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From: Susanna S. <sa...@eb...> - 2010-04-13 16:48:53
|
Apologies for cross-posting .. *** NEW and Noteworthy Recognizing the increasing synergy in medical and biological ontology research and development, biomedical Knowledge Representation Working Group (KR-WG) of the American Medical Informatics Association (AMIA) has chosen the Bio-Ontologies SIG as the venue of the KR-WG's biannual knowledge representation in medicine meetings (KR-MED, www.kr-med.org <http://www.kr-med.org/>). Bio-Ontologies 2010 will serve as host to KR-MED 2010 in the biannual meeting series. In order to attend the biannual KR-MED meeting, please register for the Bio-Ontology SIG. *** Call for paper and posters We invite submissions for Bio-Ontologies 2010: Semantic Applications in Life Sciences at the 18th annual conference on Intelligent Systems for Molecular Biology (ISMB) 2010, July 9-13, Boston, MA (http://www.iscb.org/ismb2010). *** Key Dates - Submissions Due: April 16th (Friday) - Notifications: May 7th (Friday) - Final Version Due: May 14th (Friday) - Workshop: July 9th-10th (Friday and Saturday) *** Selected papers from Bio-Ontologies 2009 will be out soon in Journal of Biomedical Semantics. See table of contents below: 1. Phillip Lord: /An evolutionary approach to function./ 2. Clement Jonquet, Mark A. Musen and Nigam H. Shah: /Building a Biomedical Ontology Recommender Web Service./ 3. The OBI Consortium: /Modeling biomedical experimental processes with OBI./ 4. David Shotton: /CiTO, the Citation Typing Ontology, and its use for annotation of reference lists and visualization of citation networks./ 5. Allyson Lister, Phillip Lord, Matthew Pocock and Anil Wipat: /Annotation of SBML Models Through Rule-Based Semantic Integration./ 6. Jose Cruz-Toledo, Michel Dumontier, Marc Parisien and Francois Major: /RKB: A Semantic Web Knowledge Base for RNA./ 7. Matthias Samwald and Holger Stenzhorn: /Simple, Ontology-Based Representation of Biomedical Statements through Fine-Granular Entity Tagging and New Web Standards./ URL: coming soon ... *** Introduction Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology and life sciences. It has existed as a SIG at ISMB (http://www.iscb.org/ismb2010) for 12 years. We are interested in approachs to organising, presenting and disseminating knowledge in life sciences. We invite papers and poster submissions in traditional areas, such as the biological and medical applications of ontologies, newly developed biomedical ontologies, and the use of ontologies in data sharing standards. In addition, We invite submissions on a wide range of topics including, but not limited to: - Semantic and/or Scientific Wikis. - Collaborative curation platforms - Collaborative ontology authoring and peer-review mechanisms - Automated ontology learning - Ontology design patterns and guidelines - Ontology evaluation - Mapping between ontologies - Biological and medical applications of ontologies - "Flash updates" on newly developed or existing ontologies - Use of ontologies in data standards - Semantic Web enabled applications (such as for enhanced publishing and for capturing scientific discourse) - Research in ontology languages and its effect on biomedical ontologies *** Instructions to Authors We are inviting three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the meeting. Posters will be exhibited during the 2 days for at least one poster session. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies (e.g. the Foundational Model of Anatomy). Posters authors can also indicate a desire to provide a flash update. Unsuccessful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2010). ** Programme The SIG will run for two days this year. On each day, the morning session will have an invited keynote and selected papers; while the afternoon session will have a panel session and selected talks. One of the talks session will have "flash updates" from groups developing bio-ontologies as part of large international, collaborative consortia and from selected poster presenters. 09:00-10:00 Keynote 10:00-12:00 Research Talks (with coffee break) 12:00-13:30 Lunch and Poster Session 13:30-16:00 Research Talks (with coffee break) 16:00-17:30 Panel Session 17:30-close and Poster Session This year's keynote speakers will by Andrew Rzhetsky (July 10th) and Tim Clark (July 9th) *** Organisers Nigam Shah, Stanford University Larisa Soldatova, University of Wales, Aberystwyth Susanna-Assunta Sansone, EBI Susie Stephens, Johnson & Johnson *** Templates Submission templates are available from the website (http://www.bio-ontologies.org.uk/submissions). *** Programme Committee The programme committee is confirmed. See: http://www.bio-ontologies.org.uk/reviewers -- |
|
From: Susanna S. <sa...@eb...> - 2010-02-03 17:14:55
|
<<apologies for cross-posting>> ** Call for Papers Submissions are now invited Bio-Ontologies 2010: Semantic Applications in Life Sciences, a SIG at Intelligent Systems for Molecular Biology (ISMB) 2010, July 9-13, Boston, MA (http://www.iscb.org/ismb2010) *** Key Dates - Submissions Due: April 16th (Friday) - Notifications: May 7th (Friday) - Final Version Due: May 14th (Friday) - Workshop: July 9th-10th (Friday and Saturday) *** Introduction Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology. It has existed as a SIG at ISMB (http://www.iscb.org/ismb2010) for 12 years now, making it one of the longest running. We are interested in approachs to organising, presenting and disseminating knowledge in life sciences. We invite papers in traditional areas, such as the biological applications of ontologies, newly developed Bio-Ontologies, and the use of ontologies in data sharing standards. In addition, We invite submissions on a wide range of topics including, but not limited to: - Semantic and/or Scientific Wikis. - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms - Automated ontology learning - Mapping between ontologies - Biological Applications of Ontologies - "Flash updates" on Newly Developed or Existing Bio-Ontologies - Use of Ontologies in Data Standards - Semantic Web enabled applications (such as for enhanced publishing and for capturing scientific discourse) - Research in Ontology Languages and its Effect on Bio-Ontologies *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2010). *** Instructions to Authors We are inviting three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the 2 days for at least one poster session. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies (e.g. the Foundational Model of Anatomy). Posters authors can also indicate a desire to provide a flash update. Unsuccessful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. ** Programme The SIG will run for two days this year. On each day, the morning session will have an invited keynote and selected papers; while the afternoon session will have a panel session and selected talks. One of the talks session will have "flash updates" from groups developing bio-ontologies as part of large international, collaborative consortia and from selected poster presenters. 09:00-10:00 Keynote 10:00-12:00 Research Talks (with coffee break) 12:00-13:30 Lunch and Poster Session 13:30-16:00 Research Talks (with coffee break) 16:00-17:30 Panel Session 17:30-close and Poster Session This year's keynote speakers will by Andrew Rzhetsky (July 10th) and Tim Clark (July 9th) *** Templates Submission templates are available from the website (http://sites.google.com/site/bioontologies/submissions). *** Organisers Nigam Shah, Stanford University Larisa Soldatova, University of Wales, Aberystwyth Susanna-Assunta Sansone, EBI Susie Stephens, Johnson & Johnson -- Susanna-Assunta Sansone, PhD Project Coordinator http://isatab.sf.net http://biosharing.org http://www.ebi.ac.uk/net-project |
|
From: Adrien C. <co...@st...> - 2009-09-04 01:23:08
|
=======================================================================
CALL FOR ABSTRACTS - PSB Workshop: GPD-Rxn Workshop
=======================================================================
GPD-Rxn WORKSHOP: Genotype-Phenotype-Drug Relationship Extraction from
Text
Co-located with the Pacific Symposium on Biocomputing,
January 4-8 2010, The Big Island of Hawaii
The aim of this workshop is to bring together researchers working on the
automatic or semi-automatic extraction of relationships between
biomedical entities from research literature. The workshop will focus
particularly on methods for the extraction of Genotype-Phenotype,
Genotype-Drug, and Phenotype-Drug relationships and the use of the
relationships for advancing pharmacogenomic research.
CALL FOR PARTICIPATION
Advances in concept recognition have led to the development of various
tools that enable the identification of biomedical entities and
relationships between them in text. The aim of the GPD-Rxn workshop is
to examine the current state of art and discuss the next steps for
making the extraction of relationships between biomedical entities
integral to the curation and knowledge management workflow in
Pharmacogenomics. The workshop will focus particularly on the extraction
of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships
that are of interest to Pharmacogenomics.
Extracting and structuring such text-mined relationships is a key to
support the evaluation and the validation of multiple hypotheses that
emerge form high throughput translational studies spanning multiple
measurement modalities. In order to advance this agenda, it is essential
that existing relationship extraction methods be compared to one another
and that a community wide benchmark corpus emerges; against which future
methods can be compared. The workshop aims to bring together researchers
working on the automatic or semi-automatic extraction of relationships
between biomedical entities from research literature in order to
identify the key groups interested in creating such a benchmark.
IMPORTANT TOPICS RELEVANT TO THIS WORKSHOP
* Natural Language Processing methods for the extraction of
relationships
* Machine learning methods for the characterization of biomedical
relationships
* Use of prior knowledge to improve relationship extraction
* Ontologies for relationships
* Applications and uses of text-extracted relationships
Approaches that combine text-mining and knowledge-based systems are of
special interest.
ABSTRACTS
We are soliciting both research and position abstracts (up to 500 words)
related to the topics mentioned above. The GPD-Rxn workshop will combine
invited talks, talks selected from abstract submissions to this call,
and a panel discussion. Submitted abstracts that will be reviewed by the
co-chairs for selecting submitted talks. In addition, other relevant
submissions will have the possibility to be presented a poster-session
at the end of the workshop. Workshop participants must register for PSB;
abstracts may be submitted prior to registering. Authors of accepted
abstracts must register for PSB as soon as they are notified of paper
acceptance.
Abstracts should be emailed to Adrien Coulet (coulet at stanford dot edu).
CO-CHAIRS
*Adrien Coulet
*Nigam Shah
*Larry Hunter
*Chitta Baral
*Russ B. Altman
IMPORTANT DATES
*Abstract deadline: September 15, 2009
*Speaker notification: October 15, 2009
*Deadline for early registration: October 31, 2009
*Workshop: Date to be announced; will be scheduled during the main
conference (January 5-8, 2010)
LINKS
PSB 2010: http://psb.stanford.edu/
GPD-Rxn Workshop: http://psb.stanford.edu/gdprxn-workshop.html
CONTACT
Adrien Coulet, coulet at stanford dot edu
|
|
From: Adrien C. <co...@st...> - 2009-07-28 18:53:40
|
=======================================================================
CALL FOR ABSTRACTS - PSB Workshop: GPD-Rxn Workshop
=======================================================================
GPD-Rxn WORKSHOP: Genotype-Phenotype-Drug Relationship Extraction from
Text
Co-located with the Pacific Symposium on Biocomputing,
January 4-8 2010, The Big Island of Hawaii
The aim of this workshop is to bring together researchers working on the
automatic or semi-automatic extraction of relationships between
biomedical entities from research literature. The workshop will focus
particularly on methods for the extraction of Genotype-Phenotype,
Genotype-Drug, and Phenotype-Drug relationships and the use of the
relationships for advancing pharmacogenomic research.
CALL FOR PARTICIPATION
Advances in concept recognition have led to the development of various
tools that enable the identification of biomedical entities and
relationships between them in text. The aim of the GPD-Rxn workshop is
to examine the current state of art and discuss the next steps for
making the extraction of relationships between biomedical entities
integral to the curation and knowledge management workflow in
Pharmacogenomics. The workshop will focus particularly on the extraction
of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships
that are of interest to Pharmacogenomics.
Extracting and structuring such text-mined relationships is a key to
support the evaluation and the validation of multiple hypotheses that
emerge form high throughput translational studies spanning multiple
measurement modalities. In order to advance this agenda, it is essential
that existing relationship extraction methods be compared to one another
and that a community wide benchmark corpus emerges; against which future
methods can be compared. The workshop aims to bring together researchers
working on the automatic or semi-automatic extraction of relationships
between biomedical entities from research literature in order to
identify the key groups interested in creating such a benchmark.
IMPORTANT TOPICS RELEVANT TO THIS WORKSHOP
* Natural Language Processing methods for the extraction of
relationships
* Machine learning methods for the characterization of biomedical
relationships
* Use of prior knowledge to improve relationship extraction
* Ontologies for relationships
* Applications and uses of text-extracted relationships
Approaches that combine text-mining and knowledge-based systems are of
special interest.
ABSTRACTS
We are soliciting both research and position abstracts (up to 500 words)
related to the topics mentioned above. The GPD-Rxn workshop will combine
invited talks, talks selected from abstract submissions to this call,
and a panel discussion. Submitted abstracts that will be reviewed by the
co-chairs for selecting submitted talks. In addition, other relevant
submissions will have the possibility to be presented a poster-session
at the end of the workshop. Workshop participants must register for PSB;
abstracts may be submitted prior to registering. Authors of accepted
abstracts must register for PSB as soon as they are notified of paper
acceptance.
Abstracts should be emailed to Adrien Coulet (coulet at stanford dot edu).
CO-CHAIRS
*Adrien Coulet
*Nigam Shah
*Larry Hunter
*Chitta Baral
*Russ B. Altman
IMPORTANT DATES
*Abstract deadline: September 15, 2009
*Speaker notification: October 15, 2009
*Deadline for early registration: October 31, 2009
*Workshop: Date to be announced; will be scheduled during the main
conference (January 5-8, 2010)
LINKS
PSB 2010: http://psb.stanford.edu/
GPD-Rxn Workshop: http://psb.stanford.edu/gdprxn-workshop.html
CONTACT
Adrien Coulet, coulet at stanford dot edu
|
|
From: Susanna-Assunta S. <sa...@eb...> - 2009-06-10 13:01:16
|
** Call for Participation Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology. We are pleased to announce the programme for Bio-Ontologies 2009: Knowledge in Biology, at SIG at Intelligent Systems for Molecular Biology, with papers and posters on a wide range of topics. ** Programme This year's keynote speaker will by Barend Mons (http://en.wikipedia.org/wiki/Barend_Mons). This year's panel will be - Barend Mons - Andrew Su - Dawn Field The full programme is now available at: http://bio-ontologies.org.uk/programme.html *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Susie Stephens, Eli Lilly Larisa Soldatova, University of Wales, Aberystwyth ** Registration All registration will be handled by ISCB. Further details are available http://www.iscb.org/ismbeccb2009/registration.php ** Bio-Ontologies 2008 Papers from last years SIG have now been published in BMC Bioinformatics. http://www.biomedcentral.com/1471-2105/10?issue=S5 |
|
From: Susanna S. <sa...@eb...> - 2009-04-07 17:25:36
|
** Apologies for cross posting **
Call for Papers - Deadline for submission Friday
Submissions are invited Bio-Ontologies 2009: Knowledge in Biology, a SIG
at Intelligent Systems for Molecular Biology 2009.
http://www.bio-ontologies.org.uk/cfp.html
Key Dates
* Submissions Due: April 10th (Friday)
* Notifications: May 1st (Friday)
* Final Version Due: May 8th (Friday)
* Workshop: June 28th (Sunday)
Introduction
Bio-Ontologies: Knowledge in Biology provides a forum for discussion of
the latest and most cutting-edge research in ontologies and more
generally the organisation, presentation and dissemination of knowledge
in biology. It has existed as a SIG at ISMB for 11 years now, making it
one of the longest running.
We are interested in any formal or informal approach to organising,
presenting and disseminating knowledge in biology.
We invite submissions on a wide range of topics including, but not
limited to:
* Semantic and/or Scientific Wikis.
* Multimedia Blogs
* Folksonomies
* Tag Clouds
* Collaborative Curation Platforms
* Collaborative Ontology Authoring and Peer-Review Mechanisms
* Biological Applications of Ontologies
* Reports on Newly Developed or Existing Bio-Ontologies
* Tools for Developing Ontologies
* Use of Ontologies in Data Communication Standards
* Use of Semantic Web technologies in Bioinformatics
* Implications of Bio-Ontologies or the Semantic Web for Drug Discovery
* Research in Ontology Languages and its Effect on Bio-Ontologies
Programme
This year's keynote speaker will by Barend Mons.
Submissions
Submissions are now open and can be submitted through EasyChair:
https://www.easychair.org/login.cgi?conf=bioontologies2009
Instructions to Authors
We are inviting two types of submissions.
* Short papers, up to 4 pages.
* Poster abstracts, up to 1/2 page.
Following review, successful papers will be presented at the
Bio-Ontologies SIG. Poster abstracts will be provided poster space and
time will be allocated during the day for at least one poster session.
Unsuccessful papers will automatically be considered for poster
presentation; there is no need to submit both on the same topic.
Organisers
Phillip Lord, Newcastle University
Susanna-Assunta Sansone, EBI
Nigam Shah, Stanford
Susie Stephens, Eli Lilly
Larisa Soldatova, University of Wales, Aberystwyth
Programme Committee
The programme committee, organised alphabetically is:
Michael Bada, University of Colorado Denver
Olivier Bodenreider, National Library Medicine
Kei Cheung, Yale Center for Medical Informatics
Paolo Ciccarese, Harvard
Sudeshna Das, Harvard
Michel Dumontier, Carleton University
Wacek Kusnierczyk, Norwegian University of Science and Technology
Cliff Joslyn, Pacific Northwest National Laboratory
Midori Harris, European Bioinformatics Institute
James Malone, European Bioinformatics Institute
Robin McEntire, Independent Consultant
Parsa Mirhaji, University of Texas
David Newman, ECS, University of Southampton
Chimezie Ogbuji, The Cleveland Clinic Foundation
Alexandre Passant, DERI
Alan Ruttenberg, Science Commons
Phillippe Rocca-Serra, European Bioinformatics Institute
Matthias Samwald, DERI
Robert Stevens, University of Manchester
Yimin Wang, Eli Lilly
Mark Wilkinson, Medical Genetics, U. of British Columbia
Jenna Zhou, Eli Lilly
and the conference organisers.
Templates
Submission templates are available at:
http://bio-ontologies.org.uk/submissions.html
<http://bio-ontologies.org.uk>
--
|
|
From: Susanna S. <sa...@eb...> - 2009-03-24 12:25:35
|
** Apologies for cross posting **
Call for Papers
Submissions are invited Bio-Ontologies 2009: Knowledge in Biology, a SIG
at Intelligent Systems for Molecular Biology 2009.
http://www.bio-ontologies.org.uk/cfp.html
Key Dates
* Submissions Due: April 10th (Friday)
* Notifications: May 1st (Friday)
* Final Version Due: May 8th (Friday)
* Workshop: June 28th (Sunday)
Introduction
Bio-Ontologies: Knowledge in Biology provides a forum for discussion of
the latest and most cutting-edge research in ontologies and more
generally the organisation, presentation and dissemination of knowledge
in biology. It has existed as a SIG at ISMB for 11 years now, making it
one of the longest running.
We are interested in any formal or informal approach to organising,
presenting and disseminating knowledge in biology.
We invite submissions on a wide range of topics including, but not
limited to:
* Semantic and/or Scientific Wikis.
* Multimedia Blogs
* Folksonomies
* Tag Clouds
* Collaborative Curation Platforms
* Collaborative Ontology Authoring and Peer-Review Mechanisms
* Biological Applications of Ontologies
* Reports on Newly Developed or Existing Bio-Ontologies
* Tools for Developing Ontologies
* Use of Ontologies in Data Communication Standards
* Use of Semantic Web technologies in Bioinformatics
* Implications of Bio-Ontologies or the Semantic Web for Drug Discovery
* Research in Ontology Languages and its Effect on Bio-Ontologies
Programme
This year's keynote speaker will by Barend Mons.
Submissions
Submissions are now open and can be submitted through EasyChair:
https://www.easychair.org/login.cgi?conf=bioontologies2009
Instructions to Authors
We are inviting two types of submissions.
* Short papers, up to 4 pages.
* Poster abstracts, up to 1/2 page.
Following review, successful papers will be presented at the
Bio-Ontologies SIG. Poster abstracts will be provided poster space and
time will be allocated during the day for at least one poster session.
Unsuccessful papers will automatically be considered for poster
presentation; there is no need to submit both on the same topic.
Organisers
Phillip Lord, Newcastle University
Susanna-Assunta Sansone, EBI
Nigam Shah, Stanford
Susie Stephens, Eli Lilly
Larisa Soldatova, University of Wales, Aberystwyth
Programme Committee
The programme committee, organised alphabetically is:
Michael Bada, University of Colorado Denver
Olivier Bodenreider, National Library Medicine
Kei Cheung, Yale Center for Medical Informatics
Paolo Ciccarese, Harvard
Sudeshna Das, Harvard
Michel Dumontier, Carleton University
Wacek Kusnierczyk, Norwegian University of Science and Technology
Cliff Joslyn, Pacific Northwest National Laboratory
Midori Harris, European Bioinformatics Institute
James Malone, European Bioinformatics Institute
Robin McEntire, Independent Consultant
Parsa Mirhaji, University of Texas
David Newman, ECS, University of Southampton
Chimezie Ogbuji, The Cleveland Clinic Foundation
Alexandre Passant, DERI
Alan Ruttenberg, Science Commons
Phillippe Rocca-Serra, European Bioinformatics Institute
Matthias Samwald, DERI
Robert Stevens, University of Manchester
Yimin Wang, Eli Lilly
Mark Wilkinson, Medical Genetics, U. of British Columbia
Jenna Zhou, Eli Lilly
and the conference organisers.
Templates
Submission templates are available at:
http://bio-ontologies.org.uk/submissions.html
<http://bio-ontologies.org.uk>
--
|
|
From: Susanna S. <sa...@eb...> - 2009-02-18 12:41:21
|
- Apologies for cross posting - *** Call for Papers* Submissions are now invited _* Bio-Ontologies 2009: Knowledge in Biology*_ (_Stockholm, June 28th, 2009_)* *** **a SIG at Intelligent Systems for Molecular Biology (ISMB/ECCB) 2009 (http://bio-ontologies.org.uk) **** Key Dates* - Submissions Due: April 10th (Friday) - Notifications: May 1st (Friday) - Final Version Due: May 8th (Friday) - Workshop: June 28th (Sunday) * *** Introduction* Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology. It has existed as a SIG at ISMB (http://www.iscb.org/ismbeccb2009) for 11 years now, making it one of the longest running. We are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. We invite submissions on a wide range of topics including, but not limited to: - Semantic and/or Scientific Wikis. - Multimedia Blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for Drug Discovery - Research in Ontology Languages and its Effect on Bio-Ontologies *** Programme* This year's keynote speaker will by Barend Mons (http://en.wikipedia.org/wiki/Barend_Mons). * *** Submissions* Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2009). * *** Instructions to Authors* We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccessful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. **** Organisers* Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Susie Stephens, Lily Larisa Soldatova, University of Wales, Aberystwyth * *** Programme Committee* The programme committee, organised alphabetically is: Michael Bada, University of Colorado Denver Olivier Bodenreider, National Library Medicine Prof. Kei Cheung, Yale Center for Medical Informatics Paolo Ciccarese, Harvard Sudeshna Das, Harvard Michel Dumontier, Carleton University Wacek Kusnierczyk, Norwegian University of Science and Technology Cliff Joslyn, Pacific Northwest National Laboratory Midori Harris, European Bioinformatics Institute James Malone, European Bioinformatics Institute Robin McEntire, Independent Consultant Parsa Mirhaji, University of Texas David Newman, ECS, University of Southampton Chimezie Ogbuji, The Cleveland Clinic Foundation Alan Passant, DERI Alan Ruttenberg, Science Commons Phillippe Rocca-Serra, European Bioinformatics Institute Matthias Samwald, DERI Robert Stevens, University of Manchester Yimin Wang, Lily Mark Wilkinson, Medical Genetics, U. of British Columbia Jenna Zhou, Lily and the conference organisers. * *** Templates* Submission templates are available from the website (http://bio-ontologies.org.uk). -- Susanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project |
|
From: Susanna-Assunta S. <sa...@eb...> - 2008-08-08 16:06:20
|
Dear colleagues, We would like to inform you that the paper describing the Minimum Information for Biological and Biomedical Investigations (MIBBI) project -- http://www.mibbi.org/ -- has been published this month in Nature Biotechnology. This represents a significant step towards a comprehensive set complementary reporting guidelines for the biosciences; both by describing our work to date, and by acting as a beacon for new participants. A PDF of the paper is freely-available for download: http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf This paper: 1. Describes the foundational work performed by the ever-growing list of participants in this project. 2. Provides analysis of the various MI specifications registered at the site (scope, conflicts, etc.), including the MSI's CIMR 3. Addresses the view of funders and publishers on the enforcement of consensual reporting guidelines. 4. Outlines our plans for future work, which all are strongly encouraged to monitor, and in which all are invited to participate. Any questions can be directed to: Chris Taylor Susanna-Assunta Sansone Dawn Field Yours Sincerely, Susanna, Chris and Dawn, on behalf of all authors. -- |
|
From: Susanna <sa...@eb...> - 2008-06-26 10:51:00
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- Apologies for cross posting - Bio-Ontologies 2008: Knowledge in Biology - Sunday 20th July- a SIG at Intelligent Systems for Molecular Biology (ISMB) 2008 *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** **THE PROGRAMME IS NOW AVAILABLE** http://bio-ontologies.org.uk/download/Bio-Ontologies2008.pdf **REGISTRATION IS OPEN** http://www.iscb.org/ismb2008/registration.php **PAPERS FROM LAST YEAR - PUBLISHED** http://www.biomedcentral.com/1471-2105/9?issue=S5 The best papers from this year will also be published in BMC Bioinformatics. See you in Toronto! The Program Chairs: Phillip Lord (1), Susanna-A. Sansone (2), Nigam Shah (3), Matt Cockerill (4) 1. School of Computing Science, University of Newcastle, UK 2. EMBL-EBI The European Bioinformatics Institute, Cambridge, UK 3. Center for Biomedical Informatics, Stanford University, USA 4. BioMedCentral *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** The Bio-Ontologies Meeting has existed as a Special Interest Group meeting at ISMB for more than a decade, making it one of the longest running SIG meetings. The Bio-Ontologies SIG meeting has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. As result, this year we are broadening the scope of SIG to include formal and informal approaches to organising, presenting and disseminating knowledge in biology. Keynote This year's keynote speaker will be Professor Philip E. Bourne, from the Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD. Panel Session This year's panel session will have the following members: - Philip E. Bourne, UCSD - Helen Parkinson, European Bioinformatics Institute - Matt Cockerill, BioMed Central - Mark Wilkinson, University of British Columbia Programme Committee We also wish to thank the programme committee for their excellent input and guidance - the programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK James Malone, EBI Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Susie M. Stephens, Eli Lilly Robert Stevens, University of Manchester and the conference organisers. -- |
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From: Susanna <sa...@eb...> - 2008-04-25 13:16:28
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- Apologies for cross posting - **One Week to the Submission Deadline** *** CALL FOR PAPERS AND POSTER ABSTRACTS Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Key Dates - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final Version Due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific wikis. - Multimedia blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday parallel to the main conference. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Programme This year's keynote speaker will be Professor **Philip E. Bourne**, from the Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD. Our panel session will the following members: - Philip E. Bourne, UCSD - Helen Parkinson, European Bioinformatics Institute - Matt Cockerill, BioMed Central - Mark Wilkinson, University of British Columbia *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Susie M. Stephens, Eli Lilly Robert Stevens, University of Manchester and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). -- |
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From: Susanna <sa...@eb...> - 2008-04-14 16:42:20
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Apologies for cross posting ****** CALL FOR PAPERS AND POSTER ABSTRACTS ******** Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. *** Key Dates - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final Version Due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific wikis. - Multimedia blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday parallel to the main conference. *** Programme This year's keynote speaker will be Professor **Philip E. Bourne**, from the Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD. Our panel session will the following members: - Philip E. Bourne, UCSD - Helen Parkinson, European Bioinformatics Institute - Matt Cockerill, BioMed Central - Mark Wilkinson, University of British Columbia *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. *** Best papers in BMC Bioinformatics The best papers from Bio-Ontologies 2008: Knowledge in Biology will be published in BMC Bioinformatics. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Susie M. Stephens, Eli Lilly Robert Stevens, University of Manchester and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). -- |
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From: Susanna-A S. <sa...@eb...> - 2008-03-09 18:30:29
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- Apologies for cross posting - ****** CALL FOR PAPERS AND POSTER ABSTRACTS ******** Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology (Toronto, July 20th, 2008), a SIG at Intelligent Systems for Molecular Biology (ISMB). *** Key Dates *** - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final version due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction *** Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific Wikis - Multimedia Blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday, July 20th parallel to the main conference. *** Submissions *** Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors *** We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. *** Organisers *** Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee *** The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Robert Stevens, University of Manchester and the conference organisers. *** Templates *** Submission templates are available from the website (http://bio-ontologies.org.uk). -- Susanna-Assunta Sansone, PhD www.ebi.ac.uk/net-project |
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From: Susanna <sa...@eb...> - 2007-09-28 15:40:38
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Dear Members, The MSI papers have been published. Thanks for your contribution! Susanna ******** Special issue papers in Metabolomics Journal (http://springerlink.metapress.com/content/j85g85483103/?p=c2b8952a7cdb44398c0c4f2f7291c0c6&pi=0) Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., Sumner, L.W., Goodacre, R., Hardy, N.W., Taylor, C., Fostel, J., Kristal, B. Kaddurah-Daouk, R., Mendes, P., van Ommen, B., Lindon, J.C. & Sansone, S.-A. (2007) The metabolomics standards initiative (MSI). Metabolomics 3, 175-178. Griffin, J.L., Nicholls, A.W., Daykin, C., Heald, S., Keun, H., Schuppe-Koistinen, I., Griffiths, J.R., Cheng, L., Rocca-Serra, P., Rubtsov, D.V. & Robertson, D. (2007) Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments. Metabolomics 3, 179-188. van der Werf, M.J., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, T., Portais. J.C., Wittmann, C., Hooks, M., Tomassini, A., Oldiges, M., Fostel, J. & Sauer, U. (2007) Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments. Metabolomics 3, 189-194. Fiehn, O., Sumner, L.W., Rhee, S.Y., Ward, J., Dickerson, J., Lange, B.M., Lane, G., Roessner, U., Last, R. & Nikolau1, B. (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics 3, 195-201. Morrison, N., Bearden, D., Bundy, J.G., Collette, T., Currie, F., Davey, M.P., Haigh, N.S., Hancock, D., Jones, O.A.H., Rochfort, S., Sansone, S.-A., S(tys, D., Teng, Q., Field, D. & Viant, M.R. (2007) Standard reporting requirements for biological samples in metabolomics experiments: environmental context. Metabolomics 3, 203-210. Sumner, L.W., Amberg, A., Barrett, D., Beger, R., Beale, M.H., Daykin, C., Fan, T.W.-M., Fiehn, O., Goodacre, R., Griffin, J.L., Hardy, N., Higashi, R., Kopka, J., Lindon, J.C., Lane, A.N., Marriott, P., Nicholls, A.W., Reily, M.D. & Viant, M. (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3, 211-221. Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.R., Günther, U., Griffin, J.L. & Hardy, N. (2007) Proposed reporting requirements for the description of NMR-based metabolomics experiments. Metabolomics 3, 223-229. Goodacre, R., Broadhurst, D., Smilde, A., Kristal, B.S., Baker, J.D., Beger, R., Bessant, C., Connor, S., Capuani, G., Craig, A., Ebbels, T., Kell, D.B., Manetti, C., Newton, J., Paternostro, G., Somorjai, R., Sjöström, M., Trygg, J. & Wulfert, F. (2007) Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 3, 231-241. Hardy, N.W. & Taylor, C.F. (2007) A roadmap for the establishment of standard data exchange structures for metabolomics. Metabolomics 3, 243-248. Sansone, S.-A., Schober, D., Atherton, H.J., Fiehn, O., Jenkins, H., Rocca-Serra, P., Rubtsov, D.V., Spasic, I., Soldatova, L., Taylor, C., Tseng, A., Viant, M.R. & The Ontology Working Group Members (2007) Metabolomics standards initiative - ontology working group - work in progress. Metabolomics 3, 249-256. *** Correspondence in Nature Biotechnology (http://www.nature.com/nbt/journal/v25/n8/full/nbt0807-846b.html) Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O. (2007) The Metabolomics Standards Initiative. Nat Biotechnol. 2007 Aug;25(8):846-8. *** -- Susanna-Assunta Sansone, PhD Project - Coordinator www.ebi.ac.uk/net-project |
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From: Sumner, L. <lws...@no...> - 2007-09-14 02:18:07
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I thought you might be interested in the recent update notice from the plant ontology db. Lloyd =20 Plant Ontology Consortium is happy to announce the release #0907 of PO database! http://www.plantontology.org <http://www.plantontology.org/>=20 =20 * Ontology update - 1109 PO terms - 32104 annotations visit http://www.plantontology.org/docs/release_notes/index.html for more details =20 * New version of PO browser (http://www.plantontology.org/amigo/go.cgi) - New interface - New users guide - New tutorials - New feature: added "GO" (Gene Ontology) associations link to Arabidopsis genes =20 * POC Website updates (http://www.plantontology.org/) - added "Request PO terms" feature on navigation menu - added "POC Outreach Activities" link in "Documentation" page - Updated "Mail Archives" - Updated "PO website usage statistics" - Updated "Tutorials" =20 * POC and plant community - Welcome experts from Medicago, Populus, Rosaceae, Solanaceae, Vitis fields to join plant ontology development Please email to po...@pl... or subscribe po-dev mailing list =20 - Phenote (a phenotype annotation tool using ontologies http:// www.phenote.org/) has added "plant" configuration, plus PO and other plant related ontologies for curation. Contact Nicole Washington ( NLW...@lb... ) for more information about downloading and using Phenote tool =20 - Meet POC members in international conferences @ 8th Agricultural Ontology Service (AOS) workshop, Rome, Italy =20 Sep 21-22 @ 5th International Symposium of Rice Functional Genomics, Tsukuba, Japan Oct 15-17 @ 2nd International Biocuration meeting, San Jose, CA Oct 25-28 =20 =20 =20 The Plant Ontology Consortium web: http:www.plantontology.org e-mail: po...@pl... submit requests at: http://sourceforge.net/tracker/?func=3Dadd&group_id=3D76834&atid=3D835555= =20 =20 =20 =20 |
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From: Susanna-A S. <sa...@eb...> - 2007-06-19 23:01:40
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** Apologies for cross posting ** Bio-Ontologies SIG Workshop Vienna, Austria: July 20 2007 "Bio-Ontologies: ten years past and looking to the future" 15th ISMB & 6th ECCB Vienna, Austria: July 18-25, 2007 *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** The programme is now available: http://bio-ontologies.org.uk/download/Bio-Ontologies2007.pdf REGISTRATION IS OPEN: http://www.iscb.org/ismbeccb2007/registration/ See you in Vienna! The Program Chairs: Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), Susanna-A. Sansone (4) 1. School of Computer Science, University of Manchester, UK 2. School of Computing Science, University of Newcastle, UK 3. GlaxoSmithKline, USA 4. EMBL-EBI The European Bioinformatics Institute, Cambridge, UK *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** The long-standing ISMB Bio-Ontologies SIG is in its tenth consecutive year. This year the workshop will have a celebratory and reflective discussion on "Bio-Ontologies: ten years past and looking to the future". About the Bio-Ontologies SIG workshop The workshop will continue offer an informal environment for presentation and discussion of ontologies and their role in providing a mechanism for organising, sharing and reconciling data. This year, to celebrate its tenth anniversary, we have invited four presenters from the first bio-ontologies tutorial and meeting organisers to sit on a panel, namely: Mark Musen, Peter Karp, Russ Altman and Steffen Schulze-Kremer They will be asked to present positions on the following questions: 1. What has been the best thing to have happened in bio-ontologies in the past ten years? 2. What has been the worst thing to have happened in bio-ontologies in the past ten years? 3. How must bio-ontologies progress in the next ten years? 4. How must bio-ontologies not progress in the next ten years Program Committee Abstracts have been reviewed by the Program Committee, including the Program Chairs and additionally: David Benton, Suzanna Lewis, Chris Mungall, Alan Ruttenberg, Andrew Gibson, James Butler, Kei Cheung, Frank Gibson. publication of the Proceedings Following the workshop some of the presentations will be invited to submit a full paper for further publication in a BMC Bioinformatics Supplement. Websites: Bio-Ontologies SIG workshop: http://bio-ontologies.org.uk <http://bio-ontologies.org.uk/> ISMB & ECCB main conference website http://www.iscb.org/ismbeccb2007 -- |
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From: anne f. <ann...@we...> - 2007-05-25 14:12:44
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From: Susanna <sa...@eb...> - 2007-04-26 17:11:08
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** Apologies for cross posting ** CALL FOR PAPERS and POSTER ABSTRACTS (Deadline May 1st) Proceedings in BMC Bioinformatics *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** Bio-Ontologies SIG Workshop Vienna, Austria: July 20 2007 "Bio-Ontologies: ten years past and looking to the future" *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** 15th ISMB & 6th ECCB Vienna, Austria: July 18-25, 2007 CALL FOR PAPERS and POSTER ABSTRACTS (Deadline May 1st) Proceedings in BMC Bioinformatics The long-standing ISMB Bio-Ontologies SIG is in its tenth consecutive year. This year the workshop will have a celebratory and reflective discussion on "Bio-Ontologies: ten years past and looking to the future". PROGRAM CHAIRS: Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), Susanna-A. Sansone (4) 1. School of Computer Science, University of Manchester, UK 2. School of Computing Science, University of Newcastle, UK 3. GlaxoSmithKline, USA 4. EMBL-EBI The European Bioinformatics Institute, Cambridge, UK WEBSITES: Bio-Ontologies SIG workshop: http://bio-ontologies.org.uk ISMB & ECCB main conference website http://www.iscb.org/ismbeccb2007 ABOUT THE BIO-ONTOLOGIES SIG WORKSHOP The workshop will continue offer an informal environment for presentation and discussion of ontologies and their role in providing a mechanism for organising, sharing and reconciling data. This year, to celebrate its tenth anniversary, we have invited four presenters from the first bio-ontologies tutorial and meeting organisers to sit on a panel, namely: Mark Musen, Peter Karp, Russ Altman and Steffen Schulze-Kremer They will be asked to present positions on the following questions: 1. What has been the best thing to have happened in bio-ontologies in the past ten years? 2. What has been the worst thing to have happened in bio-ontologies in the past ten years? 3. How must bio-ontologies progress in the next ten years? 4. How must bio-ontologies not progress in the next ten years CALL FOR PAPERS AND POSTER ABSTRACT: We are inviting two types of submissions SHORT PAPER papers (up to 4 pages) and POSTER ABSTRACT (up to 1/2 page) from any aspect doing bio-ontology research or using bio-ontologies to do bioinformatics research. Topics include, but are not restricted to: - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - The implications of Bio-Ontologies or the Semantic Web for the drug discovery process - Current Research In Ontology Languages and its implication for Bio-Ontologies PROGRAM COMMITTEE Abstracts will be reviewed by the Program Committee, including the Program Chairs and additionally: David Benton, Suzanna Lewis, Chris Mungall and Alan Ruttenberg. PUBLICATION OF THE PROCEEDINGS The Programme Committee will also select those papers, which are suitable for further publication in a BMC Bioinformatics Supplement. Authors will be invited to resubmit full papers. DEADLINES Submissions due: May 1st 2007 Notification of acceptance: May 21st 2007 Final versions due: May 31st 2007 Workshop: July 20th 2007 -- Susanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: sa...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK room: A229 |
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From: Susanna <sa...@eb...> - 2007-04-11 09:47:25
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** Apologies for cross posting ** CALL FOR PAPERS and POSTER ABSTRACTS Submissions by May 1 *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** Bio-Ontologies SIG Workshop, Vienna, Austria: July 20 2007 "Bio-Ontologies: ten years past and looking to the future" *^**^***^****^****^****^****^****^****^****^****^****^*****^**^***^** 15th ISMB & 6th ECCB, Vienna, Austria: from July 18 to 25, 2007 CALL FOR PAPERS and POSTER ABSTRACTS Submissions by May 1 The long-standing ISMB Bio-Ontologies SIG is in its tenth consecutive year. This year the workshop will have a celebratory and reflective discussion on "Bio-Ontologies: ten years past and looking to the future". PROGRAM CHAIRS Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), Susanna-A. Sansone (4) 1. School of Computer Science, University of Manchester, UK 2. School of Computing Science, University of Newcastle, UK 3. GlaxoSmithKline, USA 4. EMBL-EBI The European Bioinformatics Institute, Cambridge, UK WEBSITES Bio-Ontologies SIG workshop: http://bio-ontologies.org.uk ISMB & ECCB main conference website http://www.iscb.org/ismbeccb2007 ABOUT THE BIO-ONTOLOGIES SIG WORKSHOP The workshop will continue offer an informal environment for presentation and discussion of ontologies and their role in providing a mechanism for organising, sharing and reconciling data. This year, to celebrate its tenth anniversary, we have invited four presenters from the first bio-ontologies tutorial and meeting organisers to sit on a panel, namely: Mark Musen, Peter Karp, Russ Altman and Steffen Schulze-Kremer They will be asked to present positions on the following questions: 1. What has been the best thing to have happened in bio-ontologies in the past ten years? 2. What has been the worst thing to have happened in bio-ontologies in the past ten years? 3. How must bio-ontologies progress in the next ten years? 4. How must bio-ontologies not progress in the next ten years CALL FOR PAPERS AND POSTER ABSTRACT We are inviting two types of submissions SHORT PAPER papers (up to 4 pages) and POSTER ABSTRACT (up to 1/2 page) from any aspect doing bio-ontology research or using bio-ontologies to do bioinformatics research. Topics include, but are not restricted to: - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - The implications of Bio-Ontologies or the Semantic Web for the drug discovery process - Current Research In Ontology Languages and its implication for Bio-Ontologies PROGRAM COMMITTEE Abstracts will be reviewed by the Program Committee, including the Program Chairs, David Benton, Suzanna Lewis, Chris Mungall and Alan Ruttenberg. DEADLINES Submissions due: May 1 2007 Notification of acceptance: May 21 2007 Final versions due: May 31 2007 Workshop: July 20 2007 -- Susanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: sa...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK room: A229 |
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From: Susanna-Assunta S. <sa...@eb...> - 2007-03-07 12:56:35
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Dear All, here an update on two topics. **Naming convention document** The MSI-PSI Community Practice document on "Guidelines for the development of Controlled Vocabularies" is now available for comments. It has been posted at the MSI OWG website (http://msi-ontology.sourceforge.net/recommendations) and at by PSI at their new website (http://www.psidev.info/index.php?q=node/100) **Ontology for Biomedical Investigation** With the OBI group, we are still in the process of collecting terms for BioMaterial, instruments (inlcuding the MSI NMR.owl), design etc. If you want to follow the discussion, please, register to the OBI dev list (http://obi.sourceforge.net/resources/index.php). Otherwise, as soon as an intital list of common terms and definitions is put together, I suggest we have a call to discuss it within the MSI community and suggest changes or make comments. Best regards, Susanna |
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From: Susanna-A S. <sa...@eb...> - 2007-02-22 15:11:22
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** Sorry for cross posting **
CALL FOR PAPERS and POSTER ABSTRACTS
*^**^***^****^****^****^****^****^****^****^****^****^****^***^**^*
Bio-Ontologies SIG Workshop
Vienna, Austria: July 19th 2007
"Bio-Ontologies: ten years past and looking to the future"
*^**^***^****^****^***^**^*
15th Annual International Conference on Intelligent Systems for
Molecular Biology (ISMB)
& 6th European Conference on Computational Biology (ECCB), Vienna,
Austria: July 18-25, 2007
*^**^***^****^****^****^****^****^****^****^****^****^****^****^****^****^***^**^*
CALL FOR PAPERS and POSTER ABSTRACTS
The long-standing ISMB Bio-Ontologies SIG is in its tenth consecutive
year. This year the workshop will have a celebratory and reflective
discussion on "Bio-Ontologies: ten years past and looking to the future".
Program chairs:
Robert Stevens (1), Phillip Lord (2), Robin McEntire (3),
Susanna-Assunta Sansone (4)
1. School of Computer Science, University of Manchester, United Kingdom
2. School of Computing Science, University of Newcastle, United Kingdom
3. GlaxoSmithKline, USA
4. EMBL-EBI The European Bioinformatics Institute, Cambridge,
United Kingdom
Websites:
Bio-Ontologies SIG workshop http://bio-ontologies.org.uk
<http://bio-ontologies.org.uk/>
ISMB/ECCB main conference website http://www.iscb.org/ismbeccb2007/
About the Bio-Ontologies SIG workshop
The workshop will continue offer an informal environment for
presentation and discussion of ontologies and their role in providing a
mechanism for organising, sharing and reconciling data. This year, o
celebrate its tenth anniversary, we have invited four presenters from
the first bio-ontologies tutorial and meeting organisers to sit on a
panel, namely:
- Mark Musen
- Peter Karp
- Russ Altman
- Steffen Schulze-Kremer
They will be asked to present positions on the following questions:
1. What has been the best thing to have happened in bio-ontologies in
the past ten years?
2. What has been the worst thing to have happened in bio-ontologies
in the past ten years?
3. How must bio-ontologies progress in the next ten years?
4. How must bio-ontologies not progress in the next ten years
Call for papers and poster abstract:
We are inviting two types of submissions SHORT PAPER papers (up to 4
pages) and POSTER ABSTRACT (up to 1/2 page) from any aspect doing
bio-ontology research or using bio-ontologies to do bioinformatics
research. Topics include, but are not restricted to:
- Biological Applications of Ontologies
- Reports on Newly Developed or Existing Bio-Ontologies
- Tools for Developing Ontologies
- Use of Ontologies in Data Communication Standards
- Use of Semantic Web technologies in Bioinformatics
- The implications of Bio-Ontologies or the Semantic Web for
the drug discovery process
- Current Research In Ontology Languages and its implication
for Bio-Ontologies
DETAILS AND DEADLINE FOR SUBMISSIONS:
May 1st, 2007
Full submission details will be soon available at
http://bio-ontologies.org.uk/submissions.php
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From: Agnieszka L. <a.l...@uq...> - 2006-11-22 03:24:00
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I am a new member of the metabolomics society and I am very interested in generation of metabolomics standards. I have worked for the past 5 years with microarrays and I realize the need for such standards across all of the -omics fields. Moreover, especially in ontology there is a great need to develop sensible vocabulary and ability for cross-referencing to enzymes involved in reactions we are measuring by metabonomic methods. Regards, Agnieszka ____________ Dr Agnieszka M. Lichanska (PhD) Oral Biology and Pathology School of Dentistry 5th Floor MacGregor Building, St. Lucia University of Queensland 4072 Australia Phone:+61 7 3365 3074 Fax: +61 7 3365 1109 e-mail: A.L...@uq... website: http://www.uq.edu.au/~uqalicha/ |
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From: Susanna <sa...@eb...> - 2006-09-20 10:52:46
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Dear All, (sorry for cross-posting) ** Teleconference: Hopefully many of you will attend the Metabomeeting 3 in London (see=20 announcement below). Also in the view of this event, I hope we can=20 restart our teleconferences the coming month and prepare our=20 presentation to the meeting (MSI WGs's chairs will give short updates on=20 the status of the activities). ** NMR CV: Daniel has been working in structuring the first draft of NMR CV under=20 FuGO top level classes and add definitions with your help. He will be=20 sending an email in the next few days, as now we are ready to post it=20 under OBO (as MSI OWG - NMR CV- draft v1). This will give us=20 'visibility' and hopefully encourage others to join the WG and enlarge=20 the CV. ** NMR format: We also hope that the Format WG will soon come up with a formal in XML,=20 so we can ensure the CV fulfil its need. ** Sample processing CV (chromatography, centrifugation etc..): As you know this activity is being carried out under the HUPO-PSI=20 umbrella, as part of the Sample processing WG (see:=20 http://psidev.sourceforge.net/sp). Daniel and myself are putting=20 together a list of terms to fulfil the needs of the spML. We will=20 circulate a first draft in the next few weeks. Also, next week, I will=20 attend the PSI meeting (http://psidev.sourceforge.net/meetings/2006-09)=20 to follow this activity in representation of the MSI OWG. Best regards, Susanna -------- Original Message -------- Subject: Metabomeeting 3, Imperial College London, 18th & 19th December=20 2006 - 2nd announcement Date: Wed, 6 Sep 2006 12:33:54 +0100 From: "metabomeeting committee" <met...@go...> To: met...@go... References: <7f8...@ma...> The organizing committee are pleased to welcome you to Metabomeeting 3,=20 a two-day workshop on metabolic profiling to be held at Imperial College=20 London on 18th and 19th December 2006 . The meeting is a UK and European=20 forum for scientists from academia, government and industry interested=20 in discussing the techniques and applications of metabolic profiling=20 (metabolomics / metabonomics). It is intended to be a friendly and=20 informal opportunity to present and discuss the latest developments.=20 This meeting follows on from successful Metabomeeting workshops held in=20 Cambridge in July 2005 and January 2006. Conference website: http://www.thempf.org/MM3/MM3_main.html Important dates: =95 30th September 2006 =96 deadline for abstracts for platform presen= tations =95 31st October 2006 =96 deadline for abstracts for posters =95 30th November 2006 =96 registration deadline Registration fees: =95 Academic =A350 =95 Industrial =A3100 =95 Student =A325 Confirmed speakers include: Jeremy Nicholson (Imperial), Doug Kell (Manchester), Roy Goodacre=20 (Manchester), Colin Turnbull (Imperial), David Fell (Oxford Brookes), =20 John Griffiths (St Georges Hospital, London), Mark Viant (Birmingham), =20 Ian Wilson (AstraZeneca), Julian Griffin (Cambridge), Andrew Nicholls (GS= K) We would like to acknowledge the generous support of the following=20 organizations for sponsoring this meeting. =95 BBSRC =95 Bruker Biospin =95 Waters =95 Biorad =95 Chenomx =95 Sanofi-Aventis =95 Eli Lilly =95 Servier/IRIS =95 AstraZeneca Best regards The organising committee Tim Ebbels Jake Bundy Hector Keun Imperial College London --=20 Susanna-Assunta Sansone, PhD Project Coordinator =09 The European Bioinformatics Institute email: sa...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK =20 Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html = =20 =20 |
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From: Schober <sc...@eb...> - 2006-09-08 09:58:42
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Dear msi community, Within the next weeks, the msi-ontology group would like to submit the msi-nmr ontology to the OBO ontology resource. There are still open issues concerning ontology import and modularization of the top level classes, i.e. weather the imported FuGO reference ontology should contain top level classes that were 'borrowed' from the BFO top level ontology. A second issue is where the imported ontologies will be imported from (a web repository or a relative path to a local or co-submitted repository file). Another open issue is what to do when a synonymous class is found in more than one ontology ( as is currently the case with the administrative class MSI:_obsolete and the FuGO:deleted_classes ). Sometimes MSI classes have to be passed up to FuGO and sometimes it will be the other way round. I have posted the latest version *msi-nmr070906.owl* on our website under: http://msi-ontology.sourceforge.net/protected/NMR-CVs/NMR_Ontology/msi-nmr_FuGObinned/ username: meta_onto_page password: 444 I recommend using the latest Protege Version and start the .pprj file for easier viewing. Feedback is very welcome. This version already imports the new FuGO V0.3 (latest cleaned up version from yesterday 07. Sept. 06). Currently the msi-nmr ontology itself is a pure taxonomy of 247 classes in owl-DL format. So far no properties other than annotation properties were assigned to classes. There could however be some experimental properties inherited from FuGO. I applied the latest naming conventions and as you can see FuGO uses these too, - also the new metadata recommendations. Under our webspace you will also find an excel file *nmr_terms_lack_last_defs.xls* with the last 37 nmr terms that still lack definitions. If you could provide a few I would be glad to receive them. There are another 30 or so terms without definitions, but these are mainly the ones 1. which do not need definitions due to their 'instance' character, e.g. brand names for NMR Software 2. where it is not clear, weather they belong into this domain ontology or into FuGO or even BFO. 3. administrative classes (the ones starting with an "_") I am working also on the Sample Processing CV which will also integrate terms for column chromatography (which will come from the MeMo schema thanks to Irina Spasic). If you know of other existing terminological resources for the sample processing (except the PSI spML) and column chromatography, I would be glad to know them. Best regards, Daniel Schober -- Daniel Schober Ontologist, FuGO-Project The European Bioinformatics Institute email: sc...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494410 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html Personal Page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 Room: A2-37 |
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From: Susanna <sa...@eb...> - 2006-08-29 13:41:20
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**** Sorry for the multiple postings ***** Dear All, This is just a note to flag the *special issue of OMICS journal on data standards*. The online version is *free* and available at the following URL: http://www.liebertonline.com/toc/omi/10/2;jsessionid=nWAx67n0VoVdcUfY8Z It containts 20 invited articles, including a piece on MSI, MGED and PSI. Best regards, Susanna -- Susanna-Assunta Sansone, PhD Project Coordinator The European Bioinformatics Institute (EBI) EMBL Outstation - Hinxton Wellcome Trust Genome Campus Cambridge CB10 1SD, UK |
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