a small
team of researchers. One main aspect will be the development, and support as
well as the integration of new features inside our local instances of
BioPortal: http://bioportal.lirmm.fr and http://agroportal.lirmm.fr
More detailed here:
http://www.lirmm.fr/sifr/positions
We are happy to announce the release of BioPortal 4.20. We have had a number of
"silent releases" since the last announced 4.14 release in February 2015. These
releases concentrated almost exclusively on infrastructure improvements and
thus most of these improvements are not direct
/program.html#schedule.
Registration is open at http://icbo2015.fc.ul.pt/registration.html.
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opean Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: + 44 (0) 1223 494 676
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May 18th: http://icbo2015.fc.ul.pt/callposters.html
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he subject line.
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We are happy to announce the release of BioPortal 4.14. We have had a
number of "silent releases" since the last announced 4.10 release in
September 2014. We are pleased to announce the latest BioPortal release
and fill you in on features that have been released silently in the
int
The Protege Team
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envisioned the NCBC
program as a 10-year initiative to create national infrastructure for
biomedical computing. Alas, the 10 years of funding that have allowed us to
create tools such as BioPortal, the NCBO Annotator, the NCBO Resource Index,
and many other widely used technologies will be
tenance and
integration of new services inside our local instance of BioPortal.
More detailed here: http://bit.ly/1rAo4EV
Regards,
---
Dr. Clement JONQUET - PhD in
e our local instance of BioPortal.
More detailed here: http://bit.ly/1rAo4EV
Regards,
---
Dr. Clement JONQUET - PhD in Informatics - Assistant Professor
PI of
e our local instance of BioPortal.
More detailed here: http://bit.ly/1rAo4EV
Regards,
---
Dr. Clement JONQUET - PhD in Informatics - Assistant Professor
PI of
We are happy to announce the release of BioPortal 4.10. We have had a
number of "silent releases" since the 4.6 release in late April. We are
pleased to announce the latest BioPortal release and fill you in on
features that have been released silently in the interim:
. Reengi
mas Timpka, Linköping University, Sweden
- Kai Xu, Middlesex University, UK
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f the Scientific Program Committee.
Sponsorship
We offer a variety of sponsorship options. Interested parties are invited to
contact the organizers at <mailto:i...@swat4ls.org> i...@swat4ls.org .
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rson, copied on this message.
Thanks for your time and for helping us to serve the community better.
Mark Musen
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and for helping us to serve the community better.
Mark___
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contact the organizers at i...@swat4ls.org .
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tute, Cambridge, UK)
Alexis Nasr (Aix Marseille Université, France)
Richard Power (The Open University, UK)
Allan Third (The Open University, UK)
SUPPORTED BY
The Swiss National Science Foundation (SNSF)
The State University of New York at Buffalo
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biopo
/jobdetail.ftl?job=62946
(Senior Research Software Developer)
Successful candidates will be working in a close collaboration with the
Protégé team members.
Best regards,
The Protégé Team
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We are happy to announce the release of BioPortal 4.6. We have had a
number of "silent releases" since the 4.0 release last September. These
releases were concentrated mainly on performance and stability issues for
the new system and included only a few user-visible changes. We are
Workshop>
..
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schedule and logistics details are available
here<http://ncorwiki.buffalo.edu/index.php/Ontology_and_Imaging_Informatics>
..
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On 9/25/13 10:49 PM, Ray Fergerson wrote:
We are very happy to finally announce, after a year of planning and
development work, the release of the reengineering of BioPortal.
Because this is a huge change we care labeling this release BioPortal 4.0.
The primary distinguishing feature of
We are very happy to finally announce, after a year of planning and
development work, the release of the reengineering of BioPortal. Because
this is a huge change we care labeling this release BioPortal 4.0.
The primary distinguishing feature of this release is the replacement of
several
NCBO BioPortal Users,
We are replacing the backend of BioPortal with an RDF Triple-store based
system. To facilitate this conversion, we will disable ontology
submissions and updates starting tomorrow, September 17, 2013. We expect
that submissions and updates will be enabled again by the end
contact: icbo2...@gmail.com
>
> Organizing Committee
> Co-Scientific Chair: Michel Dumontier
> Co-Scientific Chair: Christopher Baker
> Local Organizer: Gregory Butler
> Programme Chair: Robert Hoehndorf
> Workshop and Tutorial Chair: Chris Mungall
> Poster and Demonstration Chair: Trish Whetzel
> Proceedings and Special Issue Chair: Janna Hastings
> Early Career Chair: Melissa Haendel
> Sponsorship and Publicity Chair: Sivaram Arabandi
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...@manchester.ac.uk, University of Manchester
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We are happy to announce the release of BioPortal 3.12.
Our development team remains primarily focused on replacing the BioPortal
backend infrastructure with an RDF triple store and revising the BioPortal
API. Little of this infrastructure work is visible yet but it will become
more so in the
itter.com/#!/bioontology
Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
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FYI
Original Message
Subject:[bioportal-announce] NCBO Spring Developer Events
Date: Wed, 30 Jan 2013 10:59:24 -0800
From: Trish Whetzel
To: NCBO User Support ,
annou...@bioontology.org, ncbo-publicta...@mailman.stanford.edu
The National Center for
to answer development questions.
We will also have separate sessions to provide training on the NCBO Web
services, the BioPortal SPARQL endpoint, and other topics of interest requested
by participants. If you are thinking of incorporating semantics into your
software application, the Hackathon
We are pleased to announce the release of BioPortal 3.11. The major
changes in this release are:
. We have made significant improvements to the performance of the
UI, specifically on displaying terms. You should see many fewer timeouts
and "Bioportal Error" pages.
.
The next NCBO Webinar will be presented by Tania Tudorache and Matthew
Horridge from Stanford University on "Editing and Publishing OWL 2 and OBO
ontologies with WebProtégé and BioPortal" at 10:00am PDT, Wednesday, Oct.
10. Below is information on how to join the online meeting via
We are pleased to announce the release of BioPortal 3.10. The major changes in
this release are:
Revised UI for the Resource Index. This new UI supports the BioPortal slice
mechanism. The new UI is also much faster than the previous one.
Updated ontologies available for use with the Annotator
-- Forwarded message --
From: Trish Whetzel
Date: Wed, Jun 20, 2012 at 2:43 AM
Subject: [bioportal-announce] BioPortal 3.9 Released
To: annou...@bioontology.org
We are pleased to announce the release of BioPortal 3.9. The major new
features in this release are:
· We
We are pleased to announce the release of BioPortal 3.9. The major new features
in this release are:
· We have revised the search interface, both for specifying a search
and in the format of the returned results. The new “advanced search” capability
allows users to specify more
-- Forwarded message --
From: Trish Whetzel
Date: Tue, May 22, 2012 at 12:18 AM
Subject: [bioportal-announce] BioPortal 3.8 Released
To: annou...@bioontology.org
We are pleased to announce the release of BioPortal 3.8. The major new
feature in this release is the regeneration of
We are pleased to announce the release of BioPortal 3.8. The major new feature
in this release is the regeneration of various automated mappings:
· We have regenerated all mappings based on UMLS CUIs. Thus terms in
different UMLS ontologies which share the same CUI are now mapped to
ollowing account creation.
Link: http://bioportal.bioontology.org/accounts/new .
Kingsley
On Thu, Apr 12, 2012 at 10:33 PM, Kingsley Idehen
mailto:kide...@openlinksw.com>>wrote:
On 4/10/12 5:06 PM, M. Scott Marshall wrote:
PM, Kingsley Idehen wrote:
> On 4/13/12 4:13 PM, M. Scott Marshall wrote:
>
>> Looks like you found it. For others interested, it can be found as a
>> New Account link on this page:
>> http://www.bioontology.org/**wiki/index.php/SPARQL_**BioPortal<http://www.bioontology.o
.
Link: http://bioportal.bioontology.org/accounts/new .
Kingsley
On Thu, Apr 12, 2012 at 10:33 PM, Kingsley Idehen
wrote:
On 4/10/12 5:06 PM, M. Scott Marshall wrote:
Note that the BioPortal SPARQL endpoint has moved into beta. It has a
(web) user interface, documentation, and example q
Hope that helps,
>> Scott
>
>
> Okay!
>
> Found the API Key following account creation.
>
> Link: http://bioportal.bioontology.org/accounts/new .
>
> Kingsley
>
>>
>> On Thu, Apr 12, 2012 at 10:33 PM, Kingsley Idehen
>> wrote:
>>
ing account creation.
Link: http://bioportal.bioontology.org/accounts/new .
Kingsley
On Thu, Apr 12, 2012 at 10:33 PM, Kingsley Idehen
wrote:
On 4/10/12 5:06 PM, M. Scott Marshall wrote:
Note that the BioPortal SPARQL endpoint has moved into beta. It has a
(web) user interface, documentation,
Just register to get an account on bioportal - the apikey will be listed on
the account details:
http://bioportal.bioontology.org/login
m.
On Fri, Apr 13, 2012 at 2:05 PM, Kingsley Idehen wrote:
> On 4/12/12 6:12 PM, M. Scott Marshall wrote:
>
>> Hi Kingsley,
>>
>&
Key?
Kingsley
Hope that helps,
Scott
On Thu, Apr 12, 2012 at 10:33 PM, Kingsley Idehen
wrote:
On 4/10/12 5:06 PM, M. Scott Marshall wrote:
Note that the BioPortal SPARQL endpoint has moved into beta. It has a
(web) user interface, documentation, and example queries:
http://sparql.bioontology.org/
N
PM, M. Scott Marshall wrote:
>>
>> Note that the BioPortal SPARQL endpoint has moved into beta. It has a
>> (web) user interface, documentation, and example queries:
>>
>> http://sparql.bioontology.org/
>>
>> Nice!
>>
>> -Scott
>
>
> Do
On 4/10/12 5:06 PM, M. Scott Marshall wrote:
Note that the BioPortal SPARQL endpoint has moved into beta. It has a
(web) user interface, documentation, and example queries:
http://sparql.bioontology.org/
Nice!
-Scott
Do I need an API Key to access the SPARQL endpoint?
Please try this
Note that the BioPortal SPARQL endpoint has moved into beta. It has a
(web) user interface, documentation, and example queries:
http://sparql.bioontology.org/
Nice!
-Scott
-- Forwarded message --
From: Ray Fergerson
Date: Tue, Apr 10, 2012 at 10:01 PM
Subject: [bioportal
We are pleased to announce the release of BioPortal 3.7. The major new
features in this release are:
. The term search web service and UI now supports some simple
Boolean logic. The format is backwards compatible with our previous format
so entering "heart attack" still
The next NCBO Webinar will be presented TOMORROW by Rob Wynden from UCSF on
"Health Ontology Mapper(HOM) and extending the reach of BioPortal" at
10:00am Pacific Time, Wednesday, March 7. Below is information on how to
join the online meeting via WebEx and accompanying teleconferenc
-- Forwarded message --
From: Trish Whetzel
Date: Tue, Feb 7, 2012 at 1:05 AM
Subject: [bioportal-announce] NCBO Hackathon - March 26-27 at Stanford
University
To: annou...@bioontology.org, ncbo-publicta...@lists.stanford.edu
NCBO Hackathon
Date: March 26-27, 2012
Location
Center-for-Biomedical-Ontology/127444774011153
Follow NCBO on Twitter: http://twitter.com/#!/bioontology
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We are pleased to announce the release of BioPortal 3.6. This was mostly a
bug-fix release but there was one major new feature:
* Created "alternate entry points" for BioPortal. These URL's limit
the ontologies that are visible in BioPortal, allowing users to focus on a
shar
The National Center for Biomedical Ontology is pleased to announce the release
of BioPortal 3.5. New features include updates to the Web interface and Web
services:
Added ability for logged-in users to filter which ontologies appear in their
BioPortal display
Updated Annotator page to simplify
The National Center for Biomedical Ontology is pleased to announce the release
of BioPortal 3.4. New features include updates to the Web interface and Web
services:
Revised the Term Mappings tab to ease the creation of term-to-term mappings*
Limited access to “Private” ontologies via the Browse
The National Center for Biomedical Ontology is pleased to announce the release
of BioPortal 3.3. New features include updates to the Web interface and Web
services:
Added Get Properties Web service,
http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
Updated Search
://twitter.com/#!/bioontology
and "Like" us on Facebook:
http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
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The National Center for Biomedical Ontology is pleased to announce the release
of BioPortal 3.2. New features include updates to the Web interface and Web
services:
Added Ontology Recommender feature,
http://bioportal.bioontology.org/recommender
Added support for access control for viewing
ttp://www.bioontology.org
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The National Center for Biomedical Ontology is pleased to announce the release
of BioPortal 3.1. New features include updates to the Web interface and Web
services:
Support for loading OWL 2 ontologies
Security Framework, part 2 - The apikey parameter is now required for all Web
services
-- Forwarded message --
From: Cassandra Petrachenko
Date: Tue, Jul 5, 2011 at 11:45 PM
Subject: [bioportal-announce] REMINDER: BioPortal User Survey - closes July 15
To: bioportal-annou...@mailman.stanford.edu
Dear BioPortal User:
Thanks to everyone who has completed our survey
lable only until July
1 and that there are limited places available.
Trish
Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whet...@stanford.edu
http://www.bioontology.org
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This is a reminder that the apikey parameter will be required at the end of
June for all NCBO Web service calls. To obtain your API Key, login to BioPortal
and go to your Account page where your API Key will be displayed. Web service
calls that do not include the apikey parameter and a valid
/dc/elements/1.1/creator. If your ontology uses different
properties for this content, login to BioPortal and use the "Administer" link
for your ontology to update this information. For any questions, email
supp...@bioontology.org.
Best,
Trish
Trish Whetzel, PhD
Outreach Coord
Agenda:
- BioPortal UI Update
- Notes feature
- Annotator Excel Add-in
Below are WebEx details:
---
To start or join the online meeting
---
Go to
https://stanford.webex.com/stanford/j.php
FYI
-- Forwarded message --
From: Trish Whetzel
Date: Thu, May 19, 2011 at 10:25 PM
Subject: [bioportal-announce] BioPortal 3.0 Released
To: annou...@bioontology.org
The National Center for Biomedical Ontology is pleased to announce the
release of BioPortal 3.0. New features
The National Center for Biomedical Ontology is pleased to announce the release
of BioPortal 3.0. New features include updates to the Web interface and Web
services:
Web interface updates
Browse page now displays ontology features, e.g. size of the ontology, number
of notes added to the
; November 15, 2013
http://grants.nih.gov/grants/guide/pa-files/PAR-11-209.html
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rce Index and Bio-Mixer.
>
> Trish
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The National Center for Biomedical Ontology is pleased to announce the
release of *BioPortal 2.5*, a Web-based platform for browsing, visualizing,
mapping, and commenting on biomedical ontologies and terminologies. Our new
release of BioPortal includes many new features, Web services, and bug
Hi Trish,
is it possible to have a local install of the BioPortal?
cheers,
Erick
> The National Center for Biomedical Ontology is pleased to announce the
> release of BioPortal 2.1. Highlights of this release are:
>
> -*Annotator*: a service that identifies mentions of biomedi
The National Center for Biomedical Ontology is pleased to announce the
release of BioPortal 2.1. Highlights of this release are:
-*Annotator*: a service that identifies mentions of biomedical ontology
concepts in text that users submit. You can use the annotator service to tag
automatically any
The National Center for Biomedical Ontology (NCBO) is pleased to
announce the release of BioPortal 2.0 — a Web-based application that
serves as a “one-stop shop” for accessing and sharing biomedical
ontologies. Users can browse and explore individual ontologies by
navigating either a tree
Dear HCLS interest group members,
The NCBO BioPortal Prototype is now available to the community for
testing and feedback (http://alpha.bioontology.org). This prototype
is still in its alpha stages so there will be errors, but any data you
put in will be preserved (based on a daily backup
SNOMED into
BioPortal and creating URIs for all terms in all terminologies/
ontologies. Those URIs will also probably contain the version info
for the terminology so that new terminology releases do not
invalidate older URIs. Would that work from everyone's perspective,
or are there
Hello everyone,
I response to comments from this community on the Terms of Use for
our BioPortal for accessing biomedical ontologies, we have revised
the language. Please see: http://bioontology.org/terms.html
Let us know if you have any other feedback or requirements for BioPortal.
Thanks
public to
contribute). In addition, people can add other types of requirements
other than URI if they would to see other functionality in
BioPortal.
Thanks
Daniel
At 07:55 AM 1/17/2007, Kashyap, Vipul wrote:
Daniel,
Thanks for the news. ICD and SNOMED are the two biggies used in
healthcare and th
MAIL PROTECTED] On Behalf Of Daniel Rubin
Sent: Wednesday, January 17, 2007 10:26 AM
To: [EMAIL PROTECTED]
Cc: w3c semweb hcls; [EMAIL PROTECTED]
Subject: Re: Answers to questions about BioPortal
We will be adding terminologies such as ICD and SNOMED into BioPortal and
creating URIs fo
We will be adding terminologies such as ICD and SNOMED into BioPortal and
creating URIs for all terms in all terminologies/ontologies. Those URIs
will also probably contain the version info for the terminology so that
new terminology releases do not invalidate older URIs. Would that work
from
aniel Rubin <[EMAIL PROTECTED]>
11/01/2007 04:43
To
Dirk Colaert/AMIPU/[EMAIL PROTECTED]
cc
"w3c semweb hcls" ,
[EMAIL PROTECTED]
Subject
Re: Answers to questions about BioPortal
This is a very good.point; permanent URIs is a reasonable requirement we
will aim to prov
> I too, am not clear about the use case for instance versioning? So if
> "Tom"
> is an instance of the class "Person", what does it mean to have multiple
> versions of Tom? Maybe there are some use cases that make sense in the
> lifesciences context?
>
> ---Vipul
Have an example for this one: If
I think this is a very important thread of discussion and we should probably
discuss this at some length.
Even before we discuss implementation mechanisms, we need to understand this
issue at the level of functional requirements. Some issues that arise are:
1. Everytime a new version of a conce
to Dirk's original point below, this is a requirement for OBO Foundry
ontologies - "the original URI should still point to the old term or concept,
even if it is deprecated" - though I take it not all BioPortal ontologies
will follow the OBO Foundry guidelines.
There's also b
Are we talking about versioning at a very high granularity level (e.g., a URI
that points to an entire ontology)? Should we also consider versioning at
finer granularity levels such as the levels of concepts or terms and their
relationships within an ontology? Some of these concepts, terms and
William Bug wrote:
Here, here.
I also would join Chimezie in saying I don't want to ruffle feathers
on this issue, but if either NCBO and/or NLM/NCBI would start
experimenting with a more broadly deployed LSID Registry & Resolution
Service (NCBO for ontologies and NLM/NCBI for BioRDF data s
s for BioPortal, it would be good to
elicit them now.
Daniel
At 11:53 PM 1/9/2007, [EMAIL PROTECTED] wrote:
One comment on
versioning issues (question2) . The matter is more complex than the
answer suggests. If a clinical system ever refers to a URI in BioPortal
this URI should stay forever. Even if a new ve
And the metadata (AnnotationProperties) I mentioned previously are
designed to support the ability manage versioning at the level of
nodes and edges. Again - it's just a proposal at this point, but its
in recognition of this need you stated more eloquently than I in your
previous post on t
recated" - though I take it not all
BioPortal ontologies will follow the OBO Foundry guidelines.
There's also been a lot of work on ontology class metadata standards
recently - much focused within the OBI ontology development group -
with a specific eye toward helping to support
a job for LSID's... oops! Said a dirty word!
;-)
Cheers all!
M
On Tue, 09 Jan 2007 23:53:49 -0800, <[EMAIL PROTECTED]> wrote:
One comment on versioning issues (question2) . The matter is more
complex
than the answer suggests. If a clinical system ever refers to a
URI in
Bi
On the format of URI (slash vs hash), it would be worth hearing from
the as much of the W3C community as possible, as there could be
differences of opinion. At this point, we are collecting the requirements.
In terms of synchronization, BioPortal will serve up the "current
version"
ning issues (question2) . The matter is more
complex
than the answer suggests. If a clinical system ever refers to a
URI in
BioPortal this URI should stay forever. Even if a new version of the
ontology is deployed the original URI should still point to the
old term
or concept, even if it is dep
ion2) . The matter is more
complex
than the answer suggests. If a clinical system ever refers to a
URI in
BioPortal this URI should stay forever. Even if a new version of the
ontology is deployed the original URI should still point to the
old term
or concept, even if it is deprecated. So version
On Tue, 09 Jan 2007 23:53:49 -0800, <[EMAIL PROTECTED]> wrote:
One comment on versioning issues (question2) . The matter is more
complex
than the answer suggests. If a clinical system ever refers to a
URI in
BioPortal this URI should stay forever. Even if a new version of the
ontology is
> wrote:
One comment on versioning issues (question2) . The matter is more complex
than the answer suggests. If a clinical system ever refers to a URI in
BioPortal this URI should stay forever. Even if a new version of the
ontology is deployed the original URI should still point to the old
rs to a URI in
BioPortal this URI should stay forever. Even if a new version of the
ontology is deployed the original URI should still point to the old term
or concept, even if it is deprecated. So versioning is more than a
development or collaboration issue. I don't know wether the answer giv
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