From rakesh at pieriandx.com  Sat Jul  1 12:34:24 2017
From: rakesh at pieriandx.com (Rakesh Nagarajan)
Date: Sat, 1 Jul 2017 14:34:24 -0500
Subject: [bioontology-support] HPO
In-Reply-To: <CAOaXRCeEet-56Cz7BJTVG_Bv8AtRTYxeEbxSpJaQsd-y+_W0zg@mail.gmail.com>
References: <CAOaXRCe4cTtQY5V33x6dmJfBhQS2BVBBELK5X=tabtxeHrnBOA@mail.gmail.com>
 <f2e80391-e7dc-db88-224d-4be121411347@lirmm.fr>
 <CAOaXRCdjVAa_ic3zYzbZYeKSpnYMHxDr4SMKo9p=y=Dez30tyA@mail.gmail.com>
 <3EEE530C-F1C7-4681-84A1-1FBFA81B48FE@stanford.edu>
 <CAOaXRCeEet-56Cz7BJTVG_Bv8AtRTYxeEbxSpJaQsd-y+_W0zg@mail.gmail.com>
Message-ID: <CAOaXRCf3TvKX_Mp2xs6_cQdaZRnDDQNg2CfxufHei7-3eGP_NQ@mail.gmail.com>

Hello,
     I am trying to get ancestors for an ontology (MESH). For some valid
MESH terms, I get the following error:

{

   - -
   "errors": [
      - "The input class id 'D017326' is not a valid IRI"
   ],
   - "status": 400

}


even though the term itself exists in the BioPortal browser when I navigate
here:
http://bioportal.bioontology.org/ontologies/MESH/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD017326&jump_to_nav=true

Can you fix this?

Thanks,
Rakesh

On Mon, May 22, 2017 at 9:10 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
wrote:

> Jennifer,
>      Thanks a lot!
>
> Rakesh
>
> On Mon, May 22, 2017 at 4:40 PM, Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Hello Rakesh,
>>
>>
>> On May 6, 2017, at 12:23 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
>> wrote:
>>
>> Hello,
>>      I got the above response to the HPO ontology. How can you list an
>> ontology on your site and not have it loaded appropriately to browse it?
>>
>>
>>
>> As long as users upload valid OWL or OBO ontologies, it?s not our
>> intention that they should experience issues while browsing.
>>
>> In the case of the HP ontology, I found and fixed a problem in our source
>> code that was preventing correct calculation of the set of root classes.  I
>> deployed that fix today, and the HP ontology is now fully parsed and
>> available for browsing.
>>
>> Kind regards,
>> Jennifer
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
>
> *The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.*
>



-- 

*The materials in this email are private and may contain Protected Health
Information. If you are not the intended recipient, be advised that any
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From vendetti at stanford.edu  Mon Jul  3 11:17:22 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 3 Jul 2017 18:17:22 +0000
Subject: [bioontology-support] HPO
In-Reply-To: <CAOaXRCf3TvKX_Mp2xs6_cQdaZRnDDQNg2CfxufHei7-3eGP_NQ@mail.gmail.com>
References: <CAOaXRCe4cTtQY5V33x6dmJfBhQS2BVBBELK5X=tabtxeHrnBOA@mail.gmail.com>
 <f2e80391-e7dc-db88-224d-4be121411347@lirmm.fr>
 <CAOaXRCdjVAa_ic3zYzbZYeKSpnYMHxDr4SMKo9p=y=Dez30tyA@mail.gmail.com>
 <3EEE530C-F1C7-4681-84A1-1FBFA81B48FE@stanford.edu>
 <CAOaXRCeEet-56Cz7BJTVG_Bv8AtRTYxeEbxSpJaQsd-y+_W0zg@mail.gmail.com>
 <CAOaXRCf3TvKX_Mp2xs6_cQdaZRnDDQNg2CfxufHei7-3eGP_NQ@mail.gmail.com>
Message-ID: <7CCAB221-1217-487B-A127-438D13ACD25E@stanford.edu>

Hello Rakesh,

I tested a REST API call to get ancestors for the term you listed below:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD017326/ancestors<http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D017326/ancestors>

The call returns data with no errors. Perhaps the error you receive is due to improperly encoding the term ID? It would help if you could send an example of how you?re trying to retrieve the ancestors.

Kind regards,
Jennifer


On Jul 1, 2017, at 12:34 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Hello,
     I am trying to get ancestors for an ontology (MESH). For some valid MESH terms, I get the following error:

{

  *
-
"errors": [
     *   "The input class id 'D017326' is not a valid IRI"
],
  *   "status": 400

}


even though the term itself exists in the BioPortal browser when I navigate here: http://bioportal.bioontology.org/ontologies/MESH/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD017326&jump_to_nav=true

Can you fix this?

Thanks,
Rakesh

On Mon, May 22, 2017 at 9:10 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:
Jennifer,
     Thanks a lot!

Rakesh

On Mon, May 22, 2017 at 4:40 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Rakesh,


On May 6, 2017, at 12:23 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Hello,
     I got the above response to the HPO ontology. How can you list an ontology on your site and not have it loaded appropriately to browse it?


As long as users upload valid OWL or OBO ontologies, it?s not our intention that they should experience issues while browsing.

In the case of the HP ontology, I found and fixed a problem in our source code that was preventing correct calculation of the set of root classes.  I deployed that fix today, and the HP ontology is now fully parsed and available for browsing.

Kind regards,
Jennifer



<Screenshot 2017-05-22 14.33.43.png>








--

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.



--

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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From jonquet at lirmm.fr  Tue Jul  4 02:25:05 2017
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Tue, 4 Jul 2017 11:25:05 +0200
Subject: [bioontology-support] AgroPortal 1.4 (beta) released - Harnessing
	the power of metadata
Message-ID: <03d601d2f4a7$8054e9d0$80febd70$@lirmm.fr>

Title: Harnessing the power of metadata to visualize the landscape of
agronomical ontologies

Tag:
<https://github.com/sifrproject/bioportal_web_ui/releases/tag/vAgro1.4>
https://github.com/sifrproject/bioportal_web_ui/releases/tag/vAgro1.4 

 

The new metadata model (release 1.3) has allowed us to implement additional
features to leverage the power of metadata within the portal: 

*	An ontology landscape page that displays diagrams and charts about
all the ontologies on the portal:  <http://agroportal.lirmm.fr/landscape>
http://agroportal.lirmm.fr/landscape . Please check this out and send
feedback!
*	A few changes to the ontology Summary page e.g.,
<http://agroportal.lirmm.fr/ontologies/ANAEETHES>
http://agroportal.lirmm.fr/ontologies/ANAEETHES 

*	A list of "additional metadata properties" for which, the backend
values are stored with standard URIs whenever possible.
*	"Get my metadata back" buttons which allow ontology developers to
download the metadata that has been edited on the portal in RDF/XML, JSON-LD
or N-triple syntax in order to copy/paste it in the original ontology file.

 

In conjunction with the PractikPharma / SIFR projects (annotation of French
clinical text with ontologies) we have implemented additional features
within the Annotator, including:

*	Plugin-in the NegEx/Context algorithm to detect negation or
temporality for annotations. E.g.
<http://services.agroportal.lirmm.fr/annotator/?text=the%20plant%20show%20no
%20sign%20of%20blight&ontologies=NALT&negation=true&display_links=false&disp
lay_context=false&apikey=1de0a270-29c5-4dda-b043-7c3580628cd5>
http://services.agroportal.lirmm.fr/annotator/?text=the%20plant%20show%20no%
20sign%20of%20blight&ontologies=NALT&negation=true&apikey=1de0a270-29c5-4dda
-b043-7c3580628cd5 
*	Additional output formats for the annotations (e.g.,  BRAT or Quaero
corpus format)  

 

Among the content change of this release we can mention:

*	Projects from the AgBioData group
*	Metadata population and curation for each ontology (feel free to
send feedback or edit)
*	Harmonisation of metadata fields (e.g., organization names, ontology
types, languages, etc.)
*	New vocabularies and ontologies such as: GACS (Global Agricultural
Concept Scheme), Soy ontology, Foodie 

 

This release includes code merge with NCBO BioPortal (5.3.0). See the
release notes for more details on additionnal features:
<https://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes>
https://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes

 

Bug fixes of this release include: 

*	Multilingual synonyms are not indexed anymore
*	Fix the partial parsing of big SKOS resources
*	Indexation of properties (see NCBO release notes)
*	Fix a few bugs in the front user interface cache 
*	Optimisation of metadata retrieval by ontology submission
*	Automatic synchronization of groups and slices

 

We are pleased to announce that AgroPortal will be featured during
<https://workshop.inra.fr/in-ovive-2017> IN-OVIVE 2017 workshop and
<http://www.efita2017.org/> EFITA 2017 conference's demonstration session
in Montpellier, week of July 3rd, 2017.

 

Contact us at  <mailto:agroportal-support at lirmm.fr>
agroportal-support at lirmm.fr 

 

AgroPortal release notes:
<https://github.com/agroportal/documentation/wiki/Release-notes>
https://github.com/agroportal/documentation/wiki/Release-notes 

 

Best regards

The AgroPortal team ;)

 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

 

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From rakesh at pieriandx.com  Tue Jul  4 15:31:00 2017
From: rakesh at pieriandx.com (Rakesh Nagarajan)
Date: Tue, 4 Jul 2017 17:31:00 -0500
Subject: [bioontology-support] HPO
In-Reply-To: <7CCAB221-1217-487B-A127-438D13ACD25E@stanford.edu>
References: <CAOaXRCe4cTtQY5V33x6dmJfBhQS2BVBBELK5X=tabtxeHrnBOA@mail.gmail.com>
 <f2e80391-e7dc-db88-224d-4be121411347@lirmm.fr>
 <CAOaXRCdjVAa_ic3zYzbZYeKSpnYMHxDr4SMKo9p=y=Dez30tyA@mail.gmail.com>
 <3EEE530C-F1C7-4681-84A1-1FBFA81B48FE@stanford.edu>
 <CAOaXRCeEet-56Cz7BJTVG_Bv8AtRTYxeEbxSpJaQsd-y+_W0zg@mail.gmail.com>
 <CAOaXRCf3TvKX_Mp2xs6_cQdaZRnDDQNg2CfxufHei7-3eGP_NQ@mail.gmail.com>
 <7CCAB221-1217-487B-A127-438D13ACD25E@stanford.edu>
Message-ID: <CAOaXRCe1pRkY9zLNHXG8V6-zO9=18CTy=NXdj4VVNiZLqj3gcQ@mail.gmail.com>

Jennifer,
     Sorry about that. I should have been clearer. In the browser, after I
log in, I cannot get to:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD055928/ancestors

[image: Inline image 1]

Here is the same term ID with the URL pattern I am using:
[image: Inline image 2]


Here is the full set of term IDs I received an error on per my log file.
Some of these are now working so I am not sure why there was an
intermittent error. I am using the URL:
http://data.bioontology.org/ontologies/MESH/classes/<Term ID>/ancestors.


On Mon, Jul 3, 2017 at 1:17 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Rakesh,
>
> I tested a REST API call to get ancestors for the term you listed below:
>
> http://data.bioontology.org/ontologies/MESH/classes/http%
> 3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD017326/ancestors
> <http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D017326/ancestors>
>
> The call returns data with no errors. Perhaps the error you receive is due
> to improperly encoding the term ID? It would help if you could send an
> example of how you?re trying to retrieve the ancestors.
>
> Kind regards,
> Jennifer
>
>
> On Jul 1, 2017, at 12:34 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
> wrote:
>
> Hello,
>      I am trying to get ancestors for an ontology (MESH). For some valid
> MESH terms, I get the following error:
>
> {
>
>    - -
>    "errors": [
>       - "The input class id 'D017326' is not a valid IRI"
>    ],
>    - "status": 400
>
> }
>
>
> even though the term itself exists in the BioPortal browser when I
> navigate here: http://bioportal.bioontology.org/ontologies/MESH/?p=
> classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%
> 2Fontology%2FMESH%2FD017326&jump_to_nav=true
>
> Can you fix this?
>
> Thanks,
> Rakesh
>
> On Mon, May 22, 2017 at 9:10 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
> wrote:
>
>> Jennifer,
>>      Thanks a lot!
>>
>> Rakesh
>>
>> On Mon, May 22, 2017 at 4:40 PM, Jennifer Leigh Vendetti <
>> vendetti at stanford.edu> wrote:
>>
>>> Hello Rakesh,
>>>
>>>
>>> On May 6, 2017, at 12:23 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
>>> wrote:
>>>
>>> Hello,
>>>      I got the above response to the HPO ontology. How can you list an
>>> ontology on your site and not have it loaded appropriately to browse it?
>>>
>>>
>>>
>>> As long as users upload valid OWL or OBO ontologies, it?s not our
>>> intention that they should experience issues while browsing.
>>>
>>> In the case of the HP ontology, I found and fixed a problem in our
>>> source code that was preventing correct calculation of the set of root
>>> classes.  I deployed that fix today, and the HP ontology is now fully
>>> parsed and available for browsing.
>>>
>>> Kind regards,
>>> Jennifer
>>>
>>>
>>>
>>> <Screenshot 2017-05-22 14.33.43.png>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>>
>> *The materials in this email are private and may contain Protected Health
>> Information. If you are not the intended recipient, be advised that any
>> unauthorized use, disclosure, copying, distribution or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited. If you have received this email in error, please immediately
>> notify the sender via telephone or return email.*
>>
>
>
>
> --
>
> *The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.*
>
>
>


-- 

*The materials in this email are private and may contain Protected Health
Information. If you are not the intended recipient, be advised that any
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action in reliance on the contents of this information is strictly
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From spencerhb at mymail.vcu.edu  Wed Jul  5 12:49:02 2017
From: spencerhb at mymail.vcu.edu (Heather Spencer)
Date: Wed, 5 Jul 2017 15:49:02 -0400
Subject: [bioontology-support] Attempting to track down the Get All Terms
	Web Service
Message-ID: <CAP+JS2BEuGoX5_z_VAF8iRtbU_BCBQKDgqgSLUmOWEkWXe5-yA@mail.gmail.com>

Hello!

I am attempting to export all the terms and properties of interest from
specific ontologies as is mentioned on the following page:

<goog_1027877686>
https://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook

The page directs you to a site that pushes you to the new page for REST
api's documentation, which I have explored some, but I was hoping for some
direction on where I could look to export from the ontologies within
BioPortal.

Thank you!

Heather Spencer
Masters of Science
Center for the Study of Biological Complexity
VCU Life Sciences
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From vendetti at stanford.edu  Wed Jul  5 15:57:20 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 5 Jul 2017 22:57:20 +0000
Subject: [bioontology-support] HPO
In-Reply-To: <CAOaXRCe1pRkY9zLNHXG8V6-zO9=18CTy=NXdj4VVNiZLqj3gcQ@mail.gmail.com>
References: <CAOaXRCe4cTtQY5V33x6dmJfBhQS2BVBBELK5X=tabtxeHrnBOA@mail.gmail.com>
 <f2e80391-e7dc-db88-224d-4be121411347@lirmm.fr>
 <CAOaXRCdjVAa_ic3zYzbZYeKSpnYMHxDr4SMKo9p=y=Dez30tyA@mail.gmail.com>
 <3EEE530C-F1C7-4681-84A1-1FBFA81B48FE@stanford.edu>
 <CAOaXRCeEet-56Cz7BJTVG_Bv8AtRTYxeEbxSpJaQsd-y+_W0zg@mail.gmail.com>
 <CAOaXRCf3TvKX_Mp2xs6_cQdaZRnDDQNg2CfxufHei7-3eGP_NQ@mail.gmail.com>
 <7CCAB221-1217-487B-A127-438D13ACD25E@stanford.edu>
 <CAOaXRCe1pRkY9zLNHXG8V6-zO9=18CTy=NXdj4VVNiZLqj3gcQ@mail.gmail.com>
Message-ID: <7CF684E7-0D05-48D4-B9E6-45A7CC8F3D82@stanford.edu>

Hello Rakesh,


On Jul 4, 2017, at 3:31 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Jennifer,
     Sorry about that. I should have been clearer. In the browser, after I log in, I cannot get to:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD055928/ancestors<http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D055928/ancestors>

[cid:0bf15552-793c-440d-83dd-823f05e1aae5 at namprd02.prod.outlook.com]





The ?not found? message you see as a result of the call indicates that there aren?t any terms in the MeSH ontology with that ID.

The MeSH ontology in BioPortal is imported from the National Library of Medicine?s UMLS [1]. We're currently serving UMLS ontologies that were bundled in their 2016AB release [2], which includes MeSH version "MSH2016_2015_08_18?.

I investigated the term ID of ?D055928? using the UMLS?s web-based Metathesaurs Browser. This term ID doesn?t exist in MeSH in their system either:


[cid:9faf4707-3bee-4e25-ac73-211a4ee3edf9 at namprd02.prod.outlook.com]






Here is the same term ID with the URL pattern I am using:
[cid:8baf617c-da30-4e51-8ce6-1d5011bfc12d at namprd02.prod.outlook.com]



You?re required to use the full and encoded term ID as part of the URL when using the classes endpoint [3] in BioPortal?s REST API.  For example, to retrieve the ancestors for MeSH?s ?Cheek? term with an ID of "http://purl.bioontology.org/ontology/MESH/D002610<http://purl.bioontology.org/ontology/MESH/D001419>?, the call would look like this:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD002610/ancestors<http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D002610/ancestors>

The only endpoint in the REST API where you can use short IDs is the search endpoint [4], which will find instances of terms IDs across all ontologies in BioPortal. Using the term ID you gave above as an example:

http://data.bioontology.org/search?q=D055928&ontologies=MESH

? returns no results, since this term doesn?t exist in any of the ontologies in BioPortal.





Here is the full set of term IDs I received an error on per my log file. Some of these are now working so I am not sure why there was an intermittent error. I am using the URL:  http://data.bioontology.org/ontologies/MESH/classes/<Term ID>/ancestors.


Please see my comments above. If you correct the <Term ID> portion of your URLs, these ?not found? errors should be resolved. As an example from the first line of your log file, change this link:

http://data.bioontology.org/ontologies/MESH/classes/D010963/ancestors

? to this:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD010963/ancestors<http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D010963/ancestors>


Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/
[2] https://wayback.archive-it.org/4253/20170417125306/https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html
[3] http://data.bioontology.org/documentation#Class
[4] http://data.bioontology.org/documentation#nav_search






On Mon, Jul 3, 2017 at 1:17 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Rakesh,

I tested a REST API call to get ancestors for the term you listed below:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD017326/ancestors<http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D017326/ancestors>

The call returns data with no errors. Perhaps the error you receive is due to improperly encoding the term ID? It would help if you could send an example of how you?re trying to retrieve the ancestors.

Kind regards,
Jennifer


On Jul 1, 2017, at 12:34 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Hello,
     I am trying to get ancestors for an ontology (MESH). For some valid MESH terms, I get the following error:

{

  *
-
"errors": [
     *   "The input class id 'D017326' is not a valid IRI"
],
  *   "status": 400

}


even though the term itself exists in the BioPortal browser when I navigate here: http://bioportal.bioontology.org/ontologies/MESH/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD017326&jump_to_nav=true

Can you fix this?

Thanks,
Rakesh

On Mon, May 22, 2017 at 9:10 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:
Jennifer,
     Thanks a lot!

Rakesh

On Mon, May 22, 2017 at 4:40 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Rakesh,


On May 6, 2017, at 12:23 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Hello,
     I got the above response to the HPO ontology. How can you list an ontology on your site and not have it loaded appropriately to browse it?


As long as users upload valid OWL or OBO ontologies, it?s not our intention that they should experience issues while browsing.

In the case of the HP ontology, I found and fixed a problem in our source code that was preventing correct calculation of the set of root classes.  I deployed that fix today, and the HP ontology is now fully parsed and available for browsing.

Kind regards,
Jennifer



<Screenshot 2017-05-22 14.33.43.png>








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From vendetti at stanford.edu  Wed Jul  5 16:18:55 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 5 Jul 2017 23:18:55 +0000
Subject: [bioontology-support] Attempting to track down the Get All
 Terms Web Service
In-Reply-To: <CAP+JS2BEuGoX5_z_VAF8iRtbU_BCBQKDgqgSLUmOWEkWXe5-yA@mail.gmail.com>
References: <CAP+JS2BEuGoX5_z_VAF8iRtbU_BCBQKDgqgSLUmOWEkWXe5-yA@mail.gmail.com>
Message-ID: <5F7B8565-CE1B-4A75-BACF-CF6D4035AE64@stanford.edu>

Hello Heather,


On Jul 5, 2017, at 12:49 PM, Heather Spencer <spencerhb at mymail.vcu.edu<mailto:spencerhb at mymail.vcu.edu>> wrote:

I am attempting to export all the terms and properties of interest from specific ontologies as is mentioned on the following page:

<x-msg://1/goog_1027877686>
https://www.bioontology.org/wiki/index.php/Sample_Code_Cookbook

The page directs you to a site that pushes you to the new page for REST api's documentation, which I have explored some, but I was hoping for some direction on where I could look to export from the ontologies within BioPortal.


Using the SNOMED CT ontology as an example, here is the REST call that would get you all of the classes in the ontology:

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

? and the one that gets you all properties:

http://data.bioontology.org/ontologies/SNOMEDCT/properties

If you don?t want all of the classes and properties, and instead want to search for particular classes or properties of interest, you can use the search endpoint like so:

http://data.bioontology.org/search?q=Organism&ontologies=SNOMEDCT

http://data.bioontology.org/property_search?q=has%20dimension&ontologies=SNOMEDCT

The search endpoints for terms [1] and properties [2] have a number of parameters you can use to customize the result set.

We also have code examples in various languages for using the REST API available in our GitHub repository:

https://github.com/ncbo/ncbo_rest_sample_code

Hope that helps.

Kind regards,
Jennifer

[1] http://data.bioontology.org/documentation#nav_search
[2] http://data.bioontology.org/documentation#nav_prop_search



Thank you!

Heather Spencer
Masters of Science
Center for the Study of Biological Complexity
VCU Life Sciences

_______________________________________________
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From l.andres.hernandez.18 at student.scu.edu.au  Wed Jul  5 22:36:26 2017
From: l.andres.hernandez.18 at student.scu.edu.au (Liliana Andres Hernandez)
Date: Thu, 6 Jul 2017 05:36:26 +0000
Subject: [bioontology-support] OMIT methods
Message-ID: <SYXPR01MB12779501BA537FB8B8B4DBD499D50@SYXPR01MB1277.ausprd01.prod.outlook.com>

Hi,


My name is Liliana Andres, I'm writing this email because I think OMIT is an excellent tool for my project. I would like to know more details about the methods that you used to develop OMIT, I've been reading your papers and I have some information, however I couldn't find version of the software and other details that could be very helpful for me. Do you have any document about the methods and version of the software? I would really appreciate your help or any details.


best,


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


[1489456786640_PastedImage]
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From vendetti at stanford.edu  Thu Jul  6 16:41:51 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Jul 2017 23:41:51 +0000
Subject: [bioontology-support] OMIT methods
In-Reply-To: <SYXPR01MB12779501BA537FB8B8B4DBD499D50@SYXPR01MB1277.ausprd01.prod.outlook.com>
References: <SYXPR01MB12779501BA537FB8B8B4DBD499D50@SYXPR01MB1277.ausprd01.prod.outlook.com>
Message-ID: <6FC074BD-64A0-4C85-A35F-1CD180F01D30@stanford.edu>

Hello Liliana,

You?ve reached the support list for the BioPortal application, which is a repository for biomedical ontologies based at Stanford University. Our application contains a copy of the OMIT ontology, but we?re not associated with the group that developed OMIT. You might try contacting them directly for help with your questions: http://omit.soc.usouthal.edu/Contact_Us/Contact_Us.html.

Kind regards,
Jennifer


On Jul 5, 2017, at 10:36 PM, Liliana Andres Hernandez <l.andres.hernandez.18 at student.scu.edu.au<mailto:l.andres.hernandez.18 at student.scu.edu.au>> wrote:

Hi,

My name is Liliana Andres, I'm writing this email because I think OMIT is an excellent tool for my project. I would like to know more details about the methods that you used to develop OMIT, I've been reading your papers and I have some information, however I couldn't find version of the software and other details that could be very helpful for me. Do you have any document about the methods and version of the software? I would really appreciate your help or any details.

best,

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

<OutlookEmoji-1489456786640_PastedImagea99e9e76-5dd2-4b1c-8e3a-f117bb5f4df2.png>
_______________________________________________
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 Jul  6 16:56:59 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 6 Jul 2017 23:56:59 +0000
Subject: [bioontology-support] Attempting to track down the Get All
 Terms Web Service
In-Reply-To: <CAP+JS2AtxMkph6n2RiqdwbMRa7sG6NGNtUQBtJtxBkm=8pNqQg@mail.gmail.com>
References: <CAP+JS2BEuGoX5_z_VAF8iRtbU_BCBQKDgqgSLUmOWEkWXe5-yA@mail.gmail.com>
 <5F7B8565-CE1B-4A75-BACF-CF6D4035AE64@stanford.edu>
 <CAP+JS2AtxMkph6n2RiqdwbMRa7sG6NGNtUQBtJtxBkm=8pNqQg@mail.gmail.com>
Message-ID: <AE9ADCA1-1631-4229-95AA-E21448AD0F87@stanford.edu>

Hello Heather,

On Jul 6, 2017, at 10:13 AM, Heather Spencer <spencerhb at mymail.vcu.edu<mailto:spencerhb at mymail.vcu.edu>> wrote:

Thank you very much for the response.
When I follow the link:

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

I receive the following error:

Status 401,

Error: You must provide a valid api key. Your api key can be obtained by logging in at ....

I have an account and an api, how do I enter the key, or have the site recognize it when using a browser?


Your API key can be passed as a parameter, e.g.:

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



I also attempted to access the resources using the python from the sample source code. In employing the classes_search.py program and entering my api key, an HTTP 400: Bad request error is returned. Advice on how to proceed?


Are you able to issue a simple curl call from the command line, e.g.:

curl -X GET 'http://data.bioontology.org/ontologies/SNOMEDCT?apikey=your_api_key_here?

?

I?m interested in ruling out issues with your API key before addressing Python errors.

Kind regards,
Jennifer

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From support at bioontology.org  Fri Jul  7 08:33:45 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 07 Jul 2017 08:33:45 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung
Message-ID: <595fa9d9c4b26_2ff3fb2c3ef0438638ac@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Fri Jul  7 14:31:53 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 07 Jul 2017 14:31:53 -0700
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
Message-ID: <595ffdc9eeae4_398f3fa5a96878e0218c6@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Jul  7 15:09:21 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 7 Jul 2017 22:09:21 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
In-Reply-To: <595ffdc9eeae4_398f3fa5a96878e0218c6@ncbo-prd-app-09.stanford.edu.mail>
References: <595ffdc9eeae4_398f3fa5a96878e0218c6@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <68C50C63-99B2-482B-B5C4-2FC9E439D9E9@stanford.edu>

Hi Matus,


On Jul 7, 2017, at 2:31 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Dear BioPortal maintainers,

I uploaded a new version of the EDAM ontology yesterday early morning, and the Summary page still looks weird. It's always appearing as the last version isn't parsed (see also * below). And depending on cookies, it behaves in weird ways.
- Clicking on Classes tab ends up with "Problem retrieving classes" or "We're sorry but something has gone wrong. We have been notified of this error."
- Clicking on the previous 1.17 leads to "We're sorry but something has gone wrong. We have been notified of this error."
- New version 1.18 still appears not parsed (see also * below), also no downloads other than OWL.

A couple of us have looked at your ontology here and we?re having trouble reproducing this issue. The UI shows 1.18 as parsed and all downloads available. We?ve tried both logged in and logged out, and in private and non-private browser windows. The classes tree also appears without errors.

[cid:A9BC77E6-BB35-4E46-A463-0567A0DAE18D at stanford.edu]
[cid:D1556687-1828-4F90-ADDC-83B61FE7CB74 at stanford.edu]


Are you still seeing this behavior on your end?


Also in a new private browser window

* At the same time, navigating to http://bioportal.bioontology.org/ontologies/EDAM?p=classes in a private browser window opens a correctly parsed hierarchy of the new version 1.18.



This behavior you describe of seeing the new version parsed in a private browser sounds like there may have been an issue with BioPortal?s HTTP cache, i.e., the ontology parsed successfully but a problem in the HTTP cache was preventing this from properly displaying in the UI. The private browsing session wouldn?t have been using the cache.



All in all, it seems to be in a messed-up state for already 36 hours or so, while we and our users really need it to work correctly, as we're relying on the very much appreciated BioPortal! (Btw., I also can't understand for years why the uploaded ontologies can't just be fully parsed immediately.) I hope it will be possible to fix the underlying problems we're currently experiencing, before the weekend.



We have a background process that checks the ontology parsing queue every 15 minutes. Your ontology isn?t particularly large, so my expectation is that you shouldn?t have to wait more than 30 minutes at the absolute most to see your new version. If this is not the case, feel free to contact us immediately and ask for help.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Fri Jul  7 16:14:26 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 7 Jul 2017 23:14:26 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung
In-Reply-To: <595fa9d9c4b26_2ff3fb2c3ef0438638ac@ncbo-prd-app-09.stanford.edu.mail>
References: <595fa9d9c4b26_2ff3fb2c3ef0438638ac@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <6418661C-144F-419E-BECD-008DB4DCD0D8@stanford.edu>

Hello Caty,


On Jul 7, 2017, at 8:33 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Caty Chung

Email: c.chung at miami.edu<mailto:c.chung at miami.edu>

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

Feedback:

Possible Bioportal issue? https://github.com/BioAssayOntology/BAO/issues/20

Bioportal displays the term "ATP quantitation using luciferase" in class "assay desig method" as well as in subclass "viability measurement method" - "ATP quantitation".

In the owl file bao_vocabulary_method.owl the term is define only for subclass "ATP quantitation"
Ontology lookup service displays the correct hierarchy.



I downloaded your ontology source file (bao_complete.owl) and opened it in the Protege ontology editing application [1]. Protege also displays ?ATP quantitation using luciferase? at two points in the tree. In addition to the subClassOf declaration you mentioned above, there?s an equivalentClass expression (beginning on line 4,682) where ?ATP quantitation using luciferase? is declared as equivalent to the anonymous intersection of ?assay design method? and a group of associated restrictions.


[cid:17D0544E-F785-4769-B0D3-44B80AA70E5B at stanford.edu]



I don?t think the hierarchy is being displayed incorrectly in either Protege or BioPortal, but I will double-check with our internal OWL experts.

It?s certainly true that Protege does a better visual job of indicating that a class is appearing at a particular place in the hierarchy due to an equivalentClass expression. The icon is different, and you?re able to see the full "Equivalent To" expression on the right-hand side.

Kind regards,
Jennifer

[1] http://protege.stanford.edu/products.php#desktop-protege


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From support at bioontology.org  Mon Jul 10 11:26:36 2017
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 10 Jul 2017 11:26:36 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Erin Hedlund
Message-ID: <5963c6dc582db_774c3fe665a8adb4794c2@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Jul 10 11:29:40 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 10 Jul 2017 18:29:40 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Erin Hedlund
In-Reply-To: <5963c6dc582db_774c3fe665a8adb4794c2@ncbo-prd-app-08.stanford.edu.mail>
References: <5963c6dc582db_774c3fe665a8adb4794c2@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <7FF16FDA-6E16-4835-A3AB-EE22712CB7C2@stanford.edu>

Hello Erin,

Thanks for contacting us. We?re aware that the search endpoint is down, and we?re looking into it now.

Kind regards,
Jennifer


On Jul 10, 2017, at 11:26 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Erin Hedlund

Email: erin.hedlund at abbvie.com<mailto:erin.hedlund at abbvie.com>

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

Feedback:

The API is giving an Internal Server Error (500).

e.g. http://data.bioontology.org/search?q=melanoma

_______________________________________________
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From vendetti at stanford.edu  Mon Jul 10 11:41:35 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 10 Jul 2017 18:41:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Erin Hedlund
In-Reply-To: <7FF16FDA-6E16-4835-A3AB-EE22712CB7C2@stanford.edu>
References: <5963c6dc582db_774c3fe665a8adb4794c2@ncbo-prd-app-08.stanford.edu.mail>
 <7FF16FDA-6E16-4835-A3AB-EE22712CB7C2@stanford.edu>
Message-ID: <249312C6-2CAB-4E59-ADA0-7D10E12A3CF8@stanford.edu>

Hello again Erin,

The search endpoint is back up.

Kind regards,
Jennifer


On Jul 10, 2017, at 11:29 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Erin,

Thanks for contacting us. We?re aware that the search endpoint is down, and we?re looking into it now.

Kind regards,
Jennifer


On Jul 10, 2017, at 11:26 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Erin Hedlund

Email: erin.hedlund at abbvie.com<mailto:erin.hedlund at abbvie.com>

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

Feedback:

The API is giving an Internal Server Error (500).

e.g. http://data.bioontology.org/search?q=melanoma

_______________________________________________
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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bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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From marc.hanauer at inserm.fr  Mon Jul 10 14:11:07 2017
From: marc.hanauer at inserm.fr (marc.hanauer at inserm.fr)
Date: Mon, 10 Jul 2017 23:11:07 +0200
Subject: [bioontology-support] [ORDO] bioportal issue
In-Reply-To: <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu>
References: <53721CEC.4010600@inserm.fr>
 <FD57126C-D6A4-43C4-8A40-BE90D25C427E@ebi.ac.uk>
 <56CDC203.5070001@inserm.fr>
 <848E2F34-E02F-4DA3-987D-7A836EBB874B@stanford.edu>
 <a65bae35-cc90-acf2-fc42-67be75ab4b45@inserm.fr>
 <876518B6-C6F6-465C-A1B2-AB055368F899@stanford.edu>
 <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu>
Message-ID: <da951031c667608b44c3a714f3e009e9@inserm.fr>

Hello Jennifer,

Sorry about that, but once again the new version of ORDO (2.4) seems to
have issues : 2.3 (Uploaded, Error Rdf)     07/05/2017     07/05/2017 
https://bioportal.bioontology.org/ontologies/ORDO

This version was produced the same way than the previous one.

Any ideas ? 

Best regards, 

---

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE 

Le 11-08-2016 19:22, Jennifer Leigh Vendetti a ?crit :

> Hello Marc, 
> 
> We've addressed the issue I mentioned below.  Version 2.2 of ORDO is parsed and available in BioPortal: 
> 
> http://bioportal.bioontology.org/ontologies/ORDO 
> 
> Apologies again that this one took us some time to address. 
> 
> Best, 
> Jennifer 
> 
> On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote: 
> 
> Hi Marc, 
> 
> I am writing with a status report regarding BioPortal's failure to handle ORDO 2.2. 
> 
> As you may already know, BioPortal uses the OWL API [1] internally for ontology parsing.  I wrote some Java code, independent of the BioPortal application, to make sure the OWL API handles your ontology properly.  The parsing succeeds, which indicates to me that your ontology file is valid.  When the OWL API parses your ontology file, it emits a very large number of "unparsed triple" messages (roughly 15.5K of them), e.g.: 
> 
> [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedProperty [1] -> http://purl.obolibrary.org/obo/ECO_0000218 [2] 
> [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedSource [3] -> _:genid120261 
> 
> The size of the output from the OWL API is causing a buffer overflow / deadlock in BioPortal's source code.  I am currently working toward fixing the issue, and hope to have something available soon. 
> 
> Apologies that this one is taking some time for us to track down / fix. 
> 
> Best, 
> Jennifer 
> 
> [1] http://owlcs.github.io/owlapi/ 
> 
> On Jun 27, 2016, at 3:18 AM, Marc Hanauer <marc.hanauer at inserm.fr> wrote: 
> 
> Hello Jennifer, 
> 
> I've made an update of our ontology (ORDO) last week as usual by putting the file on our own server. This time, the bioportal website seems to try the upload but with error. 
> 
> The version in our own server is now "2.2" but it appears with this line on bioportal: 
> 
> 2.1 (Uploaded, Error Rdf)
> 06/22/2016
> 06/22/2016
> OWL [4] | Diff [5]
> 
> Any idea ?
> 
> Best regards,
> 
> Marc HANAUER
> Directeur Adjoint / Deputy Director
> Directeur technique / Chief technology officer
> Strat?gie et Innovation
> marc.hanauer at inserm.fr
> 
> ORPHANET - INSERM US14
> Plateforme Maladies Rares / Rare Disease Platform
> 96 rue Didot
> 75014 PARIS
> FRANCE 
> Le 25/02/2016 ? 00:41, Jennifer Leigh Vendetti a ?crit : 
> Hello Marc, 
> 
> On Feb 24, 2016, at 6:45 AM, Marc Hanauer <marc.hanauer at inserm.fr> wrote: 
> 
> Dear support,
> We manage the ORDO (Orphanet Rare Disease Ontology) and we have made an update recently (2 days ago).
> Usually (for the previous version), we just update the file on our own server (keeping the same URL : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl [6] ) and then the bioportal website automatically upload it.
> 
> It seems this is not the case anymore (the version in bioportal remain v2.0 instead of the new 2.1)
> 
> Do we need to perform any manual action in order to update it on bioportal ? 
> 
> You don't need to do anything manual.  We were having some performance issues with our site and temporarily disabled the cron jobs in our production environment that pull new versions of ontologies.  The cron job has been reenabled today, so the new version of your ontology should be pulled and processed overnight. 
> 
> By the way, with our account, we still have trouble accessing the bioportal interface (when we sign in and try to reach the ORDO page, we obtain an error message which is not the case without login...) (see my previous msg below about this) 
> 
> Sorry you're having difficulties.  I tried reproducing this behavior here and so far haven't had any luck.  I've viewed your ontology in BioPortal, both when logged in and logged out (screen shot below).  I also verified that your user account of "ORDO_Orphanet" is valid, and I don't see any issues there.  Are you still seeing this behavior? 
> 
> Jennifer 
> 
> <Mail Attachment.png>
 _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support 

Links:
------
[1] http://www.w3.org/2002/07/owl#annotatedProperty
[2] http://purl.obolibrary.org/obo/ECO_0000218
[3] http://www.w3.org/2002/07/owl#annotatedSource
[4]
http://data.bioontology.org/ontologies/ORDO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
[5]
http://data.bioontology.org/ontologies/ORDO/submissions/9/download_diff?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
[6] http://www.orphadata.org/data/ORDO/ordo_orphanet.owl
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From vendetti at stanford.edu  Mon Jul 10 18:26:10 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 11 Jul 2017 01:26:10 +0000
Subject: [bioontology-support] [ORDO] bioportal issue
In-Reply-To: <da951031c667608b44c3a714f3e009e9@inserm.fr>
References: <53721CEC.4010600@inserm.fr>
 <FD57126C-D6A4-43C4-8A40-BE90D25C427E@ebi.ac.uk> <56CDC203.5070001@inserm.fr>
 <848E2F34-E02F-4DA3-987D-7A836EBB874B@stanford.edu>
 <a65bae35-cc90-acf2-fc42-67be75ab4b45@inserm.fr>
 <876518B6-C6F6-465C-A1B2-AB055368F899@stanford.edu>
 <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu>
 <da951031c667608b44c3a714f3e009e9@inserm.fr>
Message-ID: <AC3E54C3-B15F-4A31-9281-80C5E8CCC6D2@stanford.edu>

Hello Marc,

I?ve entered an issue in our tracker [1], and will have a look.

Kind regards,
Jennifer

[1] https://github.com/ncbo/bioportal-project/issues/31


On Jul 10, 2017, at 2:11 PM, marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr> wrote:


Hello Jennifer,

Sorry about that, but once again the new version of ORDO (2.4) seems to have issues : 2.3 (Uploaded, Error Rdf)     07/05/2017     07/05/2017
https://bioportal.bioontology.org/ontologies/ORDO


This version was produced the same way than the previous one.

Any ideas ?

Best regards,

---

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE


Le 11-08-2016 19:22, Jennifer Leigh Vendetti a ?crit :

Hello Marc,

We've addressed the issue I mentioned below.  Version 2.2 of ORDO is parsed and available in BioPortal:

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

Apologies again that this one took us some time to address.

Best,
Jennifer


On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Marc,

I am writing with a status report regarding BioPortal's failure to handle ORDO 2.2.

As you may already know, BioPortal uses the OWL API [1] internally for ontology parsing.  I wrote some Java code, independent of the BioPortal application, to make sure the OWL API handles your ontology properly.  The parsing succeeds, which indicates to me that your ontology file is valid.  When the OWL API parses your ontology file, it emits a very large number of "unparsed triple" messages (roughly 15.5K of them), e.g.:

[OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedProperty -> http://purl.obolibrary.org/obo/ECO_0000218
[OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedSource -> _:genid120261

The size of the output from the OWL API is causing a buffer overflow / deadlock in BioPortal's source code.  I am currently working toward fixing the issue, and hope to have something available soon.

Apologies that this one is taking some time for us to track down / fix.

Best,
Jennifer

[1] http://owlcs.github.io/owlapi/



On Jun 27, 2016, at 3:18 AM, Marc Hanauer <marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>> wrote:


Hello Jennifer,

I've made an update of our ontology (ORDO) last week as usual by putting the file on our own server. This time, the bioportal website seems to try the upload but with error.

The version in our own server is now "2.2" but it appears with this line on bioportal:

2.1 (Uploaded, Error Rdf)       06/22/2016      06/22/2016      OWL<http://data.bioontology.org/ontologies/ORDO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb> | Diff<http://data.bioontology.org/ontologies/ORDO/submissions/9/download_diff?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb>

Any idea ?

Best regards,

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE
Le 25/02/2016 ? 00:41, Jennifer Leigh Vendetti a ?crit :
Hello Marc,

On Feb 24, 2016, at 6:45 AM, Marc Hanauer <marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>> wrote:

Dear support,
We manage the ORDO (Orphanet Rare Disease Ontology) and we have made an update recently (2 days ago).
Usually (for the previous version), we just update the file on our own server (keeping the same URL : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ) and then the bioportal website automatically upload it.

It seems this is not the case anymore (the version in bioportal remain v2.0 instead of the new 2.1)

Do we need to perform any manual action in order to update it on bioportal ?


You don't need to do anything manual.  We were having some performance issues with our site and temporarily disabled the cron jobs in our production environment that pull new versions of ontologies.  The cron job has been reenabled today, so the new version of your ontology should be pulled and processed overnight.



By the way, with our account, we still have trouble accessing the bioportal interface (when we sign in and try to reach the ORDO page, we obtain an error message which is not the case without login...) (see my previous msg below about this)


Sorry you're having difficulties.  I tried reproducing this behavior here and so far haven't had any luck.  I've viewed your ontology in BioPortal, both when logged in and logged out (screen shot below).  I also verified that your user account of "ORDO_Orphanet" is valid, and I don't see any issues there.  Are you still seeing this behavior?

Jennifer



<Mail Attachment.png>


_______________________________________________
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 jmarr1990 at gmail.com  Tue Jul 11 05:13:13 2017
From: jmarr1990 at gmail.com (jason marr)
Date: Tue, 11 Jul 2017 08:13:13 -0400
Subject: [bioontology-support] Versioning Question
In-Reply-To: <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
References: <CA+EFHPuULimHKJ6+UeSgKuV0a-Bv=jmwr4pQkpR1GcQpPve+5g@mail.gmail.com>
 <0FCB9856-DEE1-4B9A-82A3-6FF5F69C45AA@stanford.edu>
 <CA+EFHPuKneu_a3mzmDjVW72kg7XU-3xSA2yDqahUSgvA99+kzA@mail.gmail.com>
 <E0067441-F9E4-4191-B0D3-8400C3C59779@stanford.edu>
 <CA+EFHPsD2KahDQkk+Oq7TTywcgc2r28gV3tot61hspyiM99S9w@mail.gmail.com>
 <CA+EFHPsZrQeGg6nSAq4dTMs7aaSffuoWaOkLqTSLxg317Ve-Mw@mail.gmail.com>
 <6473C11C-2432-452B-8B78-5A53E4DEBB12@stanford.edu>
 <CA+EFHPv2qWPP__wXVNHC2jWiJuCPbL5H4HK2mFTdiSAa_Vhzvg@mail.gmail.com>
 <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
Message-ID: <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>

Jennifer,
Is there a License restriction on SNOMEDCT? I'm unable to download via api.
Regards,
Jason

On Wed, Jun 14, 2017 at 3:43 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Jason,
>
>
> On Jun 14, 2017, at 12:03 PM, jason marr <jmarr1990 at gmail.com> wrote:
>
> Jennifer,
> Is it possible to download a subject of an ontology? Say given a class,
> download all the sub classes and properties in rdf? I see the download url
> in the doc, http://data.bioontology.org/ontologies/BRO/download . Let me
> know, thanks!
>
>
>
> I don?t think we offer exactly what you?re asking for. The download link
> downloads the entire ontology source file in whatever format was submitted
> to us.
>
> You can retrieve the subclasses of a given class using the ?descendants"
> REST call, e.g.:
>
> http://data.bioontology.org/ontologies/BRO/classes/http%
> 3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity/descendants
> <http://data.bioontology.org/ontologies/BRO/classes/http://bioontology.org/ontologies/Activity.owl#Activity/descendants>
>
> The format though is JSON (or XML if you specify that).
>
> You might have a look at tools offered by the Protege project (open source
> / freely available) [1]. I believe the desktop version of Protege has
> functionality that allows you to extract/copy/move ontology axioms. It also
> allows you to save your ontology in various formats.
>
> Kind regards,
> Jennifer
>
> [1] http://protege.stanford.edu/
>
>
>
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From support at bioontology.org  Tue Jul 11 03:28:01 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 11 Jul 2017 03:28:01 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Daniel Schober
Message-ID: <5964a831cb58e_72903fefb67c59802526a@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Tue Jul 11 08:54:25 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 11 Jul 2017 15:54:25 +0000
Subject: [bioontology-support] Versioning Question
In-Reply-To: <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>
References: <CA+EFHPuULimHKJ6+UeSgKuV0a-Bv=jmwr4pQkpR1GcQpPve+5g@mail.gmail.com>
 <0FCB9856-DEE1-4B9A-82A3-6FF5F69C45AA@stanford.edu>
 <CA+EFHPuKneu_a3mzmDjVW72kg7XU-3xSA2yDqahUSgvA99+kzA@mail.gmail.com>
 <E0067441-F9E4-4191-B0D3-8400C3C59779@stanford.edu>
 <CA+EFHPsD2KahDQkk+Oq7TTywcgc2r28gV3tot61hspyiM99S9w@mail.gmail.com>
 <CA+EFHPsZrQeGg6nSAq4dTMs7aaSffuoWaOkLqTSLxg317Ve-Mw@mail.gmail.com>
 <6473C11C-2432-452B-8B78-5A53E4DEBB12@stanford.edu>
 <CA+EFHPv2qWPP__wXVNHC2jWiJuCPbL5H4HK2mFTdiSAa_Vhzvg@mail.gmail.com>
 <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
 <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>
Message-ID: <B55DE7CE-4128-4B9E-AD0D-D93F1994C3C0@stanford.edu>

Hi Jason,

In the past there has been a license restriction on SNOMEDCT, because it was from UMLS. (You can see LIcense information on the summary page, in this case http://bioportal.bioontology.org/ontologies/SNOMEDCT.)

With the new UMLS licensing, it may be that SNOMEDCT can be made available as a download. Unfortunately we have not had the resources so far to confirm whether this is the case, and then modify the availability in the system.

I hope we can have another look at this question soon (constructive comments from members of the support list are welcome!).

John


On Jul 11, 2017, at 5:13 AM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

Jennifer,
Is there a License restriction on SNOMEDCT? I'm unable to download via api.
Regards,
Jason

On Wed, Jun 14, 2017 at 3:43 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Jason,


On Jun 14, 2017, at 12:03 PM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

Jennifer,
Is it possible to download a subject of an ontology? Say given a class, download all the sub classes and properties in rdf? I see the download url in the doc, http://data.bioontology.org/ontologies/BRO/download . Let me know, thanks!


I don?t think we offer exactly what you?re asking for. The download link downloads the entire ontology source file in whatever format was submitted to us.

You can retrieve the subclasses of a given class using the ?descendants" REST call, e.g.:

http://data.bioontology.org/ontologies/BRO/classes/http%3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity/descendants<http://data.bioontology.org/ontologies/BRO/classes/http://bioontology.org/ontologies/Activity.owl#Activity/descendants>

The format though is JSON (or XML if you specify that).

You might have a look at tools offered by the Protege project (open source / freely available) [1]. I believe the desktop version of Protege has functionality that allows you to extract/copy/move ontology axioms. It also allows you to save your ontology in various formats.

Kind regards,
Jennifer

[1] http://protege.stanford.edu/



_______________________________________________
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
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From jgraybeal at stanford.edu  Tue Jul 11 09:00:59 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 11 Jul 2017 16:00:59 +0000
Subject: [bioontology-support] Versioning Question
In-Reply-To: <B55DE7CE-4128-4B9E-AD0D-D93F1994C3C0@stanford.edu>
References: <CA+EFHPuULimHKJ6+UeSgKuV0a-Bv=jmwr4pQkpR1GcQpPve+5g@mail.gmail.com>
 <0FCB9856-DEE1-4B9A-82A3-6FF5F69C45AA@stanford.edu>
 <CA+EFHPuKneu_a3mzmDjVW72kg7XU-3xSA2yDqahUSgvA99+kzA@mail.gmail.com>
 <E0067441-F9E4-4191-B0D3-8400C3C59779@stanford.edu>
 <CA+EFHPsD2KahDQkk+Oq7TTywcgc2r28gV3tot61hspyiM99S9w@mail.gmail.com>
 <CA+EFHPsZrQeGg6nSAq4dTMs7aaSffuoWaOkLqTSLxg317Ve-Mw@mail.gmail.com>
 <6473C11C-2432-452B-8B78-5A53E4DEBB12@stanford.edu>
 <CA+EFHPv2qWPP__wXVNHC2jWiJuCPbL5H4HK2mFTdiSAa_Vhzvg@mail.gmail.com>
 <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
 <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>
 <B55DE7CE-4128-4B9E-AD0D-D93F1994C3C0@stanford.edu>
Message-ID: <91467629-815D-480A-A5FD-661FB88CE2DF@stanford.edu>

Jason,

Folllowing up on this topic, I took a quick look at the UMLS license to refresh my memory. In the case of SNOMEDCT, there is an extensive set of licensing terms applying particularly to that ontology; you may find it at https://uts.nlm.nih.gov/help/license/licensecategoryihtsdohelp.html.

These terms take precedence, and to my casual review, appear to preclude our redistribution of the content as an ontology. Thus we will not be able to make it available, sorry for that.

John

On Jul 11, 2017, at 8:54 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hi Jason,

In the past there has been a license restriction on SNOMEDCT, because it was from UMLS. (You can see LIcense information on the summary page, in this case http://bioportal.bioontology.org/ontologies/SNOMEDCT.)

With the new UMLS licensing, it may be that SNOMEDCT can be made available as a download. Unfortunately we have not had the resources so far to confirm whether this is the case, and then modify the availability in the system.

I hope we can have another look at this question soon (constructive comments from members of the support list are welcome!).

John


On Jul 11, 2017, at 5:13 AM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

Jennifer,
Is there a License restriction on SNOMEDCT? I'm unable to download via api.
Regards,
Jason

On Wed, Jun 14, 2017 at 3:43 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Jason,


On Jun 14, 2017, at 12:03 PM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

Jennifer,
Is it possible to download a subject of an ontology? Say given a class, download all the sub classes and properties in rdf? I see the download url in the doc, http://data.bioontology.org/ontologies/BRO/download . Let me know, thanks!


I don?t think we offer exactly what you?re asking for. The download link downloads the entire ontology source file in whatever format was submitted to us.

You can retrieve the subclasses of a given class using the ?descendants" REST call, e.g.:

http://data.bioontology.org/ontologies/BRO/classes/http%3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity/descendants<http://data.bioontology.org/ontologies/BRO/classes/http://bioontology.org/ontologies/Activity.owl#Activity/descendants>

The format though is JSON (or XML if you specify that).

You might have a look at tools offered by the Protege project (open source / freely available) [1]. I believe the desktop version of Protege has functionality that allows you to extract/copy/move ontology axioms. It also allows you to save your ontology in various formats.

Kind regards,
Jennifer

[1] http://protege.stanford.edu/



_______________________________________________
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

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From swt at stanford.edu  Tue Jul 11 09:13:00 2017
From: swt at stanford.edu (Samson Tu)
Date: Tue, 11 Jul 2017 09:13:00 -0700
Subject: [bioontology-support] Versioning Question
In-Reply-To: <91467629-815D-480A-A5FD-661FB88CE2DF@stanford.edu>
References: <CA+EFHPuULimHKJ6+UeSgKuV0a-Bv=jmwr4pQkpR1GcQpPve+5g@mail.gmail.com>
 <0FCB9856-DEE1-4B9A-82A3-6FF5F69C45AA@stanford.edu>
 <CA+EFHPuKneu_a3mzmDjVW72kg7XU-3xSA2yDqahUSgvA99+kzA@mail.gmail.com>
 <E0067441-F9E4-4191-B0D3-8400C3C59779@stanford.edu>
 <CA+EFHPsD2KahDQkk+Oq7TTywcgc2r28gV3tot61hspyiM99S9w@mail.gmail.com>
 <CA+EFHPsZrQeGg6nSAq4dTMs7aaSffuoWaOkLqTSLxg317Ve-Mw@mail.gmail.com>
 <6473C11C-2432-452B-8B78-5A53E4DEBB12@stanford.edu>
 <CA+EFHPv2qWPP__wXVNHC2jWiJuCPbL5H4HK2mFTdiSAa_Vhzvg@mail.gmail.com>
 <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
 <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>
 <B55DE7CE-4128-4B9E-AD0D-D93F1994C3C0@stanford.edu>
 <91467629-815D-480A-A5FD-661FB88CE2DF@stanford.edu>
Message-ID: <1049FC91-7FDB-45AF-9574-E5BA89403AA0@stanford.edu>


> On Jul 11, 2017, at 9:00 AM, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
> Jason,
> 
> Folllowing up on this topic, I took a quick look at the UMLS license to refresh my memory. In the case of SNOMEDCT, there is an extensive set of licensing terms applying particularly to that ontology; you may find it at https://uts.nlm.nih.gov/help/license/licensecategoryihtsdohelp.html <https://uts.nlm.nih.gov/help/license/licensecategoryihtsdohelp.html>. 
> 
> These terms take precedence, and to my casual review, appear to preclude our redistribution of the content as an ontology. Thus we will not be able to make it available, sorry for that.
> 

Licensees of NLM UMLS Metathesaurus in the U.S. can obtain SNOMED CT directly from NLM [1].

With best regards,
Samson
[1] https://www.nlm.nih.gov/healthit/snomedct/
-- 
Samson Tu                                                      email: swt at stanford.edu
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research 	phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944



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From jmarr1990 at gmail.com  Tue Jul 11 09:47:22 2017
From: jmarr1990 at gmail.com (jason marr)
Date: Tue, 11 Jul 2017 12:47:22 -0400
Subject: [bioontology-support] Versioning Question
In-Reply-To: <91467629-815D-480A-A5FD-661FB88CE2DF@stanford.edu>
References: <CA+EFHPuULimHKJ6+UeSgKuV0a-Bv=jmwr4pQkpR1GcQpPve+5g@mail.gmail.com>
 <0FCB9856-DEE1-4B9A-82A3-6FF5F69C45AA@stanford.edu>
 <CA+EFHPuKneu_a3mzmDjVW72kg7XU-3xSA2yDqahUSgvA99+kzA@mail.gmail.com>
 <E0067441-F9E4-4191-B0D3-8400C3C59779@stanford.edu>
 <CA+EFHPsD2KahDQkk+Oq7TTywcgc2r28gV3tot61hspyiM99S9w@mail.gmail.com>
 <CA+EFHPsZrQeGg6nSAq4dTMs7aaSffuoWaOkLqTSLxg317Ve-Mw@mail.gmail.com>
 <6473C11C-2432-452B-8B78-5A53E4DEBB12@stanford.edu>
 <CA+EFHPv2qWPP__wXVNHC2jWiJuCPbL5H4HK2mFTdiSAa_Vhzvg@mail.gmail.com>
 <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
 <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>
 <B55DE7CE-4128-4B9E-AD0D-D93F1994C3C0@stanford.edu>
 <91467629-815D-480A-A5FD-661FB88CE2DF@stanford.edu>
Message-ID: <CA+EFHPu7Uw5PPKGr8TODiuWwGTJf3G1JTncePRF8JaRonDR7Qw@mail.gmail.com>

So while I'm able to use SNOMEDCT in the other API functions, such as class
queries, i'm unable to actually download the ontology file itself. Am I
understanding that correctly?
-Jason

On Tue, Jul 11, 2017 at 12:00 PM, John Graybeal <jgraybeal at stanford.edu>
wrote:

> Jason,
>
> Folllowing up on this topic, I took a quick look at the UMLS license to
> refresh my memory. In the case of SNOMEDCT, there is an extensive set of
> licensing terms applying particularly to that ontology; you may find it at
> https://uts.nlm.nih.gov/help/license/licensecategoryihtsdohelp.html.
>
> These terms take precedence, and to my casual review, appear to preclude
> our redistribution of the content as an ontology. Thus we will not be able
> to make it available, sorry for that.
>
> John
>
> On Jul 11, 2017, at 8:54 AM, John Graybeal <jgraybeal at stanford.edu> wrote:
>
> Hi Jason,
>
> In the past there has been a license restriction on SNOMEDCT, because it
> was from UMLS. (You can see LIcense information on the summary page, in
> this case http://bioportal.bioontology.org/ontologies/SNOMEDCT.)
>
> With the new UMLS licensing, it may be that SNOMEDCT can be made available
> as a download. Unfortunately we have not had the resources so far to
> confirm whether this is the case, and then modify the availability in the
> system.
>
> I hope we can have another look at this question soon (constructive
> comments from members of the support list are welcome!).
>
> John
>
>
> On Jul 11, 2017, at 5:13 AM, jason marr <jmarr1990 at gmail.com> wrote:
>
> Jennifer,
> Is there a License restriction on SNOMEDCT? I'm unable to download via api.
> Regards,
> Jason
>
> On Wed, Jun 14, 2017 at 3:43 PM, Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Hi Jason,
>>
>>
>> On Jun 14, 2017, at 12:03 PM, jason marr <jmarr1990 at gmail.com> wrote:
>>
>> Jennifer,
>> Is it possible to download a subject of an ontology? Say given a class,
>> download all the sub classes and properties in rdf? I see the download url
>> in the doc, http://data.bioontology.org/ontologies/BRO/download . Let me
>> know, thanks!
>>
>>
>>
>> I don?t think we offer exactly what you?re asking for. The download link
>> downloads the entire ontology source file in whatever format was submitted
>> to us.
>>
>> You can retrieve the subclasses of a given class using the ?descendants"
>> REST call, e.g.:
>>
>> http://data.bioontology.org/ontologies/BRO/classes/http%3A%
>> 2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity/descendants
>> <http://data.bioontology.org/ontologies/BRO/classes/http://bioontology.org/ontologies/Activity.owl#Activity/descendants>
>>
>> The format though is JSON (or XML if you specify that).
>>
>> You might have a look at tools offered by the Protege project (open
>> source / freely available) [1]. I believe the desktop version of Protege
>> has functionality that allows you to extract/copy/move ontology axioms. It
>> also allows you to save your ontology in various formats.
>>
>> Kind regards,
>> Jennifer
>>
>> [1] http://protege.stanford.edu/
>>
>>
>>
> _______________________________________________
> 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
>
>
>
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From jgraybeal at stanford.edu  Tue Jul 11 09:48:52 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 11 Jul 2017 16:48:52 +0000
Subject: [bioontology-support] Versioning Question
In-Reply-To: <CA+EFHPu7Uw5PPKGr8TODiuWwGTJf3G1JTncePRF8JaRonDR7Qw@mail.gmail.com>
References: <CA+EFHPuULimHKJ6+UeSgKuV0a-Bv=jmwr4pQkpR1GcQpPve+5g@mail.gmail.com>
 <0FCB9856-DEE1-4B9A-82A3-6FF5F69C45AA@stanford.edu>
 <CA+EFHPuKneu_a3mzmDjVW72kg7XU-3xSA2yDqahUSgvA99+kzA@mail.gmail.com>
 <E0067441-F9E4-4191-B0D3-8400C3C59779@stanford.edu>
 <CA+EFHPsD2KahDQkk+Oq7TTywcgc2r28gV3tot61hspyiM99S9w@mail.gmail.com>
 <CA+EFHPsZrQeGg6nSAq4dTMs7aaSffuoWaOkLqTSLxg317Ve-Mw@mail.gmail.com>
 <6473C11C-2432-452B-8B78-5A53E4DEBB12@stanford.edu>
 <CA+EFHPv2qWPP__wXVNHC2jWiJuCPbL5H4HK2mFTdiSAa_Vhzvg@mail.gmail.com>
 <0350B77F-5D94-497B-8B34-60264AC8FD34@stanford.edu>
 <CA+EFHPshr2-f6J2x=FPtR3OHOT0bfV8nZp72NSyebo9PFhGGWg@mail.gmail.com>
 <B55DE7CE-4128-4B9E-AD0D-D93F1994C3C0@stanford.edu>
 <91467629-815D-480A-A5FD-661FB88CE2DF@stanford.edu>
 <CA+EFHPu7Uw5PPKGr8TODiuWwGTJf3G1JTncePRF8JaRonDR7Qw@mail.gmail.com>
Message-ID: <A4E679F0-92E0-4026-9222-19288647A817@stanford.edu>

Yes, that's right.

John

On Jul 11, 2017, at 9:47 AM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

So while I'm able to use SNOMEDCT in the other API functions, such as class queries, i'm unable to actually download the ontology file itself. Am I understanding that correctly?
-Jason

On Tue, Jul 11, 2017 at 12:00 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Jason,

Folllowing up on this topic, I took a quick look at the UMLS license to refresh my memory. In the case of SNOMEDCT, there is an extensive set of licensing terms applying particularly to that ontology; you may find it at https://uts.nlm.nih.gov/help/license/licensecategoryihtsdohelp.html.

These terms take precedence, and to my casual review, appear to preclude our redistribution of the content as an ontology. Thus we will not be able to make it available, sorry for that.

John

On Jul 11, 2017, at 8:54 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hi Jason,

In the past there has been a license restriction on SNOMEDCT, because it was from UMLS. (You can see LIcense information on the summary page, in this case http://bioportal.bioontology.org/ontologies/SNOMEDCT.)

With the new UMLS licensing, it may be that SNOMEDCT can be made available as a download. Unfortunately we have not had the resources so far to confirm whether this is the case, and then modify the availability in the system.

I hope we can have another look at this question soon (constructive comments from members of the support list are welcome!).

John


On Jul 11, 2017, at 5:13 AM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

Jennifer,
Is there a License restriction on SNOMEDCT? I'm unable to download via api.
Regards,
Jason

On Wed, Jun 14, 2017 at 3:43 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Jason,


On Jun 14, 2017, at 12:03 PM, jason marr <jmarr1990 at gmail.com<mailto:jmarr1990 at gmail.com>> wrote:

Jennifer,
Is it possible to download a subject of an ontology? Say given a class, download all the sub classes and properties in rdf? I see the download url in the doc, http://data.bioontology.org/ontologies/BRO/download . Let me know, thanks!


I don?t think we offer exactly what you?re asking for. The download link downloads the entire ontology source file in whatever format was submitted to us.

You can retrieve the subclasses of a given class using the ?descendants" REST call, e.g.:

http://data.bioontology.org/ontologies/BRO/classes/http%3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity/descendants<http://data.bioontology.org/ontologies/BRO/classes/http://bioontology.org/ontologies/Activity.owl#Activity/descendants>

The format though is JSON (or XML if you specify that).

You might have a look at tools offered by the Protege project (open source / freely available) [1]. I believe the desktop version of Protege has functionality that allows you to extract/copy/move ontology axioms. It also allows you to save your ontology in various formats.

Kind regards,
Jennifer

[1] http://protege.stanford.edu/



_______________________________________________
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



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


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From futo at stanford.edu  Thu Jul 13 11:47:53 2017
From: futo at stanford.edu (Michelle Futornick)
Date: Thu, 13 Jul 2017 18:47:53 +0000
Subject: [bioontology-support] properties not loading in BioPortal slice,
	and broken link
In-Reply-To: <MWHPR02MB2560FCF023D7DB015F0188C6BFCB0@MWHPR02MB2560.namprd02.prod.outlook.com>
References: <MWHPR02MB2560FCF023D7DB015F0188C6BFCB0@MWHPR02MB2560.namprd02.prod.outlook.com>
Message-ID: <MWHPR02MB2560D090911CD71F6BD7DB72BFAC0@MWHPR02MB2560.namprd02.prod.outlook.com>

1) http://biblio.bioportal.bioontology.org/ontologies/BIBFRAME/?p=properties

gives a "Loading..." message but doesn't display any properties

Trying to view the Properties tab for the same ontology in the "full" BioPortal does work.
http://bioportal.bioontology.org/ontologies/BIBFRAME/?p=properties

Same thing happens with another ontology:
http://biblio.bioportal.bioontology.org/ontologies/BIBLIOTEK-O/?p=properties properties don't load
http://bioportal.bioontology.org/ontologies/BIBLIOTEK-O/?p=properties properties do load

2) while viewing a BioPortal slice from any page except the slice "homepage", the definition link in

in other words, from this page:
http://biblio.bioportal.bioontology.org
clicking on the "BioPortal slice" definition link in "You are viewing the Biblio BioPortal Slice" works fine, but if you try the same from
http://biblio.bioportal.bioontology.org/ontologies/BIBLIOTEK-O
(which goes to http://biblio.bioportal.bioontology.org/ontologies/help?pop=true#slice_definition) you get
 "The page you are looking for wasn't found. Please try again."

same for another slice:
from umls.bioportal.bioontology.org the definition link works
but from http://umls.bioportal.bioontology.org/ontologies or umls.bioportal.bioontology.org/ontologies/AI-RHEUM the definition link gives the "not found" error.


Best regards,

****************

Michelle Futornick

Linked Data for Production (LD4P) Program Manager

Stanford University

Lathrop Library

Stanford, CA 94305

650-704-2053 (cell)

650-725-3656 (office)






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From spencerhb at mymail.vcu.edu  Thu Jul 13 12:57:38 2017
From: spencerhb at mymail.vcu.edu (Heather Spencer)
Date: Thu, 13 Jul 2017 15:57:38 -0400
Subject: [bioontology-support] Attempting to scrape definitions and any
	synonyms using get_labels.py
Message-ID: <CAP+JS2AuuZfWTZGz7rupZo62Cj-vjiXLNHcfRRh9pJ9u-V70ig@mail.gmail.com>

Hello!

I modified the get_labels.py sample code to also grab each class'
definition and synonym. Unfortunately, I am receiving a None Type error in
retrieving some of the definitions, and I would think none of them would be
blank, or that if they were, I would also be getting an error (the way my
code is written) for the synonyms. Pleas advise me on the possibility of a
'null' being returned from the following program for definition. The pull
comes from http://data.bioontology.org/ontologies/ICO/classes.

Thank you

Heather Spencer
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import urllib2
import json

REST_URL = "http://data.bioontology.org"
API_KEY = "0640b94d-63f7-49f3-9be5-f79354797620"


def get_json(url):
    opener = urllib2.build_opener()
    opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
    return json.loads(opener.open(url).read())

# Get all ontologies from the REST service and parse the JSON
ontologies = get_json(REST_URL+"/ontologies")

# Iterate looking for ontology with acronym BRO
bro = None
for ontology in ontologies:
    if ontology["acronym"] == "BRO":
        bro = ontology

labels = []
synonyms=[]
definition=[]

# Using the hypermedia link called `classes`, get the first page
page = get_json(bro["links"]["classes"])

# Iterate over the available pages adding labels from all classes
# When we hit the last page, the while loop will exit
next_page = page
while next_page:
    next_page = page["links"]["nextPage"]
    for bro_class in page["collection"]:
        labels.append(bro_class["prefLabel"])
        synonyms.append(bro_class["synonym"])
        if bro_class["definition"] is not None:
            definition.append(bro_class)["definition"]
        
    if next_page:
        page = get_json(next_page)


#for label in labels:
 #   print label
for synonym in synonyms:
    print synonym

From ravikeshwani.mca at gmail.com  Fri Jul 14 01:01:21 2017
From: ravikeshwani.mca at gmail.com (Ravi Keshwani)
Date: Fri, 14 Jul 2017 13:31:21 +0530
Subject: [bioontology-support] Help to find ndc number by rxnorm
In-Reply-To: <CAHHC=MmRhh+MVeZg6+U3PSuxi3r6LwEz-AKbyErHihgk6DUSvw@mail.gmail.com>
References: <CAHHC=Mn4ASsVgCdz+oPQ4k9FrknSR_Yswn_KVtc42RBH1-0=wg@mail.gmail.com>
 <CAHHC=MmRhh+MVeZg6+U3PSuxi3r6LwEz-AKbyErHihgk6DUSvw@mail.gmail.com>
Message-ID: <CAHHC=M=+L1K_+=GLaT6kJ3ZXX3giZmZZGioXPvfL_+PuuVV8Zg@mail.gmail.com>

Hello Support team,

   I have registered on your site and generated api key. I want to use your
api from my code to make a request to fetch ndc numbers through rxnormid.

Can you please help me on this ?

Thanks
Ravi keshwani
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From vendetti at stanford.edu  Fri Jul 14 09:06:38 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 14 Jul 2017 16:06:38 +0000
Subject: [bioontology-support] Help to find ndc number by rxnorm
In-Reply-To: <CAHHC=M=+L1K_+=GLaT6kJ3ZXX3giZmZZGioXPvfL_+PuuVV8Zg@mail.gmail.com>
References: <CAHHC=Mn4ASsVgCdz+oPQ4k9FrknSR_Yswn_KVtc42RBH1-0=wg@mail.gmail.com>
 <CAHHC=MmRhh+MVeZg6+U3PSuxi3r6LwEz-AKbyErHihgk6DUSvw@mail.gmail.com>
 <CAHHC=M=+L1K_+=GLaT6kJ3ZXX3giZmZZGioXPvfL_+PuuVV8Zg@mail.gmail.com>
Message-ID: <7E66CDB0-4C59-4054-B432-8AB7962CD56E@stanford.edu>

Hello Ravi,

I don?t know what you?re talking about when you say "ndc numbers". Here?s an example of a REST call using our API that will display the property value pairs for a particular class in RXNORM:

http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F581650?include=all<http://data.bioontology.org/ontologies/RXNORM/classes/http://purl.bioontology.org/ontology/RXNORM/581650?include=all>

You can look at the results to determine which property contains the value you?re interested in retrieving. Our REST API is documented here:

http://data.bioontology.org/documentation

We also provide example code in various languages in this GitHub repository:

https://github.com/ncbo/ncbo_rest_sample_code

Jennifer


On Jul 14, 2017, at 1:01 AM, Ravi Keshwani <ravikeshwani.mca at gmail.com<mailto:ravikeshwani.mca at gmail.com>> wrote:


Hello Support team,

   I have registered on your site and generated api key. I want to use your api from my code to make a request to fetch ndc numbers through rxnormid.

Can you please help me on this ?

Thanks
Ravi keshwani

_______________________________________________
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 ravikeshwani.mca at gmail.com  Fri Jul 14 09:10:18 2017
From: ravikeshwani.mca at gmail.com (Ravi Keshwani)
Date: Fri, 14 Jul 2017 21:40:18 +0530
Subject: [bioontology-support] Help to find ndc number by rxnorm
In-Reply-To: <7E66CDB0-4C59-4054-B432-8AB7962CD56E@stanford.edu>
References: <CAHHC=Mn4ASsVgCdz+oPQ4k9FrknSR_Yswn_KVtc42RBH1-0=wg@mail.gmail.com>
 <CAHHC=MmRhh+MVeZg6+U3PSuxi3r6LwEz-AKbyErHihgk6DUSvw@mail.gmail.com>
 <CAHHC=M=+L1K_+=GLaT6kJ3ZXX3giZmZZGioXPvfL_+PuuVV8Zg@mail.gmail.com>
 <7E66CDB0-4C59-4054-B432-8AB7962CD56E@stanford.edu>
Message-ID: <CAHHC=MkupJGJMXsQTDdnCg8bg_kAPwnFC-eLAOaUr1KCDzfQDA@mail.gmail.com>

Hello Jennifer,

  Thanks for your swift response. NDC stands for national drug code which
are associated with RxNormId of a drug ..

I only want NDC numbers only and no other properties. The documentation of
the Api is above my level of understanding... So it would be great if you
provide me the sample api call for same.

Thanks
Ravi keshwani
On 14-Jul-2017 9:36 PM, "Jennifer Leigh Vendetti" <vendetti at stanford.edu>
wrote:

> Hello Ravi,
>
> I don?t know what you?re talking about when you say "ndc numbers". Here?s
> an example of a REST call using our API that will display the property
> value pairs for a particular class in RXNORM:
>
> http://data.bioontology.org/ontologies/RXNORM/classes/
> http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F581650?include=all
> <http://data.bioontology.org/ontologies/RXNORM/classes/http://purl.bioontology.org/ontology/RXNORM/581650?include=all>
>
> You can look at the results to determine which property contains the value
> you?re interested in retrieving. Our REST API is documented here:
>
> http://data.bioontology.org/documentation
>
> We also provide example code in various languages in this GitHub
> repository:
>
> https://github.com/ncbo/ncbo_rest_sample_code
>
> Jennifer
>
>
> On Jul 14, 2017, at 1:01 AM, Ravi Keshwani <ravikeshwani.mca at gmail.com>
> wrote:
>
> Hello Support team,
>
>    I have registered on your site and generated api key. I want to use
> your api from my code to make a request to fetch ndc numbers through
> rxnormid.
>
> Can you please help me on this ?
>
> Thanks
> Ravi keshwani
> _______________________________________________
> 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  Fri Jul 14 09:41:28 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 14 Jul 2017 16:41:28 +0000
Subject: [bioontology-support] [ORDO] bioportal issue
In-Reply-To: <AC3E54C3-B15F-4A31-9281-80C5E8CCC6D2@stanford.edu>
References: <53721CEC.4010600@inserm.fr>
 <FD57126C-D6A4-43C4-8A40-BE90D25C427E@ebi.ac.uk> <56CDC203.5070001@inserm.fr>
 <848E2F34-E02F-4DA3-987D-7A836EBB874B@stanford.edu>
 <a65bae35-cc90-acf2-fc42-67be75ab4b45@inserm.fr>
 <876518B6-C6F6-465C-A1B2-AB055368F899@stanford.edu>
 <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu>
 <da951031c667608b44c3a714f3e009e9@inserm.fr>
 <AC3E54C3-B15F-4A31-9281-80C5E8CCC6D2@stanford.edu>
Message-ID: <F31F839C-3C5F-4D95-A076-995C715C00C1@stanford.edu>

Hello Marc,

I don?t have a  solution yet for parsing ORDO 2.4 in BioPortal, but I?ll provide a summary below of what I?ve discovered so far.

The system is having difficulty handling classes in your ontology that have annotations nested 3 levels deep. Here?s a screenshot of your ontology in the Protege ontology editor with class ?48,XXYY syndrome? highlighted:


[cid:3A8B998F-03C1-42EA-85B0-82EFE673DDC0 at hsd1.ca.comcast.net]


Note the second occurrence of hasDbXref in the screenshot where there?s an annotation on an annotation on an annotation.

I think I mentioned in a previous correspondence that we use the OWL API internally for parsing. When the OWL API loads this ontology, it inserts a blank node for these nested annotations with a blank node identifier in the form of ?_:genid?. Using the example in the screen shot above, this is a snippet of the ontology source, as loaded by the OWL API:

<Annotation>
  <annotatedSource>
    <Axiom rdf:nodeID="_:genid25">
      <annotatedSource rdf:resource="http://www.orpha.net/ORDO/Orphanet_10"/>
      <annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
      <annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD-10:Q98.8</annotatedTarget>
      <obo1:ECO_0000218 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Attributed</obo1:ECO_0000218>
    </Axiom>
  </annotatedSource>
  <annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/ECO_0000218"/>
  <annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Attributed</annotatedTarget>
  <obo1:ECO_0000218 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NTBT (narrower term maps to a broader term)</obo1:ECO_0000218>
</Annotation>

Although we can load the ontology without errors, the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store:

Illegal rdf:nodeID value '_:genid25' rapper: Failed to parse file

I went looking for a specification for what is considered valid syntax for blank node identifiers, but so far I haven?t been able to find anything. It?s unclear to me if the OWL API is generating invalid RDF, or if the Raptor RDF parser isn?t handling blank nodes that it should be. I will likely need to correspond with the developers of one or both projects.

Apologies that it hasn?t been straightforward so far to track this down.

On another note, I?m wondering if you could give me some basic information about how your OWL file is generated. Is it done programmatically? Or, do you use an ontology editing environment to maintain the ontology?

Kind regards,
Jennifer



On Jul 10, 2017, at 6:26 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Marc,

I?ve entered an issue in our tracker [1], and will have a look.

Kind regards,
Jennifer

[1] https://github.com/ncbo/bioportal-project/issues/31


On Jul 10, 2017, at 2:11 PM, marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr> wrote:


Hello Jennifer,

Sorry about that, but once again the new version of ORDO (2.4) seems to have issues : 2.3 (Uploaded, Error Rdf)     07/05/2017     07/05/2017
https://bioportal.bioontology.org/ontologies/ORDO


This version was produced the same way than the previous one.

Any ideas ?

Best regards,

---

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE


Le 11-08-2016 19:22, Jennifer Leigh Vendetti a ?crit :

Hello Marc,

We've addressed the issue I mentioned below.  Version 2.2 of ORDO is parsed and available in BioPortal:

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

Apologies again that this one took us some time to address.

Best,
Jennifer


On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Marc,

I am writing with a status report regarding BioPortal's failure to handle ORDO 2.2.

As you may already know, BioPortal uses the OWL API [1] internally for ontology parsing.  I wrote some Java code, independent of the BioPortal application, to make sure the OWL API handles your ontology properly.  The parsing succeeds, which indicates to me that your ontology file is valid.  When the OWL API parses your ontology file, it emits a very large number of "unparsed triple" messages (roughly 15.5K of them), e.g.:

[OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedProperty -> http://purl.obolibrary.org/obo/ECO_0000218
[OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedSource -> _:genid120261

The size of the output from the OWL API is causing a buffer overflow / deadlock in BioPortal's source code.  I am currently working toward fixing the issue, and hope to have something available soon.

Apologies that this one is taking some time for us to track down / fix.

Best,
Jennifer

[1] http://owlcs.github.io/owlapi/



On Jun 27, 2016, at 3:18 AM, Marc Hanauer <marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>> wrote:


Hello Jennifer,

I've made an update of our ontology (ORDO) last week as usual by putting the file on our own server. This time, the bioportal website seems to try the upload but with error.

The version in our own server is now "2.2" but it appears with this line on bioportal:

2.1 (Uploaded, Error Rdf)       06/22/2016      06/22/2016      OWL<http://data.bioontology.org/ontologies/ORDO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb> | Diff<http://data.bioontology.org/ontologies/ORDO/submissions/9/download_diff?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb>

Any idea ?

Best regards,

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE
Le 25/02/2016 ? 00:41, Jennifer Leigh Vendetti a ?crit :
Hello Marc,

On Feb 24, 2016, at 6:45 AM, Marc Hanauer <marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>> wrote:

Dear support,
We manage the ORDO (Orphanet Rare Disease Ontology) and we have made an update recently (2 days ago).
Usually (for the previous version), we just update the file on our own server (keeping the same URL : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ) and then the bioportal website automatically upload it.

It seems this is not the case anymore (the version in bioportal remain v2.0 instead of the new 2.1)

Do we need to perform any manual action in order to update it on bioportal ?


You don't need to do anything manual.  We were having some performance issues with our site and temporarily disabled the cron jobs in our production environment that pull new versions of ontologies.  The cron job has been reenabled today, so the new version of your ontology should be pulled and processed overnight.



By the way, with our account, we still have trouble accessing the bioportal interface (when we sign in and try to reach the ORDO page, we obtain an error message which is not the case without login...) (see my previous msg below about this)


Sorry you're having difficulties.  I tried reproducing this behavior here and so far haven't had any luck.  I've viewed your ontology in BioPortal, both when logged in and logged out (screen shot below).  I also verified that your user account of "ORDO_Orphanet" is valid, and I don't see any issues there.  Are you still seeing this behavior?

Jennifer



<Mail Attachment.png>


_______________________________________________
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  Fri Jul 14 09:59:21 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 14 Jul 2017 16:59:21 +0000
Subject: [bioontology-support] Attempting to scrape definitions and any
 synonyms using get_labels.py
In-Reply-To: <CAP+JS2AuuZfWTZGz7rupZo62Cj-vjiXLNHcfRRh9pJ9u-V70ig@mail.gmail.com>
References: <CAP+JS2AuuZfWTZGz7rupZo62Cj-vjiXLNHcfRRh9pJ9u-V70ig@mail.gmail.com>
Message-ID: <6C3352C8-214E-4799-8E6F-37DD6FF56DE1@stanford.edu>

Hi Heather,


On Jul 13, 2017, at 12:57 PM, Heather Spencer <spencerhb at mymail.vcu.edu<mailto:spencerhb at mymail.vcu.edu>> wrote:

Hello!

I modified the get_labels.py sample code to also grab each class' definition and synonym. Unfortunately, I am receiving a None Type error in retrieving some of the definitions, and I would think none of them would be blank


Classes in BioPortal aren?t required to have definitions. It?s left up to ontology authors if they want to provide them. "Classes with no definition" is one of the metrics we show in the BioPortal UI. Here?s a screenshot of the metrics panel for BRO, indicating that there are 11 classes without definitions:

[cid:2337B59F-BD4F-4F6F-B47D-3FF6ACA4326C at hsd1.ca.comcast.net]





, or that if they were, I would also be getting an error (the way my code is written) for the synonyms. Pleas advise me on the possibility of a 'null' being returned from the following program for definition.


We used to have a developer on the team that knew Python, but he?s since left the project. I looked at the file you sent and there's a difference in how definitions and synonyms are handled. There's an explicit check for ?None? when looking at definitions, but not for synonyms:

synonyms.append(bro_class["synonym"])
if bro_class["definition"] is not None:

If no synonyms are returned, it?s likely just appending an empty array element.


The pull comes from http://data.bioontology.org/ontologies/ICO/classes.


The source file you attached is using the BRO ontology (specified on lines 19 and 20):

if ontology["acronym"] == "BRO":
  bro = ontology

Kind regards,
Jennifer



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From vendetti at stanford.edu  Fri Jul 14 14:02:55 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 14 Jul 2017 21:02:55 +0000
Subject: [bioontology-support] Help to find ndc number by rxnorm
In-Reply-To: <CAHHC=MkupJGJMXsQTDdnCg8bg_kAPwnFC-eLAOaUr1KCDzfQDA@mail.gmail.com>
References: <CAHHC=Mn4ASsVgCdz+oPQ4k9FrknSR_Yswn_KVtc42RBH1-0=wg@mail.gmail.com>
 <CAHHC=MmRhh+MVeZg6+U3PSuxi3r6LwEz-AKbyErHihgk6DUSvw@mail.gmail.com>
 <CAHHC=M=+L1K_+=GLaT6kJ3ZXX3giZmZZGioXPvfL_+PuuVV8Zg@mail.gmail.com>
 <7E66CDB0-4C59-4054-B432-8AB7962CD56E@stanford.edu>
 <CAHHC=MkupJGJMXsQTDdnCg8bg_kAPwnFC-eLAOaUr1KCDzfQDA@mail.gmail.com>
Message-ID: <EBAC955D-BE21-451F-ABF4-D27CFF72BBB7@stanford.edu>

There is no API call that allows you to specify retrieval of a single property value pair for a class. You can use a call like this one:

http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F1242968?include=properties<http://data.bioontology.org/ontologies/RXNORM/classes/http://purl.bioontology.org/ontology/RXNORM/1242968?include=properties>

? to get all of the property value pairs for a particular class. (The call above retrieves properties for the "exenatide 2 MG Injection [Bydureon]? class from RXNORM). You?ll need to loop through the set of properties returned to pull out the NDC values (see screen shot below of JSON results).

Jennifer


[cid:DD0049A4-ADB2-49CC-8D6B-59E8005832B2 at stanford.edu]




On Jul 14, 2017, at 9:10 AM, Ravi Keshwani <ravikeshwani.mca at gmail.com<mailto:ravikeshwani.mca at gmail.com>> wrote:


Hello Jennifer,

  Thanks for your swift response. NDC stands for national drug code which are associated with RxNormId of a drug ..

I only want NDC numbers only and no other properties. The documentation of the Api is above my level of understanding... So it would be great if you provide me the sample api call for same.

Thanks
Ravi keshwani

On 14-Jul-2017 9:36 PM, "Jennifer Leigh Vendetti" <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Ravi,

I don?t know what you?re talking about when you say "ndc numbers". Here?s an example of a REST call using our API that will display the property value pairs for a particular class in RXNORM:

http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F581650?include=all<http://data.bioontology.org/ontologies/RXNORM/classes/http://purl.bioontology.org/ontology/RXNORM/581650?include=all>

You can look at the results to determine which property contains the value you?re interested in retrieving. Our REST API is documented here:

http://data.bioontology.org/documentation

We also provide example code in various languages in this GitHub repository:

https://github.com/ncbo/ncbo_rest_sample_code

Jennifer


On Jul 14, 2017, at 1:01 AM, Ravi Keshwani <ravikeshwani.mca at gmail.com<mailto:ravikeshwani.mca at gmail.com>> wrote:


Hello Support team,

   I have registered on your site and generated api key. I want to use your api from my code to make a request to fetch ndc numbers through rxnormid.

Can you please help me on this ?

Thanks
Ravi keshwani

_______________________________________________
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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From laia.subirats at gmail.com  Sat Jul 15 07:40:02 2017
From: laia.subirats at gmail.com (Laia Subirats)
Date: Sat, 15 Jul 2017 16:40:02 +0200
Subject: [bioontology-support] Missing metrics in PMR ontology
Message-ID: <CAHaRLjvJTs-XeDyvOK9P8QCO9mQi-v-Z9ENoACcUAL0TJm5XEg@mail.gmail.com>

Dear Sir/Madam,

I would like to see the metrics of my ontology in
http://bioportal.bioontology.org/ontologies/PMR, I do not know if there is
any problem. The ontology has grown considerably, from 137 to 1597 classes
and from 0 to 945 individuals.

Yours faithfully,
-- 
Laia Subirats
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From vendetti at stanford.edu  Sat Jul 15 07:51:22 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 15 Jul 2017 14:51:22 +0000
Subject: [bioontology-support] Missing metrics in PMR ontology
In-Reply-To: <CAHaRLjvJTs-XeDyvOK9P8QCO9mQi-v-Z9ENoACcUAL0TJm5XEg@mail.gmail.com>
References: <CAHaRLjvJTs-XeDyvOK9P8QCO9mQi-v-Z9ENoACcUAL0TJm5XEg@mail.gmail.com>
Message-ID: <F17D1A93-EA09-447D-A8AE-DB33C925CD14@stanford.edu>

Hello Laia,

Your latest ontology upload is now fully parsed and available in BioPortal. The metrics panel reflects the numbers you mention below.

Kind regards,
Jennifer


On Jul 15, 2017, at 7:40 AM, Laia Subirats <laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>> wrote:

Dear Sir/Madam,

I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/PMR, I do not know if there is any problem. The ontology has grown considerably, from 137 to 1597 classes and from 0 to 945 individuals.

Yours faithfully,
--
Laia Subirats
_______________________________________________
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 laia.subirats at gmail.com  Sat Jul 15 07:58:33 2017
From: laia.subirats at gmail.com (Laia Subirats)
Date: Sat, 15 Jul 2017 16:58:33 +0200
Subject: [bioontology-support] Missing metrics in PMR ontology
In-Reply-To: <F17D1A93-EA09-447D-A8AE-DB33C925CD14@stanford.edu>
References: <CAHaRLjvJTs-XeDyvOK9P8QCO9mQi-v-Z9ENoACcUAL0TJm5XEg@mail.gmail.com>
 <F17D1A93-EA09-447D-A8AE-DB33C925CD14@stanford.edu>
Message-ID: <CAHaRLjuwdUhvQ=TRHif6gFrETyak1GtYSkz4v1NpvHVMGhgS+g@mail.gmail.com>

Thank you Jennifer.

On Sat, Jul 15, 2017 at 4:51 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Laia,
>
> Your latest ontology upload is now fully parsed and available in
> BioPortal. The metrics panel reflects the numbers you mention below.
>
> Kind regards,
> Jennifer
>
>
> On Jul 15, 2017, at 7:40 AM, Laia Subirats <laia.subirats at gmail.com>
> wrote:
>
> Dear Sir/Madam,
>
> I would like to see the metrics of my ontology in
> http://bioportal.bioontology.org/ontologies/PMR, I do not know if there
> is any problem. The ontology has grown considerably, from 137 to 1597
> classes and from 0 to 945 individuals.
>
> Yours faithfully,
> --
> Laia Subirats
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>


-- 
Laia Subirats
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From support at bioontology.org  Tue Jul 18 11:40:24 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 18 Jul 2017 11:40:24 -0700
Subject: [bioontology-support] [BioPortal] Feedback from michelle
Message-ID: <596e5618793dd_256d3fdad18649081671d@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Jul 18 16:20:09 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 18 Jul 2017 23:20:09 +0000
Subject: [bioontology-support] [BioPortal] Feedback from michelle
In-Reply-To: <596e5618793dd_256d3fdad18649081671d@ncbo-prd-app-09.stanford.edu.mail>
References: <596e5618793dd_256d3fdad18649081671d@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <1014B1A7-6968-41DF-A5F5-239E28D08713@stanford.edu>

Hello Michelle,

On Jul 18, 2017, at 11:40 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: michelle

Email: futo at stanford.edu<mailto:futo at stanford.edu>

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

Feedback:

I submitted this ontology and the classes are not loading. Can you tell what is wrong?
http://bioportal.bioontology.org/ontologies/OA/



There are two issues here.

1). The pull URL entered is invalid because it points to an HTML page in GitHub. If you?d like BioPortal to pull an ontology from a remote location, you need to enter a pull URL that points to the exact location of the ontology source file. If an ontology is available in GitHub, you need to click the ?Raw? button to navigate to the raw ontology sources and enter that link in BioPortal. In the case of the OA ontology, the invalid URL is:

https://github.com/w3c/web-annotation/blob/gh-pages/vocab/wd/ontology/oa.rdf

On the above page, if you click the ?Raw? button, you get to the correct URL of the ontology source file:

https://raw.githubusercontent.com/w3c/web-annotation/gh-pages/vocab/wd/ontology/oa.rdf

I created a new submission of the ontology in BioPortal with the correct pull URL.

2). The new submission I created also failed to parse. It appears that this ontology is only available in RDF format, which BioPortal doesn?t handle. We accept ontologies in OWL, OBO, or SKOS format. I did notice that the ontology contains a property "prov:wasRevisionOf? with a value of "http://www.openannotation.org/spec/core/20130208/oa.owl?. This URL is valid and points to an OWL ontology, so it appears that there was an OWL version available at one time. If this older version is sufficient for your needs, let us know and we could assist you with attempting to upload.

Jennifer

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From Kristian.Nicolaisen at ehealthresearch.no  Wed Jul 19 06:32:39 2017
From: Kristian.Nicolaisen at ehealthresearch.no (Kristian Nicolaisen)
Date: Wed, 19 Jul 2017 13:32:39 +0000
Subject: [bioontology-support] Domain coverage
Message-ID: <842a5173f9954ab2b39a30094d6fed19@frodo.ad.ehealthresearch.no>

Hi,

I am currently working on a report on the transition to ontology based terminologies in healthcare in Norway, in that regard I am writing about BFO in general and the OBO Foundry in particular. I have a questions I hope you can help me with:

*         Are there any comparison between SNOMED CT and the OBO ontologies in regards to coverage in biomedical domains?

o   A sort of map to see what domains SNOMED covers and what domains OBO ontologies cover, and where there are overlaps


Sincerely,

Kristian Malm-Nicolaisen
Adviser/Project manager
Norwegian Centre for E-health Research
Tel: +47 950 59 001
www.ehealthresearch.no/en/
[NSE en]


______________________________________________
Tenk milj? - ikke skriv ut denne om det ikke er absolutt n?dvendig
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From j.detras at irri.org  Tue Jul 18 19:45:05 2017
From: j.detras at irri.org (Detras, Jeffrey (IRRI))
Date: Wed, 19 Jul 2017 10:45:05 +0800
Subject: [bioontology-support] NCBO virtual appliance request
Message-ID: <036B45F1-6C34-493A-860A-B22B54F79258@irri.org>

Dear NCBO support,

I would like to request for a VMWare Virtual Appliance of NCBO. My BioPortal username is ?jdetras?. I am working at the International Rice Research Institute (IRRI, http://irri.org/ <http://irri.org/>) as a data curator. I came across your Annotator tool from our collaborator in Agroportal. We would like to try it out and customize with our rice crop ontology so we need a copy for local installation. 

I hope you can grant my request.

Thank you,
Jeff
-- 

The International Rice Research Institute <http://irri.org> is a member of 
the CGIAR <http://cgiar.org> System Organization, a global research 
partnership for a food secure future.
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From jgraybeal at stanford.edu  Wed Jul 19 14:33:44 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 19 Jul 2017 21:33:44 +0000
Subject: [bioontology-support] Domain coverage
In-Reply-To: <842a5173f9954ab2b39a30094d6fed19@frodo.ad.ehealthresearch.no>
References: <842a5173f9954ab2b39a30094d6fed19@frodo.ad.ehealthresearch.no>
Message-ID: <A9A76040-6C8C-45F7-8A3F-5636205F9EF7@stanford.edu>

Kristian,

I think these kinds of domain-specific questions may not get much traction in this list, but there is a discussion list for the OBO Foundry may well garner some useful comments.

John


On Jul 19, 2017, at 6:32 AM, Kristian Nicolaisen <Kristian.Nicolaisen at ehealthresearch.no<mailto:Kristian.Nicolaisen at ehealthresearch.no>> wrote:

Hi,

I am currently working on a report on the transition to ontology based terminologies in healthcare in Norway, in that regard I am writing about BFO in general and the OBO Foundry in particular. I have a questions I hope you can help me with:
?         Are there any comparison between SNOMED CT and the OBO ontologies in regards to coverage in biomedical domains?
o   A sort of map to see what domains SNOMED covers and what domains OBO ontologies cover, and where there are overlaps


Sincerely,

Kristian Malm-Nicolaisen
Adviser/Project manager
Norwegian Centre for E-health Research
Tel: +47 950 59 001
www.ehealthresearch.no/en/<x-msg://4/www.ehealthresearch.no/en/>
<image001.jpg>


______________________________________________
Tenk milj? - ikke skriv ut denne om det ikke er absolutt n?dvendig
_______________________________________________
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
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From balhoff at renci.org  Wed Jul 19 15:05:14 2017
From: balhoff at renci.org (James Balhoff)
Date: Wed, 19 Jul 2017 22:05:14 +0000
Subject: [bioontology-support] Domain coverage
In-Reply-To: <A9A76040-6C8C-45F7-8A3F-5636205F9EF7@stanford.edu>
References: <842a5173f9954ab2b39a30094d6fed19@frodo.ad.ehealthresearch.no>
 <A9A76040-6C8C-45F7-8A3F-5636205F9EF7@stanford.edu>
Message-ID: <EF47178D-12E3-4E48-A5F8-580CD73C93D5@renci.org>

Kristian,

I agree with John; it would be good to ask this on the OBO-discuss list here: https://sourceforge.net/projects/obo/lists/obo-discuss

FYI it will be moving to a Google group sometime soon, but the Sourceforge address works for now.

Best regards,
Jim

____________________________________________
James P. Balhoff, Ph.D.
Renaissance Computing Institute (RENCI)
University of North Carolina at Chapel Hill



On Jul 19, 2017, at 5:33 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Kristian,

I think these kinds of domain-specific questions may not get much traction in this list, but there is a discussion list for the OBO Foundry may well garner some useful comments.

John


On Jul 19, 2017, at 6:32 AM, Kristian Nicolaisen <Kristian.Nicolaisen at ehealthresearch.no<mailto:Kristian.Nicolaisen at ehealthresearch.no>> wrote:

Hi,

I am currently working on a report on the transition to ontology based terminologies in healthcare in Norway, in that regard I am writing about BFO in general and the OBO Foundry in particular. I have a questions I hope you can help me with:
?         Are there any comparison between SNOMED CT and the OBO ontologies in regards to coverage in biomedical domains?
o   A sort of map to see what domains SNOMED covers and what domains OBO ontologies cover, and where there are overlaps


Sincerely,

Kristian Malm-Nicolaisen
Adviser/Project manager
Norwegian Centre for E-health Research
Tel: +47 950 59 001
www.ehealthresearch.no/en/<x-msg://4/www.ehealthresearch.no/en/>
<image001.jpg>


______________________________________________
Tenk milj? - ikke skriv ut denne om det ikke er absolutt n?dvendig
_______________________________________________
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
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Thu Jul 20 01:04:56 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 20 Jul 2017 01:04:56 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Siddharth
Message-ID: <59706428a91f3_54a3f864965420825439@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Jul 20 10:56:36 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 20 Jul 2017 17:56:36 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Siddharth
In-Reply-To: <59706428a91f3_54a3f864965420825439@ncbo-prd-app-09.stanford.edu.mail>
References: <59706428a91f3_54a3f864965420825439@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <02DAAA83-7EC9-4480-92A0-4091DDB5D887@stanford.edu>

Hello Siddharth,

This issue is now fixed.

Kind regards,
Jennifer


On Jul 20, 2017, at 1:04 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Siddharth

Email: siddharthsingh63 at gmail.com<mailto:siddharthsingh63 at gmail.com>

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

Feedback:

Hi,

The following links are not working since yesterday :

http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=root

http://bioportal.bioontology.org/ajax/classes/treeview?ontology=MEDDRA&conceptid=root

The error message received for both is "We're sorry but something has gone wrong. We have been notified of this error."

Regards,
Siddharth

_______________________________________________
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 siddharthsingh63 at gmail.com  Thu Jul 20 11:09:51 2017
From: siddharthsingh63 at gmail.com (Siddharth Singh)
Date: Thu, 20 Jul 2017 23:39:51 +0530
Subject: [bioontology-support] [BioPortal] Feedback from Siddharth
In-Reply-To: <02DAAA83-7EC9-4480-92A0-4091DDB5D887@stanford.edu>
References: <59706428a91f3_54a3f864965420825439@ncbo-prd-app-09.stanford.edu.mail>
 <02DAAA83-7EC9-4480-92A0-4091DDB5D887@stanford.edu>
Message-ID: <CA+dvypGB-EuELcK1gZ1n1CWNxXtwj2k7kszpoRm4uvCtsaJPow@mail.gmail.com>

Great, thanks!

On 20-Jul-2017 23:26, "Jennifer Leigh Vendetti" <vendetti at stanford.edu>
wrote:

> Hello Siddharth,
>
> This issue is now fixed.
>
> Kind regards,
> Jennifer
>
>
> On Jul 20, 2017, at 1:04 AM, support at bioontology.org wrote:
>
> Name: Siddharth
>
> Email: siddharthsingh63 at gmail.com
>
> Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA
>
>
> *Feedback:*
>
> Hi,
>
> The following links are not working since yesterday :
>
> http://bioportal.bioontology.org/ontologies/MEDDRA?p=
> classes&conceptid=root
>
> http://bioportal.bioontology.org/ajax/classes/treeview?
> ontology=MEDDRA&conceptid=root
>
> The error message received for both is "We're sorry but something has gone
> wrong. We have been notified of this error."
>
> Regards,
> Siddharth
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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From support at bioontology.org  Fri Jul 21 08:22:34 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 21 Jul 2017 08:22:34 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Katy Wolstencroft
Message-ID: <59721c3a26083_a223fceebce6b30147f4@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Jul 21 11:11:33 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 21 Jul 2017 18:11:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Katy
	Wolstencroft
In-Reply-To: <59721c3a26083_a223fceebce6b30147f4@ncbo-prd-app-08.stanford.edu.mail>
References: <59721c3a26083_a223fceebce6b30147f4@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <1775E40F-D037-4445-A919-BBCF1BCE0029@stanford.edu>

Hello Katy,


On Jul 21, 2017, at 8:22 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Katy Wolstencroft

Email: k.j.wolstencroft at liacs.leidenuniv.nl<mailto:k.j.wolstencroft at liacs.leidenuniv.nl>

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

Feedback:

I uploaded an ontology to bioportal when I worked in another institute. I would like to release a new version and upload it to bioportal, but I can no longer access my old account. My email address has changed, so I can't request a new password.

The ontology I uploaded previously is this one:
https://bioportal.bioontology.org/ontologies/JERM

I was previously at the University of Manchester, but now I am working in Leiden. I am still associated with the SEEK project, which created the ontology. We would like to update this as a matter of urgency now.



I modified your account object in our system to use your new email address of k.j.wolstencroft at liacs.leidenuniv.nl<http://liacs.leidenuniv.nl>. You should be able to enter your account name (kwolstencroft) and email address in the form below on our site to reset your password:

http://bioportal.bioontology.org/lost_pass

Let me know if you experience any issues.

Kind regards,
Jennifer



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From jonquet at lirmm.fr  Fri Jul 21 12:39:38 2017
From: jonquet at lirmm.fr (jonquet)
Date: Fri, 21 Jul 2017 21:39:38 +0200
Subject: [bioontology-support]
	[rda-agrdatainterop-ig][vocabulary_services][rda-agrisemantics-wg]
	TR: Postdoc position on AgroPortal,
	GACS and ontology alignment in Montpellier, France
Message-ID: <013e01d30257$ce18abd0$6a4a0370$@lirmm.fr>

Hello all, 

Just a quick email to ask you to share the postdoc offer we have in
Montpellier to work on AgriSemantics related stuff : AgroPortal, ontology
mapping and GACS !

It still open. A candidate from this community will be perfect!

 

Bye 

Happy summer.

Clement

-----------------------------------------------------------

The NUMEV Labex (http://www.lirmm.fr/numev) and AgroPortal project (
<http://agroportal.lirmm.fr> http://agroportal.lirmm.fr) which builds an
ontology repository for agronomy are offering a 1-year postdoc position for
2017-2018 in Montpellier, to work on agronomical ontologies and their
alignments as well as take part in the international GACS initiative
(http://www.agrisemantics.org/gacs/). 

 

Abstract: 

Standards vocabularies and ontologies are key elements to achieve data
interoperability. The AgroPortal project (http://agroportal.lirmm.fr)
develops and supports a reference ontology repository for agronomy, plant
sciences, biodiversity and nutrition. We have already designed and
implemented an advanced prototype offering ontology-based services that
hosts 64 ontologies or vocabularies including some reference resources in
the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. One of the
challenges when dealing with multiple ontologies is to determine their
overlap and align them.

We are offering a postdoc position to develop ontology mapping capabilities
to align AgroPortal ontologies and participate into the international Global
Agricultural Concept Scheme (GACS) project. With the experience and
technology developed with the YAM++ application (LIRMM's ontology alignment
matcher), we will make AgroPortal a state-of-the-art platform for mapping
extraction, generation, validation, evaluation, storage and retrieval by
adopting a complete semantic web and linked open data approach and engaging
the community for curation. We will first focus on the ontologies of the
Montpellier community (agronomy, food, biodiversity) and then join the GACS
project (integration of Agrovoc, NALt & CABt) in partnership with RDA
AgriSemantics working group.

 

More detail here: 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.pdf 

or 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.html 

 

Please, consider transferring  the job description in your labs and
networks.

 

Best regards

Clement 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

 

 



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From jonquet at lirmm.fr  Fri Jul 21 12:40:04 2017
From: jonquet at lirmm.fr (jonquet)
Date: Fri, 21 Jul 2017 21:40:04 +0200
Subject: [bioontology-support]
	[rda-agrdatainterop-ig][vocabulary_services][rda-agrisemantics-wg]
	TR: Postdoc position on AgroPortal,
	GACS and ontology alignment in Montpellier, France
Message-ID: <013e01d30257$ce18abd0$6a4a0370$@lirmm.fr>

Hello all, 

Just a quick email to ask you to share the postdoc offer we have in
Montpellier to work on AgriSemantics related stuff : AgroPortal, ontology
mapping and GACS !

It still open. A candidate from this community will be perfect!

 

Bye 

Happy summer.

Clement

-----------------------------------------------------------

The NUMEV Labex (http://www.lirmm.fr/numev) and AgroPortal project (
<http://agroportal.lirmm.fr> http://agroportal.lirmm.fr) which builds an
ontology repository for agronomy are offering a 1-year postdoc position for
2017-2018 in Montpellier, to work on agronomical ontologies and their
alignments as well as take part in the international GACS initiative
(http://www.agrisemantics.org/gacs/). 

 

Abstract: 

Standards vocabularies and ontologies are key elements to achieve data
interoperability. The AgroPortal project (http://agroportal.lirmm.fr)
develops and supports a reference ontology repository for agronomy, plant
sciences, biodiversity and nutrition. We have already designed and
implemented an advanced prototype offering ontology-based services that
hosts 64 ontologies or vocabularies including some reference resources in
the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. One of the
challenges when dealing with multiple ontologies is to determine their
overlap and align them.

We are offering a postdoc position to develop ontology mapping capabilities
to align AgroPortal ontologies and participate into the international Global
Agricultural Concept Scheme (GACS) project. With the experience and
technology developed with the YAM++ application (LIRMM's ontology alignment
matcher), we will make AgroPortal a state-of-the-art platform for mapping
extraction, generation, validation, evaluation, storage and retrieval by
adopting a complete semantic web and linked open data approach and engaging
the community for curation. We will first focus on the ontologies of the
Montpellier community (agronomy, food, biodiversity) and then join the GACS
project (integration of Agrovoc, NALt & CABt) in partnership with RDA
AgriSemantics working group.

 

More detail here: 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.pdf 

or 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.html 

 

Please, consider transferring  the job description in your labs and
networks.

 

Best regards

Clement 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

 

 



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From jonquet at lirmm.fr  Fri Jul 21 12:30:23 2017
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Fri, 21 Jul 2017 12:30:23 -0700
Subject: [bioontology-support] TR: Postdoc position on AgroPortal,
	GACS and ontology alignment in Montpellier, France
Message-ID: <013e01d30257$ce18abd0$6a4a0370$@lirmm.fr>

Hello all, 

Just a quick email to ask you to share the postdoc offer we have in
Montpellier to work on AgriSemantics related stuff : AgroPortal, ontology
mapping and GACS !

It still open. A candidate from this community will be perfect!

 

Bye 

Happy summer.

Clement

-----------------------------------------------------------

The NUMEV Labex (http://www.lirmm.fr/numev) and AgroPortal project (
<http://agroportal.lirmm.fr> http://agroportal.lirmm.fr) which builds an
ontology repository for agronomy are offering a 1-year postdoc position for
2017-2018 in Montpellier, to work on agronomical ontologies and their
alignments as well as take part in the international GACS initiative
(http://www.agrisemantics.org/gacs/). 

 

Abstract: 

Standards vocabularies and ontologies are key elements to achieve data
interoperability. The AgroPortal project (http://agroportal.lirmm.fr)
develops and supports a reference ontology repository for agronomy, plant
sciences, biodiversity and nutrition. We have already designed and
implemented an advanced prototype offering ontology-based services that
hosts 64 ontologies or vocabularies including some reference resources in
the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. One of the
challenges when dealing with multiple ontologies is to determine their
overlap and align them.

We are offering a postdoc position to develop ontology mapping capabilities
to align AgroPortal ontologies and participate into the international Global
Agricultural Concept Scheme (GACS) project. With the experience and
technology developed with the YAM++ application (LIRMM's ontology alignment
matcher), we will make AgroPortal a state-of-the-art platform for mapping
extraction, generation, validation, evaluation, storage and retrieval by
adopting a complete semantic web and linked open data approach and engaging
the community for curation. We will first focus on the ontologies of the
Montpellier community (agronomy, food, biodiversity) and then join the GACS
project (integration of Agrovoc, NALt & CABt) in partnership with RDA
AgriSemantics working group.

 

More detail here: 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.pdf 

or 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.html 

 

Please, consider transferring  the job description in your labs and
networks.

 

Best regards

Clement 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

 

 

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From jonquet at lirmm.fr  Fri Jul 21 12:39:54 2017
From: jonquet at lirmm.fr (jonquet)
Date: Fri, 21 Jul 2017 21:39:54 +0200
Subject: [bioontology-support]
	[rda-agrdatainterop-ig][vocabulary_services][rda-agrisemantics-wg]
	TR: Postdoc position on AgroPortal,
	GACS and ontology alignment in Montpellier, France
Message-ID: <013e01d30257$ce18abd0$6a4a0370$@lirmm.fr>

Hello all, 

Just a quick email to ask you to share the postdoc offer we have in
Montpellier to work on AgriSemantics related stuff : AgroPortal, ontology
mapping and GACS !

It still open. A candidate from this community will be perfect!

 

Bye 

Happy summer.

Clement

-----------------------------------------------------------

The NUMEV Labex (http://www.lirmm.fr/numev) and AgroPortal project (
<http://agroportal.lirmm.fr> http://agroportal.lirmm.fr) which builds an
ontology repository for agronomy are offering a 1-year postdoc position for
2017-2018 in Montpellier, to work on agronomical ontologies and their
alignments as well as take part in the international GACS initiative
(http://www.agrisemantics.org/gacs/). 

 

Abstract: 

Standards vocabularies and ontologies are key elements to achieve data
interoperability. The AgroPortal project (http://agroportal.lirmm.fr)
develops and supports a reference ontology repository for agronomy, plant
sciences, biodiversity and nutrition. We have already designed and
implemented an advanced prototype offering ontology-based services that
hosts 64 ontologies or vocabularies including some reference resources in
the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. One of the
challenges when dealing with multiple ontologies is to determine their
overlap and align them.

We are offering a postdoc position to develop ontology mapping capabilities
to align AgroPortal ontologies and participate into the international Global
Agricultural Concept Scheme (GACS) project. With the experience and
technology developed with the YAM++ application (LIRMM's ontology alignment
matcher), we will make AgroPortal a state-of-the-art platform for mapping
extraction, generation, validation, evaluation, storage and retrieval by
adopting a complete semantic web and linked open data approach and engaging
the community for curation. We will first focus on the ontologies of the
Montpellier community (agronomy, food, biodiversity) and then join the GACS
project (integration of Agrovoc, NALt & CABt) in partnership with RDA
AgriSemantics working group.

 

More detail here: 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.pdf 

or 

http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.html 

 

Please, consider transferring  the job description in your labs and
networks.

 

Best regards

Clement 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

 

 



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From support at bioontology.org  Tue Jul 25 14:00:10 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 25 Jul 2017 14:00:10 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Halina Labikova
Message-ID: <5977b15abdd51_58363ff72692b94c936b4@ncbo-prd-app-09.stanford.edu.mail>

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From mdorf at stanford.edu  Wed Jul 26 15:49:04 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 26 Jul 2017 22:49:04 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Halina Labikova
In-Reply-To: <5977b15abdd51_58363ff72692b94c936b4@ncbo-prd-app-09.stanford.edu.mail>
References: <5977b15abdd51_58363ff72692b94c936b4@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <28763B7E-3811-4D6E-85CA-50188ECB81E2@stanford.edu>

Hi Halina,

Thank you for getting in touch. We import NCI Thesaurus from the NIH/NCI repository, located here:

ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NCI_Thesaurus/Thesaurus.owl

Unfortunately, we don?t have any control over the content of the ontology. If you think there?s a discrepancy that needs the authors? attention, you try contacting them directly.

 https://ncit.nci.nih.gov/ncitbrowser/

Thanks!

Michael


On Jul 25, 2017, at 2:00 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Halina Labikova

Email: halina.labikova at evinance.com<mailto:halina.labikova at evinance.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FNCIT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fncicb.nci.nih.gov<http://252Fncicb.nci.nih.gov>%252Fxml%252Fowl%252FEVS%252FThesaurus.owl%2523C35607

Feedback:

Hello,

There is one ontology that is present twice, under two separate codes:

C35607 - Blood Alkaline Phosphatase Increased
A laboratory test result which indicates an increased level of alkaline phosphatase in a biological specimen.

https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C35607#

C122821 - Elevated Alkaline Phosphatase
An elevated concentration of alkaline phosphatase in the blood.

https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C122821

Regards,
Halina

_______________________________________________
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 marc.hanauer at inserm.fr  Thu Jul 27 08:49:40 2017
From: marc.hanauer at inserm.fr (Marc Hanauer)
Date: Thu, 27 Jul 2017 17:49:40 +0200
Subject: [bioontology-support] [ORDO] bioportal issue
In-Reply-To: <F31F839C-3C5F-4D95-A076-995C715C00C1@stanford.edu>
References: <53721CEC.4010600@inserm.fr>
 <FD57126C-D6A4-43C4-8A40-BE90D25C427E@ebi.ac.uk> <56CDC203.5070001@inserm.fr>
 <848E2F34-E02F-4DA3-987D-7A836EBB874B@stanford.edu>
 <a65bae35-cc90-acf2-fc42-67be75ab4b45@inserm.fr>
 <876518B6-C6F6-465C-A1B2-AB055368F899@stanford.edu>
 <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu>
 <da951031c667608b44c3a714f3e009e9@inserm.fr>
 <AC3E54C3-B15F-4A31-9281-80C5E8CCC6D2@stanford.edu>
 <F31F839C-3C5F-4D95-A076-995C715C00C1@stanford.edu>
Message-ID: <426ea122-5b25-8056-63c5-4747701190cd@inserm.fr>

Hello Jennifer,

The structure was exactly the same in ORDO V2.3 (especially for this 
exemple of annotation embeded).

The OWL file is code generated and then checked with Protegee. We have 
try to reproduce your issue using OWL API but we never succeed to have 
this kind of axiom.

Please feel free to contact our developper Samuel Demarest (in cc) who's 
in charge of the generating code if you have any other question. I'll be 
back in september.

Best regards,

www.orpha.net <https://www.orpha.net> | Twitter @Orphanet 
<https://twitter.com/Orphanet>
*Marc HANAUER*
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE
Le 14/07/2017 ? 18:41, Jennifer Leigh Vendetti a ?crit :
> Hello Marc,
>
> I don?t have a  solution yet for parsing ORDO 2.4 in BioPortal, but 
> I?ll provide a summary below of what I?ve discovered so far.
>
> The system is having difficulty handling classes in your ontology that 
> have annotations nested 3 levels deep. Here?s a screenshot of your 
> ontology in the Protege ontology editor with class ?48,XXYY syndrome? 
> highlighted:
>
>
>
>
> Note the second occurrence of hasDbXref in the screenshot where 
> there?s an annotation on an annotation on an annotation.
>
> I think I mentioned in a previous correspondence that we use the OWL 
> API internally for parsing. When the OWL API loads this ontology, it 
> inserts a blank node for these nested annotations with a blank node 
> identifier in the form of ?_:genid?. Using the example in the screen 
> shot above, this is a snippet of the ontology source, as loaded by the 
> OWL API:
>
> <Annotation>
>   <annotatedSource>
>     <Axiom *rdf:nodeID="_:genid25"*>
>       <annotatedSource 
> rdf:resource="http://www.orpha.net/ORDO/Orphanet_10"/>
>       <annotatedProperty 
> rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
>       <annotatedTarget 
> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD-10:Q98.8</annotatedTarget>
>       <obo1:ECO_0000218 
> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Attributed</obo1:ECO_0000218>
>     </Axiom>
>   </annotatedSource>
>   <annotatedProperty 
> rdf:resource="http://purl.obolibrary.org/obo/ECO_0000218"/>
>   <annotatedTarget 
> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Attributed</annotatedTarget>
>   <obo1:ECO_0000218 
> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NTBT (narrower 
> term maps to a broader term)</obo1:ECO_0000218>
> </Annotation>
>
> Although we can load the ontology without errors, the second step in 
> the parsing process fails when we attempt to serialize the data to 
> ntriples format to load it into our RDF store:
>
> /Illegal rdf:nodeID value '_:genid25' rapper: Failed to parse file/
>
> I went looking for a specification for what is considered valid syntax 
> for blank node identifiers, but so far I haven?t been able to find 
> anything. It?s unclear to me if the OWL API is generating invalid RDF, 
> or if the Raptor RDF parser isn?t handling blank nodes that it should 
> be. I will likely need to correspond with the developers of one or 
> both projects.
>
> Apologies that it hasn?t been straightforward so far to track this down.
>
> On another note, I?m wondering if you could give me some basic 
> information about how your OWL file is generated. Is it done 
> programmatically? Or, do you use an ontology editing environment to 
> maintain the ontology?
>
> Kind regards,
> Jennifer
>
>
>
>> On Jul 10, 2017, at 6:26 PM, Jennifer Leigh Vendetti 
>> <vendetti at stanford.edu <mailto:vendetti at stanford.edu>> wrote:
>>
>> Hello Marc,
>>
>> I?ve entered an issue in our tracker [1], and will have a look.
>>
>> Kind regards,
>> Jennifer
>>
>> [1] https://github.com/ncbo/bioportal-project/issues/31
>>
>>
>>> On Jul 10, 2017, at 2:11 PM, marc.hanauer at inserm.fr 
>>> <mailto:marc.hanauer at inserm.fr> wrote:
>>>
>>> Hello Jennifer,
>>>
>>> Sorry about that, but once again the new version of ORDO (2.4) seems 
>>> to have issues : 2.3 (Uploaded, Error Rdf)     07/05/2017  07/05/2017
>>> https://bioportal.bioontology.org/ontologies/ORDO
>>>
>>> This version was produced the same way than the previous one.
>>>
>>> Any ideas ?
>>>
>>> Best regards,
>>>
>>> ---
>>>
>>>
>>> Marc HANAUER
>>> Directeur Adjoint / Deputy Director
>>> Directeur technique / Chief technology officer
>>> Strat?gie et Innovation
>>> marc.hanauer at inserm.fr <mailto:marc.hanauer at inserm.fr>
>>>
>>> ORPHANET - INSERM US14
>>> Plateforme Maladies Rares / Rare Disease Platform
>>> 96 rue Didot
>>> 75014 PARIS
>>> FRANCE
>>>
>>>
>>> Le 11-08-2016 19:22, Jennifer Leigh Vendetti a ?crit :
>>>
>>>> Hello Marc,
>>>> We've addressed the issue I mentioned below.  Version 2.2 of ORDO 
>>>> is parsed and available in BioPortal:
>>>> http://bioportal.bioontology.org/ontologies/ORDO
>>>> Apologies again that this one took us some time to address.
>>>> Best,
>>>> Jennifer
>>>>> On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti 
>>>>> <vendetti at stanford.edu <mailto:vendetti at stanford.edu>> wrote:
>>>>>
>>>>> Hi Marc,
>>>>> I am writing with a status report regarding BioPortal's failure to 
>>>>> handle ORDO 2.2.
>>>>> As you may already know, BioPortal uses the OWL API [1] internally 
>>>>> for ontology parsing.  I wrote some Java code, independent of the 
>>>>> BioPortal application, to make sure the OWL API handles your 
>>>>> ontology properly.  The parsing succeeds, which indicates to me 
>>>>> that your ontology file is valid.  When the OWL API parses your 
>>>>> ontology file, it emits a very large number of "unparsed triple" 
>>>>> messages (roughly 15.5K of them), e.g.:
>>>>> [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> 
>>>>> http://www.w3.org/2002/07/owl#annotatedProperty -> 
>>>>> http://purl.obolibrary.org/obo/ECO_0000218
>>>>> [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> 
>>>>> http://www.w3.org/2002/07/owl#annotatedSource -> _:genid120261
>>>>> The size of the output from the OWL API is causing a buffer 
>>>>> overflow / deadlock in BioPortal's source code.  I am currently 
>>>>> working toward fixing the issue, and hope to have something 
>>>>> available soon.
>>>>> Apologies that this one is taking some time for us to track down / 
>>>>> fix.
>>>>> Best,
>>>>> Jennifer
>>>>> [1] http://owlcs.github.io/owlapi/
>>>>>
>>>>>> On Jun 27, 2016, at 3:18 AM, Marc Hanauer <marc.hanauer at inserm.fr 
>>>>>> <mailto:marc.hanauer at inserm.fr>> wrote:
>>>>>>
>>>>>> Hello Jennifer,
>>>>>>
>>>>>> I've made an update of our ontology (ORDO) last week as usual by 
>>>>>> putting the file on our own server. This time, the bioportal 
>>>>>> website seems to try the upload but with error.
>>>>>>
>>>>>> The version in our own server is now "2.2" but it appears with 
>>>>>> this line on bioportal:
>>>>>>
>>>>>> 2.1 (Uploaded, Error Rdf) 	06/22/2016 	06/22/2016 	OWL 
>>>>>> <http://data.bioontology.org/ontologies/ORDO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb> 
>>>>>> | Diff 
>>>>>> <http://data.bioontology.org/ontologies/ORDO/submissions/9/download_diff?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb> 
>>>>>>
>>>>>>
>>>>>> *
>>>>>> *Any idea ?
>>>>>>
>>>>>> Best regards,
>>>>>> *
>>>>>> Marc HANAUER*
>>>>>> Directeur Adjoint / Deputy Director
>>>>>> Directeur technique / Chief technology officer
>>>>>> Strat?gie et Innovation
>>>>>> marc.hanauer at inserm.fr
>>>>>>
>>>>>> ORPHANET - INSERM US14
>>>>>> Plateforme Maladies Rares / Rare Disease Platform
>>>>>> 96 rue Didot
>>>>>> 75014 PARIS
>>>>>> FRANCE
>>>>>> Le 25/02/2016 ? 00:41, Jennifer Leigh Vendetti a ?crit :
>>>>>>> Hello Marc,
>>>>>>>
>>>>>>>> On Feb 24, 2016, at 6:45 AM, Marc Hanauer 
>>>>>>>> <marc.hanauer at inserm.fr> wrote:
>>>>>>>>
>>>>>>>> Dear support,
>>>>>>>> We manage the ORDO (Orphanet Rare Disease Ontology) and we have 
>>>>>>>> made an update recently (2 days ago).
>>>>>>>> Usually (for the previous version), we just update the file on 
>>>>>>>> our own server (keeping the same URL : 
>>>>>>>> http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ) and then 
>>>>>>>> the bioportal website automatically upload it.
>>>>>>>>
>>>>>>>> It seems this is not the case anymore (the version in bioportal 
>>>>>>>> remain v2.0 instead of the new 2.1)
>>>>>>>>
>>>>>>>> Do we need to perform any manual action in order to update it 
>>>>>>>> on bioportal ?
>>>>>>> You don't need to do anything manual.  We were having some 
>>>>>>> performance issues with our site and temporarily disabled the 
>>>>>>> cron jobs in our production environment that pull new versions 
>>>>>>> of ontologies.  The cron job has been reenabled today, so the 
>>>>>>> new version of your ontology should be pulled and processed 
>>>>>>> overnight.
>>>>>>>
>>>>>>>>
>>>>>>>> By the way, with our account, we still have trouble accessing 
>>>>>>>> the bioportal interface (when we sign in and try to reach the 
>>>>>>>> ORDO page, we obtain an error message which is not the case 
>>>>>>>> without login...) (see my previous msg below about this)
>>>>>>> Sorry you're having difficulties.  I tried reproducing this 
>>>>>>> behavior here and so far haven't had any luck.  I've viewed your 
>>>>>>> ontology in BioPortal, both when logged in and logged out 
>>>>>>> (screen shot below).  I also verified that your user account of 
>>>>>>> "ORDO_Orphanet" is valid, and I don't see any issues there.  Are 
>>>>>>> you still seeing this behavior?
>>>>>>> Jennifer
>>>>>>> <Mail Attachment.png>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu 
>>>>> <mailto:bioontology-support at lists.stanford.edu>
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>

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From support at bioontology.org  Fri Jul 28 00:50:26 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 28 Jul 2017 00:50:26 -0700
Subject: [bioontology-support] [BioPortal] Feedback from onkar singh
Message-ID: <597aecc2a15f6_51933fdde689253437757@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Mon Jul 31 05:54:19 2017
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 31 Jul 2017 05:54:19 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Marvin Martens
Message-ID: <597f287b613ed_7eb43f9427c87044502ce@ncbo-prd-app-09.stanford.edu.mail>

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From terry.chamberlin at genelux.com  Mon Jul 31 11:46:45 2017
From: terry.chamberlin at genelux.com (Terry Chamberlin)
Date: Mon, 31 Jul 2017 18:46:45 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Marvin Martens
In-Reply-To: <597f287b613ed_7eb43f9427c87044502ce@ncbo-prd-app-09.stanford.edu.mail>
References: <597f287b613ed_7eb43f9427c87044502ce@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <CY1PR11MB084159AAB4D16E0D8B6E0CE282B20@CY1PR11MB0841.namprd11.prod.outlook.com>

Would you please unsubscribe my email address from these notifications:

terry.chamberlin at genelux.com<mailto:terry.chamberlin at genelux.com>

Thank You, Terry

-------------------------------------------------
Ms. Terry A. Chamberlin, CCRA
Director, Clinical Trial Operations
Genelux Corporation
Ph: +1.858.210.6808
Fax: +1.858.483.0025
Email: terry.chamberlin at genelux.com

From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of support at bioontology.org
Sent: Monday, July 31, 2017 5:54 AM
To: support at bioontology.org; marvin.martens at maastrichtuniversity.nl
Subject: [bioontology-support] [BioPortal] Feedback from Marvin Martens


Name: Marvin Martens

Email: marvin.martens at maastrichtuniversity.nl<mailto:marvin.martens at maastrichtuniversity.nl>

Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPW%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPW_0000001

Feedback:

Dear BioPortal group,
I am working on pathways on WikiPathways, which uses your Pathway ontology. However, I work on a type of pathways that is not in there, and is different: Adverse Outcome Pathways. They are pathways that cover multiple cell types, multiple processes, and often multiple biological levels. I think it would be a great addition if we could work on an ontology for this kind of patway, as it is a growing concept and soon many more of these pathways will be made in wikipathways. Could you tell me what is the best thing to do? What are the possibilities?
Kind regards,
Marvin
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From c.chung at med.miami.edu  Mon Jul 31 10:43:46 2017
From: c.chung at med.miami.edu (Chung, Caty Elizabeth)
Date: Mon, 31 Jul 2017 17:43:46 +0000
Subject: [bioontology-support] BioPortal:  DTO
Message-ID: <DM5PR07MB3516C372C3285918883BCA13B9B20@DM5PR07MB3516.namprd07.prod.outlook.com>

Hello,


On the BioPortal site, we changed from private to public and release the Ontology, it has been parsing since 07/20/2017


Can you guide us to the issue, why it does not finish the parsing, indexing, metrics and annotation for:

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


Caty
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