Trish Whetzel | 1 Feb 09:07 2010
Picon

NCBO Webinar - James Malone, Feb. 3

The next NCBO Webinar will be held Wednesday, February 3 at 10am PT. Please note there will not be a VOIP option and attendees must call into the teleconference.


The Webinar will be presented by Dr. James Malone, from the European Bioinformatics Institute. The title of the presentation will be “Modeling gene expression sample variables with an application ontology”. Below is information on how to join the online meeting and accompanying teleconference. For a schedule of the 2010 presentations or for more information about the NCBO Seminar series, see: http://www.bioontology.org/seminar-series.

TITLE: Modeling gene expression sample variables with an application ontology

ABSTRACT: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies help in providing annotation solutions, however, for cross-domain investigations, multiple ontologies are needed to represent the experimental data. Such ontologies are subject to rapid change, are often very large and are not interoperable and present complexities that are a barrier to users of biological resources. In this talk I will present our approach to curating gene expression experimental data with an application ontology, the Experimental Factor Ontology (EFO), designed to meet cross-domain, application focused use cases. I will also describe the additional querying power such an ontology now gives us in our applications, such as the Gene Expression Atlas and ArrayExpress at EBI. Our approach demonstrates a successful methodology for consuming and applying domain ontologies in a real-world data repository application.

WEBEX DETAILS:
Topic: NCBO Webinar Series
Date: February 3, 2010
Time: 10:00 am, Pacific Standard Time (San Francisco, GMT-08:00)
Meeting Number: 926 719 478
Meeting Password: ncbomeeting


-------------------------------------------------------
To join the online meeting (Now from iPhones too!)
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NNzlkODFlYWVm&RT=MiM0
2. Enter your name and email address.
3. Enter the meeting password: ncbomeeting
4. Click "Join Now".
5. Follow the instructions that appear on your screen.

To view in other time zones or languages, please click the link:
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NNzlkODFlYWVm&ORT=MiM0

-------------------------------------------------------
To join the audio conference only
-------------------------------------------------------
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=107799137&tollFree=0

Access code:926 719 478

-------------------------------------------------------
For assistance
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/mc
2. On the left navigation bar, click "Support".

You can contact me at:
whetzel <at> stanford.edu


To update this meeting to your calendar program (for example Microsoft Outlook), click this link:
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&ICS=UMI&LD=1&RD=2&ST=1&SHA2=sscJxPSrxubkyAnBruXELuZe4XBKeHnhQa70aJiFfUI=&RT=MiM0


WebEx will automatically setup Meeting Manager for Windows the first time you join a meeting. To save time, you can setup prior to the meeting by clicking this link:
https://stanford.webex.com/stanford/meetingcenter/mcsetup.php




http://www.webex.com



IMPORTANT NOTICE: This WebEx service includes a feature that allows audio and any documents and other materials exchanged or viewed during the session to be recorded. By joining this session, you automatically consent to such recordings. If you do not consent to the recording, do not join the session.

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Peter Yim | 1 Feb 09:22 2010

Re: Ontology Summit 2010: virtual Panel Sessions on "Training Requirements for Ontologists" - Thu 2010.02.04

Re: OntologySummit2010: "Creating the Ontologists of the Future"
Virtual Panel Session-3 - "Training Requirements for Ontologists"

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_01_14

Coming up this week is our Ontology Summit 2010: virtual panel
Session-3 on education and training "Requirements" for the
ontologists. Please register your attendance for this session and mark
your calendar for the "Quality" panel session-4 the will featured in
the immediately following week (Thu 2010.02.11).

In this upcoming 4-Feb-2010 panel session-3, entitled: "What Are We
Training For?" our chair, Dr. Amanda Vizedom will be joined by an
expert panel that includes Professor Denise Bedford, Dr. Michael
Uschold, Dr. John Sowa (... more). Together, they will address the
title question, as well as "What do working ontologists need to know?"
and "What do ontologists need to be able to do?" The aim is to develop
a richer and more clear picture of the requirements of employability
(those trained are well-prepared for the available jobs) and
deployability (those who hire trained ontologists find them ready and
able to perform the needed work). The session will then be opened to
all participants for Q&A and discussion with the co-chairs and the
panel. Our goal will be to the goal is to bring a strong "end-user"
voice to the discussion, and to stimulate thinking and discussion
across the Summit community as a whole.

*RSVP* by emailing the sender (<mailto:peter.yim <at> cim3.com>, offline
please)  or add yourself directly to the session page if you are
already an Ontolog or prior-year ontology-summit community member) so
that we can prepare enough resources to support everyone.

We shall look forward to your participation this Thursday!

Regards.  =ppy

For and on behalf of the OntologySummit2010
anel Session-3 chairs, Dr. Amanda Vizedom

and Members of the OntologySummit2010 Organizing Committee

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010
--

------- Forwarded message (updated) --------
From: Peter Yim <peter.yim <at> cim3.com>
Date: Mon, Jan 11, 2010 at 2:38 PM
Subject: Ontology Summit 2010: virtual Panel Sessions on "Content,"
"Requirements" & "Quality" - Jan-14, Feb-4 & Feb-11.
To: "[ontolog-invitation]" <ontolog-invitation <at> ontolog.cim3.net>

****************** Headlines ***********************

*Thu 14 Jan 2010* - OntologySummit2010: "Content" Panel Discussion,
Session-2 - Co-chairs: Professor Michael Gruninger and Dr. Leo Obrst
- see details on the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_01_14

*Thu 4 Feb 2010* - OntologySummit2010: "Requirements" Panel
Discussion, Session-3 - Co-chairs: Dr. Amanda Vizedom - see details on
the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_02_04

*Thu 11 Feb 2010* - OntologySummit2010: "Quality" Panel Discussion,
Session-4 - Co-chairs: Professor Barry Smith and Dr. Fabian Neuhaus  -
see details on the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_02_11

*Register your attendance* by emailing <peter.yim <at> cim3.com> off-line
or register yourself directly to the wiki session page.
Please specify the date of name of the session(s) you are registering
for.  ... *RSVP* (register for the Jan-14 session now!)

********************* Details ************************

This is our 5th Ontology Summit, a joint initiative by NIST, Ontolog,
NCOR, NCBO and IAOA with the support of our co-sponsors. The theme
adopted for this Summit is: "Creating the Ontologists of the Future"
and was launched on 10-Dec-2009. Like previous years, this Ontology
Summit will comprise of three months of virtual discourse, over our
archived mailing lists, wiki, and virtual panel sessions (like this
one), and will culminate in a 2-day face-to-face workshop/symposium to
be held on Mon & Tue, 15 & 16-March-2010 at NIST (Gaithersburg,
Maryland, USA.) ...

These sessions, like all Ontolog virtual events, are open and free of
charge. Anyone who is interested, or (better still) who may have
something to contribute, is welcome. Please refer to event details on
the session pages, to which the hyperlink is given above, where you
will find session agenda, conference call dial-in, slides and other
pertinent information. Feel free to pass this invitation along to
colleagues who may also find these sessions to be of interest.

*RSVP* by emailing Peter Yim at <peter.yim <at> cim3.com> offline with your
name, affiliation and session you are attending (or add yourself
directly to the session page if you are already an Ontolog or Ontology
Summit community member) so that we can prepare enough resources to
support everyone. [Please state clearly the date of the session you
are registering for in your email.] ... All respondents will be
subscribed (if they aren't already so) to the [ontology-summit]
mailing list so they are participate in the virtual discourse.

These sessions will be recorded and made available in a publicly
accessible archive. Therefore, before participating, please make sure
you are cognizant of our IPR policy (ref:
http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid32).

Regards.  =ppy

Peter Yim
Co-convener, Ontolog

For and on behalf of the

OntologySummit2010 - General Co-chairs,
Dr. Steven Ray (CMU) & Professor Barry Smith (SUNY-Buffalo)

and Members of the
OntologySummit2010 Organizing Committee

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010
--

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Guillermo Barsky | 1 Feb 14:00 2010
Picon

Guillermo Barsky/Sistemas/Administracion/OSDE/OSDE está ausente de la oficina.

Estaré ausente de la oficina desde el 29/01/2010 y no volveré hasta el 15/02/2010.

Ante una urgencia, comunicarse con Raúl Luna.

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Peter Yim | 1 Feb 18:34 2010

Fwd: Ontology Summit 2010: virtual Panel Sessions on "Training Requirements for Ontologists" - Thu 2010.02.04

ERRATA ... (thanks to AmandaVizedom and RaviSharma for catching it
simultaneously)

Sorry folks ... the first link on my last message should have read:

  http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_02_04

(and not: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_01_14
 which is for the last "Content" panel session ... a good refresher,
though, as a preparation for coming to this one.)

Regards.  =ppy
--

---------- Forwarded message (*updated) ----------
From: Peter Yim <peter.yim <at> cim3.com>
Date: Mon, Feb 1, 2010 at 12:17 AM
Subject: Re: Ontology Summit 2010: virtual Panel Sessions on "Training
Requirements for Ontologists" - Thu 2010.02.04
To: "[ontolog-invitation]" <ontolog-invitation <at> ontolog.cim3.net>

Re: OntologySummit2010: "Creating the Ontologists of the Future"
Virtual Panel Session-3 - "Training Requirements for Ontologists"

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_02_04 *

Coming up this week is our Ontology Summit 2010: virtual panel
Session-3 on education and training "Requirements" for the
ontologists. Please register your attendance for this session and mark
your calendar for the "Quality" panel session-4 the will featured in
the immediately following week (Thu 2010.02.11).

In this upcoming 4-Feb-2010 panel session-3, entitled: "What Are We
Training For?" our chair, Dr. Amanda Vizedom will be joined by an
expert panel that includes Professor Denise Bedford, Dr. Michael
Uschold, Dr. John Sowa (... more). Together, they will address the
title question, as well as "What do working ontologists need to know?"
and "What do ontologists need to be able to do?" The aim is to develop
a richer and more clear picture of the requirements of employability
(those trained are well-prepared for the available jobs) and
deployability (those who hire trained ontologists find them ready and
able to perform the needed work). The session will then be opened to
all participants for Q&A and discussion with the co-chairs and the
panel. Our goal will be to the goal is to bring a strong "end-user"
voice to the discussion, and to stimulate thinking and discussion
across the Summit community as a whole.

*RSVP* by emailing the sender (<mailto:peter.yim <at> cim3.com>, offline
please)  or add yourself directly to the session page if you are
already an Ontolog or prior-year ontology-summit community member) so
that we can prepare enough resources to support everyone.

We shall look forward to your participation this Thursday!

Regards.  =ppy

For and on behalf of the OntologySummit2010
anel Session-3 chairs, Dr. Amanda Vizedom

and Members of the OntologySummit2010 Organizing Committee

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010
--

------- Forwarded message (updated) --------
From: Peter Yim <peter.yim <at> cim3.com>
Date: Mon, Jan 11, 2010 at 2:38 PM
Subject: Ontology Summit 2010: virtual Panel Sessions on "Content,"
"Requirements" & "Quality" - Jan-14, Feb-4 & Feb-11.
To: "[ontolog-invitation]" <ontolog-invitation <at> ontolog.cim3.net>

****************** Headlines ***********************

*Thu 14 Jan 2010* - OntologySummit2010: "Content" Panel Discussion,
Session-2 - Co-chairs: Professor Michael Gruninger and Dr. Leo Obrst
- see details on the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_01_14

*Thu 4 Feb 2010* - OntologySummit2010: "Requirements" Panel
Discussion, Session-3 - Co-chairs: Dr. Amanda Vizedom - see details on
the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_02_04

*Thu 11 Feb 2010* - OntologySummit2010: "Quality" Panel Discussion,
Session-4 - Co-chairs: Professor Barry Smith and Dr. Fabian Neuhaus  -
see details on the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_02_11

*Register your attendance* by emailing <peter.yim <at> cim3.com> off-line
or register yourself directly to the wiki session page.
Please specify the date of name of the session(s) you are registering
for.  ... *RSVP* (register for the Jan-14 session now!)

********************* Details ************************

This is our 5th Ontology Summit, a joint initiative by NIST, Ontolog,
NCOR, NCBO and IAOA with the support of our co-sponsors. The theme
adopted for this Summit is: "Creating the Ontologists of the Future"
and was launched on 10-Dec-2009. Like previous years, this Ontology
Summit will comprise of three months of virtual discourse, over our
archived mailing lists, wiki, and virtual panel sessions (like this
one), and will culminate in a 2-day face-to-face workshop/symposium to
be held on Mon & Tue, 15 & 16-March-2010 at NIST (Gaithersburg,
Maryland, USA.) ...

These sessions, like all Ontolog virtual events, are open and free of
charge. Anyone who is interested, or (better still) who may have
something to contribute, is welcome. Please refer to event details on
the session pages, to which the hyperlink is given above, where you
will find session agenda, conference call dial-in, slides and other
pertinent information. Feel free to pass this invitation along to
colleagues who may also find these sessions to be of interest.

*RSVP* by emailing Peter Yim at <peter.yim <at> cim3.com> offline with your
name, affiliation and session you are attending (or add yourself
directly to the session page if you are already an Ontolog or Ontology
Summit community member) so that we can prepare enough resources to
support everyone. [Please state clearly the date of the session you
are registering for in your email.] ... All respondents will be
subscribed (if they aren't already so) to the [ontology-summit]
mailing list so they are participate in the virtual discourse.

These sessions will be recorded and made available in a publicly
accessible archive. Therefore, before participating, please make sure
you are cognizant of our IPR policy (ref:
http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid32).

Regards.  =ppy

Peter Yim
Co-convener, Ontolog

For and on behalf of the

OntologySummit2010 - General Co-chairs,
Dr. Steven Ray (CMU) & Professor Barry Smith (SUNY-Buffalo)

and Members of the
OntologySummit2010 Organizing Committee

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010
--

_________________________________________________________________
Msg Archives: http://ontolog.cim3.net/forum/ontology-summit
Subscribe/Config: http://ontolog.cim3.net/mailman/listinfo/ontology-summit/
Unsubscribe: mailto:ontology-summit-leave <at> ontolog.cim3.net
Community Files: http://ontolog.cim3.net/file/work/OntologySummit2010/
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Obrst, Leo J. | 1 Feb 21:11 2010
Picon

Axiome?

Folks,

I am trying to use the AXIOME tab in Protégé 3.4.2, Build 562. But there are no sub-tabs available,
contrary to the documentation. It says it is available in Config, but it's not in Help/About Plugins. The
online documentation says it is in 3.4.2, but it apparently is not,
http://protegewiki.stanford.edu/index.php/Axiom%C3%A9#Installation. Was it excluded from this
build for some  reason, or is it broken?

Thanks,
Leo

_____________________________________________ 
Dr. Leo Obrst		The MITRE Corporation, Information Semantics 
lobrst <at> mitre.org  	Information Discovery & Understanding, Command & Control Center
Voice: 703-983-6770	7515 Colshire Drive, M/S H305 
Fax: 703-983-1379	McLean, VA 22102-7508, USA

  

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Obrst, Leo J. | 1 Feb 21:37 2010
Picon

Re: Axiome?

Also, there is a jar file in the plugins folder.

Thanks,
Leo

-----Original Message-----
From: protege-discussion-bounces <at> mailman.stanford.edu
[mailto:protege-discussion-bounces <at> mailman.stanford.edu] On Behalf Of Obrst, Leo J.
Sent: Monday, February 01, 2010 3:12 PM
To: protege-discussion <at> mailman.stanford.edu
Subject: [protege-discussion] Axiome?

Folks,

I am trying to use the AXIOME tab in Protégé 3.4.2, Build 562. But there are no sub-tabs available,
contrary to the documentation. It says it is available in Config, but it's not in Help/About Plugins. The
online documentation says it is in 3.4.2, but it apparently is not,
http://protegewiki.stanford.edu/index.php/Axiom%C3%A9#Installation. Was it excluded from this
build for some  reason, or is it broken?

Thanks,
Leo

_____________________________________________ 
Dr. Leo Obrst		The MITRE Corporation, Information Semantics 
lobrst <at> mitre.org  	Information Discovery & Understanding, Command & Control Center
Voice: 703-983-6770	7515 Colshire Drive, M/S H305 
Fax: 703-983-1379	McLean, VA 22102-7508, USA

  

_______________________________________________
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protege-discussion <at> lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/protege-discussion

Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
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Olivier Biot | 1 Feb 23:59 2010
Picon

API method for finding all instances through a transitive property?

Imagine I have a Part class in which I defined the transitive
"isPartOf" property between Part instances. From a given Part instance
I want to follow the "isPartOf" property up to the top Part instance
to which it is connected through the "isPartOf" property.

A simple instantiation of this is given below:
1. Belgium isPartOf WesternEurope
2. Poland isPartOf EasternEurope
3. WesternEurope isPartOf Europe
4. EasternEurope isPartOf Europe
5. Europe isPartOf TheWorld
6. Africa isPartOf TheWorld

If I start at Belgium I want to see: { WesternEurope, Europe, TheWorld }.
Starting from Poland I want to see: { EasternEurope, Europe, TheWorld }.
Starting from Africa I want to see: { TheWorld }.

How do I do this with the Protege-OWL API?

Best regards,

Olivier
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alaa hedib | 2 Feb 23:23 2010
Picon

DL query error message


i have FaCT++ only in Resoner menu, but when i Switch to it i receive this  message "inconsistent ontology exception FaCT++. kernel inconsistent ontology " and still have the old DLquery error 
 Alaa

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Obrst, Leo J. | 3 Feb 02:14 2010
Picon

Re: Axiome?

Apparently no one is using Axiome?

Thanks,
Leo

_____________________________________________ 
Dr. Leo Obrst		The MITRE Corporation, Information Semantics 
lobrst <at> mitre.org  	Information Discovery & Understanding, Command & Control Center
Voice: 703-983-6770	7515 Colshire Drive, M/S H305 
Fax: 703-983-1379	McLean, VA 22102-7508, USA

  

-----Original Message-----
From: protege-discussion-bounces <at> mailman.stanford.edu
[mailto:protege-discussion-bounces <at> mailman.stanford.edu] On Behalf Of Obrst, Leo J.
Sent: Monday, February 01, 2010 3:38 PM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Axiome?

Also, there is a jar file in the plugins folder.

Thanks,
Leo

-----Original Message-----
From: protege-discussion-bounces <at> mailman.stanford.edu
[mailto:protege-discussion-bounces <at> mailman.stanford.edu] On Behalf Of Obrst, Leo J.
Sent: Monday, February 01, 2010 3:12 PM
To: protege-discussion <at> mailman.stanford.edu
Subject: [protege-discussion] Axiome?

Folks,

I am trying to use the AXIOME tab in Protégé 3.4.2, Build 562. But there are no sub-tabs available,
contrary to the documentation. It says it is available in Config, but it's not in Help/About Plugins. The
online documentation says it is in 3.4.2, but it apparently is not,
http://protegewiki.stanford.edu/index.php/Axiom%C3%A9#Installation. Was it excluded from this
build for some  reason, or is it broken?

Thanks,
Leo

_____________________________________________ 
Dr. Leo Obrst		The MITRE Corporation, Information Semantics 
lobrst <at> mitre.org  	Information Discovery & Understanding, Command & Control Center
Voice: 703-983-6770	7515 Colshire Drive, M/S H305 
Fax: 703-983-1379	McLean, VA 22102-7508, USA

  

_______________________________________________
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protege-discussion <at> lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/protege-discussion

Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
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Saeed Hassanpour | 3 Feb 08:55 2010
Picon

Re: [protege-discussion] Axiome?

Hi Leo,

For now on could you please post the question to protege-owl mailing
list <protege-owl <at> lists.stanford.edu>?

Axiome works based on syntactic structure of rules and tries to parse
them. So if there is a structural/syntactic problem with rules, it
returns blank. I suggest to review the rules to make sure that they
are syntactically correct.
If everything looks right in the rule base, you can send the rule base
+ ontology to me, I 'll be happy to take a look and find out what
causes the problem.

Best,
Saeed
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Gmane