Nabble - w3.org - semantic web

Extended Deadline, Visual Interfaces to the Social and Semantic Web, Hong Kong, 7th February 2010 (workshop co-located with IUI2010)

2009-12-01T03:01:56Z

Hi all,

Due to a postponement of the early bird registration deadline for
Intelligent User Interfaces 2010 (IUI2010) in Hong Kong, we have
decided to extend the deadline for submissions to the VISSW2010
workshop (Visual Interfaces to the Social and Semantic Web). The
revised dates are as follows:

* Paper submission deadline: 14th December, 2009 (11:59pm Hawaii time)
* Notification of acceptance: 5th January, 2010
* Camera-ready paper submission deadline: TBD

If you have any questions about the workshop please contact: vissw2010
[at] easychair [dot] org

Cheers,

Tom.

2009/10/20 Tom Heath <tom.heath@...>:

> [apologies if you see this announcement more than once...]
>
> CALL FOR PAPERS
> ------------------------------
> 2nd International Workshop on Visual Interfaces to the Social and
> Semantic Web (VISSW2010)
> In conjunction with the International Conference on Intelligent User
> Interfaces (IUI2010)
> Hong Kong, 7th February 2010
> http://www.smart-ui.org/events/vissw2010/
>
> INTRODUCTION
> -----------------------
>
> The continued growth and importance of the Social Web has resulted in
> ever increasing volumes of data created, published and consumed by
> users. This vast amount of data takes many forms, including text,
> images, video and more recently streams of status information from
> applications such as Twitter. Not only is this data accessible through
> more traditional means, such as desktop and laptop computers, but also
> via diverse platforms such as mobile phones and set-top boxes that
> bring unique constraints in terms of computing resources and user
> interfaces. Through the increasing availability of Web APIs, data that
> has traditionally been coupled with a specific application may now be
> exposed through novel interfaces developed by third parties, providing
> functionality not previously anticipated by the data owner.
>
> In tandem with the growth of the Social Web, the Web at large has
> experienced a significant evolution into a Web not just of linked
> documents, but also of Linked Data. This development, which exploits
> the Semantic Web technology stack, allows relationships to be
> expressed between items in distributed data sets, paving the way for
> integration of raw data from multiple, heterogeneous sources. Coupled
> with the increasing availability of APIs that expose structured (if
> not linked) data from the Social Web, application developers have a
> wealth of data available to them upon which they can build compelling
> visual interfaces.
>
> The ability to easily integrate vast amounts of data from across the
> Social and Semantic Web raises significant and exciting research
> challenges, not least of which how to provide effective access to and
> navigation across vast, heterogeneous and interconnected data sources.
> However, the need for intelligent and visual human interfaces to this
> evolving Web is not limited simply to the modalities of searching and
> browsing, important as these are. As the Web becomes increasingly
> populated with data, continues to evolve from a read-mainly to a
> read-write medium, and the level of social interaction supported on
> the Web increases, there is also a pressing need to support end-users
> who engage in a wide range of online tasks, such as publishing and
> sharing their own data on the Web.
>
> This workshop aims to bring together researchers and practitioners
> from diverse, complementary fields to discuss the latest research
> results and challenges in designing, implementing, and evaluating
> intelligent interfaces to structured or Linked Data in the context of
> the Social or Semantic Web. The workshop will serve as an opportunity
> for researchers to gain feedback on their work, and to identify
> potential collaborations with their peers. We believe that the
> potential for fostering links between a variety of facets of the IUI
> community will help to ensure an exciting workshop program.
>
> Information about the previous workshop can be found at:
> http://www.smart-ui.org/events/vissw2010/
>
> TOPICS OF INTEREST
> ----------------------------------
>
> Topics of interest include, but are not limited to:
>
> * Interfaces
> o Novel visualisation of structured, linked and aggregated
> data, originating from multiple sources.
> o Novel interfaces for high-volume transient data, e.g.
> feeds, streams and sensors.
> o 'Living' interfaces to constantly evolving data,
> vocabularies, and emerging links between them.
> o Task-centric interfaces for structured and/or Linked Data.
> o Interface components for displaying/interacting with
> aggregated, heterogeneous Linked Data, e.g. components for displaying
> provenance information.
> o Lightweight components and processes for casual users to
> publish/share their own content on the Web.
> o Ontology-based visualization of collections of data.
> * Interaction Paradigms
> o Novel interaction paradigms for textual, photos, music,
> videos, etc. on alternative platforms (e.g. mobile devices, set-top
> boxes, shared/public displays).
> o Novel interaction paradigms with structured, linked and
> aggregated data.
> o Investigation of task-centric interaction paradigms beyond
> search and browse.
> o Ontology-based interaction with collections of data.
> o Semantic models for interaction and their reuse on the web
> * Empirical Studies and Evaluation
> o Empirical studies that can guide the development of
> interfaces for Linked Data.
> o Use cases which present novel visualization requirements
> and expose interesting interaction challenges on the Social and
> Semantic Web.
> o Lessons learned from user-studies, pilot systems and live
> deployments in the Social and Semantic Web.
>
> SUBMISSIONS
> -----------------------
>
> We welcome three types of submissions:
>
> * Full papers which should be between 6 and 10 pages.
> * Short papers and position papers which should be up to 5 pages.
> * Demo papers which should be a 2 page description with a
> screenshot of the working prototype or preferably a link to an online
> demo.
>
> Submissions must be in PDF format and prepared according to the IUI
> format. Papers will be peer-reviewed by three independent reviewers.
> Papers can be submitted via the EasyChair system at:
> http://www.easychair.org/conferences?conf=vissw2010 . Accepted papers
> will be published in CEUR-WS.org proceedings.
>
> IMPORTANT DATES
> ------------------------------
>
> * Paper submission deadline: 30th November, 2009 (11:59pm Hawaii time)
> * Notification of acceptance: 18th December, 2009
> * Camera-ready paper submission deadline: 12th January, 2010
>
> REGISTRATION
> ------------------------
>
> Please refer to the main conference website for registration details:
> http://www.iuiconf.org/
>
> ORGANISERS
> ----------------------
>
> * Siegfried Handschuh, DERI, NUI Galway, Ireland
> * Tom Heath, Talis Information Ltd, UK
> * VinhTuan Thai, DERI, NUI Galway, Ireland
> * Ian Dickinson, Epimorphics Ltd, UK
> * Lora Aroyo, VU Amsterdam, The Netherlands
> * Valentina Presutti, Semantic Technology Laboratory (STLab), ISTC, Italy
>
> PROGRAMME COMMITTEE
> ------------------------------------------
>
> * Peter Brusilovsky, University of Pittsburgh, US
> * Karen Church, Telefonica Research, ES
> * Duane Degler, Design for Context, US
> * Bertrand Delacretaz, Day, CH
> * Aldo Gangemi, CNR-ISTC, IT
> * Alain Giboin, INRIA, FR
> * Michael Hausenblas, DERI, NUI Galway, IE
> * Nathalie Henry, Microsoft Research, US
> * David Karger, MIT, US
> * Nicholas J. Kings, BT, UK
> * Georgi Kobilarov, FU Berlin, DE
> * Steffen Lohmann, University of Duisburg, DE
> * Wolfgang Maass, University of St.Gallen, CH
> * Knud Möller, DERI, NUI Galway, IE
> * Enrico Motta, The Open University, UK
> * Alexandre Passant, DERI, NUI Galway, IE
> * Adam Perer, IBM Research, IL
> * Massimo Romanelli, DFKI, DE
> * Lloyd Rutledge, Open Universiteit, NL
> * Harald Sack, Hasso-Plattner-Institut, DE
> * Sebastian Schaffert, Salzburg Research, AT
> * Bernhard Schandl, Uni Vienna, AT
> * Daniel Schwabe, PUC-Rio, BR
> * Barry Smyth, University College Dublin, IE
> * Carlo Torniai, Simon Fraser University, CA
> * Fabio Vitali, University of Bologna, IT
> * Earl Wagner, Northwestern University, US
> * Jun Zhao, Oxford University, UK
>
> CONTACT INFORMATION
> --------------------------------------
>
> If you have any questions, please feel free to contact the workshop
> organizers at: vissw2010 [at] easychair [dot] org
>
>
> --
> Dr Tom Heath
> Researcher
> Platform Division
> Talis Information Ltd
> T: 0870 400 5000
> W: http://www.talis.com/
>

--
Dr Tom Heath
Researcher
Platform Division
Talis Information Ltd
T: 0870 400 5000
W: http://www.talis.com/

From forum: w3.org - semantic-web

Sesame 2.3.0 released

2009-12-01T02:56:24Z

Dear all,

We have just released Sesame 2.3.0. Sesame 2.3.0 has major improvements
on three subjects: NativeStore performance, query optimization and the
SeRQL query language. Of course, there's also the usual set of bug
fixes. For more info, please visit http://www.openrdf.org/

Regards,

Arjohn Kampman

--
Arjohn Kampman, Senior Software Engineer
Aduna - Semantic Power
www.aduna-software.com

From forum: w3.org - semantic-web

ISO/DIS 25964-1 now available

2009-12-01T01:18:30Z

At last everyone can access a Draft of ISO 25964-1 “Thesauri and
interoperability with other vocabularies. Thesauri for information
retrieval” . You can view and comment on it *free of charge* on the BSI
site (see details below). Comments on the associated draft XML schema
are best submitted via the NISO site.

Work has been under way since May 2008 to revise and extend the
international standards for thesauri, ISO 2788 and ISO 5964. The updated
content of these two standards, plus other material needed to support
interoperability, will be combined in a new standard ISO 25964, as follows:
ISO 25964. Thesauri and interoperability with other vocabularies
Part 1: Thesauri for information retrieval
Part 2: Interoperability with other vocabularies

Part 1, officially numbered ISO/DIS 25964-1, has been released as a
draft available for public comment until the end of February 2010.

Part 1 covers monolingual and multilingual thesauri. As well as updating
the entire content of ISO 2788 and ISO 5964, coverage includes:
guidelines for thesaurus management software;
a data model for monolingual and multilingual thesauri;
recommendations for exchange formats and protocols.
An XML schema for data exchange is included as an informative appendix,
and is available free of charge at http://www.niso.org/schemas/iso25964/
. Please click the “comments” link on this web page, to give your
feedback on the draft schema.

While the data model is not exactly the same as the SKOS model, there is
a lot of commonality between the two, and some members of the SKOS
community have proposed extensions to achieve better alignment. Let us
all hope this effort pays off!

The whole standard may be viewed online at http://drafts.bsigroup.com/.
You have to register on the site, but there is no charge for
registration, and it is easy to submit comments on each clause, whether
you are in the UK or not. Alternatively a hard copy is available from
BSI at a price of £36 (just £18 for BSI members). Place your order
online at http://shop.bsigroup.com/ (where the draft is listed under an
alternative number of 09/30165649 DC).

A copy of the whole draft may also be obtained from any of the national
standards bodies which are members of ISO, the International
Organization for Standards.

Development of the standard is based on BS 8723, which was published in
5 parts during 2005-2008. The work is managed by a Working Group known
as ISO TC46/SC9/WG8, which has participants from 15 countries and is led
by Stella Dextre Clarke of the UK. The Secretariat is provided by NISO
(USA). WG8 is now actively working on Part 2 of the standard, which will
provide guidance on mapping between vocabularies.

See official website at http://www.niso.org/workrooms/iso25964. Further
information may be found in the ASIS&T Bulletin, at
http://www.asis.org/Bulletin/Oct-08/OctNov08_DextreClark.pdf, and in an
article in the Technology Watch Report at
http://metadaten-twr.org/tag/iso-25964/ .

--
*****************************************************
Stella Dextre Clarke
Information Consultant
Luke House, West Hendred, Wantage, OX12 8RR, UK
Tel: 01235-833-298
Fax: 01235-863-298
stella@...
*****************************************************

From forum: w3.org - public-esw-thes

ECCOMAS CFD 2010 Mini-Symposium on Image Processing and Visualization

2009-11-30T10:47:34Z

Image Processing and Visualization

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

(Apologies for cross-posting)

Mini-Symposium on Image Processing and Visualization

ECCOMAS CFD 2010 - Fifth European Conference on Computational Fluid Dynamics

June 14th -17th, 2010, Lisbon, Portugal

http://www.eccomas-cfd2010.org

We would appreciate if you could distribute this information by your colleagues and co-workers.

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

Dear Colleague,

Within the ECCOMAS CFD 2010 - Fifth European Conference on Computational Fluid Dynamics (http://www.eccomas-cfd2010.org), to be held in Lisbon, Portugal, on 14-17 June 2010, we are organizing the Mini-Symposium on “Image Processing and Visualization”.

Due to your research activities in the related fields, we would like to invite you to submit an invited abstract to our mini-symposium. Your contribution is mostly welcomed, and we would be honoured if you could accept this invitation.

TOPICS OF INTEREST (not restricted to):

- Image Analysis;

- Image Restoration, Compression, Segmentation and Description;

- Object Tracking, Matching, Recognition and Reconstruction;

- Visual Inspection;

- 3D Vision;

- Data Processing, Modeling and Analysis;

- Scientific Visualization;

- Enhanced Visualization;

- Human Computer Interaction;

- Simulation and Animation;

- Virtual Reality;

- Software Development for Image Processing and Visualization;

- Grid Computing in Image Processing and Visualization;

- Applications of Image Processing and Visualization on fluid dynamics.

IMPORTANT DATES:

Deadline for submission of abstracts: December 31, 2009;

Notification of acceptance: January 15, 2010;

Submission of camera-ready manuscripts: March 31, 2010.

ABSTRACT SUBMISSION:

Please go to the abstract submission page (http://www.eccomas-cfd2010.org/abstractSubmission.php) and select the Mini-Symposium on “Image Processing and Visualization”.

Please, see the Instructions for Authors at: http://www.eccomas-cfd2010.org/authorsInstructions.php

With kind regards,

João Manuel R. S. Tavares, University of Porto, Portugal, tavares@...

Renato Natal Jorge, University of Porto, Portugal, rnatal@...

(Organizers of the Mini-Symposium on “Image Processing and Visualization”)

From forum: w3.org - semantic-web

FLoC 2010: Call for Papers

2009-11-30T09:19:07Z

2010 FEDERATED LOGIC CONFERENCE (FLoC'10)

Edinburgh, Scotland, U.K.
July 9-21, 2010
http://www.floc-conference.org

CALL FOR PAPERS

* The fifth Federated Logic Conference (FLoC'10) will be held in
Edinburgh, Scotland, U.K. (www.edinburgh.org), in July 2010, at the
School of Informatics at University of Edinburgh (www.inf.ed.ac.uk).

* The following conferences will participate in FLoC:
- CAV 2010: Int'l Conference on Computer-Aided Verification
- CSF 2010: IEEE Computer Security Foundations Symposium
- ICLP 2010: Int'l Conference on Logic Programming
- IJCAR 2010: Int'l Joint Conference on Automated Reasoning
- ITP 2010: Int'l Conference on Interactive Theorem Proving
- LICS 2010: IEEE Symposium on Logic in Computer Science
- RTA 2010: Int'l Conference on Rewriting Techniques and Applications
- SAT 2010: Int'l Conference on Theory and Applications of
Satisfiability Testing

* Plenary events involving all the conferences are planned. In addition
to the participating conferences, FLoC'10 will host a number of
pre- and post-conference workshops. There will be receptions in the
Edinburgh Castle and at the National Galleries of Scotland.

* Travel support for US student participants is expected.

* Detailed calls for papers (as well as submission instructions) for each
of the participating conferences can be found at the FLoC'10 website at
http://www.floc-conference.org

* Important dates:
- CAV 2010:
PC chairs: Byron Cook, Paul Jackson, Tayssir Touili
Jan 11: abstract submission deadline
Jan 15: paper submission deadline
- CSF 2010:
PC chairs: Michael Backes, Andrew Myers
Feb 04: abstract submission deadline
Feb 08: paper submission deadline
- ICLP 2010:
PC chairs: Manuel Hermenegildo, Torsten Schaub
Jan 26: paper registration deadline
Feb 02: paper submission deadline
- IJCAR 2010:
PC chairs: Jürgen Giesl, Reiner Hähnle
Jan 15: abstract submission deadline
Jan 22: paper submission deadline
- ITP 2010:
PC chairs: Matt Kaufmann, Lawrence C. Paulson
Jan 15: abstract submission deadline
Jan 22: paper submission deadline
- LICS 2010:
PC chair: Jean-Pierre Jouannaud
Jan 10: abstract submission deadline
Jan 17: paper submission deadline
- RTA 2010:
PC chair: Christopher Lynch
Jan 15: abstract submission deadline
Jan 22: paper submission deadline
- SAT 2010:
PC chairs: Ofer Strichman, Stefan Szeider
Feb 01: abstract submission deadline
Feb 08: paper submission deadline

* FLoC'10 Steering Committee:
- General Chair: Moshe Y. Vardi
- Conference Co-chairs: Leonid Libkin, Gordon Plotkin
- CAV Representative: Edmund Clarke
- ICLP Representative: Manuel Hermenegildo
- IJCAR Representative: Alan Bundy
- ITP Representative: Tobias Nipkow
- LICS Representative: Martin Abadi
- RTA Representative: Juergen Giesl
- SAT Representative: Enrico Giunchiglia
- EasyChair Representative: Andrei Voronkov

----------------------
You are subscribed to the FLoC 2010 mailing list.
To unsubscribe please send an email to majordomo@...
with the keywords unsubscribe floc2010 in the message body.

From forum: w3.org - public-semweb-lifesci

HCLS Telcon Reminder

2009-11-30T08:38:14Z

Here's the reminder for Thursday's HCLS call. See
http://esw.w3.org/topic/HCLSIG/Meetings/2009-12-03_Conference_Call for
up-to-date details, snapshot pasted below.

New participants please see http://esw.w3.org/topic/HCLSIG and
http://esw.w3.org/topic/HTML/Teleconferences and info about mibbit in
this message. Note: there is now a clickable link for mibbit below.

Cheers,
Scott

Conference Details

* Date of Call: Thursday December 3, 2009
* Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British
Summer Time (BST), 17:00 Central European Time (CET)
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS").
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page
for details, or see Web IRC), Quick Start: Use mibbit for IRC access.
* Duration: ~1h
* Convener: Scott, Susie
* Scribe: TBD

Agenda

* News Updates by BioRDF, COI, LODD, Pharma Ontology, Scientific
Discourse, Terminology - All
* Recent EU FP7 grant proposal, other grant possibilities - Scott
* SWAT4LS notes - Scott
* C-SHALS - All
* RDB2RDF Status - Eric
* AOB

++++
IRC
++++

* If you do not have an IRC client installed on your computer, you can
get one of the many free one (search "irc client" and your platform), or
you can use a web-based client.

Mibbit QuickStart (fill in your name at the prompt):
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls

One possible web-based client you might try is Mibbit
(http://www.mibbit.com/chat/). If you use mibbit, fill out the blanks
like this: you need to click on "Server" (highlighted in red in attached
image) to reveal the "Server address" field. NOTE: this meeting will use
the "hcls" channel.

mibbitexample.PNG (28K) Download Attachment

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-30T08:19:05Z

I'm following a similar strategy, but have been folowing the MGED
ontology where possible. I've finished aligning the IDF portion, and
have started on SDRF. MGED ontology is missing a property and class
for what is often termed as ProtocolApplication, which usually serves
as an edge between derived from and derived nodes, while linking to
the protocol used for the derivation. I am planning on creating this
link in a MAGE extensions ontology, but would like to vet the
structure here:

ProtocolApplication is a class.

New properties:

has_derivation_source
has_derivative

And then ProtocolApplication would have the restrictions:

has_protocol some Protocol

I don't put, domains, etc. on the derived properties to allow use in
directly describing derivations if people so choose. There is no
superclass for all nodes that can be derived or derived from, so I'm
not bothering with restrictions for those, although I could add a
union restriction to it.

If this structure us acceptable to people, I can publish the ontology
for general use pretty quickly, and let us work from the same data
structure. I would appreciate any feedback.

Jim

On Monday, November 30, 2009, Helena Deus <helenadeus@...> wrote:

> @Kei,
>
>
>
> When you said data structure, did you mean the RDF structure
> For now, all I have is the java object returned by parser. I've been using Limpopo, which creates an object that I can then parse to RDF uing Jena. The challenge, though, has been coming up with the predicates to formalize the relationships between the various elements. I'm using the XML structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate the structure that will contain the data. My plan is to then create the RDF triples that use the attributes described in those documents and populate them with the data from the MAGE-TAB java object created by Limpopo.
>
> Right now all I have is a very raw RDF/XML document describing the relationships in the IDF structure: http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf
> The triples for that had to be encoded manually using Jena by reading the model.
> @Satya and Jun
> I would very much like to be involved in that effort, do you already have a URL that I can look at?
>
> ThanksLena
> On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung <kei.cheung@...> wrote:
> Hi Lena et al,
>
> When you said data structure, did you mean the RDF structure. If so, is a pointer to the structure that we can look at?
>
> As discussed during yesterday's call, Jun and Satya will help create a wiki page for listing some of the requirements for provenance/workflow in the context of gene lists, perhaps we should also use it to help coordinate some of the future activities (people also brought up Taverna during the call yesterday). Please coordinate with Satya and Jun.
>
> Cheers,
>
> -Kei
>
> Helena Deus wrote:
>
> Hi all,
>
> I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-)
> If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow?
>
> Thanks!
> Lena
>
>
>
>
> On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmiller53@... <mailto:mdmiller53@...>> wrote:
>
>    hi all,
>
>    (from the minutes)
>
>    "Yolanda/Kei/Scott: semantic annotation/description of workflow
>    would enable the retrieval of data relevant to that workflow (i.e..
>    data that could be used to populate that workflow for a different
>    experimental scenario)"
>
>    what is typically in a MAGE-TAB/MAGE-ML document are the protocols
>    for how the source was processed into the extract then how the
>    hybridization, feature extraction, error and normalization were
>    performed. these are interesting and different protocols can
>    cause differences at this level but it is pretty much a known art
>    and usually not of too much interest or variability.
>
>    what is usually missing from those documents, along with the final
>    gene list, is how that gene list was obtained, what higher level
>    analysis was used, that is generally only in the paper unfortunately.
>
>    cheers,
>    michael
>    .
>    ----- Original Message ----- From: "Kei Cheung"
>
>    <kei.cheung@... <mailto:kei.cheung@...>>
>    To: "HCLS" <public-semweb-lifesci@...
>
>    <mailto:public-semweb-lifesci@...>>
>    Sent: Monday, November 23, 2009 1:27 PM
>    Subject: Re: BioRDF Telcon
>
>
>
>    Today's BioRDF minutes are available at the following:
>
>    http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
>
>    Thanks to Rob for scribing.
>
>    Cheers,
>
>    -Kei
>
>    Kei Cheung wrote:
>
>    This is a reminder that the next BioRDF telcon call will
>    be held at 11 am EDT (5 pm CET) on Monday, November 23
>    (see details below).
>
>    Cheers,
>
>    -Kei
>
>    == Conference Details ==
>    * Date of Call: Monday November 23, 2009
>    * Time of Call: 11:00 am Eastern Time
>    * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>    * Dial-In #: +33.4.89.06.34.99 (Nice, France)
>    * Dial-In #: +44.117.370.6152 (Bristol, UK)
>    * Participant Access Code: 4257 ("HCLS")
>
>    * IRC Channel: irc.w3.org <http://irc.w3.org> port 6665
>    channel #
>

--
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@... | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@...
http://tw.rpi.edu

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-30T07:47:03Z

@Kei,

When you said data structure, did you mean the RDF structure

For now, all I have is the java object returned by parser. I've been using Limpopo, which creates an object that I can then parse to RDF uing Jena. The challenge, though, has been coming up with the predicates to formalize the relationships between the various elements. I'm using the XML structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate the structure that will contain the data. My plan is to then create the RDF triples that use the attributes described in those documents and populate them with the data from the MAGE-TAB java object created by Limpopo.

Right now all I have is a very raw RDF/XML document describing the relationships in the IDF structure: http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf

The triples for that had to be encoded manually using Jena by reading the model.

@Satya and Jun

I would very much like to be involved in that effort, do you already have a URL that I can look at?

Thanks

Lena

On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung <kei.cheung@...> wrote:

Hi Lena et al,

When you said data structure, did you mean the RDF structure. If so, is a pointer to the structure that we can look at?

As discussed during yesterday's call, Jun and Satya will help create a wiki page for listing some of the requirements for provenance/workflow in the context of gene lists, perhaps we should also use it to help coordinate some of the future activities (people also brought up Taverna during the call yesterday). Please coordinate with Satya and Jun.

Cheers,

-Kei

Helena Deus wrote:

Hi all,

I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-)
If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser. However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow?

Thanks!
Lena

On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmiller53@... <mailto:mdmiller53@...>> wrote:

hi all,

(from the minutes)

"Yolanda/Kei/Scott: semantic annotation/description of workflow
would enable the retrieval of data relevant to that workflow (i.e.
data that could be used to populate that workflow for a different
experimental scenario)"

what is typically in a MAGE-TAB/MAGE-ML document are the protocols
for how the source was processed into the extract then how the
hybridization, feature extraction, error and normalization were
performed. these are interesting and different protocols can
cause differences at this level but it is pretty much a known art
and usually not of too much interest or variability.

what is usually missing from those documents, along with the final
gene list, is how that gene list was obtained, what higher level
analysis was used, that is generally only in the paper unfortunately.

cheers,
michael
.
----- Original Message ----- From: "Kei Cheung"
<kei.cheung@... <mailto:kei.cheung@...>>

To: "HCLS" <public-semweb-lifesci@...
<mailto:public-semweb-lifesci@...>>

Sent: Monday, November 23, 2009 1:27 PM
Subject: Re: BioRDF Telcon

Today's BioRDF minutes are available at the following:

http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call

Thanks to Rob for scribing.

Cheers,

-Kei

Kei Cheung wrote:

This is a reminder that the next BioRDF telcon call will
be held at 11 am EDT (5 pm CET) on Monday, November 23
(see details below).

Cheers,

-Kei

== Conference Details ==
* Date of Call: Monday November 23, 2009
* Time of Call: 11:00 am Eastern Time
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS")
* IRC Channel: irc.w3.org <http://irc.w3.org> port 6665

channel #HCLS (see W3C IRC page for details, or see Web
IRC), Quick Start: Use
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
<http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls>
for IRC access.
* Duration: ~1 hour
* Frequency: bi-weekly
* Convener: Kei Cheung
* Scribe: to-be-determined

== Agenda ==
* Roll call & introduction (Kei)
* RDF representation of microarray experiment and data (All)
* Provenance and workflow (All)

From forum: w3.org - public-semweb-lifesci

Translational Medicine Ontology Telcon

2009-11-30T07:31:30Z

Just a heads up that we won't be having a Translational Medicine Ontology call this week, so the next call will be on Dec. 10.

Thanks for all of your work on the paper. :-)

Cheers,

Susie

== Conference Details ==
* Date of Call: Thursday December 10 2009
* Time of Call: 12:00am - 1:00pm ET
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 42572 ("HCLS2").
* IRC Channel: irc.w3.org port 6665 channel #HCLS2

* Duration: 1h
* Convener: Susie

== Agenda ==
* Paper Submission - Susie
* Ontology Update - Colin
* Next Steps - All
* AOB

From forum: w3.org - public-semweb-lifesci

Upper and domain ontologies

2009-11-29T07:34:17Z

Hi all:

I have the following doubt involving upper ontologies and domain
ontologies. Upper ontologies are often described using FOL and modal
logics because they deal with general semantics and intended meaning.
Its implementation in the Semantic Web is in DL, much less expressive.
For example, DOLCE UltraLite is a implementation in DL of the upper
ontology DOLCE. Therefore, if I develop a domain ontology, which one of
the following approaches is the proper choice?

(1) Develop the domain ontology in DL, importing a well-known DL
implementation of the upper ontology.

(2) Develop the domain ontology in DL, importing the upper FOL ontology.
Then, create a DL implementation importing upper concepts from a
well-known DL implementation.

IMHO, the second approach guarantees that the concepts of the domain
ontology are consistent with the intended meaning of the upper ontology.
However, available tools, such as Protege, are focused in the first
approach. I think these tools makes easy to develop domain ontologies
that claim to be based in the upper ontology but can violate some of its
axioms that can not be expressed in DL.

This question is relevant in my field (GIS). I realize that we are using
more and more the layered approach to develop domain ontologies, and I
have the impression that we are just cherry picking the upper ontologies
(the approach 1) rather than develop something with a shared semantics
(the approach 2).

Many thanks for considering my questions.

Best,

fjlopez

----------------------------------------------------------------------------------------------------------
Francisco J. Lopez-Pellicer
IAAA, Universidad de Zaragoza, Spain

From forum: w3.org - semantic-web

Upper and domain ontologies

2009-11-29T07:32:19Z

From forum: w3.org - semantic-web

ANNOUNCEMENT: Raptor RDF Parser Library 1.4.20

2009-11-28T18:15:35Z

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Raptor RDF Parser Library 1.4.20
http://librdf.org/raptor/

Raptor is a free software / Open Source C library that provides a set
of Resource Description Framework (RDF) parsers and serializers that
both generate RDF triples by parsing syntaxes and serialize RDF
triples into a syntax. It is a mature, portable and high performance
library that works across many systems and architectures.

It parses the following syntax into RDF triples:
RDF/XML, N-Triples, TRiG, Turtle, GRDDL (including microformats
hCard and hCal) and RSS tag soup for RSSes, Atom 0.3 and Atom 1.0.
and serializes RDF triples into the following syntaxes:
RDF/XML, RDF/XML abbreviated, RDF/XML XMP, N-Triples,
Atom 1.0, RSS 1.0, Graphviz DOT, Turtle and JSON.

*** WARNING: FUTURE ABI and API CHANGES ***
Releases of the raptor 1.4.x series will include bug fixes only and no
new features. New development has moved to raptor 2 where a planned
ABI and API break will happen. There may be preview releases of
raptor 2 with 1.9.x numbering.

The main changes in this version since the last release 2009-07-20 are:
* Turtle serializing performance improvement by Chris Cannam
* librdfa RDFa parser updates to fix empty datatype, xml:lang and
1-char prefixes by Manu Sporny
* Fix a crash when the GRDDL parser reported errors
* Enable large file support for 32-bit systems
* Several resilience improvements by Lauri Aalto
* Other minor portability and bug fixes
* Fixed reported issues: 0000306 0000307 0000310 and 0000312.

For full details of the changes see the Raptor 1.4.20 release notes at
http://librdf.org/raptor/RELEASE.html#rel1_4_20

Binary deb packages for Debian unstable will be made available
later via the standard debian archive and download.librdf.org.

Sources are also available from the Redland SourceForge mirror site
at http://sourceforge.net/projects/librdf/ although the site is such
a usability disaster that I'm not likely to use it anymore.

The http://librdf.org/ site lets you browse and check out the latest
version of the sources in Subversion and use Raptor in various demos
as part of Redland such as Triplr http://triplr.org/

For more information on Redland, Raptor or Rasqal please join
the redland-dev list by visiting http://librdf.org/lists/
or visit IRC channel #redland on irc.freenode.net

Dave
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From forum: w3.org - semantic-web

Re: Using DBpedia resources as skos:Concepts?

2009-11-27T18:23:40Z

On Fri, Nov 27, 2009 at 2:27 PM, martin <martin@...> wrote:

I believe that we are running into a problem if we interpret SKOS:Concept too widely, and allow persons and other particulars be regarded as SKOS:Concept.
SKOS:Concept clearly has been designed initially to cover universals, i.e., concepts in the narrower sense, which have "instances" in the real world. This is why SKOS:Concept has properties broader/narrower:

"The word "broader" should read here as "has broader concept"; the subject of a skos:broader statement is the more specific concept involved in the assertion and its object is the more generic one. "

This clearly does not apply to persons, events and generally not to all "particulars".

[...]

In library classification, persons, such as Shakespeare, may appear as subjects. At least the library of congress describes clearly such concepts as books talking about "Shakespeare", and not as the person itself. In this case, the concept "books about Shakespeare" clearly qualifies as SKOS:Concept. Narrower concepts may be "books about Shakespeare's comedies" or "Shakespeare biographies". The example demonstrates, that a person as literary subject is distinct from identifying the person.
There is no contradiction to classify a URI for "Shakespeare" as both a literary subject(SKOS:Concept) and a real person (foaf:person)). However, that does not make every person a subject, and persons behave like a subject!

Martin-

You may be getting confused by the major changes that were made to SKOS in 2008, which altered the semantics of skos:broader.
The initial design of SKOS can be seen at: http://www.w3.org/2001/sw/Europe/reports/thes/1.0/guide/20040504/

One of the design requirements for SKOS, R-CompatibilityWithISO2788, required compatibility with ISO-2788.
Since ISO 2788 and its kin provide for the instantive relationship (BTI) the notion of skos:Concept cannot exclude individuals.

"Subjects" are what "documents" are "about"; if X is "about" Y, Y is a "subject" and X is a "document". Subjects are intentional. They aren't about what things are, they are what things are about.

An antelope, in a museum is a document about the subject of antelopes.
An antelope with a tattoo of a frog, in a museum, is an antelope and a document, and is about the subject of antelopes, and about the subject of frogs. It is not a frogelope.
Should this antelope escape, it remains an antelope, but is not a document, and is not about anything.

Simon

From forum: w3.org - public-esw-thes

Re: Using DBpedia resources as skos:Concepts?

2009-11-27T11:27:03Z

Dear All,

I believe that we are running into a problem if we interpret SKOS:Concept too widely, and allow
persons and other particulars be regarded as SKOS:Concept.
SKOS:Concept clearly has been designed initially to cover universals, i.e., concepts in
the narrower sense, which have "instances" in the real world. This is why SKOS:Concept
has properties broader/narrower:

"The word "broader" should read here as "has broader concept"; the subject of a skos:broader statement is the more specific concept involved
in the assertion and its object is the more generic one. "

This clearly does not apply to persons, events and generally not to all "particulars".

In the semantic Web, we seek clarity by formal ontologies. If we let creep in the
bad practices of decades of abuse of database schemata, because in later use they do not fit what we
initially anticipated, we render the whole idea of ontologies and unambiguous
communication useless.

If we nevertheless introduce a person as a "SKOS:Concept", and regard that we ignore
not applicable properties, i.e., the broader/narrower, we have a schema that deliberately
describes "unintented models".

Nicola Guarino and others regard as one of the most important tasks of a formal ontology
to avoid as much as possible unintended models.
(GUARINO, N. 1998. Formal Ontology and Information Systems. In Formal Ontology in Information Systems. In Proceedings of the 1st
International Conference, Trento, Italy, 6-8 June 1998, N. GUARINO Ed. IOS Press, 3-15)

We invite, for instance, abuse of "broader" of a person as a group it belongs to, or as
its parents. This would obviously be quite counterproductive. No interoperability is served,
if a KOS is declared as SKOS compatible, but does not use it in an unambiguous sense. Even if
SKOS would declare one kind of use as preferred, it would blur semantics and confuse future reasoning
systems. Persons do not behave like classes of things.

In library classification, persons, such as Shakespeare, may appear as subjects. At least the library of congress
describes clearly such concepts as books talking about "Shakespeare", and not as the person itself.
In this case, the concept "books about Shakespeare" clearly qualifies as SKOS:Concept. Narrower concepts
may be "books about Shakespeare's comedies" or "Shakespeare biographies". The example demonstrates,
that a person as literary subject is distinct from identifying the person.
There is no contradiction to classify a URI for "Shakespeare" as both a literary subject(SKOS:Concept)
and a real person (foaf:person)). However, that does not make every person a subject, and persons behave like a subject!

Leaving the definition of concepts deliberately open, such as SKOS:Concept between universals and particulars, is highly
counterproductive in the general Semantic Web framework.

a) A too wide definition that must be withdrawn later causes backwards incompatibility.
b) A narrower definition can be broadened at a later time, if the impact is well understood

c) RDF is designed so that different ontologies can be freely combined. This requires some foresight
at which levels of specialization/generalization other ontologies my fit in:
SKOS Concept currently combines all properties of labelling (preferred etc.) and defining vocabulary with the semantic
properties that hold only for universals.
If the concepts of labelling are regarded to be useful for KOS about persons, objects, places, periods and events,
no other adequate ontology for the latter can make use of these obviously applicable SKOS properties, without
buying in the unintended semantic properties.

RDF does not foresee to partially reuse properties of a class. Therefore the intended mixing of ontolgies does only
work if no ontology concentrates more properties in a class than are applicable to this class only.

Therefore I strongly recommend:
Either, SKOS to take a clear position and state that it is only about universals, or better,

==> split SKOS:Concept into two levels, for instance: "SKOS:Concept IsA SKOS:Entity", such that
SKOS:Entity would describe labeling and Vocabularies a term belongs to, and SKOS:Concept would
specialize SKOS:Entity to universals. This splitting is obviously backwards compatible with all current
SKOS applications.

Then, foaf:person or VIAF:person??? or ULAN:person could be declared as IsA "SKOS:Entity", without interfering
with the semantics of universals, and everybody can reuse the management of multiple vocabularies proposed by SKOS.

As a practical example, the CIDOC CRM (ISO21127) was deliberately designed to be SKOS compatible from the very conception
of SKOS on, i.e., crm:E55_Type same_as SKOS:Concept, so that a clear interface between factual metadata and terminology
represented as data (SKOS approach) can be guaranteed. If now SKOS takes a fuzzy stance to how particulars fit into it,
SKOS becomes not only incompatible with the CRM, because there is no reasonable class it could fit to, but also with many
other ontologies, and any other dedicated KOS scheme of particulars.

Best,

Martin
--

--------------------------------------------------------------
Dr. Martin Doerr | Vox:+30(2810)391625 |
Principle Researcher | Fax:+30(2810)391638 |
| Email: martin@... |
|
Center for Cultural Informatics |
Information Systems Laboratory |
Institute of Computer Science |
Foundation for Research and Technology - Hellas (FORTH) |
|
Vassilika Vouton,P.O.Box1385,GR71110 Heraklion,Crete,Greece |
|
Web-site: http://www.ics.forth.gr/isl |
--------------------------------------------------------------

From forum: w3.org - public-esw-thes

n-ary relations in OWL

2009-11-26T23:20:49Z

-----BEGIN PGP SIGNED MESSAGE-----
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Dear All,

We had a few questions with regards to the scope of n-ary relations in OWL

Questions:

1) Is satisfiability on OWL2 + n-ary relation undecidable?
Or is it an open question?

2) For the DL with n-ary relations in Section 5.7 [1],
the proof of decidability uses reification
can't we do the same proof for OWL+n-ary relations?
Do we need intersection and negation of roles for this?

3) Let R be an n-ary relation and C_R the reification of R, i.e.
the class coding R. Can't we express in OWL that the tuples are
uniquely represented by elements in R?
Would it be easy to prove that we cannot express this in OWL?
Actually I am not sure I understand how you express that tuples are
uniquely represented in the DL
of [1] (see Definition 5.11 and Theorem 5.12).

[1] Calvanese and De Giacomo. Expressive Description Logics.

Monika
- --
Dr Monika Solanki
F27 Department of Computer Science
University of Leicester
Leicester LE1 7RH
United Kingdom
Google Coordinates: 52.653791,-1.158414
Tel: +44 116 252 3828
Web: http://www.cs.le.ac.uk/people/ms491/

Times Higher Education University of the Year 2008/09
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From forum: w3.org - semantic-web

test

2009-11-26T23:08:39Z

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- --
Dr Monika Solanki
F27 Department of Computer Science
University of Leicester
Leicester LE1 7RH
United Kingdom
Google Coordinates: 52.653791,-1.158414
Tel: +44 116 252 3828
Web: http://www.cs.le.ac.uk/people/ms491/

Times Higher Education University of the Year 2008/09
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From forum: w3.org - semantic-web

Spanish translation of SKOS Primer

2009-11-26T03:45:45Z

Dear Colleagues,

It is available the Spanish translation of the document "SKOS Simple Knowledge Organization System Primer (W3C Working Group Note 18 August 2009)"

http://skos.um.es/TR/skos-primer

I hope it will be useful to the SKOS community.

Regards

--

Ph.D. Juan Antonio Pastor Sánchez
Senior Lecturer - Dep. Information and Documentation
Faculty Communication and Documentation
University of Murcia
phone: +34 868 88 8780
http://webs.um.es/pastor
pastor@...

From forum: w3.org - public-esw-thes

Re: TheSoz available in SKOS and SPARQL

2009-11-26T02:47:14Z

Ah, oops. The form is under "contact", so I did not figure it was a requirement for "download".
I'm very dumb when it comes to interfaces :(

Thanks

Bernard

2009/11/26 Zapilko, Benjamin <Benjamin.Zapilko@...>

Dear Bernard,

just leave your email-address in the form and the download will work :-)

Cheers,
Ben

-----Ursprüngliche Nachricht-----
Von: public-esw-thes-request@... im Auftrag von Bernard Vatant
Gesendet: Do 26.11.2009 09:44
An: Sure, York
Cc: public-esw-thes
Betreff: Re: TheSoz available in SKOS and SPARQL

York

Great news ... but the "download" button brings me back to the top of the
page :(

Bernard

2009/11/26 Sure, York <york.sure@...>

> Dear SKOS-lovers,
>
> the Thesaurus for the Social Sciences (TheSoz) is an interconnected
> vocabulary in English and German on the social sciences, which contains
> about 11,600 entries and covers topics of all social science disciplines and
> related or interdisciplinary connected topics. Its publication aims at
> providing a vocabulary for resources relevant for or related to the social
> sciences on the web of Linked Open Data.
>
> The thesaurus is maintained by the GESIS - Leibniz Institute for the Social
> Sciences and is published under a Creative Commons (by-nc-nd) license.
>
> It is published as a SKOS RDF/XML dump version which can be downloaded at <
> http://www.gesis.org/en/services/tools-standards/social-science-thesaurus/
> >.
> (Please scroll down the page!)
>
> The thesaurus is furthermore available via a SPARQL endpoint at <
> http://multiweb.gesis.org/thesoz/sparql>.
>
> This is a very early version (v0.2) and we're looking forward to get some
> feedback for future improvements.
>
> Further details about the conversion of the TheSoz to SKOS can be found in
> the GESIS technical report 2009/07, available at <
> http://www.gesis.org/fileadmin/upload/forschung/publikationen/gesis_reihen/gesis_methodenberichte/2009/TechnicalReport_09_07.pdf
> >.
>
> Kind regards,
> York Sure and Benjamin Zapilko
>
> --
> Prof. Dr. York Sure
> Scientific Director
> GESIS - Leibniz Institute for the Social Sciences
> Information Processes in the Social Sciences (IPS)
> Lennéstr. 30, D-53113 Bonn
> Tel: + 49 (0) 228 / 22 81-145
> Fax: + 49 (0) 228 / 22 81-121
> Web: http://www.gesis.org
>
> Professor for Applied Informatics in the Social Sciences
> University of Koblenz-Landau
> WeST - Institute for Web Science and Technologies
> Universitaetsstr. 1, D-56070 Koblenz
> Web: http://west.uni-koblenz.de
>
>
>
>
>

--
Bernard Vatant
Senior Consultant
Vocabulary & Data Engineering
Tel: +33 (0) 971 488 459
Mail: bernard.vatant@...
----------------------------------------------------
Mondeca
3, cité Nollez 75018 Paris France
Web: http://www.mondeca.com
Blog: http://mondeca.wordpress.com
----------------------------------------------------

--
Bernard Vatant
Senior Consultant
Vocabulary & Data Engineering
Tel: +33 (0) 971 488 459
Mail: bernard.vatant@...
----------------------------------------------------
Mondeca
3, cité Nollez 75018 Paris France
Web: http://www.mondeca.com
Blog: http://mondeca.wordpress.com
----------------------------------------------------

From forum: w3.org - public-esw-thes

AW: TheSoz available in SKOS and SPARQL

2009-11-26T02:33:31Z

Dear Bernard,

just leave your email-address in the form and the download will work :-)

Cheers,
Ben

-----Ursprüngliche Nachricht-----
Von: public-esw-thes-request@... im Auftrag von Bernard Vatant
Gesendet: Do 26.11.2009 09:44
An: Sure, York
Cc: public-esw-thes
Betreff: Re: TheSoz available in SKOS and SPARQL

York

Great news ... but the "download" button brings me back to the top of the
page :(

Bernard

2009/11/26 Sure, York <york.sure@...>

> Dear SKOS-lovers,
>
> the Thesaurus for the Social Sciences (TheSoz) is an interconnected
> vocabulary in English and German on the social sciences, which contains
> about 11,600 entries and covers topics of all social science disciplines and
> related or interdisciplinary connected topics. Its publication aims at
> providing a vocabulary for resources relevant for or related to the social
> sciences on the web of Linked Open Data.
>
> The thesaurus is maintained by the GESIS - Leibniz Institute for the Social
> Sciences and is published under a Creative Commons (by-nc-nd) license.
>
> It is published as a SKOS RDF/XML dump version which can be downloaded at <
> http://www.gesis.org/en/services/tools-standards/social-science-thesaurus/
> >.
> (Please scroll down the page!)
>
> The thesaurus is furthermore available via a SPARQL endpoint at <
> http://multiweb.gesis.org/thesoz/sparql>.
>
> This is a very early version (v0.2) and we're looking forward to get some
> feedback for future improvements.
>
> Further details about the conversion of the TheSoz to SKOS can be found in
> the GESIS technical report 2009/07, available at <
> http://www.gesis.org/fileadmin/upload/forschung/publikationen/gesis_reihen/gesis_methodenberichte/2009/TechnicalReport_09_07.pdf
> >.
>
> Kind regards,
> York Sure and Benjamin Zapilko
>
> --
> Prof. Dr. York Sure
> Scientific Director
> GESIS - Leibniz Institute for the Social Sciences
> Information Processes in the Social Sciences (IPS)
> Lennéstr. 30, D-53113 Bonn
> Tel: + 49 (0) 228 / 22 81-145
> Fax: + 49 (0) 228 / 22 81-121
> Web: http://www.gesis.org
>
> Professor for Applied Informatics in the Social Sciences
> University of Koblenz-Landau
> WeST - Institute for Web Science and Technologies
> Universitaetsstr. 1, D-56070 Koblenz
> Web: http://west.uni-koblenz.de
>
>
>
>
>

From forum: w3.org - public-esw-thes

Re: TheSoz available in SKOS and SPARQL

2009-11-26T00:44:00Z

York

Great news ... but the "download" button brings me back to the top of the page :(

Bernard

2009/11/26 Sure, York <york.sure@...>

Dear SKOS-lovers,

the Thesaurus for the Social Sciences (TheSoz) is an interconnected vocabulary in English and German on the social sciences, which contains about 11,600 entries and covers topics of all social science disciplines and related or interdisciplinary connected topics. Its publication aims at providing a vocabulary for resources relevant for or related to the social sciences on the web of Linked Open Data.

The thesaurus is maintained by the GESIS - Leibniz Institute for the Social Sciences and is published under a Creative Commons (by-nc-nd) license.

It is published as a SKOS RDF/XML dump version which can be downloaded at <http://www.gesis.org/en/services/tools-standards/social-science-thesaurus/>.
(Please scroll down the page!)

The thesaurus is furthermore available via a SPARQL endpoint at <http://multiweb.gesis.org/thesoz/sparql>.

This is a very early version (v0.2) and we're looking forward to get some feedback for future improvements.

Further details about the conversion of the TheSoz to SKOS can be found in the GESIS technical report 2009/07, available at <http://www.gesis.org/fileadmin/upload/forschung/publikationen/gesis_reihen/gesis_methodenberichte/2009/TechnicalReport_09_07.pdf>.

Kind regards,
York Sure and Benjamin Zapilko

--
Prof. Dr. York Sure
Scientific Director
GESIS - Leibniz Institute for the Social Sciences
Information Processes in the Social Sciences (IPS)
Lennéstr. 30, D-53113 Bonn
Tel: + 49 (0) 228 / 22 81-145
Fax: + 49 (0) 228 / 22 81-121
Web: http://www.gesis.org

Professor for Applied Informatics in the Social Sciences
University of Koblenz-Landau
WeST - Institute for Web Science and Technologies
Universitaetsstr. 1, D-56070 Koblenz
Web: http://west.uni-koblenz.de

From forum: w3.org - public-esw-thes

TheSoz available in SKOS and SPARQL

2009-11-25T21:59:07Z

Dear SKOS-lovers,

the Thesaurus for the Social Sciences (TheSoz) is an interconnected vocabulary in English and German on the social sciences, which contains about 11,600 entries and covers topics of all social science disciplines and related or interdisciplinary connected topics. Its publication aims at providing a vocabulary for resources relevant for or related to the social sciences on the web of Linked Open Data.

The thesaurus is maintained by the GESIS - Leibniz Institute for the Social Sciences and is published under a Creative Commons (by-nc-nd) license.

It is published as a SKOS RDF/XML dump version which can be downloaded at <http://www.gesis.org/en/services/tools-standards/social-science-thesaurus/>.
(Please scroll down the page!)

The thesaurus is furthermore available via a SPARQL endpoint at <http://multiweb.gesis.org/thesoz/sparql>.

This is a very early version (v0.2) and we're looking forward to get some feedback for future improvements.

Further details about the conversion of the TheSoz to SKOS can be found in the GESIS technical report 2009/07, available at <http://www.gesis.org/fileadmin/upload/forschung/publikationen/gesis_reihen/gesis_methodenberichte/2009/TechnicalReport_09_07.pdf>.

Kind regards,
York Sure and Benjamin Zapilko

--
Prof. Dr. York Sure
Scientific Director
GESIS - Leibniz Institute for the Social Sciences
Information Processes in the Social Sciences (IPS)
Lennéstr. 30, D-53113 Bonn
Tel: + 49 (0) 228 / 22 81-145
Fax: + 49 (0) 228 / 22 81-121
Web: http://www.gesis.org

Professor for Applied Informatics in the Social Sciences
University of Koblenz-Landau
WeST - Institute for Web Science and Technologies
Universitaetsstr. 1, D-56070 Koblenz
Web: http://west.uni-koblenz.de

From forum: w3.org - public-esw-thes

No Telcons for the remainder of the week

2009-11-25T10:38:53Z

For the sake of clarity, there will be no telcons for Terminology, HCLS,
TMO, and Scientific Discourse for the remainder of the week due to the
Thanksgiving holidays in the U.S.

Cheers,
Scott

From forum: w3.org - public-semweb-lifesci

Re: LODD Minutes

2009-11-25T09:04:32Z

On Wed, Nov 25, 2009 at 5:56 PM, Susie Stephens
<susie.stephens@...> wrote:
> Minutes from today's LODD call are now available.
> http://esw.w3.org/topic/HCLSIG/LODD/Meetings/2009-11-25_Conference_Call

Did my email of yesterday not reach the list?

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

From forum: w3.org - public-semweb-lifesci

LODD Minutes

2009-11-25T08:56:38Z

Minutes from today's LODD call are now available.

http://esw.w3.org/topic/HCLSIG/LODD/Meetings/2009-11-25_Conference_Call

Susie

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-24T12:26:09Z

mdmiller wrote:
> hi all,
>
> the MAGE-TAB also can have (and often does) good phenotypic
> information on the sources (patients, mice, etc) of the samples used
> plus the experimental factors.
I think it's also important for EFO to be harmonized with existing
ontologies like the one in NCBO.

Cheers,

-Kei

>
> it does typically have the method to process from the raw to the
> processed data but what i meant was the information on how the
> normalized processed data was reduced to the gene list.
>
> cheers,
> michael
>
> ----- Original Message -----
> *From:* Helena Deus <mailto:helenadeus@...>
> *To:* mdmiller <mailto:mdmiller53@...>
> *Cc:* Kei Cheung <mailto:kei.cheung@...> ; HCLS
> <mailto:public-semweb-lifesci@...>
> *Sent:* Tuesday, November 24, 2009 10:06 AM
> *Subject:* Re: BioRDF Telcon
>
> Hi all,
>
> I apologize for missing the call yesterday! It seems you had a
> pretty interesting discussion! :-)
> If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML
> into RDF would result in obtaining only the raw and processed data
> files but not the mechanism used to process it nor the resulting
> gene list. That's also what I concluded after looking at the data
> structure created by Tony Burdett's Limpopo parser.
> However, having the raw data as linked data is already a great
> start! Kei, should I be looking into Taverna in order to
> reprocessed the raw files with a traceable analysis workflow?
>
> Thanks!
> Lena
>
>
>
> On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmiller53@...
> <mailto:mdmiller53@...>> wrote:
>
> hi all,
>
> (from the minutes)
>
> "Yolanda/Kei/Scott: semantic annotation/description of
> workflow would enable the retrieval of data relevant to that
> workflow (i.e. data that could be used to populate that
> workflow for a different experimental scenario)"
>
> what is typically in a MAGE-TAB/MAGE-ML document are the
> protocols for how the source was processed into the extract
> then how the hybridization, feature extraction, error and
> normalization were performed. these are interesting and
> different protocols can cause differences at this level but it
> is pretty much a known art and usually not of too much
> interest or variability.
>
> what is usually missing from those documents, along with the
> final gene list, is how that gene list was obtained, what
> higher level analysis was used, that is generally only in the
> paper unfortunately.
>
> cheers,
> michael
> .
> ----- Original Message ----- From: "Kei Cheung"
> <kei.cheung@... <mailto:kei.cheung@...>>
> To: "HCLS" <public-semweb-lifesci@...
> <mailto:public-semweb-lifesci@...>>
> Sent: Monday, November 23, 2009 1:27 PM
> Subject: Re: BioRDF Telcon
>
>
>
> Today's BioRDF minutes are available at the following:
>
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
>
> Thanks to Rob for scribing.
>
> Cheers,
>
> -Kei
>
> Kei Cheung wrote:
>
> This is a reminder that the next BioRDF telcon call
> will be held at 11 am EDT (5 pm CET) on Monday,
> November 23 (see details below).
>
> Cheers,
>
> -Kei
>
> == Conference Details ==
> * Date of Call: Monday November 23, 2009
> * Time of Call: 11:00 am Eastern Time
> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> * Dial-In #: +33.4.89.06.34.99 (Nice, France)
> * Dial-In #: +44.117.370.6152 (Bristol, UK)
> * Participant Access Code: 4257 ("HCLS")
> * IRC Channel: irc.w3.org <http://irc.w3.org> port
> 6665 channel #HCLS (see W3C IRC page for details, or
> see Web IRC), Quick Start: Use
> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
> <http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls>
> for IRC access.
> * Duration: ~1 hour
> * Frequency: bi-weekly
> * Convener: Kei Cheung
> * Scribe: to-be-determined
>
> == Agenda ==
> * Roll call & introduction (Kei)
> * RDF representation of microarray experiment and data
> (All)
> * Provenance and workflow (All)
>
>
>
>
>
>
>
>
>
>

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-24T12:19:21Z

Hi Lena et al,

When you said data structure, did you mean the RDF structure. If so, is
a pointer to the structure that we can look at?

As discussed during yesterday's call, Jun and Satya will help create a
wiki page for listing some of the requirements for provenance/workflow
in the context of gene lists, perhaps we should also use it to help
coordinate some of the future activities (people also brought up Taverna
during the call yesterday). Please coordinate with Satya and Jun.

Cheers,

-Kei

Helena Deus wrote:

> Hi all,
>
> I apologize for missing the call yesterday! It seems you had a pretty
> interesting discussion! :-)
> If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into
> RDF would result in obtaining only the raw and processed data files
> but not the mechanism used to process it nor the resulting gene list.
> That's also what I concluded after looking at the data structure
> created by Tony Burdett's Limpopo parser.
> However, having the raw data as linked data is already a great start!
> Kei, should I be looking into Taverna in order to reprocessed the raw
> files with a traceable analysis workflow?
>
> Thanks!
> Lena
>
>
>
> On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmiller53@...
> <mailto:mdmiller53@...>> wrote:
>
> hi all,
>
> (from the minutes)
>
> "Yolanda/Kei/Scott: semantic annotation/description of workflow
> would enable the retrieval of data relevant to that workflow (i.e.
> data that could be used to populate that workflow for a different
> experimental scenario)"
>
> what is typically in a MAGE-TAB/MAGE-ML document are the protocols
> for how the source was processed into the extract then how the
> hybridization, feature extraction, error and normalization were
> performed. these are interesting and different protocols can
> cause differences at this level but it is pretty much a known art
> and usually not of too much interest or variability.
>
> what is usually missing from those documents, along with the final
> gene list, is how that gene list was obtained, what higher level
> analysis was used, that is generally only in the paper unfortunately.
>
> cheers,
> michael
> .
> ----- Original Message ----- From: "Kei Cheung"
> <kei.cheung@... <mailto:kei.cheung@...>>
> To: "HCLS" <public-semweb-lifesci@...
> <mailto:public-semweb-lifesci@...>>
> Sent: Monday, November 23, 2009 1:27 PM
> Subject: Re: BioRDF Telcon
>
>
>
> Today's BioRDF minutes are available at the following:
>
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
>
> Thanks to Rob for scribing.
>
> Cheers,
>
> -Kei
>
> Kei Cheung wrote:
>
> This is a reminder that the next BioRDF telcon call will
> be held at 11 am EDT (5 pm CET) on Monday, November 23
> (see details below).
>
> Cheers,
>
> -Kei
>
> == Conference Details ==
> * Date of Call: Monday November 23, 2009
> * Time of Call: 11:00 am Eastern Time
> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> * Dial-In #: +33.4.89.06.34.99 (Nice, France)
> * Dial-In #: +44.117.370.6152 (Bristol, UK)
> * Participant Access Code: 4257 ("HCLS")
> * IRC Channel: irc.w3.org <http://irc.w3.org> port 6665
> channel #HCLS (see W3C IRC page for details, or see Web
> IRC), Quick Start: Use
> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
> <http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls>
> for IRC access.
> * Duration: ~1 hour
> * Frequency: bi-weekly
> * Convener: Kei Cheung
> * Scribe: to-be-determined
>
> == Agenda ==
> * Roll call & introduction (Kei)
> * RDF representation of microarray experiment and data (All)
> * Provenance and workflow (All)
>
>
>
>
>
>
>
>
>
>

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-24T12:16:57Z

Hi Michael et al,

Thanks for pointing out the kind of metadata captured in MAGE-TAB. Yes,
we have discussed what kind of semantic information might be needed for
describing gene lists. In addition to recording how the gene lists were
obtained, we might need to keep track of how these gene lists might be
used by other people (beyond the paper).

Cheers,

-Kei

mdmiller wrote:

> hi all,
>
> (from the minutes)
>
> "Yolanda/Kei/Scott: semantic annotation/description of workflow would
> enable the retrieval of data relevant to that workflow (i.e. data that
> could be used to populate that workflow for a different experimental
> scenario)"
>
> what is typically in a MAGE-TAB/MAGE-ML document are the protocols for
> how the source was processed into the extract then how the
> hybridization, feature extraction, error and normalization were
> performed. these are interesting and different protocols can cause
> differences at this level but it is pretty much a known art and
> usually not of too much interest or variability.
>
> what is usually missing from those documents, along with the final
> gene list, is how that gene list was obtained, what higher level
> analysis was used, that is generally only in the paper unfortunately.
>
> cheers,
> michael
> .
> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
> To: "HCLS" <public-semweb-lifesci@...>
> Sent: Monday, November 23, 2009 1:27 PM
> Subject: Re: BioRDF Telcon
>
>
>> Today's BioRDF minutes are available at the following:
>>
>> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
>>
>>
>> Thanks to Rob for scribing.
>>
>> Cheers,
>>
>> -Kei
>>
>> Kei Cheung wrote:
>>> This is a reminder that the next BioRDF telcon call will be held at
>>> 11 am EDT (5 pm CET) on Monday, November 23 (see details below).
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>> == Conference Details ==
>>> * Date of Call: Monday November 23, 2009
>>> * Time of Call: 11:00 am Eastern Time
>>> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>>> * Dial-In #: +33.4.89.06.34.99 (Nice, France)
>>> * Dial-In #: +44.117.370.6152 (Bristol, UK)
>>> * Participant Access Code: 4257 ("HCLS")
>>> * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page
>>> for details, or see Web IRC), Quick Start: Use
>>> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
>>> for IRC access.
>>> * Duration: ~1 hour
>>> * Frequency: bi-weekly
>>> * Convener: Kei Cheung
>>> * Scribe: to-be-determined
>>>
>>> == Agenda ==
>>> * Roll call & introduction (Kei)
>>> * RDF representation of microarray experiment and data (All)
>>> * Provenance and workflow (All)
>>>
>>>
>>
>>
>>
>>
>
>

From forum: w3.org - public-semweb-lifesci

Re: Differentially Expressed Gene Lists

2009-11-24T12:16:47Z

Hi Misha and All,

I believe there is a complementary relationship between paper-based gene
lists and the gene lists produced by Atlas. Different methods may
produce different lists of genes (there should be some overlap though)
for the same experiment. It's good to consider the possibility of
integrating GeneSigDB and Atlas. I also believe SDA is complementary to
the paper-based approach and database approach. It is a
practice/framework recommended for authors/editors to enter things like
gene lists in a machine readable format. FEBS Letters (published by
Elsevier) has experimented with SDA. That's why I wonder if a similar
experiment can be done for gene lists.

Cheers

-Kei

Misha Kapushesky wrote:

> Hi,
>
> Just to add to what Michael said, I will be in Boston around Christmas
> and one of the goals of this visit is to talk to the GeneSigDB guys
> about integrating it somehow with our Atlas, as gene list/signature
> curation is something a lot of our users demand frequently.
>
> Cheers,
>
> Misha
>
> On Mon, Nov 23, 2009 at 9:08 PM, Kei Cheung <kei.cheung@...> wrote:
>
>> Since there seems to be an interest in exploring how to represent
>> differentially expressed gene list, I'm cc'ing this to the HCLS list (Scott
>> also suggested doing this). In addition to Michael's suggestion (see below),
>> the following is a reference to Structured Digital Abstract (SDA) for those
>> who are interested.
>>
>> http://www.nature.com/nature/journal/v447/n7141/full/447142a.html
>>
>> Cheers,
>>
>> -Kei
>>
>> mdmiller wrote:
>>
>>> hi all,
>>>
>>> SDA does sound useful but it still has the hurdle that the writers of the
>>> abstract need to be aware and care to use such structures or someone else
>>> needs to add such structure afterwards.
>>>
>>> as i mentioned at the F2F, there is GeneSigDB [1] hosted at dana farber,
>>> which is curating gene lists from papers. this is very useful in that it
>>> pulls out into a structured database the genes of interest from papers but
>>> has the limitation that it doesn't provide the signatures of interest.
>>>
>>> there is also the matter of the algorithm that, given a new gene
>>> expression profile, provides a score as to inclusion or exclusion from the
>>> biomarker. i'm not a bioinformaticists but my understanding is such
>>> algorithms may depend on more than just the signatures, they might depend on
>>> the values of some higher level algorithm, i.e. there may not be one size
>>> fits all algorithms to determine membership.
>>>
>>> i also won't be able to make the call.
>>>
>>> cheers,
>>> michael
>>>
>>> [1]: http://compbio.dfci.harvard.edu/genesigdb/
>>>
>>> Michael Miller
>>> mdmiller53@...
>>>
>>> ----- Original Message ----- From: "Helen Parkinson" <parkinson@...>
>>> To: "Kei Cheung" <kei.cheung@...>
>>> Cc: <marshall@...>; "mdmiller" <mdmiller53@...>; "Misha
>>> Kapushesky" <ostolop@...>; "Eric Prud'hommeaux" <eric@...>;
>>> "Matthias Samwald" <samwald@...>
>>> Sent: Monday, November 23, 2009 5:58 AM
>>> Subject: Re: Differentially Expressed Gene Lists
>>>
>>>
>>>
>>>> I should have read the spec for the SDA. Sounds useful.
>>>>
>>>> Kei Cheung wrote:
>>>>
>>>>> Helen Parkinson wrote:
>>>>>
>>>>>
>>>>>>> I've been wondering how structured digital abstract (SDA) can be
>>>>>>> applied to gene lists. There has been a pilot application of SDA by FEBS in
>>>>>>> terms of interactions with links to MINT. Perhaps, a similar thing can be
>>>>>>> done for gene lists with links to databases like ArrayExpress and GEO. Mark
>>>>>>> Gerstein and I are working on a paper describing some extension of SDA
>>>>>>> (Matthias is also a co-author).
>>>>>>>
>>>>>>>
>>>>>> Gene lists don't really appear in abstracts either often, one or two
>>>>>> genes of interest are mentioned. I'd be happy to take a look at a subset of
>>>>>> papers though to confirm/deny this. If that would help
>>>>>>
>>>>> Many people misunderstood that structured digital abstract applies only
>>>>> to abstracts (I know the name is misleading unforunately), it can be applied
>>>>> to representing key findings described in the paper. The abstract I'm
>>>>> looking at is the following:
>>>>>
>>>>> http://www.ncbi.nlm.nih.gov/pubmed/16242812
>>>>>
>>>>> It mentions explicitly that one of the key findings is a differently
>>>>> gene list of 225 genes across different conditions. Four of the validated
>>>>> genes are also mentioned in the abstract:
>>>>>
>>>>> apolipoprotein J, interleukin-1 receptor-associated kinase 1, tissue
>>>>> inhibitor of metalloproteinase 3, and casein kinase 2, beta.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>>> The job of creating an OWL/RDF representation of microarray
>>>>>>>> experiement results should *start* with differentially expressed genes and
>>>>>>>> experimental conditions. I would hope that it doesn't start with text mining
>>>>>>>> ill-defined text sources (such as figures). On the bright side, if the
>>>>>>>> experiment of interest is included in Gene Expression Atlas, we are all set,
>>>>>>>> right? We just need a way to export the RDF.
>>>>>>>>
>>>>>>>
>>>>>>> I'm planning to give a short presentation including an example during
>>>>>>> the BioRDF call tomorrow.
>>>>>>>
>>>>>> I'll miss this unfortunately, as will Misha. Yes, if the experiment is
>>>>>> in Atlas we can now export rdf and we have a prototype working.
>>>>>>
>>>>> Look forward to seeing the protoype. SDA can be seen as a bridge between
>>>>> databases and literature. It fits both bottom-up and top-down approach.
>>>>>
>>>>>
>>>>>>>> BTW, I've pasted Kei's reminder below for the next BioRDF call
>>>>>>>> (tomorrow). It would be great if you could call in and help us to figure
>>>>>>>> this out.
>>>>>>>>
>>>>>> Apologies, I have 30 days holiday to use before the end of the year, so
>>>>>> I won't make this.
>>>>>>
>>>>> Have a good vacation.
>>>>>
>>>>> -Kei
>>>>>
>>>>>
>>>>>>>> Cheers,
>>>>>>>> Scott
>>>>>>>>
>>>>>>>> n.b. Does anybody mind if I post this to the mailing list?
>>>>>>>>
>>>>>>> It's fine with me if people think nothing is controversal or premature
>>>>>>> here. :-)
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> -Kei
>>>>>>>
>>>>>>>
>>>>>>>> -------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>> This is a reminder that the next BioRDF telcon call will be held at
>>>>>>>> 11 am EDT (5 pm CET) on Monday, November 23 (see details below).
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> -Kei
>>>>>>>>
>>>>>>>> == Conference Details ==
>>>>>>>> * Date of Call: Monday November 23, 2009
>>>>>>>> * Time of Call: 11:00 am Eastern Time
>>>>>>>> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>>>>>>>> * Dial-In #: +33.4.89.06.34.99 (Nice, France)
>>>>>>>> * Dial-In #: +44.117.370.6152 (Bristol, UK)
>>>>>>>> * Participant Access Code: 4257 ("HCLS")
>>>>>>>> * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page
>>>>>>>> for details, or see Web IRC), Quick Start: Use
>>>>>>>> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC
>>>>>>>> access.
>>>>>>>> * Duration: ~1 hour
>>>>>>>> * Frequency: bi-weekly
>>>>>>>> * Convener: Kei Cheung
>>>>>>>> * Scribe: to-be-determined
>>>>>>>>
>>>>>>>> == Agenda ==
>>>>>>>> * Roll call & introduction (Kei)
>>>>>>>> * RDF representation of microarray experiment and data (All)
>>>>>>>> * Provenance and workflow (All)
>>>>>>>>
>>>>>>>>
>>>>>>>>> mdmiller wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> hi scott,
>>>>>>>>>>
>>>>>>>>>> typically it will not, the data will be the raw data, usually in
>>>>>>>>>> the format from the feature extractor at the feature/spot level and then the
>>>>>>>>>> error corrected and normalized data at the sequence/gene/transcript level.
>>>>>>>>>> one could include the final gene list in the MAGE-TAB by adding the
>>>>>>>>>> appropriate columns to the MAGE-TAB and have the Derived Data File column
>>>>>>>>>> contain the name of the appropriate file but in general the gene list is
>>>>>>>>>> only in the paper, often as supplemental data. in fact i can't think of a
>>>>>>>>>> single case where it is included, helen, can you?
>>>>>>>>>>
>>>>>>>>>> cheers,
>>>>>>>>>> michael
>>>>>>>>>>
>>>>>>>>>> ----- Original Message ----- From: "M. Scott Marshall"
>>>>>>>>>> <marshall@...>
>>>>>>>>>> To: <mdmiller53@...>
>>>>>>>>>> Cc: "kc28" <kei.cheung@...>
>>>>>>>>>> Sent: Friday, November 13, 2009 6:50 PM
>>>>>>>>>> Subject: BioRDF
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>
>>>>>>>>>>> One of the things that has come up during the BioRDF call is "we
>>>>>>>>>>> need to confirm whether MAGE-TAB contains gene lists or not". In other
>>>>>>>>>>> words, we will need to represent gene lists in RDF.
>>>>>>>>>>>
>>>>>>>>>>> Ok, my quick interpretation between other things,
>>>>>>>>>>> Scott
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> M. Scott Marshall
>>>>>>>>>>> Leiden University Medical Center / University of Amsterdam
>>>>>>>>>>> http://staff.science.uva.nl/~marshall
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>> --
>>>> Helen Parkinson, PhD
>>>> ArrayExpress Production Coordinator,
>>>> Microarray Informatics Team, EBI
>>>>
>>>> EBI 01223 494672
>>>> Skype: helen.parkinson.ebi
>>>>
>>>>
>>>>
>>>
>>
>>
>
>

From forum: w3.org - public-semweb-lifesci

Re: SKOS support in Drupal

2009-11-24T10:31:33Z

There is another way in which this is key. For those of us who have
both a Drupal site and an ontology repository they like to use -- hmm,
maybe MMI is the only one like that has both, but you could use
*anyone's* repository -- this is very powerful. We can manage the
Drupal taxonomies using the repository (or can at least export the
Drupal taxonomies to the repository).

So our community's work developing ontology and metadata
classification systems for our Drupal site can be exported to the
publicly visible list of community vocabularies, instead of being
hidden behind Drupal. Generalizing this, imagine if the http://metadataregistry.org
site contained all the classification systems that were used to
organize various Drupal sites -- now you have exposed a collection of
vocabularies that have been thought about and used to classify
content, which is a pretty powerful resource.

I'm not sure what the 'minimum criteria' are for a vocabulary to be
SKOS, we have a lot of OWL-DL vocabularies on the MMI ontology site
[1]. Few of them will be of a scope worth packaging with the system,
though, they're mostly about science stuff.

John

[1] MMI Ontology Registry: http://mmisw.org/or

On Nov 24, 2009, at 02:45, Dan Morrison wrote:

> Thanks Sean, that's definitely the sort of list I'm looking for. My
> browser history indicates I've found a *few* of them before. (and
> many more are defunct, damn)
> I still can't see any that will empower a killer app for the social,
> 2.0 or "semantic" web. I've found lists of economic terminology, but
> to sell it as an enhancement to a CMS, I need things more
> accessible, something that a blogger, marketer, corporate or
> institution would want to use to enhance the metadata of their
> readable content, not just academic data dumps.
> The broadest re-usable source I've found so far is MeSH which grew
> up to support PUBMed (I think). But it's not SKOS. So if there were
> a SKOS resource that was in any way authoritative, and not just a
> proof-of-concept, I'd love to link right in and embed it.
> (taxonomy_xml for the Drupal CMS is designed to feed from published
> external sources, it's not distributed with data itself (beyond
> samples).

John Graybeal <mailto:jgraybeal@...>
phone: 858-534-2162
Development Manager
Ocean Observatories Initiative Cyberinfrastructure Project: http://ci.oceanobservatories.org
Marine Metadata Interoperability Project: http://marinemetadata.org

From forum: w3.org - public-esw-thes

Re: BioRDF Telcon

2009-11-24T10:19:16Z

hi all,

the MAGE-TAB also can have (and often does) good phenotypic information on the sources (patients, mice, etc) of the samples used plus the experimental factors.

it does typically have the method to process from the raw to the processed data but what i meant was the information on how the normalized processed data was reduced to the gene list.

cheers,

michael

----- Original Message -----

From: helenadeus@...

To: mdmiller53@...

Cc: kei.cheung@... ; public-semweb-lifesci@...

Sent: Tuesday, November 24, 2009 10:06 AM

Subject: Re: BioRDF Telcon

Hi all,

I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-)

If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser.

However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow?

Thanks!

Lena

On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmiller53@...> wrote:

hi all,

(from the minutes)

"Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario)"

what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability.

what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately.

cheers,
michael
.
----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
To: "HCLS" <public-semweb-lifesci@...>
Sent: Monday, November 23, 2009 1:27 PM
Subject: Re: BioRDF Telcon

Today's BioRDF minutes are available at the following:

http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call

Thanks to Rob for scribing.

Cheers,

-Kei

Kei Cheung wrote:

This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below).

Cheers,

-Kei

== Conference Details ==
* Date of Call: Monday November 23, 2009
* Time of Call: 11:00 am Eastern Time
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS")
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
* Duration: ~1 hour
* Frequency: bi-weekly
* Convener: Kei Cheung
* Scribe: to-be-determined

== Agenda ==
* Roll call & introduction (Kei)
* RDF representation of microarray experiment and data (All)
* Provenance and workflow (All)

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-24T10:06:29Z

Hi all,

I apologize for missing the call yesterday! It seems you had a pretty interesting discussion! :-)

If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF would result in obtaining only the raw and processed data files but not the mechanism used to process it nor the resulting gene list. That's also what I concluded after looking at the data structure created by Tony Burdett's Limpopo parser.

However, having the raw data as linked data is already a great start! Kei, should I be looking into Taverna in order to reprocessed the raw files with a traceable analysis workflow?

Thanks!

Lena

On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmiller53@...> wrote:

hi all,

(from the minutes)

"Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario)"

what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how the source was processed into the extract then how the hybridization, feature extraction, error and normalization were performed. these are interesting and different protocols can cause differences at this level but it is pretty much a known art and usually not of too much interest or variability.

what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately.

cheers,
michael
.
----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
To: "HCLS" <public-semweb-lifesci@...>
Sent: Monday, November 23, 2009 1:27 PM
Subject: Re: BioRDF Telcon

Today's BioRDF minutes are available at the following:

http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call

Thanks to Rob for scribing.

Cheers,

-Kei

Kei Cheung wrote:

This is a reminder that the next BioRDF telcon call will be held at 11 am EDT (5 pm CET) on Monday, November 23 (see details below).

Cheers,

-Kei

== Conference Details ==
* Date of Call: Monday November 23, 2009
* Time of Call: 11:00 am Eastern Time
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS")
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
* Duration: ~1 hour
* Frequency: bi-weekly
* Convener: Kei Cheung
* Scribe: to-be-determined

== Agenda ==
* Roll call & introduction (Kei)
* RDF representation of microarray experiment and data (All)
* Provenance and workflow (All)

From forum: w3.org - public-semweb-lifesci

Re: BioRDF Telcon

2009-11-24T07:59:37Z

hi all,

(from the minutes)

"Yolanda/Kei/Scott: semantic annotation/description of workflow would enable
the retrieval of data relevant to that workflow (i.e. data that could be
used to populate that workflow for a different experimental scenario)"

what is typically in a MAGE-TAB/MAGE-ML document are the protocols for how
the source was processed into the extract then how the hybridization,
feature extraction, error and normalization were performed. these are
interesting and different protocols can cause differences at this level but
it is pretty much a known art and usually not of too much interest or
variability.

what is usually missing from those documents, along with the final gene
list, is how that gene list was obtained, what higher level analysis was
used, that is generally only in the paper unfortunately.

cheers,
michael
.
----- Original Message -----
From: "Kei Cheung" <kei.cheung@...>
To: "HCLS" <public-semweb-lifesci@...>
Sent: Monday, November 23, 2009 1:27 PM
Subject: Re: BioRDF Telcon

> Today's BioRDF minutes are available at the following:
>
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
>
> Thanks to Rob for scribing.
>
> Cheers,
>
> -Kei
>
> Kei Cheung wrote:
>> This is a reminder that the next BioRDF telcon call will be held at 11 am
>> EDT (5 pm CET) on Monday, November 23 (see details below).
>>
>> Cheers,
>>
>> -Kei
>>
>> == Conference Details ==
>> * Date of Call: Monday November 23, 2009
>> * Time of Call: 11:00 am Eastern Time
>> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>> * Dial-In #: +33.4.89.06.34.99 (Nice, France)
>> * Dial-In #: +44.117.370.6152 (Bristol, UK)
>> * Participant Access Code: 4257 ("HCLS")
>> * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for
>> details, or see Web IRC), Quick Start: Use
>> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for
>> IRC access.
>> * Duration: ~1 hour
>> * Frequency: bi-weekly
>> * Convener: Kei Cheung
>> * Scribe: to-be-determined
>>
>> == Agenda ==
>> * Roll call & introduction (Kei)
>> * RDF representation of microarray experiment and data (All)
>> * Provenance and workflow (All)
>>
>>
>
>
>
>

From forum: w3.org - public-semweb-lifesci

Re: SKOS support in Drupal

2009-11-24T05:42:07Z

Dan Morrison wrote:
>
> If anyone can link to a SKOS file that represents a glossary,
> taxonomy, or restricted vocabulary in any useful field, I can point
> the machine at it and see what happens. So far results have been
> surprisingly good, but I'm sure that some tuning may be needed if I
> feed it enough astual data.
>
Dan, check out http://metadataregistry.org. Everything behind the
"vocabularies" link is SKOS.

Regards,
Diane Hillmann

From forum: w3.org - public-esw-thes

Second call for papers: NMR sub-workshop on ontologies

2009-11-24T03:52:59Z

Sincere apologies for multiple postings.

======================================================
CALL FOR PAPERS

The NMR'2010 Workshop on

Commonsense and Non-Monotonic Reasoning for Ontologies

http://ksg.meraka.org.za/nmronto2010

Collocated With KR'2010

May 14-16 2010

Sutton Place, Toronto, Canada
======================================================

-- Workshop Description --

Classical reasoning over ontologies has reached the point where it can deal with large real-world ontologies.. This can largely be attributed to advances in research on description logics (DLs). A good example is the medical ontology SNOMED-CT, containing over 300,000 concepts and millions of binary relationships between them. SNOMED-CT can be represented as a DL ontology, and its subsumption hierarchy can be computed in a matter of minutes.

The obvious next step now is to extend reasoning over ontologies to cover non-classical cases, such as commonsense reasoning, a well established branch of AI. The first steps in that direction have been done by the ontology community, and while research along these lines has already resulted in initial tangible results, there is a need for a more coherent approach in order to speed up progress.

This need provides interesting challenges to both the ontology and commonsense reasoning communities. For the commonsense reasoning community it is a chance to determine to what extent techniques developed in its sub-areas, like e.g. non-monotonic reasoning (NMR), can be tailored to the requirements of the ontology community. For the ontology community it is an opportunity to determine whether existing results in this area can be sharpened and improved on by referring to results in the broader area of commonsense reasoning.

The topic of the workshop will hence be combining commonsense reasoning approaches and techniques with ontologies. One of the main motivations is to bring ideas from the well developed area of non-monotonic reasoning, like e.g. reasoning about actions, argumentation and belief revision, for discussion in the realm of ontology engineering: evolution, debugging, update, merging, etc. Certainly these tasks can benefit from most of the advances in NMR and give new insights for research in that area as well.

Commonsense and Non-Monotonic Reasoning for Ontologies will be of interest to:

- Researchers in the ontology community, particularly DL researchers, interested in extending ontological reasoning to non-classical cases.
- Researchers in the knowledge representation and commonsense reasoning community interested in applying existing NMR techniques to the area of ontologies.

This workshop will focus on an emerging hot topic. As such, one of its immediate outcomes will be boosting a new and exciting hybrid research domain combining commonsense reasoning and knowledge engineering for ontologies.

-- Topics of Interest --

Submissions are welcome on the role of commonsense and non-monotonic reasoning for ontologies in areas that include but are not limited to the following ones:

- Ontology Debugging and Update
- Ontology Merging, Alignment and Integration
- Inconsistency Handling
- Belief Revision and Theory Change for ontologies
- Uncertainty Handling, Defeasible Reasoning and Argumentation in ontologies
- Heuristic and Approximate Reasoning
- NMR methods for light-weight DL ontologies
- Planning and Reasoning about Action and Change on the Semantic Web
- Rules and Ontologies
- Temporal and Spatial Reasoning
- Ontology Fault Diagnosis and Repair
- Preferences and Ontologies
- Formal Concept Analysis and Ontologies

-- Submission Instructions --

Authors are kindly requested to follow the instructions for authors on the NMR website at
http://www.cs.sfu.ca/news/conferences/NMR/2010/NMR_2010/Author_Instructions.html

Please submit to http://www.easychair.org/conferences/?conf=nmronto2010

-- Important Dates

- Papers due: January 29 (Friday), 2010
- Notification: March 1 (Monday), 2010
- Final version: April 6 (Tuesday), 2010
- Workshop: May 14-16, 2010

-- Additional Information --

Please visit the NMR website at
http://www.cs.sfu.ca/news/conferences/NMR/2010/NMR_2010/NMR10.html

for more information about NMR, the venue of the workshop, the city of Toronto, accommodation and travel tips.

-- Workshop Chairs --

- Ivan José Varzinczak (Meraka Institute, South Africa)
http://ksg.meraka.org.za/~ivarzinczak

- Renata Wassermann (Universidade de São Paulo, Brazil)
http://www.ime.usp.br/~renata

-- Program Committee --

- Grigoris Antoniou (University of Crete and Information Systems Laboratory, Greece)
- Fábio Cozman (Universidade de São Paulo, Brazil)
- Giorgos Flouris (University of Crete and Information Systems Laboratory, Greece)
- Norman Foo (University of New South Wales, Australia)
- Zhisheng Huang (Free University of Amsterdam, Netherlands)
- Jos Lehmann (University of Edinburgh, United Kingdom)
- Maurice Pagnucco (University of New South Wales, Australia)
- Jeff Pan (University of Aberdeen, United Kingdom)
- Bijan Parsia (University of Manchester, United Kingdom)
- Laurent Perrussel (Université de Toulouse 1, France)
- Guilin Qi (Universitaet Karlsruhe, Germany)

--
Renata Wassermann
Associate Professor
Computer Science Department
University of São Paulo

From forum: w3.org - semantic-web

Re: SKOS support in Drupal

2009-11-24T02:45:12Z

On 24/11/2009, at 10:48 PM, Sean Bechhofer wrote:

The SKOS implementation report [1] cited a number of vocabularies that were using SKOS. How about one of those?

Cheers,

Sean

[1] http://www.w3.org/2006/07/SWD/SKOS/reference/20090315/implementation.html

Thanks Sean, that's definitely the sort of list I'm looking for. My browser history indicates I've found a *few* of them before. (and many more are defunct, damn)

I still can't see any that will empower a killer app for the social, 2.0 or "semantic" web. I've found lists of economic terminology, but to sell it as an enhancement to a CMS, I need things more accessible, something that a blogger, marketer, corporate or institution would want to use to enhance the metadata of their readable content, not just academic data dumps.

The broadest re-usable source I've found so far is MeSH which grew up to support PUBMed (I think). But it's not SKOS. So if there were a SKOS resource that was in any way authoritative, and not just a proof-of-concept, I'd love to link right in and embed it. (taxonomy_xml for the Drupal CMS is designed to feed from published external sources, it's not distributed with data itself (beyond samples).

If I could find a SKOS leader-in-the-field of:

- Music genres

- fiction genres

- ethnologies, world languages

- foods, recipes by type or influence

- geography/regions

- mythology

- geneology

- car makes & models

- art classifications or materials

- political groups

- religious sects

... heck I dunno, just SOMETHING that had meaning, represents abstract knowledge in the real world, and would actually be a benefit to certain folk putting together a web site.

That's what I'd like to sell, I need to be able to say if you add this rich, semantic data to your information architecture, it will be helpful.

I do not have any example of this in SKOS yet, though I know the promise is there. I just don't understand why I've failed to find it yet.

Thanks for the input, I've now followed every hopeful link on that page... but :-(

Yes, Dan, if you want to play with something, maybe one of the IVOA astronomy vocabularies can be nice. Especially because there are a couple of "small" vocs with a clear hierarchical structure there, such as [2].
And then you could have a try with bigger vocabularies. But be careful, things such as subject heading lists (like LCSH at [3]) are more like "networks" of concepts that are not really intended at for global hierarchical browsing, as they maybe have some thousands of "top" nodes...

Cheers,

Antoine

[2] http://www.ivoa.net/rdf/Vocabularies/vocabularies-20091007/AVM/
[3] http://id.loc.gov

I've been supporting importing the Library of Congress Subject Headings for a little while - They support content-negotiation properly and made my spider happy! I found that the consumer I wrote a year before there was any producer just started working on it without modification. That was gobsmacking.

At the time it was "If anyone ever does start serving vocabs up in RDF/XML with proper content-headers, I'll be able to read it this way, pity nobody does". When I discovered LOC had started doing so *and* my reader just worked, I poured myself a martini and stopped work for the day!

I solved the scaling problem when I was working on the Encyclopedia of Life project (hundreds of thousands of taxons). And refined it when importing MeSH (25,000 terms). So the LOC was small fry compared to them. :-)

I'll look further into the Astronomy one, which did at least look self-contained. Still a bit academic to use as a show-pony for why SKOS is any use to humans ;-)

I need some kick-ass real (public domain) list that a site-builder would WANT to start using. No more "samples" :-)

.dan.

From forum: w3.org - public-esw-thes