Re: Answers to questions about BioPortal

2007-01-19 Thread Suzanna Lewis
I added this requirement (URI for most current version) to the wiki  
since it is essential for the operation of the software we use. Be  
nice to have the chaining between versions as well.


-S

On Jan 17, 2007, at 7:26 AM, Daniel Rubin wrote:

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 everyone's perspective,  
or are there other requirements (for example, I could imagine it  
would be nice is there were another layer that permitted people to  
refer to a URI that pointed to the current version of a term,  
though it could be quite a bit of work to provide that service).

Daniel


___
Daniel Rubin, MD, MS
Clinical Asst. Professor, Radiology
Research Scientist, Stanford Medical Informatics
Scientific Director, National Center of Biomedical Ontology
MSOB X-215
Stanford, CA 94305
650-725-5693


At 02:03 AM 1/17/2007, [EMAIL PROTECTED] wrote:

I don't know if any commercial clinical system is rteally using  
URI's right now, but I think this will come. If an URI is the  
ultiimate and unique way of pointing to a resource then future  
systems should use URI's to 'codify' diagnoses for example in  
stead of storing a local code in the data base. Currently many  
systems store the combination of a coding system (ICD, SNOMED) +  
the specific code + a locally deployed repository. However,  
conceptually this is the same of pointing to the SNOMED or ICD URI  
in the SNOMED/URI ontology residing at some site.


By the way also by using codesystem/code combinations you have the  
versioning problem. Code System is also holding version info.

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871


Daniel Rubin [EMAIL PROTECTED]

11/01/2007 04:43
To
Dirk Colaert/AMIPU/[EMAIL PROTECTED]
cc
w3c semweb hcls public-semweb-lifesci@w3.org, public-semweb- 
[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 provide. Though I am intrigued with  
your use case about clinical systems referring to a URI. Are you  
aware of any commercial system that is contemplating referring to  
entities on the semantic Web via URI? We'd certainly be interested  
in catalyzing commercial efforts use these technologies  
effectively, and it would be particularly nice if we could get  
these systems using public knowledge sources such as terminologies  
instead of embedding them in the code...
BTW--if there are other requirements 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  
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 given to question 3 solves this.


__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871


Daniel Rubin [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]

10/01/2007 01:46

To

w3c semweb hcls public-semweb-lifesci@w3.org

cc
Subject

Answers to questions about BioPortal





Dear HCLSIG users,

We have received a number of questions/comments from you for our  
BioPortal sneak preview. Please continue to provide comments/ 
suggestions as this will help us to ensure BioPortal meets the  
community needs. We have collected the following recent feedback  
from several different members of this list, and would like to  
summarize our responses to them below to clarify some of the  
recent questions:


1. Looking at the interface, it is not clear to me how best to  
reference an element of the ontologies there-- is there a URI  
mechanism that can be used directly by outside researchers? How does

this relate to the DOID # (i.e., namespaces)?

Yes, a URI mechanism will be made available soon. Ontologies will  
have their own namespaces defined by the authors, or if none is  
provided, we will create one based on our bioontology.org namespace.


2. Also, can you provide more details on how the BioPortal will  
provide versioning? Last I understood, there were no SVN  
capabilities with the BioPortal - has that changed or did I  
misunderstand the set-up?


It is important to understand that BioPortal is a Web application  
that accesses an ontology library, and that it is not a content  
management system (such as cvs

Re: Answers to questions about BioPortal

2007-01-17 Thread dirk . colaert
I don't know if any commercial clinical system is rteally using URI's 
right now, but I think this will come. If an URI is the ultiimate and 
unique way of pointing to a resource then future systems should use URI's 
to 'codify' diagnoses for example in stead of storing a local code in the 
data base. Currently many systems store the combination of a coding system 
(ICD, SNOMED) + the specific code + a locally deployed repository. 
However, conceptually this is the same of pointing to the SNOMED or ICD 
URI in the SNOMED/URI ontology residing at some site.

By the way also by using codesystem/code combinations you have the 
versioning problem. Code System is also holding version info. 
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871



Daniel Rubin [EMAIL PROTECTED] 
11/01/2007 04:43

To
Dirk Colaert/AMIPU/[EMAIL PROTECTED]
cc
w3c semweb hcls public-semweb-lifesci@w3.org, 
[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 provide. Though I am intrigued with your use case about 
clinical systems referring to a URI. Are you aware of any commercial 
system that is contemplating referring to entities on the semantic Web via 
URI? We'd certainly be interested in catalyzing commercial efforts use 
these technologies effectively, and it would be particularly nice if we 
could get these systems using public knowledge sources such as 
terminologies instead of embedding them in the code...
BTW--if there are other requirements 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 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 given 
to question 3 solves this. 

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871 


Daniel Rubin [EMAIL PROTECTED] 
Sent by: [EMAIL PROTECTED] 

10/01/2007 01:46 
To
w3c semweb hcls public-semweb-lifesci@w3.org 
cc
Subject
Answers to questions about BioPortal 





Dear HCLSIG users,

We have received a number of questions/comments from you for our BioPortal 
sneak preview. Please continue to provide comments/suggestions as this 
will help us to ensure BioPortal meets the community needs. We have 
collected the following recent feedback from several different members of 
this list, and would like to summarize our responses to them below to 
clarify some of the recent questions:

1. Looking at the interface, it is not clear to me how best to reference 
an element of the ontologies there-- is there a URI mechanism that can be 
used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?

Yes, a URI mechanism will be made available soon. Ontologies will have 
their own namespaces defined by the authors, or if none is provided, we 
will create one based on our bioontology.org namespace.

2. Also, can you provide more details on how the BioPortal will provide 
versioning? Last I understood, there were no SVN capabilities with the 
BioPortal - has that changed or did I misunderstand the set-up?

It is important to understand that BioPortal is a Web application that 
accesses an ontology library, and that it is not a content management 
system (such as cvs and subversion). BioPortal stores the released 
versions of ontologies and indexes their content.  For ontology 
development, the authors use their preferred local systems (local cvs, 
svn, sourceforge, or gforge). When they create a new version that is ready 
to be released publicly, it is submitted directly to BioPortal by the 
author. In some cases, we may be able to set up URL pull into BioPortal on 
a regular basis.

3. Will there be a general way to identify deprecated terms in the 
ontologies posted in BioPortal, how does LexGrid handle this information?

Yes, and LexGrid provides this functionality. 

4. Are you [Mark Musen] the person to request updates of information 
currently displayed on the site?

You can contact Daniel Rubin.

5. The terms of service says: Except as expressly prohibited on the Site, 
you are permitted to view, copy, print and distribute publications and 
documents within this Site, subject to your agreement that:... You will 
display the below copyright notice and other proprietary notices on every 
copy you make I read this as saying that anything submitted to the 
repository would be copyright Copyright (c) 2005-2006, The Board

Re: Answers to questions about BioPortal

2007-01-17 Thread Daniel Rubin



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 everyone's perspective, or are there other requirements (for
example, I could imagine it would be nice is there were another layer
that permitted people to refer to a URI that pointed to the current
version of a term, though it could be quite a bit of work to provide that
service).
Daniel

___

Daniel Rubin, MD, MS
Clinical Asst. Professor, Radiology
Research Scientist, Stanford Medical Informatics
Scientific Director, National Center of Biomedical Ontology
MSOB X-215
Stanford, CA 94305
650-725-5693

At 02:03 AM 1/17/2007, [EMAIL PROTECTED] wrote:
I don't know if any
commercial clinical system is rteally using URI's right now, but I think
this will come. If an URI is the ultiimate and unique way of pointing to
a resource then future systems should use URI's to 'codify' diagnoses for
example in stead of storing a local code in the data base. Currently many
systems store the combination of a coding system (ICD, SNOMED) + the
specific code + a locally deployed repository. However, conceptually this
is the same of pointing to the SNOMED or ICD URI in the SNOMED/URI
ontology residing at some site. 
By the way also by using codesystem/code combinations you
have the versioning problem. Code System is also holding
version info. 
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa
Healthcare
mobile: +32 497 470 871 

Daniel Rubin [EMAIL PROTECTED]

11/01/2007 04:43 
To

Dirk Colaert/AMIPU/[EMAIL PROTECTED] 
cc

w3c semweb hcls public-semweb-lifesci@w3.org,
[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 provide. Though I am intrigued with your use case about
clinical systems referring to a URI. Are you aware of any commercial
system that is contemplating referring to entities on the semantic Web
via URI? We'd certainly be interested in catalyzing commercial efforts
use these technologies effectively, and it would be particularly nice if
we could get these systems using public knowledge sources such as
terminologies instead of embedding them in the code...
BTW--if there are other requirements 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 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
given to question 3 solves this. 

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa
Healthcare
mobile: +32 497 470 871 

Daniel Rubin [EMAIL PROTECTED] 
Sent by: [EMAIL PROTECTED] 

10/01/2007 01:46 

To


w3c semweb hcls
public-semweb-lifesci@w3.org 

cc
Subject


Answers to questions about BioPortal 


Dear HCLSIG users,
We have received a number of questions/comments from you for our
BioPortal sneak preview. Please continue to provide comments/suggestions
as this will help us to ensure BioPortal meets the community needs. We
have collected the following recent feedback from several different
members of this list, and would like to summarize our responses to them
below to clarify some of the recent questions:

1. Looking at the interface, it is not clear to me how best to reference
an element of the ontologies there-- is there a URI mechanism that can be
used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?
Yes, a URI mechanism will be made available soon. Ontologies will have
their own namespaces defined by the authors, or if none is provided, we
will create one based on our bioontology.org namespace.
2. Also, can you provide more details on how the BioPortal will provide
versioning? Last I understood, there were no SVN capabilities with the
BioPortal - has that changed or did I misunderstand the
set-up?
It is important to understand that BioPortal is a Web application that
accesses an ontology library, and that it is not a content
management system (such as cvs and subversion). BioPortal stores the
released versions of ontologies and indexes their content. For
ontology development, the authors use their preferred local systems
(local cvs, svn, sourceforge, or gforge). When they create a new version
that is ready to be released publicly, it is submitted directly to
BioPortal by the author. In some cases, we may be able to set up URL pull
into BioPortal

RE: Answers to questions about BioPortal

2007-01-17 Thread Kashyap, Vipul
Daniel,

 

Thanks for the news. ICD and SNOMED are the two biggies used in healthcare and
this would a very useful services.

Hopefully, you have got an exhaustive set of wish lists/requirements from
various communities.

 

Was wondering if you are planning to make the requirements and/or spec open to
the public?

This would be valuable to both the HCLS and other W3C communities!

 

Best regards,

 

---Vipul

 

===

Vipul Kashyap, Ph.D.

Senior Medical Informatician

Clinical Informatics RD, Partners HealthCare System

Phone: (781)416-9254

Cell: (617)943-7120

http://www.partners.org/cird/AboutUs.asp?cBox=StaffstAb=vik

 

To keep up you need the right answers; to get ahead you need the right questions

---John Browning and Spencer Reiss, Wired 6.04.95



From: [EMAIL PROTECTED]
[mailto:[EMAIL 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 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 other requirements (for example, I could
imagine it would be nice is there were another layer that permitted people to
refer to a URI that pointed to the current version of a term, though it could be
quite a bit of work to provide that service).
Daniel


___



Daniel Rubin, MD, MS
Clinical Asst. Professor, Radiology
Research Scientist, Stanford Medical Informatics
Scientific Director, National Center of Biomedical Ontology
MSOB X-215
Stanford, CA 94305
650-725-5693


At 02:03 AM 1/17/2007, [EMAIL PROTECTED] wrote:

I don't know if any commercial clinical system is rteally using URI's
right now, but I think this will come. If an URI is the ultiimate and unique way
of pointing to a resource then future systems should use URI's to 'codify'
diagnoses for example in stead of storing a local code in the data base.
Currently many systems store the combination of a coding system (ICD, SNOMED) +
the specific code + a locally deployed repository. However, conceptually this is
the same of pointing to the SNOMED or ICD URI in the SNOMED/URI ontology
residing at some site. 

By the way also by using codesystem/code combinations you have the
versioning problem. Code System is also holding version info. 
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871 


Daniel Rubin [EMAIL PROTECTED] 

11/01/2007 04:43 

To

Dirk Colaert/AMIPU/[EMAIL PROTECTED] 

cc

w3c semweb hcls public-semweb-lifesci@w3.org,
[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 provide. Though I am intrigued with your use case about clinical
systems referring to a URI. Are you aware of any commercial system that is
contemplating referring to entities on the semantic Web via URI? We'd certainly
be interested in catalyzing commercial efforts use these technologies
effectively, and it would be particularly nice if we could get these systems
using public knowledge sources such as terminologies instead of embedding them
in the code...
BTW--if there are other requirements 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 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 given to question 3 solves this. 

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871 


Daniel Rubin [EMAIL PROTECTED] 
Sent by: [EMAIL PROTECTED] 

10/01/2007 01:46 


To


w3c semweb hcls public-semweb-lifesci@w3.org 


cc
Subject


Answers to questions about BioPortal 





Dear HCLSIG users,

We have

RE: Answers to questions about BioPortal

2007-01-17 Thread Daniel Rubin



Actually this is a very good idea, and we have created a section on our
wiki for gathering requirements from the public:

http://www.bioontology.org/wiki/index.php/Public_Requirements
We have seeded this with URI requirements that we have gathered from this
community. Alas, we do not yet have a wish list/requirements
from various communities, but this is exactly what we want, and we hope
that this wiki mechanism will improve our outreach to that end.
If there are others who would be valuable to contribute, feel free to
encourage them to participate (the wiki is open to the 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 this would a very useful services.
Hopefully, you have got an exhaustive set of “wish lists/requirements”
from various communities.

Was wondering if you are planning to make the requirements and/or spec
open to the public?
This would be valuable to both the HCLS and other W3C communities!

Best regards,

---Vipul

===
Vipul Kashyap, Ph.D.
Senior Medical Informatician
Clinical Informatics RD, Partners HealthCare System
Phone: (781)416-9254
Cell: (617)943-7120

http://www.partners.org/cird/AboutUs.asp?cBox=StaffstAb=vik

To keep up you need the right
answers; to get ahead you need the right questions
---John Browning and Spencer Reiss, Wired 6.04.95


From:
[EMAIL PROTECTED]
[
mailto:[EMAIL 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 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 other requirements (for
example, I could imagine it would be nice is there were another layer
that permitted people to refer to a URI that pointed to the current
version of a term, though it could be quite a bit of work to provide that
service).
Daniel

___
Daniel Rubin, MD, MS
Clinical Asst. Professor, Radiology
Research Scientist, Stanford Medical Informatics
Scientific Director, National Center of Biomedical Ontology
MSOB X-215
Stanford, CA 94305
650-725-5693

At 02:03 AM 1/17/2007, [EMAIL PROTECTED] wrote:

I don't know if any commercial
clinical system is rteally using URI's right now, but I think this will
come. If an URI is the ultiimate and unique way of pointing to a resource
then future systems should use URI's to 'codify' diagnoses for example in
stead of storing a local code in the data base. Currently many systems
store the combination of a coding system (ICD, SNOMED) + the specific
code + a locally deployed repository. However, conceptually this is the
same of pointing to the SNOMED or ICD URI in the SNOMED/URI ontology
residing at some site. 
By the way also by using codesystem/code combinations you
have the versioning problem. Code System is also holding
version info. 
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa
Healthcare
mobile: +32 497 470 871 

Daniel Rubin [EMAIL PROTECTED]

11/01/2007 04:43 
To

Dirk Colaert/AMIPU/[EMAIL PROTECTED] 
cc

w3c semweb hcls public-semweb-lifesci@w3.org,
[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 provide. Though I am intrigued with your use case about
clinical systems referring to a URI. Are you aware of any commercial
system that is contemplating referring to entities on the semantic Web
via URI? We'd certainly be interested in catalyzing commercial efforts
use these technologies effectively, and it would be particularly nice if
we could get these systems using public knowledge sources such as
terminologies instead of embedding them in the code...
BTW--if there are other requirements 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 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
given to question 3 solves this. 

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa
Healthcare
mobile: +32 497 470 871

RE: Answers to questions about BioPortal

2007-01-11 Thread Kashyap, Vipul


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 concept is created, should the version of the
ontology be updated?
2. If yes, should the new version be a major version or minor version?
3. If no, is it OK for a version of ontology (say v1) to be linked to multiple
versions of a concept (say v1, v2, etc...)
...
Of course, if we extend this thinking to multiple levels of granularity, say
properties, axioms, etc. this could give rise to a large number of
configurations.

A key issue we need to think about is what kind of business rules or
lifecycles need to be defined to appropriately link various versions at
multiple levels of granularity and best practices around these. 

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


  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
 their
  relationships may evolve over time. We many need a versioning scheme for
  these. I think some of these finer granularity versioning examples can
 be
  found in the UMLS (Unified Medical Language System). At the instance
 level,
  we may need versioning as well. Also, the semantics of versioning may be
  unclear sometimes. For example, two different SNPs (Single Necleotide
  Polymorphisms) that were submitted to dbSNP may refer to the same
 location in
  the genome. Do we say they are two different versions of the same SNP?
 There
  may not be a standard notion/definition of versioning for biomedical
  entities.
 
 I think that both types, high-level e.g. this is a new release of the
 ontology, and low-level, e.g. a term (class or property) is deprecated,
 are needed. Not sure about versioning at the instance level.
 
 Mechanisms that I have seen or am aware of are either 1) add annotation
 properties in the ontology for this purpose or 2) use a database backend
 that provides a mechanism to store information about deprecated terms.
 The database backend solution may be too heavy weight for a general
 solution?. As for the annotation property mechanism. the developers of the
 MGED Ontology have put together a policy of how to indicate deprecated
 terms for this resource:
 https://www.cbil.upenn.edu/magewiki/index.php/TermDeprecationPolicy
 Although there may be some items that are particular to the MGED Ontology
 and it's peculiarities, I believe that there are also items that can be
 generalized for use with other ontologies.
 
 Cheers,
 Trish





THE INFORMATION TRANSMITTED IN THIS ELECTRONIC COMMUNICATION IS INTENDED ONLY 
FOR THE PERSON OR ENTITY TO WHOM IT IS ADDRESSED AND MAY CONTAIN CONFIDENTIAL 
AND/OR PRIVILEGED MATERIAL.  ANY REVIEW, RETRANSMISSION, DISSEMINATION OR OTHER 
USE OF OR TAKING OF ANY ACTION IN RELIANCE UPON, THIS INFORMATION BY PERSONS OR 
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INFORMATION IN ERROR, PLEASE CONTACT THE SENDER AND THE PRIVACY OFFICER, AND 
PROPERLY DISPOSE OF THIS INFORMATION.





RE: Answers to questions about BioPortal

2007-01-11 Thread Nigam Haresh Shah

 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 the instance is of a the class Tumor then
on giving treatment it changes in size, shape etc, and might ultimately
disappear. On each visit we are observing a different version of the tumor
instance [in Tom].

Regards,
Nigam.



Re: Answers to questions about BioPortal

2007-01-10 Thread dirk . colaert
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 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 given 
to question 3 solves this.

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871



Daniel Rubin [EMAIL PROTECTED] 
Sent by: [EMAIL PROTECTED]
10/01/2007 01:46

To
w3c semweb hcls public-semweb-lifesci@w3.org
cc

Subject
Answers to questions about BioPortal







Dear HCLSIG users,

We have received a number of questions/comments from you for our BioPortal 
sneak preview. Please continue to provide comments/suggestions as this 
will help us to ensure BioPortal meets the community needs. We have 
collected the following recent feedback from several different members of 
this list, and would like to summarize our responses to them below to 
clarify some of the recent questions:

1. Looking at the interface, it is not clear to me how best to reference 
an element of the ontologies there-- is there a URI mechanism that can be 
used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?

Yes, a URI mechanism will be made available soon. Ontologies will have 
their own namespaces defined by the authors, or if none is provided, we 
will create one based on our bioontology.org namespace.

2. Also, can you provide more details on how the BioPortal will provide 
versioning? Last I understood, there were no SVN capabilities with the 
BioPortal - has that changed or did I misunderstand the set-up?

It is important to understand that BioPortal is a Web application that 
accesses an ontology library, and that it is not a content management 
system (such as cvs and subversion). BioPortal stores the released 
versions of ontologies and indexes their content.  For ontology 
development, the authors use their preferred local systems (local cvs, 
svn, sourceforge, or gforge). When they create a new version that is ready 
to be released publicly, it is submitted directly to BioPortal by the 
author. In some cases, we may be able to set up URL pull into BioPortal on 
a regular basis.

3. Will there be a general way to identify deprecated terms in the 
ontologies posted in BioPortal, how does LexGrid handle this information?

Yes, and LexGrid provides this functionality. 

4. Are you [Mark Musen] the person to request updates of information 
currently displayed on the site?

You can contact Daniel Rubin.

5. The terms of service says: Except as expressly prohibited on the Site, 
you are permitted to view, copy, print and distribute publications and 
documents within this Site, subject to your agreement that:... You will 
display the below copyright notice and other proprietary notices on every 
copy you make I read this as saying that anything submitted to the 
repository would be copyright Copyright (c) 2005-2006, The Board of
Trustees of Leland Stanford Junior University. All rights reserved., 
which I would guess some would consider unacceptable.

This is not the intended interpretation and we will change the wording of 
the terms.

6. Termination of Use: You agree that The National Center for Biomedical 
Ontology may, in its sole discretion, at any time terminate your access to 
the Site and any account(s) you may have in connection
with the Site. Access to the Site may be monitored by The National Center 
for Biomedical Ontology.  This is scary. There ought to be explicit cause 
for termination, otherwise people might be reluctant to entrust their work 
to the site.

We will modify the terms to declare the conditions that would be a cause 
for termination.

7. Disclaimer: ... PROVIDED ON AN AS IS AND AS AVAILABLE BASIS... . 
(B The W3C has taken steps to ensure that access to the files hosted at 
the W3C domain will be maintained under a variety of circumstances, using 
mirrors, externals services, etc. It would be desirable that similar 
actions be taken by the NCBO, and some mention of them included in the 
terms of service, particularly if URIs in the bioontology.org namespace 
are to be used.

NCBO sites are hosted by Stanford Information Technology Services, the 
same people who host the Stanford Hospital clinical database and Highwire 
Press.  We anticipate having reliable availability of the services we 
provide.

8. Use of ontologies: Only the submitter of the ontology will be able to 
modify it or submit new versions.  B In a project such as ours that is 
group oriented, it is likely that individuals will come and go. I think 
there needs to be some notion of group access so that we aren't vulnerable 
to a key individual becoming unavailable.

Yes, 

RE: Answers to questions about BioPortal

2007-01-10 Thread Xiaoshu Wang
  Yes, a URI mechanism will be made available soon. Ontologies will have
their own namespaces defined  by  
  the authors, or if none is provided, we will create one based on our
bioontology.org namespace.
 
If the authors have their own namespace URI, that means they have to
maintain a copy of the ontology at their own site. I wonder how will the
synchronization between the bioportal to the external site be established?  
 
If an ontology is to adopt the URI that the bioportal provides, I wonder
what kind of URI, in terms of the hash vs. slash, that the bioportal will
support.  For a samll sized ontology, the hash URI would be sufficient and
ideal.  But if the ontology's size is huge, I do believe the slash URI
should be used to avoid the unnecessary import. From the implementation
point of view, however, supporting slash URI would take a lot more hassle
than supporting the hash URI. I wonder if bioportal will be able to support
that?
 
Xiaoshu



Re: Answers to questions about BioPortal

2007-01-10 Thread Mark Wilkinson


H... sounds like 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
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 given
to question 3 solves this.

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871



Daniel Rubin [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
10/01/2007 01:46

To
w3c semweb hcls public-semweb-lifesci@w3.org
cc

Subject
Answers to questions about BioPortal







Dear HCLSIG users,

We have received a number of questions/comments from you for our  
BioPortal

sneak preview. Please continue to provide comments/suggestions as this
will help us to ensure BioPortal meets the community needs. We have
collected the following recent feedback from several different members of
this list, and would like to summarize our responses to them below to
clarify some of the recent questions:

1. Looking at the interface, it is not clear to me how best to reference
an element of the ontologies there-- is there a URI mechanism that can be
used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?

Yes, a URI mechanism will be made available soon. Ontologies will have
their own namespaces defined by the authors, or if none is provided, we
will create one based on our bioontology.org namespace.

2. Also, can you provide more details on how the BioPortal will provide
versioning? Last I understood, there were no SVN capabilities with the
BioPortal - has that changed or did I misunderstand the set-up?

It is important to understand that BioPortal is a Web application that
accesses an ontology library, and that it is not a content management
system (such as cvs and subversion). BioPortal stores the released
versions of ontologies and indexes their content.  For ontology
development, the authors use their preferred local systems (local cvs,
svn, sourceforge, or gforge). When they create a new version that is  
ready

to be released publicly, it is submitted directly to BioPortal by the
author. In some cases, we may be able to set up URL pull into BioPortal  
on

a regular basis.

3. Will there be a general way to identify deprecated terms in the
ontologies posted in BioPortal, how does LexGrid handle this information?

Yes, and LexGrid provides this functionality.

4. Are you [Mark Musen] the person to request updates of information
currently displayed on the site?

You can contact Daniel Rubin.

5. The terms of service says: Except as expressly prohibited on the  
Site,

you are permitted to view, copy, print and distribute publications and
documents within this Site, subject to your agreement that:... You will
display the below copyright notice and other proprietary notices on every
copy you make I read this as saying that anything submitted to the
repository would be copyright Copyright (c) 2005-2006, The Board of
Trustees of Leland Stanford Junior University. All rights reserved.,
which I would guess some would consider unacceptable.

This is not the intended interpretation and we will change the wording of
the terms.

6. Termination of Use: You agree that The National Center for Biomedical
Ontology may, in its sole discretion, at any time terminate your access  
to

the Site and any account(s) you may have in connection
with the Site. Access to the Site may be monitored by The National Center
for Biomedical Ontology.  This is scary. There ought to be explicit  
cause
for termination, otherwise people might be reluctant to entrust their  
work

to the site.

We will modify the terms to declare the conditions that would be a cause
for termination.

7. Disclaimer: ... PROVIDED ON AN AS IS AND AS AVAILABLE BASIS... .
(B The W3C has taken steps to ensure that access to the files hosted at
the W3C domain will be maintained under a variety of circumstances, using
mirrors, externals services, etc. It would be desirable that similar
actions be taken by the NCBO, and some mention of them included in the
terms of service, particularly if URIs in the bioontology.org namespace
are to be used.

NCBO sites are hosted by Stanford Information Technology Services, the
same people who host the Stanford Hospital clinical database and Highwire
Press.  We anticipate having reliable availability of the services we
provide.

8. Use of ontologies: Only the submitter of the ontology will be able to
modify it or submit new versions.  B In a project such as ours that is
group oriented, it is likely that individuals will come and go. I think

Re: Answers to questions about BioPortal

2007-01-10 Thread Alan Ruttenberg


I guess  what I'm trolling for is some more careful description of  
the desired behavior. Some examples would be helpful, etc.
My feeling is the technical management of how to arrange a uri/lsid  
is much easier than specifying and agreeing upon what the versioning  
behavior should be.


For instance, BioPAX took the strategy of using a different namespace  
for each of its versions. That cleanly separates which version you  
are referring to. Too cleanly - people who want to integrate data  
from the two versions now need to think too hard about how to do that.


-Alan

On Jan 10, 2007, at 12:23 PM, Chimezie Ogbuji wrote:



Well, (not to open up a can of worms) ontology versioning can be  
handled as a mechanism 'built-in' to the protocol (as is the case  
with LSID) or via an HTTP resolution service (such as PURL).  I'm  
more familiar with the latter scenario than the former.  Assuming  
you have a static PURL address for the ontology you can specify  
which version the request is redirected to.


This is similar to the way W3C spec URLs work (from what I gather).  
There is usually a 'latest' link (which is always static) which  
redirects the a location specific to the current 'version'.  I  
think this is a good model to follow for managing ontology  
locations (per version).



On Wed, 10 Jan 2007, Mark Wilkinson wrote:
H... sounds like 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

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 given

to question 3 solves this.
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871
Daniel Rubin [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
10/01/2007 01:46
To
w3c semweb hcls public-semweb-lifesci@w3.org
cc
Subject
Answers to questions about BioPortal
Dear HCLSIG users,
We have received a number of questions/comments from you for our  
BioPortal
sneak preview. Please continue to provide comments/suggestions as  
this

will help us to ensure BioPortal meets the community needs. We have
collected the following recent feedback from several different  
members of
this list, and would like to summarize our responses to them  
below to

clarify some of the recent questions:
1. Looking at the interface, it is not clear to me how best to  
reference
an element of the ontologies there-- is there a URI mechanism  
that can be

used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?
Yes, a URI mechanism will be made available soon. Ontologies will  
have
their own namespaces defined by the authors, or if none is  
provided, we

will create one based on our bioontology.org namespace.
2. Also, can you provide more details on how the BioPortal will  
provide
versioning? Last I understood, there were no SVN capabilities  
with the

BioPortal - has that changed or did I misunderstand the set-up?
It is important to understand that BioPortal is a Web application  
that
accesses an ontology library, and that it is not a content  
management

system (such as cvs and subversion). BioPortal stores the released
versions of ontologies and indexes their content.  For ontology
development, the authors use their preferred local systems (local  
cvs,
svn, sourceforge, or gforge). When they create a new version that  
is ready
to be released publicly, it is submitted directly to BioPortal by  
the
author. In some cases, we may be able to set up URL pull into  
BioPortal on

a regular basis.
3. Will there be a general way to identify deprecated terms in the
ontologies posted in BioPortal, how does LexGrid handle this  
information?

Yes, and LexGrid provides this functionality.
4. Are you [Mark Musen] the person to request updates of information
currently displayed on the site?
You can contact Daniel Rubin.
5. The terms of service says: Except as expressly prohibited on  
the Site,
you are permitted to view, copy, print and distribute  
publications and
documents within this Site, subject to your agreement that:...  
You will
display the below copyright notice and other proprietary notices  
on every

copy you make I read this as saying that anything submitted to the
repository would be copyright Copyright (c) 2005-2006, The Board of
Trustees of Leland Stanford Junior University. All rights  
reserved.,

which I would guess some would consider unacceptable.
This is not the intended interpretation and we will change the  
wording of

the terms.
6. Termination of Use: You agree that The 

Re: Answers to questions about BioPortal

2007-01-10 Thread Alan Ruttenberg


How will LSIDs help?
-Alan

On Jan 10, 2007, at 11:19 AM, Mark Wilkinson wrote:



H... sounds like 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

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  
given

to question 3 solves this.

__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871



Daniel Rubin [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
10/01/2007 01:46

To
w3c semweb hcls public-semweb-lifesci@w3.org
cc

Subject
Answers to questions about BioPortal







Dear HCLSIG users,

We have received a number of questions/comments from you for our  
BioPortal
sneak preview. Please continue to provide comments/suggestions as  
this

will help us to ensure BioPortal meets the community needs. We have
collected the following recent feedback from several different  
members of

this list, and would like to summarize our responses to them below to
clarify some of the recent questions:

1. Looking at the interface, it is not clear to me how best to  
reference
an element of the ontologies there-- is there a URI mechanism that  
can be

used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?

Yes, a URI mechanism will be made available soon. Ontologies will  
have
their own namespaces defined by the authors, or if none is  
provided, we

will create one based on our bioontology.org namespace.

2. Also, can you provide more details on how the BioPortal will  
provide
versioning? Last I understood, there were no SVN capabilities with  
the

BioPortal - has that changed or did I misunderstand the set-up?

It is important to understand that BioPortal is a Web application  
that

accesses an ontology library, and that it is not a content management
system (such as cvs and subversion). BioPortal stores the released
versions of ontologies and indexes their content.  For ontology
development, the authors use their preferred local systems (local  
cvs,
svn, sourceforge, or gforge). When they create a new version that  
is ready

to be released publicly, it is submitted directly to BioPortal by the
author. In some cases, we may be able to set up URL pull into  
BioPortal on

a regular basis.

3. Will there be a general way to identify deprecated terms in the
ontologies posted in BioPortal, how does LexGrid handle this  
information?


Yes, and LexGrid provides this functionality.

4. Are you [Mark Musen] the person to request updates of information
currently displayed on the site?

You can contact Daniel Rubin.

5. The terms of service says: Except as expressly prohibited on  
the Site,
you are permitted to view, copy, print and distribute publications  
and
documents within this Site, subject to your agreement that:... You  
will
display the below copyright notice and other proprietary notices  
on every

copy you make I read this as saying that anything submitted to the
repository would be copyright Copyright (c) 2005-2006, The Board of
Trustees of Leland Stanford Junior University. All rights reserved.,
which I would guess some would consider unacceptable.

This is not the intended interpretation and we will change the  
wording of

the terms.

6. Termination of Use: You agree that The National Center for  
Biomedical
Ontology may, in its sole discretion, at any time terminate your  
access to

the Site and any account(s) you may have in connection
with the Site. Access to the Site may be monitored by The National  
Center
for Biomedical Ontology.  This is scary. There ought to be  
explicit cause
for termination, otherwise people might be reluctant to entrust  
their work

to the site.

We will modify the terms to declare the conditions that would be a  
cause

for termination.

7. Disclaimer: ... PROVIDED ON AN AS IS AND AS AVAILABLE  
BASIS... .
(B The W3C has taken steps to ensure that access to the files  
hosted at
the W3C domain will be maintained under a variety of  
circumstances, using

mirrors, externals services, etc. It would be desirable that similar
actions be taken by the NCBO, and some mention of them included in  
the
terms of service, particularly if URIs in the bioontology.org  
namespace

are to be used.

NCBO sites are hosted by Stanford Information Technology Services,  
the
same people who host the Stanford Hospital clinical database and  
Highwire

Press.  We anticipate having reliable availability of the services we
provide.

8. Use of ontologies: Only the submitter of the ontology will 

RE: Answers to questions about BioPortal

2007-01-10 Thread Daniel Rubin


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 as defined by the authors of the ontologies. They can either 
push those to us, or if they prefer, they can discuss with us the 
possibilities for pull at regular intervals.

Daniel

At 07:37 AM 1/10/2007, Xiaoshu Wang wrote:
  Yes, a URI mechanism will be made available soon. Ontologies 
will have their own namespaces defined  by
  the authors, or if none is provided, we will create one based 
on our bioontology.org namespace.


If the authors have their own namespace URI, that means they have to 
maintain a copy of the ontology at their own site. I wonder how will 
the synchronization between the bioportal to the external site be 
established?


If an ontology is to adopt the URI that the bioportal provides, I 
wonder what kind of URI, in terms of the hash vs. slash, that the 
bioportal will support.  For a samll sized ontology, the hash URI 
would be sufficient and ideal.  But if the ontology's size is huge, 
I do believe the slash URI should be used to avoid the unnecessary 
import. From the implementation point of view, however, supporting 
slash URI would take a lot more hassle than supporting the hash URI. 
I wonder if bioportal will be able to support that?


Xiaoshu





Re: Answers to questions about BioPortal

2007-01-10 Thread kc28


Hi,

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 their relationships may evolve over time. We many 
need a versioning scheme for these. I think some of these finer 
granularity versioning examples can be found in the UMLS (Unified 
Medical Language System). At the instance level, we may need versioning 
as well. Also, the semantics of versioning may be unclear sometimes. For 
example, two different SNPs (Single Necleotide Polymorphisms) that were 
submitted to dbSNP may refer to the same location in the genome. Do we 
say they are two different versions of the same SNP? There may not be a 
standard notion/definition of versioning for biomedical entities.


Just my two-cent thought,

-Kei

Alan Ruttenberg wrote:



I guess  what I'm trolling for is some more careful description of  
the desired behavior. Some examples would be helpful, etc.
My feeling is the technical management of how to arrange a uri/lsid  
is much easier than specifying and agreeing upon what the versioning  
behavior should be.


For instance, BioPAX took the strategy of using a different namespace  
for each of its versions. That cleanly separates which version you  
are referring to. Too cleanly - people who want to integrate data  
from the two versions now need to think too hard about how to do that.


-Alan

On Jan 10, 2007, at 12:23 PM, Chimezie Ogbuji wrote:



Well, (not to open up a can of worms) ontology versioning can be  
handled as a mechanism 'built-in' to the protocol (as is the case  
with LSID) or via an HTTP resolution service (such as PURL).  I'm  
more familiar with the latter scenario than the former.  Assuming  
you have a static PURL address for the ontology you can specify  
which version the request is redirected to.


This is similar to the way W3C spec URLs work (from what I gather).  
There is usually a 'latest' link (which is always static) which  
redirects the a location specific to the current 'version'.  I  think 
this is a good model to follow for managing ontology  locations (per 
version).



On Wed, 10 Jan 2007, Mark Wilkinson wrote:

H... sounds like 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

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 
given

to question 3 solves this.
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa Healthcare   mobile: +32 497 470 871
Daniel Rubin [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
10/01/2007 01:46
To
w3c semweb hcls public-semweb-lifesci@w3.org
cc
Subject
Answers to questions about BioPortal
Dear HCLSIG users,
We have received a number of questions/comments from you for our  
BioPortal
sneak preview. Please continue to provide comments/suggestions as  
this

will help us to ensure BioPortal meets the community needs. We have
collected the following recent feedback from several different  
members of

this list, and would like to summarize our responses to them  below to
clarify some of the recent questions:
1. Looking at the interface, it is not clear to me how best to  
reference
an element of the ontologies there-- is there a URI mechanism  that 
can be

used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?
Yes, a URI mechanism will be made available soon. Ontologies will  
have
their own namespaces defined by the authors, or if none is  
provided, we

will create one based on our bioontology.org namespace.
2. Also, can you provide more details on how the BioPortal will  
provide
versioning? Last I understood, there were no SVN capabilities  with 
the

BioPortal - has that changed or did I misunderstand the set-up?
It is important to understand that BioPortal is a Web application  
that

accesses an ontology library, and that it is not a content  management
system (such as cvs and subversion). BioPortal stores the released
versions of ontologies and indexes their content.  For ontology
development, the authors use their preferred local systems (local  
cvs,
svn, sourceforge, or gforge). When they create a new version that  
is ready

to be released publicly, it is submitted directly to BioPortal by  the
author. In some cases, we may be able to set up URL pull into  
BioPortal on

a regular basis.
3. Will there be a general way to 

Re: Answers to questions about BioPortal

2007-01-10 Thread Daniel Rubin



This is a very good.point; permanent URIs is a reasonable requirement we
will aim to provide. Though I am intrigued with your use case about
clinical systems referring to a URI. Are you aware of any commercial
system that is contemplating referring to entities on the semantic Web
via URI? We'd certainly be interested in catalyzing commercial efforts
use these technologies effectively, and it would be particularly nice if
we could get these systems using public knowledge sources such as
terminologies instead of embedding them in the code...
BTW--if there are other requirements 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 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 given to question 3
solves this. 
__
Dr. Dirk Colaert MD
Advanced Clinical Application Research Manager
Agfa
Healthcare
mobile: +32 497 470 871 

Daniel Rubin [EMAIL PROTECTED]

Sent by: [EMAIL PROTECTED]

10/01/2007 01:46 
To

w3c semweb hcls public-semweb-lifesci@w3.org

cc
Subject

Answers to questions about BioPortal 


Dear HCLSIG users,
We have received a number of questions/comments from you for our
BioPortal sneak preview. Please continue to provide comments/suggestions
as this will help us to ensure BioPortal meets the community needs. We
have collected the following recent feedback from several different
members of this list, and would like to summarize our responses to them
below to clarify some of the recent questions:

1. Looking at the interface, it is not clear to me how best to reference
an element of the ontologies there-- is there a URI mechanism that can be
used directly by outside researchers? How does
this relate to the DOID # (i.e., namespaces)?

Yes, a URI mechanism will be made available soon. Ontologies will have
their own namespaces defined by the authors, or if none is provided, we
will create one based on our bioontology.org namespace.

2. Also, can you provide more details on how the BioPortal will provide
versioning? Last I understood, there were no SVN capabilities with the
BioPortal - has that changed or did I misunderstand the set-up?

It is important to understand that BioPortal is a Web application that
accesses an ontology library, and that it is not a content
management system (such as cvs and subversion). BioPortal stores the
released versions of ontologies and indexes their content. For
ontology development, the authors use their preferred local systems
(local cvs, svn, sourceforge, or gforge). When they create a new version
that is ready to be released publicly, it is submitted directly to
BioPortal by the author. In some cases, we may be able to set up URL pull
into BioPortal on a regular basis.

3. Will there be a general way to identify deprecated terms in the
ontologies posted in BioPortal, how does LexGrid handle this
information?

Yes, and LexGrid provides this functionality. 

4. Are you [Mark Musen] the person to request updates of information
currently displayed on the site?

You can contact Daniel Rubin.

5. The terms of service says: Except as expressly prohibited on the
Site, you are permitted to view, copy, print and distribute publications
and documents within this Site, subject to your agreement that:... You
will display the below copyright notice and other proprietary notices on
every copy you make I read this as saying that anything submitted
to the repository would be copyright Copyright (c) 2005-2006, The
Board of
Trustees of Leland Stanford Junior University. All rights
reserved., which I would guess some would consider
unacceptable.

This is not the intended interpretation and we will change the wording of
the terms.

6. Termination of Use: You agree that The National Center for
Biomedical Ontology may, in its sole discretion, at any time terminate
your access to the Site and any account(s) you may have in
connection
with the Site. Access to the Site may be monitored by The National Center
for Biomedical Ontology. This is scary. There ought to be
explicit cause for termination, otherwise people might be reluctant to
entrust their work to the site.

We will modify the terms to declare the conditions that would be a cause
for termination.

7. Disclaimer: ... PROVIDED ON AN AS IS AND AS
AVAILABLE BASIS... . (B The W3C has taken steps to
ensure that access to the files hosted at the W3C domain will be
maintained under a variety of circumstances, using mirrors, externals
services, etc. It would be desirable that similar actions be taken by the
NCBO, and some mention of them included in the terms of service,
particularly if 

Re: Answers to questions about BioPortal

2007-01-10 Thread William Bug
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 this thread, that many biomedical ontology  
developers have gradually come to recognize must be addressed.


Daniel Rubin has also begun to work with the SKOS developers to help  
them continue to evolve this resource so we'll also have a annotation  
standard for managing the variety of lexical elements associated with  
an ontology.  Daniel has been soliciting SKOS Use Cases from those  
biomedical ontology projects currently making use of SKOS.  We're  
just talking low-hanging fruit here - e.g., we all use the same  
AnnotationProperties to specify associated synonyms, misspellings,  
preferred terms, etc..


Cheers,
Bill

On Jan 10, 2007, at 10:10 PM, kc28 wrote:


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 sets and/or data sets with ontology-centric annotations), I  
think there would be many interested in making use of it.



Agreed. The whole point of the semantic web is to come up with a  
standard that can broadly be applied to interconnect or integrate  
ontologies/data sets across different organizations (e.g., NCBO and  
NLM/NCBI).


Cheers,

-Kei

-Kei


Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging   Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology  Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - [EMAIL PROTECTED]






Re: Answers to questions about BioPortal

2007-01-10 Thread kc28


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 sets and/or 
data sets with ontology-centric annotations), I think there would be 
many interested in making use of it.



Agreed. The whole point of the semantic web is to come up with a 
standard that can broadly be applied to interconnect or integrate 
ontologies/data sets across different organizations (e.g., NCBO and 
NLM/NCBI).


Cheers,

-Kei

-Kei



Re: Answers to questions about BioPortal

2007-01-10 Thread Trish Whetzel


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 their 
relationships may evolve over time. We many need a versioning scheme for 
these. I think some of these finer granularity versioning examples can be 
found in the UMLS (Unified Medical Language System). At the instance level, 
we may need versioning as well. Also, the semantics of versioning may be 
unclear sometimes. For example, two different SNPs (Single Necleotide 
Polymorphisms) that were submitted to dbSNP may refer to the same location in 
the genome. Do we say they are two different versions of the same SNP? There 
may not be a standard notion/definition of versioning for biomedical 
entities.


I think that both types, high-level e.g. this is a new release of the 
ontology, and low-level, e.g. a term (class or property) is deprecated, 
are needed. Not sure about versioning at the instance level.


Mechanisms that I have seen or am aware of are either 1) add annotation 
properties in the ontology for this purpose or 2) use a database backend 
that provides a mechanism to store information about deprecated terms. 
The database backend solution may be too heavy weight for a general 
solution?. As for the annotation property mechanism. the developers of the 
MGED Ontology have put together a policy of how to indicate deprecated 
terms for this resource: 
https://www.cbil.upenn.edu/magewiki/index.php/TermDeprecationPolicy
Although there may be some items that are particular to the MGED Ontology 
and it's peculiarities, I believe that there are also items that can be 
generalized for use with other ontologies.


Cheers,
Trish



Re: Answers to questions about BioPortal

2007-01-10 Thread Trish Whetzel


Hi Bill,

Is the work that you mention below part of that for BIRN and is there a 
pointer to a policy?


Also, have you found it necessary to be able to re-create the graph within 
the same version of the ontology on a day-to-day basis or is a 
version-to-version basis acceptable?


Trish

As 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 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 the link between deprecated classes and those 
classes to which the original semantic content covered by the defunct class 
has been transferred.  To fully represent this evolutionary graph, there will 
likely be a need for some ruled-based formalism to deal with scenarios where 
the deprecated class has not simply been decomposed into 2 or more newer 
classes - or scenarios where multiple deprecated classes map to multiple 
current classes. Even under the simple case where 1 entity -- 2 entities, 
rules may be required to more fully and formally express the semantic 
transference asserted by the ontological evolutionary graph.


For the time being, we at least are working to include metadata properties to 
make it possible to - in theory - reconstruct the ontology graph as it 
existed on a particular date.