depending on which ontology you query. Below is the result of trying to do that superclass mapping I described above. The first class listed is just whatever ontology you query ? you don?t get an order that you can infer the subclass relationship from.

Thanks much,
Ross

GAMUTS query (first the GAMUTS entity, then the DOID entity):

{
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_rest-5Fbackup-5Fmappings_c18b9c30-2Db904-2D0136-2D06f7-2D005056010074&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=5ANX5S8KIqApDislC4-94TQGA8rNTbDR9e4-2gKAXdQ&e=>",
        "source": "REST",
        "classes": [
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gamuts.net_entity-23abdominal-5For-5Fpelvic-5Finflammatory-5Fdisease&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=4ZcxeqAZRQgPyX8G58td8PUgTmUxMG_o9vWsANEU1UE&e=>",
                ?.
            },
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_DOID-5F1003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=OZhp8d6j16e2MFdHiTQ-uv2W2nrNs_t0uF_RRr5atqc&e=>",
                ?.
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_metadata_mapping-5Fprocesses_-2Drwfilice-2Dc180dc40-2Db904-2D0136-2D06f6-2D005056010074&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=dg5_dUiibEM1xmXX3qs6W3RCekgnHKZS1FJBuywWmTA&e=>",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_users_rwfilice&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=wM4Hr7RaHctvwhiOzXIfYWv6miU1S8MvjN9t1rdnN-0&e=>",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_rdfs-23subClassOf&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=9IJAWfwDA5zpgeTjultqHOa6LeIYW43u2eChFg8ss1c&e=>",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
}

And the DOID query (first the DOID entity, then the GAMUTS entity):

    {
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_rest-5Fbackup-5Fmappings_c18b9c30-2Db904-2D0136-2D06f7-2D005056010074&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=5ANX5S8KIqApDislC4-94TQGA8rNTbDR9e4-2gKAXdQ&e=>",
        "source": "REST",
        "classes": [
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_DOID-5F1003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=OZhp8d6j16e2MFdHiTQ-uv2W2nrNs_t0uF_RRr5atqc&e=>",
                ?.
            },
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gamuts.net_entity-23abdominal-5For-5Fpelvic-5Finflammatory-5Fdisease&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=4ZcxeqAZRQgPyX8G58td8PUgTmUxMG_o9vWsANEU1UE&e=>",
                ?.
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_metadata_mapping-5Fprocesses_-2Drwfilice-2Dc180dc40-2Db904-2D0136-2D06f6-2D005056010074&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=dg5_dUiibEM1xmXX3qs6W3RCekgnHKZS1FJBuywWmTA&e=>",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_users_rwfilice&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=wM4Hr7RaHctvwhiOzXIfYWv6miU1S8MvjN9t1rdnN-0&e=>",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_rdfs-23subClassOf&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=9IJAWfwDA5zpgeTjultqHOa6LeIYW43u2eChFg8ss1c&e=>",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
        "@id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_rest-5Fbackup-5Fmappings_c18b9c30-2Db904-2D0136-2D06f7-2D005056010074&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=5ANX5S8KIqApDislC4-94TQGA8rNTbDR9e4-2gKAXdQ&e=>",
        "@type": "http://data.bioontology.org/metadata/Mapping<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_metadata_Mapping&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=arcxB8t9O3ReZRqBG4nWsqzEgXLReAd0GqVmv0YTpSg&s=0YD7JwFK_8c_uCffFCg0CbVPZesfwvI8DHIsscuF9uw&e=>"
    },

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, September 25, 2018 8:16 PM
To: Filice, Ross W
Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings

** ATTENTION: This email originated from outside of the MedStar network.
** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.


Hi Ross,

My apologies that you?ve had to endure some back and forth with us. We?re a small team and I wasn?t able to look at this in some detail until today. The example code in our repository is outdated in more ways than I thought. I haven?t had time to modify the code, so instead I?ll add some information here about the JSON structure you need to use, along with some screenshots from testing in Postman.

This is the JSON structure that the mappings endpoint is expecting (which is simpler / has less nesting than the older version):

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":"SNOMEDCT"
  }
}

The ?classes? hash contains the data for the classes you want to create a mapping between, with the class ID on the left-hand side and the ontology acronym on the right-hand side.

You can also add the ?source", ?source_name", and ?comment" key value pairs as before, but they aren?t required. What I listed above is the minimum structure you need to create the mapping. Here is a another example with the additional pairs added:

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "source" : "vendetti",
  "source_name" : "Jennifer's Test Mapping Data",
  "comment" : "Creates a same as mapping between Melanoma (NCIT) and Malignant melanoma (SNOMEDCT)",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":?SNOMEDCT"
  }
}


If you want to test this in Postman, you?ll need header information like the following (please enter your API key where I?ve indicated):


<image001.png>


? and here is the body text:


<image002.png>


Clicking the Send button should result in a ?201 Created? status with a result that contains the mapping creation date, etc.:


<image003.png>


? and here is what it looks like in BioPortal (you may have to refresh the SNOMEDCT page):


<image004.png>


You can select the Malignant melanoma class in SNOMEDCT:

https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_SNOMEDCT_-3Fp-3Dclasses-26conceptid-3Dhttp-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=zHivVLJLDcMIQFj9sE8C_14WSL_Z9eUbxxMinrNUYvk&e=>

? and click the Class Mappings tab to view this in the production application. I created one of the mappings with a source_name, and one without. I?ll delete the test mappings in a day or two.

Let me know if you?re still having difficulties.

Kind regards,
Jennifer





On Sep 24, 2018, at 6:53 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks Jennifer. If I change to classes instead of terms as such:

{
 "creator" : "http://data.bioontology.org/user/rwfilice<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_rwfilice&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=9Kvl2F4iwxRotzPXcZeeuNimPXKgiegqHo8890U7kDU&e=>",
 "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
 "source" : "rwfilice",
 "source_name" : "rwfilice Mapping Data",
 "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",
 "classes" : [ {
   "ontology" : "NCIT",
   "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=KguElG_zro0KoJR-Tgb6CUu4Ty7E4Ozt68nY482TGE0&e=>" ]
 }, {
   "ontology" : "SNOMEDCT",
   "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=J5RkphjbVpl59HJk-oKWEHhgdo8lEq6ZBMvdlM8kk_w&e=>" ]
 } ]
}

I get an Internal Server Error (500)

Any further help would be much appreciated.
Thanks much,
Ross

-----Original Message-----
From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Monday, September 24, 2018 7:32 PM
To: Filice, Ross W
Cc: John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings


** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.

Hello Ross,



Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors.



Kind regards,

Jennifer







On Sep 24, 2018, at 10:37 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:







Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error:







{"errors":["Input does not contain classes"],"status":400}







I'm submitting the JSON object as provided by the github code:







{



"creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=",



"relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=",



"source" : "[USER]",



"source_name" : "[USER] Mapping Data",



"comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",



"terms" : [ {



  "ontology" : "NCIT",



  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ]



}, {



  "ontology" : "SNOMEDCT",



  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ]



} ]



}







Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings:







https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e=







It includes parameters "source" "id" "process" and "classes" without any other information.







Thanks much,



Ross







-----Original Message-----



From: John Graybeal [mailto:jgraybeal at stanford.edu]



Sent: Thursday, August 30, 2018 7:14 PM



To: Filice, Ross W



Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>



Subject: Re: [bioontology-support] programmatic class mappings











** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.







Hi Ross,















BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=.















Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept.  At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.)















But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=:















You can also manually create mappings using our REST API:















https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e=















We have example code for programmatically creating mappings in our GitHub sample code repository:















https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e=















I hope all this helps.















John























On Aug 28, 2018, at 12:02 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:















Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other?















And similarly is there a way to map subclasses across ontologies?















Thanks much,







Ross















Ross W. Filice, M.D.







Associate Professor and Chief, Imaging Informatics







Department of Radiology, MedStar Georgetown University Hospital







Chief, Imaging Informatics







MedStar Medical Group Radiology







Clinical Informatics Scientist







National Center for Human Factors in Healthcare, MedStar Institute for Innovation















3800 Reservoir Road NW, CG 201







Washington DC, 20007







202-444-3450 PHONE







202-444-4899 FAX







ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>







https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e=















_______________________________________________







bioontology-support mailing list







bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>







https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e=















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







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://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=AF8-u_FYGJ9Bc9prtVxgWktndfWTn0vy_iu-5EXzp3o&e=

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From megapode32559 at gmail.com  Thu Oct 25 09:35:15 2018
From: megapode32559 at gmail.com (Michael Liu)
Date: Thu, 25 Oct 2018 11:35:15 -0500
Subject: [bioontology-support] Anything wrong with bioportal.bioontology.org
In-Reply-To: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
References: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
Message-ID: <CABcfS1jHnLvsip3H8=28JTC8UahE0=eEPDO+QdaU3nQBBD-6bQ@mail.gmail.com>

Hi,

I see "Problem retrieving classes" on the following URL. Is there
anything wrong?

https://bioportal.bioontology.org/ontologies/DDO/?p=classes&conceptid=root

-- 
Best wishes,
Michael

From megapode32559 at gmail.com  Thu Oct 25 01:37:28 2018
From: megapode32559 at gmail.com (Michael Liu)
Date: Thu, 25 Oct 2018 03:37:28 -0500
Subject: [bioontology-support] How to download MEDDRA?
In-Reply-To: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
References: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
Message-ID: <CABcfS1j1HM9BrSTD-w+mJH=ms-iOCb8GfHFkYUY1T0eNXnmUUw@mail.gmail.com>

Hi,

http://data.bioontology.org/ontologies/MEDDRA/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb

I got the following error message when I try to download MEDDRA. Does
this mean that there is not a way to download it? Thanks.

{
-"errors": [
"License restrictions on download for MEDDRA"
],
"status": 403
}

-- 
Best wishes,
Michael

From vendetti at stanford.edu  Thu Oct 25 17:12:24 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 26 Oct 2018 00:12:24 +0000
Subject: [bioontology-support] Anything wrong with
 bioportal.bioontology.org
In-Reply-To: <CABcfS1jHnLvsip3H8=28JTC8UahE0=eEPDO+QdaU3nQBBD-6bQ@mail.gmail.com>
References: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
 <CABcfS1jHnLvsip3H8=28JTC8UahE0=eEPDO+QdaU3nQBBD-6bQ@mail.gmail.com>
Message-ID: <C6F6E7E4-728B-4BE9-96A9-2D990A7E9F2A@stanford.edu>

Hello Michael,

Yes - there?s a bug that?s been uncovered in BioPortal recently where the Classes tab is inaccessible under certain conditions (for users logged in with a non-administrative account, attempting to view ontologies with a fair amount of class mappings). We?re working on trying to get this fixed.

In the mean time, you should be able to use the workaround of logging out of your account and then viewing the page you mention below:

https://bioportal.bioontology.org/ontologies/DDO/?p=classes&conceptid=root

Let us know if that doesn?t work for you. Apologies for the inconvenience.

Kind regards,
Jennifer


On Oct 25, 2018, at 9:35 AM, Michael Liu <megapode32559 at gmail.com<mailto:megapode32559 at gmail.com>> wrote:

Hi,

I see "Problem retrieving classes" on the following URL. Is there
anything wrong?

https://bioportal.bioontology.org/ontologies/DDO/?p=classes&conceptid=root

--
Best wishes,
Michael
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Thu Oct 25 17:21:34 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 26 Oct 2018 00:21:34 +0000
Subject: [bioontology-support] How to download MEDDRA?
In-Reply-To: <CABcfS1j1HM9BrSTD-w+mJH=ms-iOCb8GfHFkYUY1T0eNXnmUUw@mail.gmail.com>
References: <CABcfS1i9_rTnTuBCwmKoTMXVu7xDRU0dLhtxriRttsQCtGBuUA@mail.gmail.com>
 <CABcfS1j1HM9BrSTD-w+mJH=ms-iOCb8GfHFkYUY1T0eNXnmUUw@mail.gmail.com>
Message-ID: <D7C72F7A-A58A-4A83-8C99-D9C00217D6D2@stanford.edu>

Hi Michael,


> On Oct 25, 2018, at 1:37 AM, Michael Liu <megapode32559 at gmail.com> wrote:
> 
> http://data.bioontology.org/ontologies/MEDDRA/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
> 
> I got the following error message when I try to download MEDDRA. Does
> this mean that there is not a way to download it? Thanks.
> 
> {
> -"errors": [
> "License restrictions on download for MEDDRA"
> ],
> "status": 403
> }


Due to licensing restrictions, we?re not allowed to offer downloads of the MEDDRA ontology source file via our REST service, or from the BioPortal website. 

If you're a current UMLS license holder [1], please contact our technical program manager John Graybeal (cc'ed) for possible download options. (UMLS licenses are free and take about 5 business days to get approved).

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/databases/umls.html#license_request


From Carol.Dickens at choa.org  Fri Oct 26 12:12:13 2018
From: Carol.Dickens at choa.org (Dickens, Carol)
Date: Fri, 26 Oct 2018 19:12:13 +0000
Subject: [bioontology-support] BIO Medical Portal CPT CODES Table Error
Message-ID: <e3526de69d9a449f96eaa483c56e795b@choa.org>

Dorith,

There seems to be an error in your CPT table it is showing codes with more than six digits.
Can you please fix this issue?


[cid:image002.jpg at 01D46D3E.45E0FE40]



Carol Dickens, MBA- Business Intelligence & Analytics Mgmt.
Senior REDCap Administrator/BI App Analyst
Children's Healthcare of Atlanta
2800 Century Center Parkway, Suite 800
Atlanta, GA   30345
Office:  404-785-5948
Cell: 404-218-9423

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From megapode32559 at gmail.com  Wed Oct 31 05:45:25 2018
From: megapode32559 at gmail.com (Michael Liu)
Date: Wed, 31 Oct 2018 20:45:25 +0800
Subject: [bioontology-support] Why
	http://data.bioontology.org/ontologies/ONTOAD is not available?
Message-ID: <CABcfS1j0cmLdr3=EkNy0HvA7T6_64LKPZeWnZ4x5_9p5f9C3RQ@mail.gmail.com>

Hi,

I see "Internal Server Error". Is there anything wrong with it? Thanks.

http://data.bioontology.org/ontologies/ONTOAD

--
Best wishes,
Michael

From h.s.liyanage at surrey.ac.uk  Wed Oct 31 05:00:23 2018
From: h.s.liyanage at surrey.ac.uk (h.s.liyanage at surrey.ac.uk)
Date: Wed, 31 Oct 2018 12:00:23 +0000
Subject: [bioontology-support] Pregnancy Ontology
Message-ID: <AM0PR06MB58433440FFFB9790FA94B638F7CD0@AM0PR06MB5843.eurprd06.prod.outlook.com>

Dear BioPortal Team,

I have created an ontology titled "Pregnancy Ontology" on BioPortal at the following address.
https://bioportal.bioontology.org/ontologies/PREGONTO

My initial ontology upload failed during the creation of the ontology page and I have not been able to upload any OWL files since then. The issue is that there is no place to upload the ontology in this particular page (I have not come across this issue in the other ontology pages I have created).

Could you please associate the attached OWL file with this ontology and enable uploading of future updates of the OWL file. Alternatively, I would be happy to recreate the ontology page on BioPortal if you are able to delete the current page.

My use name on BioPortal is: harshanal

Thank you.

Best regards,

Harshana
Harshana Liyanage (Dr)
Research Fellow
Department of Clinical and Experimental Medicine
Faculty of Health and Medical Sciences
Room 07 PGM 02, Leggett Building, Daphne Jackson Road
University of Surrey
Tel: +44 (0) 1483 68 3836
Email: h.s.liyanage at surrey.ac.uk<mailto:h.s.liyanage at surrey.ac.uk>
Web: surrey.ac.uk<http://www.surrey.ac.uk/>

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From h.s.liyanage at surrey.ac.uk  Wed Oct 31 04:57:07 2018
From: h.s.liyanage at surrey.ac.uk (h.s.liyanage at surrey.ac.uk)
Date: Wed, 31 Oct 2018 11:57:07 +0000
Subject: [bioontology-support] Pregnancy Ontology
Message-ID: <AM0PR06MB58439ECFD5406305D43CE93CF7CD0@AM0PR06MB5843.eurprd06.prod.outlook.com>

Dear BioPortal Team,

I have created an ontology titled "Pregnancy Ontology" on BioPortal at the following address.
https://bioportal.bioontology.org/ontologies/PREGONTO

My initial ontology upload failed during the creation of the ontology page and I have not been able to upload any OWL files since then. The issue is that there is no place to upload the ontology in this particular page (I have not come across this issue in the other ontology pages I have created).

Could you please associate the attached OWL file with this ontology and enable uploading of future updates of the OWL file. Alternatively, I would be happy to recreate the ontology page on BioPortal if you are able to delete the current page.

My use name on BioPortal is: harshanal

Thank you.

Best regards,

Harshana
Harshana Liyanage (Dr)
Research Fellow
Department of Clinical and Experimental Medicine
Faculty of Health and Medical Sciences
Room 07 PGM 02, Leggett Building, Daphne Jackson Road
University of Surrey
Tel: +44 (0) 1483 68 3836
Email: h.s.liyanage at surrey.ac.uk<mailto:h.s.liyanage at surrey.ac.uk>
Web: surrey.ac.uk<http://www.surrey.ac.uk/>

[http://43bc734e13f6ef265bec-003422995f0c8d62f140f93cb947a950.r84.cf3.rackcdn.com/image001-2.png]<http://www.surrey.ac.uk/?utm_medium=internal&utm_source=emailsignature&utm_campaign=reputation+50th+brand>

[http://43bc734e13f6ef265bec-003422995f0c8d62f140f93cb947a950.r84.cf3.rackcdn.com/good-uni-guide-2.png]

Follow the University of Surrey
[cid:image002.png at 01CFEC63.939337D0]<http://bit.ly/1pjtrrk> [cid:image003.png at 01CFEC63.939337D0] <http://on.fb.me/1xY68sf>  [cid:image004.png at 01CFEC63.939337D0] <http://bit.ly/1wgOL6T>  [cid:image005.png at 01CFEC63.939337D0] <http://bit.ly/ZxiXOa>  [cid:image006.png at 01CFEC63.939337D0] <http://bit.ly/1CuWVIG>

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From jgraybeal at stanford.edu  Wed Oct 31 13:16:54 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 31 Oct 2018 20:16:54 +0000
Subject: [bioontology-support] Why
 http://data.bioontology.org/ontologies/ONTOAD is not available?
In-Reply-To: <CABcfS1j0cmLdr3=EkNy0HvA7T6_64LKPZeWnZ4x5_9p5f9C3RQ@mail.gmail.com>
References: <CABcfS1j0cmLdr3=EkNy0HvA7T6_64LKPZeWnZ4x5_9p5f9C3RQ@mail.gmail.com>
Message-ID: <5E1597D5-06D9-4512-8473-9B03F7B0229D@stanford.edu>

Thank you Michael for this report. We have taken care of some internal system issues on our side and this query is working again.

John

On Oct 31, 2018, at 5:45 AM, Michael Liu <megapode32559 at gmail.com<mailto:megapode32559 at gmail.com>> wrote:

Hi,

I see "Internal Server Error". Is there anything wrong with it? Thanks.

http://data.bioontology.org/ontologies/ONTOAD

--
Best wishes,
Michael
_______________________________________________
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


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From jgraybeal at stanford.edu  Wed Oct 31 13:24:24 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 31 Oct 2018 20:24:24 +0000
Subject: [bioontology-support] Pregnancy Ontology
In-Reply-To: <AM0PR06MB58433440FFFB9790FA94B638F7CD0@AM0PR06MB5843.eurprd06.prod.outlook.com>
References: <AM0PR06MB58433440FFFB9790FA94B638F7CD0@AM0PR06MB5843.eurprd06.prod.outlook.com>
Message-ID: <2144DE0C-B70F-43CC-BDBD-40C737681549@stanford.edu>

hello Harshana,

Sorry for your trouble, this is an unusual result which we will look into right away.

I have created an issue in GitHub so that you can track our progress:
  https://github.com/ncbo/bioportal-project/issues/101

John

On Oct 31, 2018, at 5:00 AM, h.s.liyanage at surrey.ac.uk<mailto:h.s.liyanage at surrey.ac.uk> wrote:

Dear BioPortal Team,

I have created an ontology titled ?Pregnancy Ontology? on BioPortal at the following address.
https://bioportal.bioontology.org/ontologies/PREGONTO

My initial ontology upload failed during the creation of the ontology page and I have not been able to upload any OWL files since then. The issue is that there is no place to upload the ontology in this particular page (I have not come across this issue in the other ontology pages I have created).

Could you please associate the attached OWL file with this ontology and enable uploading of future updates of the OWL file. Alternatively, I would be happy to recreate the ontology page on BioPortal if you are able to delete the current page.

My use name on BioPortal is: harshanal

Thank you.

Best regards,

Harshana
Harshana Liyanage (Dr)
Research Fellow
Department of Clinical and Experimental Medicine
Faculty of Health and Medical Sciences
Room 07 PGM 02, Leggett Building, Daphne Jackson Road
University of Surrey
Tel: +44 (0) 1483 68 3836
Email: h.s.liyanage at surrey.ac.uk<mailto:h.s.liyanage at surrey.ac.uk>
Web: surrey.ac.uk<http://www.surrey.ac.uk/>

<image001.jpg><http://www.surrey.ac.uk/?utm_medium=internal&utm_source=emailsignature&utm_campaign=reputation+50th+brand>

<image002.png>

Follow the University of Surrey
<image003.png><http://bit.ly/1pjtrrk> <image004.png><http://on.fb.me/1xY68sf> <image005.png><http://bit.ly/1wgOL6T> <image006.png><http://bit.ly/ZxiXOa> <image007.png><http://bit.ly/1CuWVIG>

Surrey Winter Statistics School (SWISS 2019)  - 14-18th January 2019 ? Book Now!<https://clininf.eu/index.php/education/swiss2019/>

<pregnancy-ontology-v0-1-20181019.owl>_______________________________________________
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  Wed Oct 31 15:20:02 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 31 Oct 2018 22:20:02 +0000
Subject: [bioontology-support] Pregnancy Ontology
In-Reply-To: <AM0PR06MB58433440FFFB9790FA94B638F7CD0@AM0PR06MB5843.eurprd06.prod.outlook.com>
References: <AM0PR06MB58433440FFFB9790FA94B638F7CD0@AM0PR06MB5843.eurprd06.prod.outlook.com>
Message-ID: <DC62B53A-63F6-4D8E-9224-EF74728FEE69@stanford.edu>

Hello Harshana,

Apologies that the initial attempt to upload your ontology failed. I deleted and recreated your ontology in our system, and uploaded the attached OWL file. Your ontology data is accessible now [1]. You can use the add button at the top of the Submissions table to upload new versions.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies/PREGONTO



On Oct 31, 2018, at 5:00 AM, h.s.liyanage at surrey.ac.uk<mailto:h.s.liyanage at surrey.ac.uk> wrote:

Dear BioPortal Team,

I have created an ontology titled ?Pregnancy Ontology? on BioPortal at the following address.
https://bioportal.bioontology.org/ontologies/PREGONTO

My initial ontology upload failed during the creation of the ontology page and I have not been able to upload any OWL files since then. The issue is that there is no place to upload the ontology in this particular page (I have not come across this issue in the other ontology pages I have created).

Could you please associate the attached OWL file with this ontology and enable uploading of future updates of the OWL file. Alternatively, I would be happy to recreate the ontology page on BioPortal if you are able to delete the current page.

My use name on BioPortal is: harshanal

Thank you.

Best regards,

Harshana
Harshana Liyanage (Dr)
Research Fellow
Department of Clinical and Experimental Medicine
Faculty of Health and Medical Sciences
Room 07 PGM 02, Leggett Building, Daphne Jackson Road
University of Surrey
Tel: +44 (0) 1483 68 3836
Email: h.s.liyanage at surrey.ac.uk<mailto:h.s.liyanage at surrey.ac.uk>
Web: surrey.ac.uk<http://www.surrey.ac.uk/>

<image001.jpg><http://www.surrey.ac.uk/?utm_medium=internal&utm_source=emailsignature&utm_campaign=reputation+50th+brand>

<image002.png>

Follow the University of Surrey
<image003.png><http://bit.ly/1pjtrrk> <image004.png><http://on.fb.me/1xY68sf> <image005.png><http://bit.ly/1wgOL6T> <image006.png><http://bit.ly/ZxiXOa> <image007.png><http://bit.ly/1CuWVIG>

Surrey Winter Statistics School (SWISS 2019)  - 14-18th January 2019 ? Book Now!<https://clininf.eu/index.php/education/swiss2019/>

<pregnancy-ontology-v0-1-20181019.owl>_______________________________________________
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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