From ludaesch at sdsc.edu  Mon May  5 05:50:41 2003
From: ludaesch at sdsc.edu (Bertram Ludaescher)
Date: Mon, 5 May 2003 05:50:41 -0700 (PDT)
Subject: [seek-ucsd] SEEK Meeting Tuesday 462
Message-ID: <200305051250.h45Cofnl014885@multivac.sdsc.edu>

Dear all:

We are meeting on Tuesday 11am in 462 at SDSC (also known as the "dark
room" ;-)

AGENDA: The upcoming SEEK technical/developers meetings!!
Specifically:

1. 11-11:45am What we want to do for SMS (see below)

2. 11:45-12:15pm (suggestion): Jenny presents the technical details of
the "schema matching" work she has done with Joseph.

Hope to see you tomorrow!

And now to the details: 



     ------------------------------------------------------------
		      Semantic Mediation System
     ------------------------------------------------------------
As you will see by going to the meeting overview at 
	http://seek.ecoinformatics.org/meetings/dev-20030510/index.html
the meeting starts on May 10th with the Semantic Mediation System
(SMS) meeting, which I coordinate.


From ludaesch at sdsc.edu  Tue May  6 08:46:22 2003
From: ludaesch at sdsc.edu (Bertram Ludaescher)
Date: Tue,  6 May 2003 08:46:22 -0700 (PDT)
Subject: [seek-ucsd] Re: SEEK Meeting Tuesday 462
In-Reply-To: <200305051250.h45Cofnl014885@multivac.sdsc.edu>
References: <200305051250.h45Cofnl014885@multivac.sdsc.edu>
Message-ID: <16055.55301.706523.353027@multivac.sdsc.edu>

Dear all:

A gentle reminder for our weekly SEEK meeting.

Today's agenda (since I didn't hear back any other suggestions) will
be the upcoming SEEK meeting. In particular, I would like to dicuss
issues of the Semantic Mediation System:

1. Brief review of what the SEEK-SMS system is supposed to do.

2. Planning what kind of presentations we could do on the SMS
technologies during our SMS session.

Bertram


>>>>> "BL" == Bertram Ludaescher <ludaesch at sdsc.edu> writes:
BL> 
BL> Dear all:
BL> 
BL> We are meeting on Tuesday 11am in 462 at SDSC (also known as the "dark
BL> room" ;-)
BL> 
BL> AGENDA: The upcoming SEEK technical/developers meetings!!
BL> Specifically:
BL> 
BL> 1. 11-11:45am What we want to do for SMS (see below)
BL> 
BL> 2. 11:45-12:15pm (suggestion): Jenny presents the technical details of
BL> the "schema matching" work she has done with Joseph.
BL> 
BL> Hope to see you tomorrow!
BL> 
BL> And now to the details: 
BL> 
BL> 
BL> 
BL>      ------------------------------------------------------------
BL> 		      Semantic Mediation System
BL>      ------------------------------------------------------------
BL> As you will see by going to the meeting overview at 
BL> 	http://seek.ecoinformatics.org/meetings/dev-20030510/index.html
BL> the meeting starts on May 10th with the Semantic Mediation System
BL> (SMS) meeting, which I coordinate.
BL> 
>> From UCSD the following people are listed for SMS:
BL>     Joseph Goguen UCSD goguen at cs.ucsd.edu 
BL>     Bertram Ludaescher SDSC ludaesch at sdsc.edu 
BL>     Liying Sui UCSD  
BL>     Shawn Bowers (new hire) UCSD  
BL>     Victor Vianu UCSD vdvianu at ucsd.edu 
BL>     Jenny Wang UCSD jwang at sdsc.edu 
BL> 
BL> 
BL> Joseph, Victor: 
BL> It would be good if we could use some of the time this Tuesday to
BL> discuss any presentations that could be prepared to trigger
BL> discussions for the SMS part of the meeting.
BL> 
BL> I encourage you to check out (the very early state of) the design for
BL> the SMS system:
BL> 
BL> http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/docs/design/design-sms-1.0.0.txt?rev=1.3&content-type=text/plain
BL> 
>> From there you will find the following ...
BL>     Milestone1 (by May 2003 Technical Meeting): 
BL>     -- Initial suggestion of languages for SW1, e.g., DATA TYPES in XML
BL>     Schema, SEMANTIC TYPES and OTHER CONSTRAINTS in OWL.
BL>     -- Overview of possible QUERY PLANNING and REASONING SUPPORT for
BL>     those languages.
BL> 
BL> 
BL> ------------------------------------------------------------
BL>                           EcoGrid
BL> ------------------------------------------------------------
BL> This is led by Raja who may call a separate meeting on this.
BL> Bing Zhu is our new member on board of SEEK! (since May 1st).
BL> Welcome Bing!!
BL> Also: We have invited our local web services czar Tony Fountain to
BL> present his work on web service architectures for ecology and other
BL> data during the SEEK meeting.
BL> It seems that the EcoGrid goes web services (AFAIK).
BL> 
BL> ------------------------------------------------------------
BL> 		Analysis and Modeling System (AMS)
BL> ------------------------------------------------------------
BL> This should be interesting for the SMS folks too. This is about the
BL> front end of the SEEK system (PtolemyII being the most likely
BL> candidate) as well as the "pipeline/workflow engine".
BL> 
BL> An interesting exercise could be to model David Stockwell's
BL> application (which he presented a while ago during our local meetings) 
BL> as an analytical pipeline.
BL> 
BL> 
BL> Bertram


From guilian at cs.ucsd.edu  Tue May  6 10:07:18 2003
From: guilian at cs.ucsd.edu (Jenny Guilian WANG)
Date: Tue, 6 May 2003 10:07:18 -0700 (PDT)
Subject: [seek-ucsd] Re: SEEK Meeting Tuesday 462
In-Reply-To: <16055.55301.706523.353027@multivac.sdsc.edu>
Message-ID: <Pine.GSO.4.33.0305061003220.29960-100000@gradlab.ucsd.edu>

Hi, all,

As Bertram suggested, I'd like to present our work on schema
matching/mapping today if most of you are interested.

Cheers,

Jenny

On Tue, 6 May 2003, Bertram Ludaescher wrote:

>
> Dear all:
>
> A gentle reminder for our weekly SEEK meeting.
>
> Today's agenda (since I didn't hear back any other suggestions) will
> be the upcoming SEEK meeting. In particular, I would like to dicuss
> issues of the Semantic Mediation System:
>
> 1. Brief review of what the SEEK-SMS system is supposed to do.
>
> 2. Planning what kind of presentations we could do on the SMS
> technologies during our SMS session.
>
> Bertram
>
>
> >>>>> "BL" == Bertram Ludaescher <ludaesch at sdsc.edu> writes:
> BL>
> BL> Dear all:
> BL>
> BL> We are meeting on Tuesday 11am in 462 at SDSC (also known as the "dark
> BL> room" ;-)
> BL>
> BL> AGENDA: The upcoming SEEK technical/developers meetings!!
> BL> Specifically:
> BL>
> BL> 1. 11-11:45am What we want to do for SMS (see below)
> BL>
> BL> 2. 11:45-12:15pm (suggestion): Jenny presents the technical details of
> BL> the "schema matching" work she has done with Joseph.
> BL>
> BL> Hope to see you tomorrow!
> BL>
> BL> And now to the details:
> BL>
> BL>
> BL>
> BL>      ------------------------------------------------------------
> BL> 		      Semantic Mediation System
> BL>      ------------------------------------------------------------
> BL> As you will see by going to the meeting overview at
> BL> 	http://seek.ecoinformatics.org/meetings/dev-20030510/index.html
> BL> the meeting starts on May 10th with the Semantic Mediation System
> BL> (SMS) meeting, which I coordinate.
> BL>
> >> From UCSD the following people are listed for SMS:
> BL>     Joseph Goguen UCSD goguen at cs.ucsd.edu
> BL>     Bertram Ludaescher SDSC ludaesch at sdsc.edu
> BL>     Liying Sui UCSD
> BL>     Shawn Bowers (new hire) UCSD
> BL>     Victor Vianu UCSD vdvianu at ucsd.edu
> BL>     Jenny Wang UCSD jwang at sdsc.edu
> BL>
> BL>
> BL> Joseph, Victor:
> BL> It would be good if we could use some of the time this Tuesday to
> BL> discuss any presentations that could be prepared to trigger
> BL> discussions for the SMS part of the meeting.
> BL>
> BL> I encourage you to check out (the very early state of) the design for
> BL> the SMS system:
> BL>
> BL> http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/docs/design/design-sms-1.0.0.txt?rev=1.3&content-type=text/plain
> BL>
> >> From there you will find the following ...
> BL>     Milestone1 (by May 2003 Technical Meeting):
> BL>     -- Initial suggestion of languages for SW1, e.g., DATA TYPES in XML
> BL>     Schema, SEMANTIC TYPES and OTHER CONSTRAINTS in OWL.
> BL>     -- Overview of possible QUERY PLANNING and REASONING SUPPORT for
> BL>     those languages.
> BL>
> BL>
> BL> ------------------------------------------------------------
> BL>                           EcoGrid
> BL> ------------------------------------------------------------
> BL> This is led by Raja who may call a separate meeting on this.
> BL> Bing Zhu is our new member on board of SEEK! (since May 1st).
> BL> Welcome Bing!!
> BL> Also: We have invited our local web services czar Tony Fountain to
> BL> present his work on web service architectures for ecology and other
> BL> data during the SEEK meeting.
> BL> It seems that the EcoGrid goes web services (AFAIK).
> BL>
> BL> ------------------------------------------------------------
> BL> 		Analysis and Modeling System (AMS)
> BL> ------------------------------------------------------------
> BL> This should be interesting for the SMS folks too. This is about the
> BL> front end of the SEEK system (PtolemyII being the most likely
> BL> candidate) as well as the "pipeline/workflow engine".
> BL>
> BL> An interesting exercise could be to model David Stockwell's
> BL> application (which he presented a while ago during our local meetings)
> BL> as an analytical pipeline.
> BL>
> BL>
> BL> Bertram
> _______________________________________________
> seek-ucsd mailing list
> seek-ucsd at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/seek-ucsd
>



From davids at sdsc.edu  Tue May  6 12:51:29 2003
From: davids at sdsc.edu (David Stockwell)
Date: Tue, 06 May 2003 12:51:29 -0700
Subject: [seek-ucsd] ToolBus
Message-ID: <3EB81241.1050302@sdsc.edu>

Here are some links to information about the ToolBus communication software
and an applications for the life sciences called PathPort.

Cheers

 http://adam.wins.uva.nl/~olivierp/toolbus/
http://www.vbi.vt.edu/pathport/xml/index.shtml
https://www.vbi.vt.edu/article/articleview/316
http://www.vbi.vt.edu/pathport/document/design/javadoc/edu/vt/vbi/pathport/client/toolbus/ToolBus.html





From davids at sdsc.edu  Tue May  6 13:00:24 2003
From: davids at sdsc.edu (David Stockwell)
Date: Tue, 06 May 2003 13:00:24 -0700
Subject: [seek-ucsd] Semantic Web Tools
In-Reply-To: <3EB81241.1050302@sdsc.edu>
References: <3EB81241.1050302@sdsc.edu>
Message-ID: <3EB81458.40606@sdsc.edu>

Here are additional tools for the semantic web
being developed at James Hendlers Lab in Maryland (MIND)

http://www.mindswap.org/

Cheers


David Stockwell wrote:

> Here are some links to information about the ToolBus communication 
> software
> and an applications for the life sciences called PathPort.
>
> Cheers
>
> http://adam.wins.uva.nl/~olivierp/toolbus/
> http://www.vbi.vt.edu/pathport/xml/index.shtml
> https://www.vbi.vt.edu/article/articleview/316
> http://www.vbi.vt.edu/pathport/document/design/javadoc/edu/vt/vbi/pathport/client/toolbus/ToolBus.html
>
>
>
> _______________________________________________
> seek-ucsd mailing list
> seek-ucsd at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/seek-ucsd





From davids at sdsc.edu  Tue May  6 13:52:38 2003
From: davids at sdsc.edu (David Stockwell)
Date: Tue, 06 May 2003 13:52:38 -0700
Subject: [seek-ucsd] Semantic Web Tools
In-Reply-To: <3EB81458.40606@sdsc.edu>
References: <3EB81241.1050302@sdsc.edu> <3EB81458.40606@sdsc.edu>
Message-ID: <3EB82096.3060405@sdsc.edu>

For an introduction,  review and bibliography of the Semantic Web see

Enhanced: Science and the Semantic Web by James Hendler at
*
*http://www.sciencemag.org/cgi/content/full/299/5606/520#note1

Cheers

David Stockwell wrote:

> Here are additional tools for the semantic web
> being developed at James Hendlers Lab in Maryland (MIND)
>
> http://www.mindswap.org/
>
> Cheers
>
>
> David Stockwell wrote:
>
>> Here are some links to information about the ToolBus communication 
>> software
>> and an applications for the life sciences called PathPort.
>>
>> Cheers
>>
>> http://adam.wins.uva.nl/~olivierp/toolbus/
>> http://www.vbi.vt.edu/pathport/xml/index.shtml
>> https://www.vbi.vt.edu/article/articleview/316
>> http://www.vbi.vt.edu/pathport/document/design/javadoc/edu/vt/vbi/pathport/client/toolbus/ToolBus.html
>>
>>
>>
>> _______________________________________________
>> seek-ucsd mailing list
>> seek-ucsd at ecoinformatics.org
>> http://www.ecoinformatics.org/mailman/listinfo/seek-ucsd
>
>
>
>
> _______________________________________________
> seek-ucsd mailing list
> seek-ucsd at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/seek-ucsd





From ludaesch at sdsc.edu  Wed May 21 08:00:30 2003
From: ludaesch at sdsc.edu (Bertram Ludaescher)
Date: Wed, 21 May 2003 08:00:30 -0700 (PDT)
Subject: [seek-ucsd] Re: [seek] request for list of publications
In-Reply-To: <3ECA46C6.8040203@nceas.ucsb.edu>
References: <3ECA46C6.8040203@nceas.ucsb.edu>
Message-ID: <16075.36761.474132.46183@multivac.sdsc.edu>

Matt:

See the list of references below. I'll be out of town until Friday.

SEEKers at UCSD: 

Please send to Matt (and please cc me) the list of publications and
presentations that were supported by SEEK funding ASAP. As indicated
in his email he is assembling the report for NSF.

So here are my references (with URL where available). I know at least
from Raja and Joseph that they have additional ones, and I suspect
that David and Victor may have too.

*** Publications ***

[ABB+03] A Modeling and Execution Environment for Distributed
Scientific Workflows, I. Altintas, S. Bhagwanani, D. Buttler,
S. Chandra, Z. Cheng, M. Coleman, T. Critchlow, A. Gupta, W. Han,
L. Liu, B. Lud?scher, C. Pu, R. Moore,A. Shoshani, and M. Vouk, In
15th Intl. Conference on Scientific and Statistical Database
Management (SSDBM), Boston, Massachussets, 2003. 
http://kbis.sdsc.edu/SciDAC-SDM/p1-ssdbm-demo.pdf

[LAG03] Compiling Abstract Scientific Workflows into Web Service
Workflows, B. Lud?scher, I. Altintas, A. Gupta, In 15th
Intl. Conference on Scientific and Statistical Database Management
(SSDBM), Boston, Massachussets, 2003. 
http://kbis.sdsc.edu/SciDAC-SDM/ludaescher-compiling.pdf

[LAG03b] B. Ludaescher, A. Gupta, and M. E. Martone. A Model-Based
Mediator System for Scientific Data Management. In T. Critchlow and
Z. Lacroix, editors, Bioinformatics: Managing Scientific Data.  Morgan
Kaufmann, 2003. to appear

[BCG+02] O. Boucelma, S. Castano, C. A. Goble, V. Josifovski,
Z. Lacroix, and B. Ludaescher. Report on the EDBT'2002 Panel on
Scientific Data Integration. SIGMOD Record, 31(4):107-112, 2002.


*** Tutorials/Classes *** 

[LAGL03] Scientific Data Integration and Mediation, B. Lud?scher,
I. Altintas, A. Gupta, and K. Lin, Tutorial at the NPACI All Hands
Meeting, San Diego, 2003
http://www.sdsc.edu/~ludaesch/Paper/ahm03-data-mediation.ppt

[Lud03] CSE-291: Ontologies in Data Integration, graduate class,
Department of Computer Science & Engineering, University of
California, San Diego, Spring 2003.
http://www.sdsc.edu/~ludaesch/CSE-291-Spring-03/


>>>>> "MJ" == Matt Jones <jones at nceas.ucsb.edu> writes:
MJ> 
MJ> Dear SEEK'ers,
MJ> We need to submit the annual report to NSF a bit early this year (at 
MJ> NSF's request), and so I have started compiling the report.  For this, I 
MJ> need a complete list of papers, book, other publications, and conference 
MJ> presentations that were supported under SEEK funding.  Could you send me 
MJ> a list with a full citation for all papers in which you were involved? 
MJ> I will also place this list on our web site, and I would like to place 
MJ> an electronic copy on the web site as well if that is permitted under 
MJ> your copyright agreement with the publisher.  So, please also send an 
MJ> electronic version of the paper if possible.
MJ> 
MJ> I need this list as soon as possible.
MJ> 
MJ> Thank you,
MJ> 
MJ> Matt
MJ> 
MJ> -- 
MJ> -------------------------------------------------------------------
MJ> Matt Jones                                     jones at nceas.ucsb.edu
MJ> http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
MJ> National Center for Ecological Analysis and Synthesis (NCEAS)
MJ> University of California Santa Barbara
MJ> Interested in ecological informatics? http://www.ecoinformatics.org
MJ> -------------------------------------------------------------------
MJ> 
MJ> _______________________________________________
MJ> seek mailing list
MJ> seek at ecoinformatics.org
MJ> http://www.ecoinformatics.org/mailman/listinfo/seek