From wynner at mail.nih.gov  Tue Sep  4 09:14:21 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Tue, 4 Sep 2018 16:14:21 +0000
Subject: [bioontology-support] searching by synonyms
In-Reply-To: <D89299C5-69FF-4E76-96F5-9381D9B29A02@stanford.edu>
References: <BL0PR0901MB244956EF1D7E3BA4DF3C1A15FB3E0@BL0PR0901MB2449.namprd09.prod.outlook.com>
 <CA25F169-D15A-4E05-B60C-BA7178E3C896@stanford.edu>
 <BL0PR0901MB2449FFB6124E64486CF6791AFB3C0@BL0PR0901MB2449.namprd09.prod.outlook.com>
 <D89299C5-69FF-4E76-96F5-9381D9B29A02@stanford.edu>
Message-ID: <BL0PR0901MB24496CFAE7EA7EB9309E0591FB030@BL0PR0901MB2449.namprd09.prod.outlook.com>

Yes!  Jennifer, this is great.  I will bronze this thread.

Thank you so much.

Rob

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Thursday, August 30, 2018 7:51 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov>
Cc: support at bioontology.org; De Coronado, Sherri (NIH/NCI) [E] <decorons at mail.nih.gov>
Subject: Re: [bioontology-support] searching by synonyms

Hi Rob,



On Aug 18, 2018, at 12:52 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi Jennifer,

Yes.  I took a look at the documentation and have tried the following calls using my key.  Neither seem to return what I?m looking for, so maybe I?m doing something wrong.

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT/search?q=Malignant

I?d like to restrict my search to just synonyms, and have classes returned that match the search value (a contains or exact match).


You can use the ?include? parameter to limit what?s returned by the API. That parameter is documented in the Common Parameters section of our API documentation:

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

You can also set the display_links parameter to false to eliminate the hypermedia links that are returned by default.

For example (this is the /search endpoint, not the /property_search endpoint):

http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&display_links=false

? the above call retrieves all classes from the NCIT ontology where the class name contains ?Malignant?. For each class in the resulting JSON, only the preferred label and synonyms are returned:


[cid:image001.png at 01D44448.CE9A9BC0]




For an exact match search, you would add the require_exact_match parameter:

http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&require_exact_match=true&display_links=false

[cid:image002.png at 01D44448.CE9A9BC0]

Is this the type of search you?re trying to accomplish?

Kind regards,
Jennifer




Can this be done through BioPortal instead?  If I go to the Advanced Search there is an option to select all properties, but is there a way to search by a single property?

Thanks!
Rob

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Thursday, August 16, 2018 7:57 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; De Coronado, Sherri (NIH/NCI) [E] <decorons at mail.nih.gov<mailto:decorons at mail.nih.gov>>
Subject: Re: [bioontology-support] searching by synonyms

Hi Rob,

Apologies, but I?m not sure I followed your question.

We do have a search endpoint in the REST API for searching by ontology properties. It?s documented here:

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

Is this what you meant?

Kind regards,
Jennifer





On Aug 16, 2018, at 4:35 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes?  I guess this would go for any one specific text property.  If I do this search using REST, could I specify my property?

Thanks,
Rob
_______________________________________________
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 hideki at biosciencedbc.jp  Mon Sep  3 21:44:31 2018
From: hideki at biosciencedbc.jp (Hideki Hatanaka)
Date: Tue, 4 Sep 2018 13:44:31 +0900
Subject: [bioontology-support] [BioPortal] Feedback from Hideki Hatanaka
In-Reply-To: <5b8e09ac821b9_16553f8a400b73f4543fc@ncbo-prd-app-09.stanford.edu.mail>
References: <5b8e09ac821b9_16553f8a400b73f4543fc@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <CAOo7UZBxBo6DWGhe0jYqBL0vSGaS_JnAj5UwbGKROJ=s5AUhoA@mail.gmail.com>

Dear Sirs,

the content of the email is different from that I input into the support form.
I wanted to show downloading was suddenly interrupted.

Sincerely yours,
Hideki
2018?9?4?(?) 13:27 <support at bioontology.org>:
>
> Name: Hideki Hatanaka
>
> Email: hideki at biosciencedbc.jp
>
> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FGAZ
>
>
> Feedback:
>
> Downloading PR, GAZ or NCBITAXON seems to stop at 1 GB .
> For example, results from downloading RDF/XML at https://bioportal.bioontology.org/ontologies/PR are :
>
> $ ls -l
> total 2129944
> -rw-r--r--@ 1 hatanaka staff 8094 9 4 05:42 Info.plist
> -rw-r--r--@ 1 hatanaka staff 1074126848 9 4 05:42 owlapi.xrdf
>
> $ tail -5 owlapi.xrdf
>
>
>
> A protein coding gene wdr68 in Dictyostelium discoideum.



-- 
Hideki Hatanaka, D.Sc.

National Bioscience Database Center (NBDC), JST
5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan
Phone:+81-90-1114-6896, +81-3-5214-8491

From nick.kennedy1 at nhs.net  Tue Sep  4 04:13:02 2018
From: nick.kennedy1 at nhs.net (KENNEDY, Nick (ROYAL DEVON AND EXETER NHS FOUNDATION TRUST))
Date: Tue, 4 Sep 2018 11:13:02 +0000
Subject: [bioontology-support] MEDDRA version
Message-ID: <6fa22fb7ddcc47eaa5696e1c1e925326@NH-SLPEX095.AD1.NHS.NET>

Dear Bioontology support,

The version of MEDDRA currently used on bioontology doesn't seem to be displayed anywhere. I've checked on http://bioportal.bioontology.org/ontologies/MEDDRA?p=summary and browsed through the other tabs on that page. From the release date given as June 2017, it seems likely that you are using version 20.0 released March 2017. Is that correct?

Best wishes,

Dr Nick Kennedy
Consultant Gastroenterologist
Direct line (01392) 40 8457
Secretary (01392) 40 2783



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From support at bioontology.org  Mon Sep  3 21:27:24 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 03 Sep 2018 21:27:24 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Hideki Hatanaka
Message-ID: <5b8e09ac821b9_16553f8a400b73f4543fc@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Tue Sep  4 03:23:22 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 04 Sep 2018 03:23:22 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5b8e5d1ad21ce_53523ff5d50e3fc023d7@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Sep  4 10:59:22 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 4 Sep 2018 17:59:22 +0000
Subject: [bioontology-support] MEDDRA version
In-Reply-To: <6fa22fb7ddcc47eaa5696e1c1e925326@NH-SLPEX095.AD1.NHS.NET>
References: <6fa22fb7ddcc47eaa5696e1c1e925326@NH-SLPEX095.AD1.NHS.NET>
Message-ID: <3DDE4CDC-2D88-4A61-8074-EC25523FD54A@stanford.edu>

Hello Nick,


On Sep 4, 2018, at 4:13 AM, KENNEDY, Nick (ROYAL DEVON AND EXETER NHS FOUNDATION TRUST) <nick.kennedy1 at nhs.net<mailto:nick.kennedy1 at nhs.net>> wrote:

The version of MEDDRA currently used on bioontology doesn?t seem to be displayed anywhere. I?ve checked on http://bioportal.bioontology.org/ontologies/MEDDRA?p=summary and browsed through the other tabs on that page. From the release date given as June 2017, it seems likely that you are using version 20.0 released March 2017. Is that correct?


We import MEDDRA into BioPortal from the National Library of Medicine?s UMLS [1]. The last release of the UMLS was 2018AA. According to their documentation, 2018AA included version 20.1 of MEDDRA from Sept., 2017. More specifics are available on their website [2].

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/
[2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html

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From vendetti at stanford.edu  Tue Sep  4 11:11:46 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 4 Sep 2018 18:11:46 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5b8e5d1ad21ce_53523ff5d50e3fc023d7@ncbo-prd-app-09.stanford.edu.mail>
References: <5b8e5d1ad21ce_53523ff5d50e3fc023d7@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <9A3C2435-B22C-45A2-8287-9A5219CA6FCF@stanford.edu>

Hello Chen,


On Sep 4, 2018, at 3:23 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org<http://252Fpurl.obolibrary.org>%252Fobo%252FFOODON_03400361

Feedback:

Dear,
1) If I want to make permanent link/ID for classes (i.e. I can access the class on BioPortal by the url/ID), should I use "http://purl.bioontology.org/ontology/ONE/XXXX"?

You can access a permanent link for a class in the BioPortal user interface on the Classes tab. I noticed a bug while looking at this functionality, in that the icon for displaying the dialog with the permanent link is barely visible. We?ll need to fix that. To get to what you?re looking for, you can use the following steps:

1. Navigate to the Classes tab for your ontology: https://bioportal.bioontology.org/ontologies/ONE?p=classes.
2. Select any class in the class tree on the left-hand side.
3. In the Details pane on the right-hand side, hover your mouse in the toolbar to the right of the "Class Mappings" tab. You should be able to see a tooltip that says ?Get a permanent link to this class?.
4. Click the link and a dialog will pop up that contains the permanent link to the class.


2) In my ontology (ONE), there are always some classes without labels randomly. But I added labels actually.

Please give an example of a class that you feel should have a label, but doesn?t.



3) For the terms I borrowed from other ontology (e.g. MeSH), if I don't add label by myself, the original label put by MeSH ontology will be used or not? i.e. in my ontology I will see "MESH:D003223" or "Congo" as label?

You?ll see Congo. This is something you can check yourself by entering what you think the label would be in the ?Jump To? search box on the Classes tab:


[cid:E62221BE-89B3-4CED-BE99-1BA0E69E3B8F at stanford.edu]


Jennifer

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From Thomas.Schneider2 at mountsinai.org  Wed Sep  5 08:31:17 2018
From: Thomas.Schneider2 at mountsinai.org (Schneider, Thomas)
Date: Wed, 5 Sep 2018 15:31:17 +0000
Subject: [bioontology-support] Problem with registration to website
Message-ID: <1DC6254D8AC2924BACB3BAAE6975FC480C0866D2@SMESEXCP014034.msnyuhealth.org>

Hi,

I am having difficulty registering to your website.  Whenever I try to register it stalls and then I get the error below.


We're sorry but something has gone wrong. We have been notified of this error.


Please let me know how I can register for this website.


Thanks,
Tom

From support at bioontology.org  Wed Sep  5 04:53:29 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 05 Sep 2018 04:53:29 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Gerhard Mayer
Message-ID: <5b8fc3b985433_564f3fe9c4eb3488564b4@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Wed Sep  5 11:56:00 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 5 Sep 2018 18:56:00 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Gerhard Mayer
In-Reply-To: <5b8fc3b985433_564f3fe9c4eb3488564b4@ncbo-prd-app-08.stanford.edu.mail>
References: <5b8fc3b985433_564f3fe9c4eb3488564b4@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <97C43287-AC94-4068-A628-7D57DF8FA810@stanford.edu>

Hello Gerhard,

The process for submitting an ontology to BioPortal is described on this wiki page:

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

Let us know if you experience any difficulties.

Kind regards,
Jennifer



On Sep 5, 2018, at 4:53 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Hello,

we developed a new cross-linker and derivatization reagents ontology.
It's a structured controlled vocabulary for cross-linking reagents and derivatization reagents used within the proteomics mass spectrometry standard mzIdenML1.2 and mzTab-M / mzTab-L

The link to the .obo file is https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo

How can we trigger the inclusion into the BioPortal portal?

Best regards,
Gerhard Mayer
HUPO-PSI ontology coordinator

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From vendetti at stanford.edu  Wed Sep  5 18:16:00 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Sep 2018 01:16:00 +0000
Subject: [bioontology-support] Problem with registration to website
In-Reply-To: <1DC6254D8AC2924BACB3BAAE6975FC480C0866D2@SMESEXCP014034.msnyuhealth.org>
References: <1DC6254D8AC2924BACB3BAAE6975FC480C0866D2@SMESEXCP014034.msnyuhealth.org>
Message-ID: <D5A39EA2-9D9E-4371-84EF-9290BE8302B3@stanford.edu>

Hi Tom,

Apologies that our site has been experiencing some instability since early this morning. We?re still investigating / doing some troubleshooting. It?s up at the moment if you?d like to do another attempt at registration.

Kind regards,
Jennifer



> On Sep 5, 2018, at 8:31 AM, Schneider, Thomas <Thomas.Schneider2 at mountsinai.org> wrote:
> 
> Hi,
> 
> I am having difficulty registering to your website.  Whenever I try to register it stalls and then I get the error below.
> 
> 
> We're sorry but something has gone wrong. We have been notified of this error.
> 
> 
> Please let me know how I can register for this website.
> 
> 
> Thanks,
> Tom
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From amassengale at rsna.org  Thu Sep  6 12:13:37 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Thu, 6 Sep 2018 19:13:37 +0000
Subject: [bioontology-support] BioPortal API route not working
Message-ID: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org>

Hi all,

We have been using the following API call without issue up until a few days ago (API key removed):

https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000

Now it is returning 0 results. What is interesting is that, considering that this query is using the subtree_root_id option, if I use a subtree directly under the root ID I?m passing in, then it returns results. This seems to be in error to be, because if I try and query a subtree on a parent of a child element, than at least that child?s elements should be returned, but instead nothing is being returned. Here is the query for the child (API key removed again):

https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID13230&roots_only=true&page=1&pagesize=1000<https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000>

Here is a visual representation of what I?m trying to do:

[cid:image001.png at 01D445EB.CD3BDAB0]

I?m trying to query the ?Anatomical entity? subtree (RID3), which returns 0 results. However, as mentioned above, when I use the ?Anatomical set? subtree (RID13230), I get some results returned.

Let me know if you need any more information,

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 vendetti at stanford.edu  Thu Sep  6 13:16:19 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Sep 2018 20:16:19 +0000
Subject: [bioontology-support] BioPortal API route not working
In-Reply-To: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org>
References: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org>
Message-ID: <07AE9960-C21D-464C-A0CF-BA73DE890C05@stanford.edu>

Hi Andrew,

This appears to have been a caching issue, possibly related to some system instability we experienced yesterday.

I?ve reset the application caches and the call you list below now returns results. Apologies for the difficulty.

Kind regards,
Jennifer



On Sep 6, 2018, at 12:13 PM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

Hi all,

We have been using the following API call without issue up until a few days ago (API key removed):

https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000

Now it is returning 0 results. What is interesting is that, considering that this query is using the subtree_root_id option, if I use a subtree directly under the root ID I?m passing in, then it returns results. This seems to be in error to be, because if I try and query a subtree on a parent of a child element, than at least that child?s elements should be returned, but instead nothing is being returned. Here is the query for the child (API key removed again):

https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID13230&roots_only=true&page=1&pagesize=1000<https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000>

Here is a visual representation of what I?m trying to do:

<image001.png>

I?m trying to query the ?Anatomical entity? subtree (RID3), which returns 0 results. However, as mentioned above, when I use the ?Anatomical set? subtree (RID13230), I get some results returned.

Let me know if you need any more information,

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 _______________________________________________
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 amassengale at rsna.org  Thu Sep  6 13:18:43 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Thu, 6 Sep 2018 20:18:43 +0000
Subject: [bioontology-support] BioPortal API route not working
In-Reply-To: <07AE9960-C21D-464C-A0CF-BA73DE890C05@stanford.edu>
References: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org>
 <07AE9960-C21D-464C-A0CF-BA73DE890C05@stanford.edu>
Message-ID: <807C8BFB-0347-4B03-BA81-EECAEC45EA5D@hq.rsna.org>

Confirmed that it?s working from our end again.

Thanks Jennifer!

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Thursday, September 6, 2018 at 3:16 PM
To: Andrew Massengale <amassengale at rsna.org>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] BioPortal API route not working

Hi Andrew,

This appears to have been a caching issue, possibly related to some system instability we experienced yesterday.

I?ve reset the application caches and the call you list below now returns results. Apologies for the difficulty.

Kind regards,
Jennifer




On Sep 6, 2018, at 12:13 PM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

Hi all,

We have been using the following API call without issue up until a few days ago (API key removed):

https://data.bioontology.org/search?ontology=RADLEX&q=head&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%26q%3Dhead%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%7C9eb6dde3697e4c23deef08d614359e07%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636718617860256947&sdata=Jo9%2B2UwC%2FTIa7dPSBWfLNIUCltoK3kdJ3tSAnlPEGrE%3D&reserved=0>

Now it is returning 0 results. What is interesting is that, considering that this query is using the subtree_root_id option, if I use a subtree directly under the root ID I?m passing in, then it returns results. This seems to be in error to be, because if I try and query a subtree on a parent of a child element, than at least that child?s elements should be returned, but instead nothing is being returned. Here is the query for the child (API key removed again):

https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID13230&roots_only=true&page=1&pagesize=1000<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fontology%3DRADLEX%26q%3Dhead%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%7C9eb6dde3697e4c23deef08d614359e07%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636718617860256947&sdata=Jo9%2B2UwC%2FTIa7dPSBWfLNIUCltoK3kdJ3tSAnlPEGrE%3D&reserved=0>

Here is a visual representation of what I?m trying to do:

<image001.png>

I?m trying to query the ?Anatomical entity? subtree (RID3), which returns 0 results. However, as mentioned above, when I use the ?Anatomical set? subtree (RID13230), I get some results returned.

Let me know if you need any more information,

Andrew M

Andrew Massengale
Team Lead | Senior Software Engineer
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From Elcio.Abrahao at lirmm.fr  Mon Sep 10 06:23:54 2018
From: Elcio.Abrahao at lirmm.fr (abrahao)
Date: Mon, 10 Sep 2018 15:23:54 +0200
Subject: [bioontology-support] Problem on the respose from the REST API for
	mappigs submission
Message-ID: <986218a9d71b8dc78cd5b93d9778af29@lirmm.fr>

Hi!

My name is Elcio Abrah?o. I worked with Clement Jonquet at Agroportal, 
FR.

I am testing the REST API from Bioportal to submit Mappings on the JSON 
format and I notice that the
response JSON did not include a valid ID for that mapping. The ID field 
come with the content NULL.

I would like to asked you if this an error or I missing something....

The request and response are attached bellow:

Thanks,

-- 
Elcio Abrah?o
AgroPortal Project - LIRMM - University of Montpellier, France.


HTTP POST with APIKEY on the headers.
REST URL: https://data.bioontology.org/mappings
REST API Key: OMITTED HERE for security

REQUEST:

{
     "creator": "http://data.bioontology.org/users/elcioabrahao",
     "source_contact_info": "pirmail at georgetown.edu,dan5 at georgetown.edu",
     "relation": [
       "http://www.geneontology.org/formats/oboinowl#hasdbxref"
     ],
     "source": "RESTTEST",
     "source_name": "PR",
     "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 
- Agroportal Project - LIRMM - 10/09/2018 11:13 - FR",
   "classes" : { "http://purl.bioontology.org/ontology/STY/T052": "STY",
     "http://www.drugtargetontology.org/dto/DTO_03100518": "DTO"
   }
}

RESPONSE:

{
     "id": null,
     "source": "REST",
     "classes": [
         {
             "obsolete": false,
             "@id": "http://purl.bioontology.org/ontology/STY/T052",
             "@type": "http://www.w3.org/2002/07/owl#Class",
             "links": {
                 "self": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052",
                 "ontology": 
"http://data.bioontology.org/ontologies/STY",
                 "children": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/children",
                 "parents": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/parents",
                 "descendants": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/descendants",
                 "ancestors": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/ancestors",
                 "instances": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/instances",
                 "tree": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/tree",
                 "notes": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/notes",
                 "mappings": 
"http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/mappings",
                 "ui": 
"http://bioportal.bioontology.org/ontologies/STY?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052",
                 "@context": {
                     "self": "http://www.w3.org/2002/07/owl#Class",
                     "ontology": 
"http://data.bioontology.org/metadata/Ontology",
                     "children": "http://www.w3.org/2002/07/owl#Class",
                     "parents": "http://www.w3.org/2002/07/owl#Class",
                     "descendants": 
"http://www.w3.org/2002/07/owl#Class",
                     "ancestors": "http://www.w3.org/2002/07/owl#Class",
                     "instances": 
"http://data.bioontology.org/metadata/Instance",
                     "tree": "http://www.w3.org/2002/07/owl#Class",
                     "notes": 
"http://data.bioontology.org/metadata/Note",
                     "mappings": 
"http://data.bioontology.org/metadata/Mapping",
                     "ui": "http://www.w3.org/2002/07/owl#Class"
                 }
             },
             "@context": {
                 "@vocab": "http://data.bioontology.org/metadata/",
                 "obsolete": 
"http://data.bioontology.org/metadata/owlobsolete"
             }
         },
         {
             "obsolete": false,
             "@id": "http://www.drugtargetontology.org/dto/DTO_03100518",
             "@type": "http://www.w3.org/2002/07/owl#Class",
             "links": {
                 "self": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518",
                 "ontology": 
"http://data.bioontology.org/ontologies/DTO",
                 "children": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/children",
                 "parents": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/parents",
                 "descendants": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/descendants",
                 "ancestors": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/ancestors",
                 "instances": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/instances",
                 "tree": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/tree",
                 "notes": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/notes",
                 "mappings": 
"http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/mappings",
                 "ui": 
"http://bioportal.bioontology.org/ontologies/DTO?p=classes&conceptid=http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518",
                 "@context": {
                     "self": "http://www.w3.org/2002/07/owl#Class",
                     "ontology": 
"http://data.bioontology.org/metadata/Ontology",
                     "children": "http://www.w3.org/2002/07/owl#Class",
                     "parents": "http://www.w3.org/2002/07/owl#Class",
                     "descendants": 
"http://www.w3.org/2002/07/owl#Class",
                     "ancestors": "http://www.w3.org/2002/07/owl#Class",
                     "instances": 
"http://data.bioontology.org/metadata/Instance",
                     "tree": "http://www.w3.org/2002/07/owl#Class",
                     "notes": 
"http://data.bioontology.org/metadata/Note",
                     "mappings": 
"http://data.bioontology.org/metadata/Mapping",
                     "ui": "http://www.w3.org/2002/07/owl#Class"
                 }
             },
             "@context": {
                 "@vocab": "http://data.bioontology.org/metadata/",
                 "obsolete": 
"http://data.bioontology.org/metadata/owlobsolete"
             }
         }
     ],
     "process": {
         "id": 
"http://data.bioontology.org/metadata/mapping_processes/-elcioabrahao-0831b590-9723-0136-cc8e-005056010074",
         "name": "REST Mapping",
         "creator": "http://data.bioontology.org/users/elcioabrahao",
         "source": "RESTTEST",
         "relation": 
"[\"http://www.geneontology.org/formats/oboinowl#hasdbxref\"]",
         "source_name": "PR",
         "comment": "Generated with the Ontology Mapping Harvest Tool - 
v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR",
         "date": "2018-09-10T05:29:05-07:00"
     },
     "@id": "",
     "@type": "http://data.bioontology.org/metadata/Mapping"
}


From Elcio.Abrahao at lirmm.fr  Mon Sep 10 06:13:32 2018
From: Elcio.Abrahao at lirmm.fr (abrahao)
Date: Mon, 10 Sep 2018 15:13:32 +0200
Subject: [bioontology-support] Problem when trying to see class details
Message-ID: <dd62fe82f13e4b188663f0b0c35cd6b7@lirmm.fr>

Hi !

My name is Elcio Abrah?o. I worked with CLement Jonquet at Agroportal, 
FR.

I just trying to query same classes on PR ontology but I only could 
access the class details when I am logged out... If I login then cames 
the folow error message only when try to access class details or the cls 
tree: "We're sorry but something has gone wrong. We have been notified 
of this error."

Finnaly, I have 2 accounts: "elcioabrahao" and "abrahao". Could you 
delete the account with ID "abrahao" please ?

I notice a problem when sumiting mappings, but I will send other email 
for this problem.

Thanks,

-- 
Elcio Abrah?o
AgroPortal Project - LIRMM - University of Montpellier, France.

From csongor.nyulas at stanford.edu  Mon Sep 10 12:31:17 2018
From: csongor.nyulas at stanford.edu (Csongor Nyulas)
Date: Mon, 10 Sep 2018 12:31:17 -0700
Subject: [bioontology-support] =?utf-8?q?Fwd=3A_Early_bird_deadline_approa?=
 =?utf-8?q?ching=3A_Register_today_to_the_Protege_Short_Course_at_Stanford?=
 =?utf-8?q?_University=2C_October_22_=E2=80=93_24=2C_2018!?=
In-Reply-To: <6ef02961-ec36-881a-6695-54723cf3df75@stanford.edu>
References: <6ef02961-ec36-881a-6695-54723cf3df75@stanford.edu>
Message-ID: <57d05cfa-3742-9c82-b487-53a02bdbd27a@stanford.edu>

In case anyone is interested in participating at the Prot?g? Short 
Course please check out the announcement below...

Csongor


-------- Forwarded Message --------
Subject: 	Early bird deadline approaching: Register today to the Protege 
Short Course at Stanford University, October 22 ? 24, 2018!
Date: 	Mon, 10 Sep 2018 12:05:09 -0700
From: 	Csongor Nyulas <csongor.nyulas at stanford.edu>
To: 	protege-announce at lists.stanford.edu
CC: 	User support for WebProtege and Protege Desktop 
<protege-user at lists.stanford.edu>, Developer support for WebProtege and 
Protege Desktop <protege-dev at lists.stanford.edu>



Dear all,

Don't miss the chance to register at reduced rate to the next Prot?g? 
Short Course, to be held at Stanford University, California between 
October 22 ? 24, 2018. *There are only two weeks until the "early bird" 
deadline!*

Register here: 
https://protege.stanford.edu/shortcourse/201810/registration.html

The Prot?g? Short Course offers a 3-day intensive training in use of the 
Prot?g? toolset, ontology development, and OWL. We cover best practices 
in ontology building and the latest Semantic Web technologies, including 
OWL 2, RDF, and SPARQL. We also cover topics such as real-world 
applications with ontologies, and data access and import from different 
data sources. The course is hands-on and is taught by the members of the 
Prot?g? team.

Read more about it at:
https://protege.stanford.edu/shortcourse/201810/

If you have any questions about the Prot?g? Short Course, please email: 
protege-shortcourse at lists.stanford.edu

Please feel free to forward this announcement to anyone who might be 
interested in the course. Thank you!

We look forward to seeing you in October!

Best regards,
The Prot?g? Team
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From support at bioontology.org  Mon Sep 10 19:52:01 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 10 Sep 2018 19:52:01 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Chad Vanderbilt
Message-ID: <5b972dd180603_177e2acee3c42f3448e0@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Mon Sep 10 18:39:54 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 10 Sep 2018 18:39:54 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Syanne Fonda
Message-ID: <5b971cea617f2_79432b28b31c6ec831656@ncbo-prd-app-08.stanford.edu.mail>

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From james at overton.ca  Mon Sep 10 12:36:00 2018
From: james at overton.ca (James A. Overton)
Date: Mon, 10 Sep 2018 15:36:00 -0400
Subject: [bioontology-support] Some trouble with OBI on Bioportal
Message-ID: <174F5073-5C3D-448D-93A1-41951AB08D12@overton.ca>

Hello,

I'm a developer for the Ontology for Biomedical Investigations (OBI). A new OBI release was published last week. On Bioportal's OBI page, I see that a new release was uploaded last week, but the ontology date is wrong, and the new classes are not appearing in the class view.

I have access to the "ontology.bio.investigations" user that administers the OBI account, but I can't figure out how to fix this.

In general I've seen a lot of errors while trying to use the OBI class view over the past week.

Some help would be appreciated.

James

From mdorf at stanford.edu  Tue Sep 11 13:19:00 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 11 Sep 2018 20:19:00 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Chad Vanderbilt
In-Reply-To: <5b972dd180603_177e2acee3c42f3448e0@ncbo-prd-app-08.stanford.edu.mail>
References: <5b972dd180603_177e2acee3c42f3448e0@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <93ED9B89-B47D-492A-B0AB-DD0E28AC91D2@stanford.edu>

Hi Chad,

Thank you for contacting us.  Our site has experienced several outages last week, which may have been the cause of the issues you?ve experienced. It is back to normal now, and I?ve verified that the URL below works as expected. Please let us know if you continue experiencing issues with BioPortal.

Thanks,

Michael


On Sep 10, 2018, at 7:52 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Chad Vanderbilt

Email: vanderbilt.chad at gmail.com<mailto:vanderbilt.chad at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FICD10PCS%252FGZC

Feedback:

Hi,

I have noticed a lot of performance issues, particularly with the CPT section in the last 2 weeks. Thank you.

-Chad Vanderbilt, MD

_______________________________________________
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  Tue Sep 11 13:21:38 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 11 Sep 2018 20:21:38 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Syanne Fonda
In-Reply-To: <5b971cea617f2_79432b28b31c6ec831656@ncbo-prd-app-08.stanford.edu.mail>
References: <5b971cea617f2_79432b28b31c6ec831656@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <D4DF903F-EF5F-45C3-8D1E-BE893F703FA2@stanford.edu>

Hi Syanne,

Thank you for contacting us. Thank you for contacting us.  Our site has experienced several outages last week and yesterday, which may have been the cause of your issue with CPT. It is back to normal now, and I?ve verified that the URL below works as expected. Please let us know if you continue experiencing issues with CPT and BioPortal.

Thanks!

Michael

On Sep 10, 2018, at 6:39 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Syanne Fonda

Email: syanne.fonda at docdoc.com<mailto:syanne.fonda at docdoc.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FCPT%252F1006069

Feedback:

Why is your CPT is not working since yesterday?
You need to fix this as soon as possible.

Thank you.

Best

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From mdorf at stanford.edu  Tue Sep 11 14:18:04 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 11 Sep 2018 21:18:04 +0000
Subject: [bioontology-support] Some trouble with OBI on Bioportal
In-Reply-To: <174F5073-5C3D-448D-93A1-41951AB08D12@overton.ca>
References: <174F5073-5C3D-448D-93A1-41951AB08D12@overton.ca>
Message-ID: <E4FA97DB-A46B-4421-BA76-4387762AFFFA@stanford.edu>

Hi James,

Thank you for contacting us. I?ve re-processed the latest version of OBI, and it appears to work as expected now.  You can adjust the release date by following this link (having previously logged in to BioPortal):

http://bioportal.bioontology.org/ontologies/OBI/submissions/37/edit

As far as errors, I must apologize, we?ve been experiencing a number of periods of instability both last and this week (Monday). The site is now back to normal, so please let us know if you continue seeing errors you reported.

Thanks!

Michael

On Sep 10, 2018, at 12:36 PM, James A. Overton <james at overton.ca<mailto:james at overton.ca>> wrote:

Hello,

I'm a developer for the Ontology for Biomedical Investigations (OBI). A new OBI release was published last week. On Bioportal's OBI page, I see that a new release was uploaded last week, but the ontology date is wrong, and the new classes are not appearing in the class view.

I have access to the "ontology.bio.investigations" user that administers the OBI account, but I can't figure out how to fix this.

In general I've seen a lot of errors while trying to use the OBI class view over the past week.

Some help would be appreciated.

James
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From mdorf at stanford.edu  Wed Sep 12 11:36:54 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 12 Sep 2018 18:36:54 +0000
Subject: [bioontology-support] Problem when trying to see class details
In-Reply-To: <dd62fe82f13e4b188663f0b0c35cd6b7@lirmm.fr>
References: <dd62fe82f13e4b188663f0b0c35cd6b7@lirmm.fr>
Message-ID: <F56F27F3-31BC-4A58-BB6D-A7102C5F0C34@stanford.edu>

Hi Elcio,

Thanks for contacting us. Is the problem still happening on your end. I have not been able to reproduce it on mine.  I?ve seen a problem like this reported on the support list before, and it was solved by clearing the browser cache, e.g., in Chrome doing something like Preferences? | Clear Browsing Data? Have you tried this? 

Another thing to note is that we?ve experienced some pockets of downtime last week, and your use may have coincided with one. When you?re logged out, you are seeing a cached response, which doesn?t always rely on our backend being up and running. When you?re logged in, the caching layer does not kick in (well, to some extent), and you are hitting the rest service.

I?ve removed the user ?abrahao? from our system.

Thanks!

Michael


> On Sep 10, 2018, at 6:13 AM, abrahao <Elcio.Abrahao at lirmm.fr> wrote:
> 
> Hi !
> 
> My name is Elcio Abrah?o. I worked with CLement Jonquet at Agroportal, FR.
> 
> I just trying to query same classes on PR ontology but I only could access the class details when I am logged out... If I login then cames the folow error message only when try to access class details or the cls tree: "We're sorry but something has gone wrong. We have been notified of this error."
> 
> Finnaly, I have 2 accounts: "elcioabrahao" and "abrahao". Could you delete the account with ID "abrahao" please ?
> 
> I notice a problem when sumiting mappings, but I will send other email for this problem.
> 
> Thanks,
> 
> -- 
> Elcio Abrah?o
> AgroPortal Project - LIRMM - University of Montpellier, France.
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From mdorf at stanford.edu  Wed Sep 12 14:51:32 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 12 Sep 2018 21:51:32 +0000
Subject: [bioontology-support] Problem on the respose from the REST API
 for	mappigs submission
In-Reply-To: <986218a9d71b8dc78cd5b93d9778af29@lirmm.fr>
References: <986218a9d71b8dc78cd5b93d9778af29@lirmm.fr>
Message-ID: <08A76D05-759D-4955-92F8-65F20B29117B@stanford.edu>

Hi again, Elcio,

This output is by design. If you look at a sample of our own mappings output, the response would look identical to yours:

https://data.bioontology.org/mappings?ontologies=SNOMEDCT,CPT

Most of the mappings in our system are of type LOOM, which are auto-inferred on the fly when you make the REST call. The other auto-generated mappings are of type CUI and SAME_URI. They aren?t stored in the system, and therefore, don?t have an ID (or the Process object) associated with them.

The mappings of type REST (manually created) are stored in our backend. They have the object ?process? populated, which serves as the identifier for the mapping. So, in short, your output looks correct! :-)

Hope this helps!

Michael

On Sep 10, 2018, at 6:23 AM, abrahao <Elcio.Abrahao at lirmm.fr<mailto:Elcio.Abrahao at lirmm.fr>> wrote:

Hi!

My name is Elcio Abrah?o. I worked with Clement Jonquet at Agroportal, FR.

I am testing the REST API from Bioportal to submit Mappings on the JSON format and I notice that the
response JSON did not include a valid ID for that mapping. The ID field come with the content NULL.

I would like to asked you if this an error or I missing something....

The request and response are attached bellow:

Thanks,

--
Elcio Abrah?o
AgroPortal Project - LIRMM - University of Montpellier, France.


HTTP POST with APIKEY on the headers.
REST URL: https://data.bioontology.org/mappings
REST API Key: OMITTED HERE for security

REQUEST:

{
   "creator": "http://data.bioontology.org/users/elcioabrahao",
   "source_contact_info": "pirmail at georgetown.edu<mailto:pirmail at georgetown.edu>,dan5 at georgetown.edu<mailto:dan5 at georgetown.edu>",
   "relation": [
     "http://www.geneontology.org/formats/oboinowl#hasdbxref"
   ],
   "source": "RESTTEST",
   "source_name": "PR",
   "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR",
 "classes" : { "http://purl.bioontology.org/ontology/STY/T052": "STY",
   "http://www.drugtargetontology.org/dto/DTO_03100518": "DTO"
 }
}

RESPONSE:

{
   "id": null,
   "source": "REST",
   "classes": [
       {
           "obsolete": false,
           "@id": "http://purl.bioontology.org/ontology/STY/T052",
           "@type": "http://www.w3.org/2002/07/owl#Class",
           "links": {
               "self": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052",
               "ontology": "http://data.bioontology.org/ontologies/STY",
               "children": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/children",
               "parents": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/parents",
               "descendants": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/descendants",
               "ancestors": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/ancestors",
               "instances": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/instances",
               "tree": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/tree",
               "notes": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/notes",
               "mappings": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/mappings",
               "ui": "http://bioportal.bioontology.org/ontologies/STY?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052",
               "@context": {
                   "self": "http://www.w3.org/2002/07/owl#Class",
                   "ontology": "http://data.bioontology.org/metadata/Ontology",
                   "children": "http://www.w3.org/2002/07/owl#Class",
                   "parents": "http://www.w3.org/2002/07/owl#Class",
                   "descendants": "http://www.w3.org/2002/07/owl#Class",
                   "ancestors": "http://www.w3.org/2002/07/owl#Class",
                   "instances": "http://data.bioontology.org/metadata/Instance",
                   "tree": "http://www.w3.org/2002/07/owl#Class",
                   "notes": "http://data.bioontology.org/metadata/Note",
                   "mappings": "http://data.bioontology.org/metadata/Mapping",
                   "ui": "http://www.w3.org/2002/07/owl#Class"
               }
           },
           "@context": {
               "@vocab": "http://data.bioontology.org/metadata/",
               "obsolete": "http://data.bioontology.org/metadata/owlobsolete"
           }
       },
       {
           "obsolete": false,
           "@id": "http://www.drugtargetontology.org/dto/DTO_03100518",
           "@type": "http://www.w3.org/2002/07/owl#Class",
           "links": {
               "self": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518",
               "ontology": "http://data.bioontology.org/ontologies/DTO",
               "children": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/children",
               "parents": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/parents",
               "descendants": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/descendants",
               "ancestors": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/ancestors",
               "instances": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/instances",
               "tree": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/tree",
               "notes": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/notes",
               "mappings": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/mappings",
               "ui": "http://bioportal.bioontology.org/ontologies/DTO?p=classes&conceptid=http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518",
               "@context": {
                   "self": "http://www.w3.org/2002/07/owl#Class",
                   "ontology": "http://data.bioontology.org/metadata/Ontology",
                   "children": "http://www.w3.org/2002/07/owl#Class",
                   "parents": "http://www.w3.org/2002/07/owl#Class",
                   "descendants": "http://www.w3.org/2002/07/owl#Class",
                   "ancestors": "http://www.w3.org/2002/07/owl#Class",
                   "instances": "http://data.bioontology.org/metadata/Instance",
                   "tree": "http://www.w3.org/2002/07/owl#Class",
                   "notes": "http://data.bioontology.org/metadata/Note",
                   "mappings": "http://data.bioontology.org/metadata/Mapping",
                   "ui": "http://www.w3.org/2002/07/owl#Class"
               }
           },
           "@context": {
               "@vocab": "http://data.bioontology.org/metadata/",
               "obsolete": "http://data.bioontology.org/metadata/owlobsolete"
           }
       }
   ],
   "process": {
       "id": "http://data.bioontology.org/metadata/mapping_processes/-elcioabrahao-0831b590-9723-0136-cc8e-005056010074",
       "name": "REST Mapping",
       "creator": "http://data.bioontology.org/users/elcioabrahao",
       "source": "RESTTEST",
       "relation": "[\"http://www.geneontology.org/formats/oboinowl#hasdbxref\"]",
       "source_name": "PR",
       "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR",
       "date": "2018-09-10T05:29:05-07:00"
   },
   "@id": "",
   "@type": "http://data.bioontology.org/metadata/Mapping"
}

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From support at bioontology.org  Wed Sep 12 22:26:23 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 12 Sep 2018 22:26:23 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Kristi Brownfield
Message-ID: <5b99f4ff1c3b7_24b72b29a20ad3a855523@ncbo-prd-app-09.stanford.edu.mail>

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From mdorf at stanford.edu  Thu Sep 13 11:31:56 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 13 Sep 2018 18:31:56 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Kristi
	Brownfield
In-Reply-To: <5b99f4ff1c3b7_24b72b29a20ad3a855523@ncbo-prd-app-09.stanford.edu.mail>
References: <5b99f4ff1c3b7_24b72b29a20ad3a855523@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <1E95416C-95F2-4177-97BE-24D346ECAF60@stanford.edu>

Hi Kristi,

Thank you for contacting us. I?ve looked up the term you were referring to, but it doesn?t contain any definition:

http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F19681004<http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http://purl.bioontology.org/ontology/SNOMEDCT/19681004>

Can you please clarify what you are looking for? Roughly twice per year the UMLS [1] publishes a release of a group of ontologies, which we import into BioPortal.  SNOMED CT is one of the ontologies that?s pulled in when we do the UMLS imports. We don?t have any control over the ontology content.

I look forward to further clarification from you.

Thanks!

Michael


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


On Sep 12, 2018, at 10:26 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Kristi Brownfield

Email: kbrownfield at wregional.com<mailto:kbrownfield at wregional.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FSNOMEDCT%252F424008009

Feedback:

I am researching Snomed code 19681004 "Nursing evaluation of patient and report (procedure)" for a quality metrix visit type permitted by CMS for a program for CPC+ CQM.

I am trying to find the definition or defining term to the "nursing ....(procedure" What required docuemation is required to link this snomed code to the note?

Thank you so much. This is a very time sensitive issue that we are trying to resolve on behalf of the CPC+ program and our hospital system and EMR Vendor.

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From markampa at pennmedicine.upenn.edu  Tue Sep 18 08:43:20 2018
From: markampa at pennmedicine.upenn.edu (Miller, Mark)
Date: Tue, 18 Sep 2018 15:43:20 +0000
Subject: [bioontology-support] Download OWL versions of UMLS components?
Message-ID: <BYAPR04MB4069430722319D7151E3C62FF71D0@BYAPR04MB4069.namprd04.prod.outlook.com>

If I try to download MDDB via http://data.bioontology.org/ontologies/MDDB/download?apikey=<my apikey>


I get the response at the end of the is email.


Are there any conditions under which you allow download of licensed UMLS components?  I have a UMLS license!  I have done the MetaMorphoSys -> MySQL -> RDF conversion in the past, but would like to avoid that overhead if possible.  (I do appreciate your contribution of the RDF conversion tool.)


thanks,

Mark Miller

ontologist, Institute for Biomedical Informatics

University of Pennsylvania


____


{

  *
-
"errors": [
     *   "License restrictions on download for MDDB"
],
  *   "status": 403

}
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From jgraybeal at stanford.edu  Tue Sep 18 13:22:12 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 18 Sep 2018 20:22:12 +0000
Subject: [bioontology-support] Download OWL versions of UMLS components?
In-Reply-To: <BYAPR04MB4069430722319D7151E3C62FF71D0@BYAPR04MB4069.namprd04.prod.outlook.com>
References: <BYAPR04MB4069430722319D7151E3C62FF71D0@BYAPR04MB4069.namprd04.prod.outlook.com>
Message-ID: <418EB8C5-0177-421D-BBC5-D9E809762B5B@stanford.edu>

Mark,

We handle requests like this on a case-by-case basis, depending on the ontology, its license, the UMLS distribution license, and sometimes my current knowledge of Intellectual Property issues.

I'll respond to you off-list once I've explore further.

John

On Sep 18, 2018, at 8:43 AM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

If I try to download MDDB via http://data.bioontology.org/ontologies/MDDB/download?apikey=<<http://data.bioontology.org/ontologies/MDDB/download?apikey=%3C>my apikey>

I get the response at the end of the is email.

Are there any conditions under which you allow download of licensed UMLS components?  I have a UMLS license!  I have done the MetaMorphoSys -> MySQL -> RDF conversion in the past, but would like to avoid that overhead if possible.  (I do appreciate your contribution of the RDF conversion tool.)

thanks,
Mark Miller
ontologist, Institute for Biomedical Informatics
University of Pennsylvania

____

{

  *
-
"errors": [
     *   "License restrictions on download for MDDB"
],
  *   "status": 403

}

_______________________________________________
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bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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From support at bioontology.org  Mon Sep 17 11:48:05 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 17 Sep 2018 11:48:05 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5b9ff6e54edc2_3fb92b263a0b0dd4660f6@ncbo-prd-app-08.stanford.edu.mail>

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From yac9016 at nyp.org  Tue Sep 18 08:42:47 2018
From: yac9016 at nyp.org (Yael Greenberg)
Date: Tue, 18 Sep 2018 15:42:47 +0000
Subject: [bioontology-support] CPT Code Library
Message-ID: <834786eeb7c348d5b359e02b19f946a0@nyp.org>

Is there a way to download the library of CPT codes and matching descriptions?
Thanks,
Yael

Yael Coppleson Greenberg, MPH
Director, NYP Analytics | NewYork-Presbyterian Hospital
yac9016 at nyp.org<mailto:yac9016 at nyp.org> | (c) 646.784.5656 | (o) 212.305.5715


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From gullyburns at gmail.com  Mon Sep 17 13:27:40 2018
From: gullyburns at gmail.com (Gully Burns)
Date: Mon, 17 Sep 2018 13:27:40 -0700
Subject: [bioontology-support] Transferring ownership of DSEO ontology
Message-ID: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com>

Dear Sir, 

Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary <http://bioportal.bioontology.org/ontologies/DSEO/?p=summary>) to a colleague? 

The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com). 

Can you advise me what the process is to switch ownership of this ontology?

Thanks

Gully
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From jgraybeal at stanford.edu  Wed Sep 19 10:50:45 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 19 Sep 2018 17:50:45 +0000
Subject: [bioontology-support] Transferring ownership of DSEO ontology
In-Reply-To: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com>
References: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com>
Message-ID: <2883DEF7-3A1B-4C6F-89C4-E1BF7165B589@stanford.edu>

Gully,

We can take care of that for you. Do you want both of the people you list as administrator?

John

On Sep 17, 2018, at 1:27 PM, Gully Burns <gullyburns at gmail.com<mailto:gullyburns at gmail.com>> wrote:

Dear Sir,

Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary) to a colleague?

The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu<mailto:lfierro at isi.edu>) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com<mailto:jl.ambite at gmail.com>).

Can you advise me what the process is to switch ownership of this ontology?

Thanks

Gully
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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From jgraybeal at stanford.edu  Wed Sep 19 18:17:29 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 20 Sep 2018 01:17:29 +0000
Subject: [bioontology-support] CPT Code Library
In-Reply-To: <834786eeb7c348d5b359e02b19f946a0@nyp.org>
References: <834786eeb7c348d5b359e02b19f946a0@nyp.org>
Message-ID: <92F0973F-539F-4F6D-89D1-9FB3FF57EC66@stanford.edu>

Yael,

Thanks for your request. I offer the following information for the list, some of which you may have received separately (thanks R Wynne!).

As you may know, you are unable to download most UMLS ontologies directly from BioPortal, because license restrictions apply. However, you can download information contained in BioPortal about those ontologies by using the BioPortal REST API. The API is documented at http://data.bioontology.org/documentation. If you decide to use the API, you?ll need to get an API key (see https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key).

So for example, REST API calls to retrieve class data will return results:
   http://data.bioontology.org/ontologies/CPT/classes?apikey=<your_api_key_here><http://data.bioontology.org/ontologies/CPT/classes?apikey=%3Cyour_api_key_here%3E>
You can use the hypermedia links in the reply to explore things like parents, children, descendants, etc.

OR, for UMLS ontologies:

There is a way to download this information directly from UMLS, with minimal processing.  The following applies for almost all sources in the UMLS Metathesaurus (which includes even more sources than BioPortal captures). You may want to reach out to the source contact for your ontology and let them know you are interested, as there may be a license on the source you are not aware of, it could give you additional access or reuse privileges beyond what UMLS offers in its license.

The CPT source is extracted via the UMLS Metathesaurus.  You need to obtain a free license[1] from NLM to download Metathesaurus.  The download includes a utility to extract a source or sources, named Metamorphosys.  Once you have an extract, it can be loaded into a database.  Some sources are small enough to load into Excel.  You will want to know which files and columns are most important to you.  More information on CPT source representation is available through UMLS[2].

John

[1] https://uts.nlm.nih.gov/license.html
[2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT/sourcerepresentation.html

On Sep 18, 2018, at 8:42 AM, Yael Greenberg <yac9016 at nyp.org<mailto:yac9016 at nyp.org>> wrote:

Is there a way to download the library of CPT codes and matching descriptions?
Thanks,
Yael

Yael Coppleson Greenberg, MPH
Director, NYP Analytics | NewYork-Presbyterian Hospital
yac9016 at nyp.org<mailto:yac9016 at nyp.org> | (c) 646.784.5656 | (o) 212.305.5715


________________________________
This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.
code:d34y
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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From jgraybeal at stanford.edu  Thu Sep 20 17:49:56 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 21 Sep 2018 00:49:56 +0000
Subject: [bioontology-support] NCBO virtual appliance
In-Reply-To: <DM5PR06MB2393E5BD147C8C47C986897CC3130@DM5PR06MB2393.namprd06.prod.outlook.com>
References: <BLUPR06MB674BE78442BC851230F6E0DC3E20@BLUPR06MB674.namprd06.prod.outlook.com>
 <017BE204-69FE-418C-A83E-B8E381C5A736@stanford.edu>
 <DM5PR06MB2393E5BD147C8C47C986897CC3130@DM5PR06MB2393.namprd06.prod.outlook.com>
Message-ID: <D02CD1B4-D9A9-49E2-B289-23D1B42E2517@stanford.edu>

Hi Chad,

I'm sorry, but I don't know what version you have right now, so I can't answer your question directly.

The Release Notes for the Virtual Appliance software are at https://www.bioontology.org/wiki/BioPortal_Virtual_Appliance_Release_Notes.

However, you may also want to know whether it is easily installable on your platform.

If you have a Virtual Appliance already, the way to find out the current releases that are available for download is to visit https://bioportal.bioontology.org/virtual_appliance.  (You'll need to be logged in to BioPortal, using the account you obtained the Virtual Appliance with, to see that page.)

The current listing show:
? Version 2.5 OVF
? Version 2.4 OVF | Amazon EC2
In summary, we have not created an Amazon EC2 version for Version 2.5 yet.

I hope this helps.

John




On Sep 20, 2018, at 3:28 PM, Shaw, Chad A. <cashaw at bcm.edu<mailto:cashaw at bcm.edu>> wrote:

Hi John

Is there a new release of the NCBO VM that we could obtain?  I think the one we have is pretty old right now.

Please let me know

Thanks
Chad
________________________________
========================
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 lfierro at isi.edu  Fri Sep 21 09:09:26 2018
From: lfierro at isi.edu (Lily Fierro)
Date: Fri, 21 Sep 2018 16:09:26 +0000
Subject: [bioontology-support] Transferring ownership of DSEO ontology
In-Reply-To: <2883DEF7-3A1B-4C6F-89C4-E1BF7165B589@stanford.edu>
References: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com>,
 <2883DEF7-3A1B-4C6F-89C4-E1BF7165B589@stanford.edu>
Message-ID: <528934fd6376469395e3617179128104@ads.isi.edu>

Hello John,


Thank you very much for your help on this! I just logged into BioPortal and can confirm that I have administrator access.


One quick question for you: is there a way to upload mappings to BioPortal in bulk? I noticed that I can add them on a class-by-class basis through the web interface, but could not find any way to upload them for multiple classes.


Thanks again!


-Lily

________________________________
From: John Graybeal <jgraybeal at stanford.edu>
Sent: Wednesday, September 19, 2018 1:50:45 PM
To: Gully Burns
Cc: support at bioontology.org; Jose-Luis Ambite; Lily Fierro
Subject: Re: [bioontology-support] Transferring ownership of DSEO ontology

Gully,

We can take care of that for you. Do you want both of the people you list as administrator?

John

On Sep 17, 2018, at 1:27 PM, Gully Burns <gullyburns at gmail.com<mailto:gullyburns at gmail.com>> wrote:

Dear Sir,

Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary) to a colleague?

The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu<mailto:lfierro at isi.edu>) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com<mailto:jl.ambite at gmail.com>).

Can you advise me what the process is to switch ownership of this ontology?

Thanks

Gully
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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From jgraybeal at stanford.edu  Fri Sep 21 11:43:48 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 21 Sep 2018 18:43:48 +0000
Subject: [bioontology-support] uploading mappings in bulk
Message-ID: <DBF77EA0-3C77-417F-B3FE-AD85D1355EC4@stanford.edu>

You're welcome Lily.

Yes, you can upload mappings through the API. 

Example code for creating API mappings is at 
  https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java 

A past thread on how to do this is at 
  http://ncbo-support.2288202.n4.nabble.com/Uploading-a-Mapping-td4653220.html#a4653222
It mentions the general info on running the above sample code:
  https://github.com/ncbo/ncbo_rest_sample_code/tree/master/java 

Links that might be useful:
  https://www.bioontology.org/wiki/index.php/BioPortal_Mappings
  http://data.bioontology.org/documentation#Mapping    -- the actual API documentation

John




> On Sep 21, 2018, at 9:09 AM, Lily Fierro <lfierro at isi.edu> wrote:
> 
> Hello John, 
> 
> Thank you very much for your help on this! I just logged into BioPortal and can confirm that I have administrator access. 
> 
> One quick question for you: is there a way to upload mappings to BioPortal in bulk? I noticed that I can add them on a class-by-class basis through the web interface, but could not find any way to upload them for multiple classes. 
> 
> Thanks again! 
> 
> -Lily 
> From: John Graybeal <jgraybeal at stanford.edu>
> Sent: Wednesday, September 19, 2018 1:50:45 PM
> To: Gully Burns
> Cc: support at bioontology.org; Jose-Luis Ambite; Lily Fierro
> Subject: Re: [bioontology-support] Transferring ownership of DSEO ontology
>  
> Gully,
> 
> We can take care of that for you. Do you want both of the people you list as administrator?
> 
> John
> 
>> On Sep 17, 2018, at 1:27 PM, Gully Burns <gullyburns at gmail.com> wrote:
>> 
>> Dear Sir, 
>> 
>> Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary) to a colleague? 
>> 
>> The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com). 
>> 
>> Can you advise me what the process is to switch ownership of this ontology?
>> 
>> Thanks
>> 
>> Gully
>> _______________________________________________
>> 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

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632




From support at bioontology.org  Mon Sep 24 02:17:17 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 24 Sep 2018 02:17:17 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Hiba Itani
Message-ID: <5ba8ab9de591c_af52b0b2911aef4536aa@ncbo-prd-app-08.stanford.edu.mail>

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From a.grigoriu at student.maastrichtuniversity.nl  Mon Sep 24 07:06:25 2018
From: a.grigoriu at student.maastrichtuniversity.nl (Grigoriu, Andreea (Stud. DKE))
Date: Mon, 24 Sep 2018 14:06:25 +0000
Subject: [bioontology-support] error report
Message-ID: <1537797983389.43171@student.maastrichtuniversity.nl>

Hi!


While working on my Internship during my Master Studies I have encountered some incosistency in your platform.

I was trying to find the metrics for various ontologies ( I was particulary interested in number of classes and properties of an ontology). Some ontologies (eg. PTS, HUGO, HGNC) were showing ( in the metric box on the ontology page->http://bioportal.bioontology.org/ontologies/HGNC/?p=summary)<http://bioportal.bioontology.org/ontologies/HGNC/?p=summary> 0 properties but once I check the properties tab (http://bioportal.bioontology.org/ontologies/HGNC/?p=properties?) I can actually see a lot of properties. This was obvious for the examples of 0 properties but now I am also wandering if there might be other inconsistencies as well in other numbers of properties or maybe even classes.


Kind regards,

Andreea Grigoriu

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From support at bioontology.org  Mon Sep 24 08:49:35 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 24 Sep 2018 08:49:35 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh
Message-ID: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>

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From Ross.W.Filice at gunet.georgetown.edu  Mon Sep 24 10:37:59 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Mon, 24 Sep 2018 13:37:59 -0400
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <D9DB15C3-DDE1-4F3B-8496-70ED78987954@stanford.edu>
References: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
 <D9DB15C3-DDE1-4F3B-8496-70ED78987954@stanford.edu>
Message-ID: <DAE74CB00EC3AD49975BE0428640870B854F0DFF42@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

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" : "http://data.bioontology.org/user/[USER]",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs",
  "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" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ]
  }, {
    "ontology" : "SNOMEDCT",
    "term" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ]
  } ]
}

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

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

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
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> 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

>   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

> 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






From vendetti at stanford.edu  Mon Sep 24 11:35:05 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 24 Sep 2018 18:35:05 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
	El-Sappagh
In-Reply-To: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>
References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu>

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 vendetti at stanford.edu  Mon Sep 24 14:19:13 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 24 Sep 2018 21:19:13 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Hiba Itani
In-Reply-To: <5ba8ab9de591c_af52b0b2911aef4536aa@ncbo-prd-app-08.stanford.edu.mail>
References: <5ba8ab9de591c_af52b0b2911aef4536aa@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <3D9790D8-1631-4BA8-8F20-F1E7DBF84408@stanford.edu>

Hello Hiba,

We offer a REST API for accessing all of the ontology data in BioPortal. CPT is one of the ontologies in our repository, so you can use the API to access CPT content. Our API is documented here:

http://data.bioontology.org/documentation

In order to use the API, you need an API key. Instructions for getting a key are available on our wiki:

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

If you have more specific question about API usage, feel free to follow up with us.

Kind regards,
Jennifer


On Sep 24, 2018, at 2:17 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Hiba Itani

Email: best.smile1988 at live.com<mailto:best.smile1988 at live.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FCPT%252F99241%26jump_to_nav%3Dtrue

Feedback:

Hello;
We are a Healthcare Management Company located in Lebanon and we are looking for a structured coding database or web api for CPT hat will enable us to manage our claims, stratify, and map our provider codes.

Kindly Let ya know what solutions can you provide.

Anticipating your feedback.

Kind Regards,
Hiba Itani

_______________________________________________
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 Sep 24 14:13:55 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 24 Sep 2018 21:13:55 +0000
Subject: [bioontology-support] error report
In-Reply-To: <1537797983389.43171@student.maastrichtuniversity.nl>
References: <1537797983389.43171@student.maastrichtuniversity.nl>
Message-ID: <8BEB2827-3B8B-484E-9CCC-33EC361252E1@stanford.edu>

Hi Andreea,


On Sep 24, 2018, at 7:06 AM, Grigoriu, Andreea (Stud. DKE) <a.grigoriu at student.maastrichtuniversity.nl<mailto:a.grigoriu at student.maastrichtuniversity.nl>> wrote:

While working on my Internship during my Master Studies I have encountered some incosistency in your platform.
I was trying to find the metrics for various ontologies ( I was particulary interested in number of classes and properties of an ontology). Some ontologies (eg. PTS, HUGO, HGNC) were showing ( in the metric box on the ontology page->http://bioportal.bioontology.org/ontologies/HGNC/?p=summary)<http://bioportal.bioontology.org/ontologies/HGNC/?p=summary> 0 properties but once I check the properties tab (http://bioportal.bioontology.org/ontologies/HGNC/?p=properties?) I can actually see a lot of properties. This was obvious for the examples of 0 properties but now I am also wandering if there might be other inconsistencies as well in other numbers of properties or maybe even classes.


The number of properties reported in the BioPortal metrics panel includes the total number of data and object properties that are declared in an ontology. It doesn?t include the number of annotation properties, but we do display annotation properties in the user interface, which is why you see more properties on the properties tab than are reported in the metrics panel.

Using one of the ontologies you listed above, I opened PTS in the Protege ontology editing environment [1] and confirmed that there are 5 object properties, and no data properties declared:


[cid:370C96D0-9508-4724-AFBB-5B3852FCEC9C at stanford.edu]


The BioPortal metrics panel reports a total of 5 properties for PTS.

I checked the other two ontologies you mentioned above. HUGO and HGNC appear to be the same OWL ontology listed under two different ontology entries in BioPortal. The ontology has no data or object properties, hence the zeros in the metrics panel. It does have 66 annotation properties though, which is why the properties tab in the BioPortal UI shows a property tree.

Honestly speaking, I don?t know the historical reason why annotation property counts weren?t included in the total property count in the metrics data. I will ask around among my colleagues to see if anyone has more information on this.

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php


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From vendetti at stanford.edu  Mon Sep 24 16:32:28 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 24 Sep 2018 23:32:28 +0000
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <DAE74CB00EC3AD49975BE0428640870B854F0DFF42@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>
Message-ID: <E4318C79-7578-4FE9-B31C-DC83A8914C42@stanford.edu>

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> 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" : "http://data.bioontology.org/user/[USER]",
>  "relation" : "http://www.w3.org/2002/07/owl#sameAs",
>  "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" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ]
>  }, {
>    "ontology" : "SNOMEDCT",
>    "term" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ]
>  } ]
> }
> 
> Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings:
> 
> http://data.bioontology.org/documentation#Mapping
> 
> 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
> 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> 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
> 
>>  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
> 
>> 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
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From Ross.W.Filice at gunet.georgetown.edu  Mon Sep 24 18:53:51 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Mon, 24 Sep 2018 21:53:51 -0400
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <E4318C79-7578-4FE9-B31C-DC83A8914C42@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>
Message-ID: <DAE74CB00EC3AD49975BE0428640870B854F0E00E6@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

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

{
  "creator" : "http://data.bioontology.org/user/rwfilice",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs",
  "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" ]
  }, {
    "ontology" : "SNOMEDCT",
    "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ]
  } ]
}

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
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> 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

> 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> 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

> 

>>  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

> 

>> 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

> 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=




From shaker_elsapagh at yahoo.com  Mon Sep 24 20:31:17 2018
From: shaker_elsapagh at yahoo.com (Shaker El-Sappagh)
Date: Tue, 25 Sep 2018 03:31:17 +0000 (UTC)
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
 El-Sappagh
In-Reply-To: <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu>
References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail>
 <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu>
Message-ID: <2032047650.1906847.1537846277280@mail.yahoo.com>

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 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 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  Tue Sep 25 17:16:11 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 26 Sep 2018 00:16:11 +0000
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <DAE74CB00EC3AD49975BE0428640870B854F0E00E6@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>
Message-ID: <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu>

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",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003":"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",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs",
  "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" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003":?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:ED5766D3-FCE4-4255-935C-D0A6B68FE2E1 at stanford.edu]


? and here is the body text:


[cid:D3BB66BE-AFEE-4E6D-8FD6-D6A928DB2F5B at stanford.edu]


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


[cid:869FDF5B-FA0E-4ED2-99F8-3597C8D29BB0 at stanford.edu]


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


[cid:5BDAE2EA-CE28-4A1E-B9B3-6BE2462EA453 at stanford.edu]


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://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http://purl.bioontology.org/ontology/SNOMEDCT/2092003>

? 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",
 "relation" : "http://www.w3.org/2002/07/owl#sameAs",
 "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" ]
 }, {
   "ontology" : "SNOMEDCT",
   "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ]
 } ]
}

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>



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



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From Ross.W.Filice at gunet.georgetown.edu  Wed Sep 26 07:20:36 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Wed, 26 Sep 2018 10:20:36 -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: <DAE74CB00EC3AD49975BE0428640870B854F0E05CB@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

That worked! Thanks very much. Ross

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 01D45582.90BA60B0]


? and here is the body text:


[cid:image002.png at 01D45582.90BA60B0]


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 01D45582.90BA60B0]


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


[cid:image004.png at 01D45582.90BA60B0]


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 alex.noury at nih.gov  Wed Sep 26 08:23:40 2018
From: alex.noury at nih.gov (Noury, Alex (NIH/NIMH) [E])
Date: Wed, 26 Sep 2018 15:23:40 +0000
Subject: [bioontology-support] Broken Link
Message-ID: <BN6PR09MB1409BB8DFADCBDC921D4880584150@BN6PR09MB1409.namprd09.prod.outlook.com>

The link to "MedDRA MSSO" on the below page is broken.  The link is on the "Summary" tab under "License Information".

http://bioportal.bioontology.org/ontologies/MEDDRA

Also, I tried to submit this comment using the form under Feedback, but there wasn't a "submit" button.  If it helps, I accessed the page using Chrome.

[cid:image001.jpg at 01D4558B.5FBD65D0]



Best,
Alex



___________________________________________________________

Alex J. Noury
Protocol Coordinator  |  ETPB, NIMH
301-496-9848  |  alex.noury at nih.gov<mailto:alex.noury at nih.gov>  |  10-CRC, 7-5331

Branch website: www.nimh.nih.gov/MoodResearch<http://www.nimh.nih.gov/MoodResearch>
Adult Bipolar & Depression Research at: www.nimh.nih.gov/JoinAStudy<http://www.nimh.nih.gov/JoinAStudy>

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From vendetti at stanford.edu  Wed Sep 26 11:32:45 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 26 Sep 2018 18:32:45 +0000
Subject: [bioontology-support] Broken Link
In-Reply-To: <BN6PR09MB1409BB8DFADCBDC921D4880584150@BN6PR09MB1409.namprd09.prod.outlook.com>
References: <BN6PR09MB1409BB8DFADCBDC921D4880584150@BN6PR09MB1409.namprd09.prod.outlook.com>
Message-ID: <06C418A2-5235-4C84-AC5E-287768017CCC@stanford.edu>

Hi Alex,


On Sep 26, 2018, at 8:23 AM, Noury, Alex (NIH/NIMH) [E] <alex.noury at nih.gov<mailto:alex.noury at nih.gov>> wrote:

The link to "MedDRA MSSO" on the below page is broken.  The link is on the "Summary" tab under "License Information".

http://bioportal.bioontology.org/ontologies/MEDDRA



At the moment we don?t have a way for end users to edit ontology license information via the BioPortal user interface. Rather, if you send us the updated license text, we can add it to the application on your behalf.




Also, I tried to submit this comment using the form under Feedback, but there wasn?t a ?submit? button.  If it helps, I accessed the page using Chrome.

<image001.jpg>


You should be able to resize the dialog window to make it a little bigger, which will reveal the ?Send Feedback? button:


[cid:24C66B2E-219D-4C7D-B26A-1FB65FDACF17 at stanford.edu]

Kind regards,
Jennifer

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From vendetti at stanford.edu  Wed Sep 26 15:26:50 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 26 Sep 2018 22:26:50 +0000
Subject: [bioontology-support] Broken Link
In-Reply-To: <BN6PR09MB140975A9CF1660A1FA55A6EA84150@BN6PR09MB1409.namprd09.prod.outlook.com>
References: <BN6PR09MB1409BB8DFADCBDC921D4880584150@BN6PR09MB1409.namprd09.prod.outlook.com>
 <06C418A2-5235-4C84-AC5E-287768017CCC@stanford.edu>
 <BN6PR09MB140975A9CF1660A1FA55A6EA84150@BN6PR09MB1409.namprd09.prod.outlook.com>
Message-ID: <4466A436-16D2-464B-9B2D-2EE4C79BAA0F@stanford.edu>

Hi Alex,


On Sep 26, 2018, at 11:38 AM, Noury, Alex (NIH/NIMH) [E] <alex.noury at nih.gov<mailto:alex.noury at nih.gov>> wrote:

Hi Jennifer,

I didn?t realize I could shrink the dialogue box.  Thanks!

About the link, I was just reporting that it?s broken.  It goes to this error page: https://www.meddra.org/node/734.  It looks like the page moved.  Here?s the current location:https://www.meddra.org/about-meddra/organisation/msso.


OK, thanks for pointing that out. I changed the link to point to the new page, and it?s now live on our production site.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Wed Sep 26 17:00:04 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 27 Sep 2018 00:00:04 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
	El-Sappagh
In-Reply-To: <2032047650.1906847.1537846277280@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>
Message-ID: <8E890E4D-A5F5-41D4-8AE0-4A68BA4D5DBB@stanford.edu>

Hello Dr. El-Sappagh,

Thank you for resubmitting your ontology in the requested format. There were still some errors that occurred during our parsing process, which I am looking into and will report back when I have more information.

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<http://us.mc1126.mail.yahoo.com/mc/compose?to=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<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 jonquet at lirmm.fr  Thu Sep 27 10:27:06 2018
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Thu, 27 Sep 2018 19:27:06 +0200
Subject: [bioontology-support] =?utf-8?q?Research_engineer_position_in_Mon?=
 =?utf-8?q?tpellier=2C_France_-_Web_architect_=E2=80=93_Semantic_web_techn?=
 =?utf-8?q?ologies_=E2=80=93_Text_and_data_mining?=
Message-ID: <6AD25A29-F837-4356-9D2B-2072351B2F76@lirmm.fr>

Dear all, 

We have a job opening in Montpellier, France to work on semantic web technologies, ontology managment and text mining workflows? at LIRMM (University of Montpellier & CNRS Informatics Research lab). 
The position is for 1 year with possible extensions.

********
A key aspect in addressing semantic interoperability is the use of terminologies, vocabularies and ontologies as a common denominator to structure data and make them interoperable. In partnership with Stanford University, LIRMM designs, develops and maintains two vocabulary and ontology repositories: (i) the SIFR BioPortal (http://bioportal.lirmm.fr <http://bioportal.lirmm.fr/>) which targets the French biomedical community and offers an ontology-based annotation workflow to semantically index text biomedical and clinical data; (ii) AgroPortal (http://agroportal.lirmm.fr <http://agroportal.lirmm.fr/>) a reference repository for semantic resources in agronomy, agriculture, food, plant sciences and biodiversity. These platforms allow us to tackle scientific problems in natural language processing, semantic annotation, ontology engineering, while being driven by concrete use cases with impacts in biomedicine and agronomy.

In the context of the ANR PractiKPharma and VisaTM projects, we are seeking a motivated, curious and interested research engineer and web developer to take hands on the platforms and prototypes developed. Your role will be both to support the current platforms and investigate technical decisions to enable the development of new features in relation to text and data mining. Within PractiKPharma, your role will consist in enhancing the SIFR Annotator to facilitate its use to annotate clinical data (in collaboration with HEGP and LORIA). Within the VisaTM project, your role will be to enable interoperation of both AgroProtal and BioPortal with the text and data mining infrastructure developed in the OpenMinTeD project (in collaboration with INRA and INIST). You will work with a small team (4 persons) at LIRMM in both a national and international context. Further extension of the proposed 12-month-contract are possible.

********

See http://www.lirmm.fr/~jonquet/positions/2018_PractiKPharma-VisaTM_IGR_position.pdf <http://www.lirmm.fr/~jonquet/positions/2018_PractiKPharma-VisaTM_IGR_position.pdf>

Regards
-------------------------------------------------------------------------------------------
Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier (LIRMM)
Coordinator of the SIFR and AgroPortal projects
EU Marie Curie fellow
 
jonquet at lirmm.fr
http://www.lirmm.fr/~jonquet
 
@Montpellier : +33/0 4 67 14 97 43
-------------------------------------------------------------------------------------------

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From support at bioontology.org  Thu Sep 27 09:19:45 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 27 Sep 2018 09:19:45 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Mohammad
Message-ID: <5bad032147acd_5c192ac93bce5f5c51971@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Sep 27 11:23:54 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 27 Sep 2018 18:23:54 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Mohammad
In-Reply-To: <5bad032147acd_5c192ac93bce5f5c51971@ncbo-prd-app-09.stanford.edu.mail>
References: <5bad032147acd_5c192ac93bce5f5c51971@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <2DCDC503-F953-4F65-AAB7-A70068EA2A4B@stanford.edu>

Hello Mohammad,

There?s a known issue with the 3rd party visualization software we use where it doesn?t work over HTTPS. You?ll need to change the protocol in your browser?s address bar to HTTP in order to see the visualizations:


[cid:5D5DA279-D11D-433F-A1C8-F7DA0B5331E4 at stanford.edu]




Apologies for the inconvenience.

Jennifer


On Sep 27, 2018, at 9:19 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Mohammad

Email: mohammad.babaei33 at yahoo.com<mailto:mohammad.babaei33 at yahoo.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FATOL%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.org<http://252Fpurl.org>%252Fobo%252FowlATOL_0002159

Feedback:

Hi, i want to know why vidualization of trait's ontologies( e.g. feed efficiency) don't draw?.
Thanks

_______________________________________________
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 jonquet at lirmm.fr  Thu Sep 27 10:27:06 2018
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Thu, 27 Sep 2018 19:27:06 +0200
Subject: [bioontology-support] =?utf-8?q?=5Bbioportal-announce=5D_Research?=
 =?utf-8?q?_engineer_position_in_Montpellier=2C_France_-_Web_architect_?=
 =?utf-8?q?=E2=80=93_Semantic_web_technologies_=E2=80=93_Text_and_data_min?=
 =?utf-8?q?ing?=
Message-ID: <6AD25A29-F837-4356-9D2B-2072351B2F76@lirmm.fr>

Dear all, 

We have a job opening in Montpellier, France to work on semantic web technologies, ontology managment and text mining workflows? at LIRMM (University of Montpellier & CNRS Informatics Research lab). 
The position is for 1 year with possible extensions.

********
A key aspect in addressing semantic interoperability is the use of terminologies, vocabularies and ontologies as a common denominator to structure data and make them interoperable. In partnership with Stanford University, LIRMM designs, develops and maintains two vocabulary and ontology repositories: (i) the SIFR BioPortal (http://bioportal.lirmm.fr <http://bioportal.lirmm.fr/>) which targets the French biomedical community and offers an ontology-based annotation workflow to semantically index text biomedical and clinical data; (ii) AgroPortal (http://agroportal.lirmm.fr <http://agroportal.lirmm.fr/>) a reference repository for semantic resources in agronomy, agriculture, food, plant sciences and biodiversity. These platforms allow us to tackle scientific problems in natural language processing, semantic annotation, ontology engineering, while being driven by concrete use cases with impacts in biomedicine and agronomy.

In the context of the ANR PractiKPharma and VisaTM projects, we are seeking a motivated, curious and interested research engineer and web developer to take hands on the platforms and prototypes developed. Your role will be both to support the current platforms and investigate technical decisions to enable the development of new features in relation to text and data mining. Within PractiKPharma, your role will consist in enhancing the SIFR Annotator to facilitate its use to annotate clinical data (in collaboration with HEGP and LORIA). Within the VisaTM project, your role will be to enable interoperation of both AgroProtal and BioPortal with the text and data mining infrastructure developed in the OpenMinTeD project (in collaboration with INRA and INIST). You will work with a small team (4 persons) at LIRMM in both a national and international context. Further extension of the proposed 12-month-contract are possible.

********

See http://www.lirmm.fr/~jonquet/positions/2018_PractiKPharma-VisaTM_IGR_position.pdf <http://www.lirmm.fr/~jonquet/positions/2018_PractiKPharma-VisaTM_IGR_position.pdf>

Regards
-------------------------------------------------------------------------------------------
Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier (LIRMM)
Coordinator of the SIFR and AgroPortal projects
EU Marie Curie fellow
 
jonquet at lirmm.fr
http://www.lirmm.fr/~jonquet
 
@Montpellier : +33/0 4 67 14 97 43
-------------------------------------------------------------------------------------------

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From support at bioontology.org  Thu Sep 27 16:47:52 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 27 Sep 2018 16:47:52 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Chris
Message-ID: <5bad6c28ef982_37582ad167b795a4124c5@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Sep 27 16:55:42 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 27 Sep 2018 23:55:42 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Chris
In-Reply-To: <5bad6c28ef982_37582ad167b795a4124c5@ncbo-prd-app-08.stanford.edu.mail>
References: <5bad6c28ef982_37582ad167b795a4124c5@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <1655EE7F-1DA1-4783-B15E-006CCAAAD7CE@stanford.edu>

Hi Chris,

I think this message from our mailing list archive may address your question:

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Jaime-Parra-MD-phD-tp4655505p4655508.html

If not, feel free to follow up again.

Kind regards,
Jennifer



On Sep 27, 2018, at 4:47 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Chris

Email: cvolzer3 at gmail.com<mailto:cvolzer3 at gmail.com>

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

Feedback:

What does "inverse of SIB" mean?

Thanks!

_______________________________________________
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 Sep 27 18:10:52 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 28 Sep 2018 01:10:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Shaker
	El-Sappagh
In-Reply-To: <2032047650.1906847.1537846277280@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>
Message-ID: <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu>

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
> 


From shaker_elsapagh at yahoo.com  Thu Sep 27 19:05:16 2018
From: shaker_elsapagh at yahoo.com (Shaker El-Sappagh)
Date: Fri, 28 Sep 2018 02:05:16 +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: <404437831.1297530.1538100316184@mail.yahoo.com>

Dear Dr. Jennifer,Thank you for your kind reply. 
I have changed the URL and uploaded the zip file for the ontology.
Thank you for your support.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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