Difference between revisions of "ISB2014 group notes"

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==Logistics==
 +
<pre>
 
The Seventh International Biocuration Conference
 
The Seventh International Biocuration Conference
Toronto, Canada
+
Dates: April 6-9,2014
April 6-9, 2014
+
Location: Toronto, Ontario, Canada
ISB2014 Posters on F1000:
+
Attendees:
    http://f1000.com/posters/browse?conferenceId=259713564
+
Caltech: Wen Chen, Xiaodong Wong, Karen Yook, Mary Ann Tuli
Schedule and links:
+
Hinxton: Paul Davis
April 6
+
OICR: Abby Cabunoc, Todd Harris, Scott Cain
18:20 - 19:20
+
</pre>
From Genome Annotation to Genomic Medicine
+
==Links==
 +
Site: [http://biocuration2014.events.oicr.on.ca/biocuration ISB_meeting]<br>
 +
Twitter feed: [http://www.wormbase.org/species/c_elegans/gene/WBGene00044623?query=bus-8#07b-d-6-7b here], search for #isb2104<br>
 +
Minutes of the meeting taken by Abby and other attendees were captured in etherpad [http://etherpad.wikimedia.org/p/isb2014 here]. (Wiki pages containing copies of these notes are included next to the note links below as etherpad notes are not permanent.)
 +
ISB2014 <br>
 +
Posters on F1000: [http://f1000.com/posters/browse?conferenceId=259713564 F1000_ISB_posters]
 +
 
 +
==Conference Schedule and links==
 +
 
 +
===April 6===
 +
==== Tim Hubbard====
 +
18:20 - 19:20<br>
 +
From Genome Annotation to Genomic Medicine<br>
 
Tim Hubbard, King’s College London, UK
 
Tim Hubbard, King’s College London, UK
  
April 7
+
===April 7===
09:00 - 10:00
+
==== Suzanna Lewis====
The World of BioCuration: Optimizing Its Impact  
+
09:00 - 10:00<br>
 +
The World of BioCuration: Optimizing Its Impact <br>
 
Suzanna Lewis, Lawrence Berkeley National Laboratory, USA
 
Suzanna Lewis, Lawrence Berkeley National Laboratory, USA
  
10:00 - 12:00
+
 
Session 1 - Clinical Annotations, Chaired by Warren Kibbe and Mathias Brochhausen
+
====Session 1 - Clinical Annotations====
 +
10:00 - 12:00<br>
 +
Chaired by Warren Kibbe and Mathias Brochhausen<br>
 
*Melissa Landrum, ClinVar: Archiving Variants and Their Relationship to Phenotypes  
 
*Melissa Landrum, ClinVar: Archiving Variants and Their Relationship to Phenotypes  
 
*J. Michael Cherry, The ClinGen Portal: A new resource to provide access to expertly curated data and evidence for clinically significant genomic variants
 
*J. Michael Cherry, The ClinGen Portal: A new resource to provide access to expertly curated data and evidence for clinically significant genomic variants
Line 25: Line 42:
 
Slides: http://www.slideshare.net/goodb/mturk-biocuration2014-pdf
 
Slides: http://www.slideshare.net/goodb/mturk-biocuration2014-pdf
  
13:00 - 14:30
+
====Session 2 - Systems Biology====
Session 2 - Systems Biology, Chaired by Henning Hermjakob and Fritz Roth
+
13:00 - 14:30<br>
http://etherpad.wikimedia.org/p/isb2014-systems
+
Chaired by Henning Hermjakob and Fritz Roth<br>
 +
http://etherpad.wikimedia.org/p/isb2014-systems [[ISB2014_Session2_Systems_Biology]]
  
 
*Robin Haw, Reactome Knowledgebase of reactions, pathways and biological processes
 
*Robin Haw, Reactome Knowledgebase of reactions, pathways and biological processes
Line 36: Line 54:
 
*Inna Kuperstein, Visualization and analysis of data using Atlas of Cancer Signalling Networks (ACSN) and NaviCell tools for integrative systems biology of cancer
 
*Inna Kuperstein, Visualization and analysis of data using Atlas of Cancer Signalling Networks (ACSN) and NaviCell tools for integrative systems biology of cancer
  
15.00 - 17.00
+
====Workshops====
Workshop 1 - BioCreative Workshop on Text Mining Applications, Chaired by Cecilia Arighi and Lynette Hirschman
+
15.00 - 17.00<br>
 +
Workshop 1 - BioCreative Workshop on Text Mining Applications, Chaired by Cecilia Arighi and Lynette Hirschman<br>
 
Workshop 2 - Automated Function Prediction, Chaired by Iddo Friedberg and Sean Mooney
 
Workshop 2 - Automated Function Prediction, Chaired by Iddo Friedberg and Sean Mooney
April 8
 
9:00 - 10:00
 
A Global Context for Prediction of Functional Trends in Protein Superfamilies
 
Patricia Babbitt, California Institute for Quantitative Biosciences (QB3), UCSF, USA
 
http://etherpad.wikimedia.org/p/isb2014-functional
 
  
10:00 - 12:00
+
===April 8===
Session 3 - Functional Annotations, Chaired by Iddo Friedberg
+
====Patricia Babbitt====
http://etherpad.wikimedia.org/p/isb2014-functional
+
9:00 - 10:00<br>
 +
A Global Context for Prediction of Functional Trends in Protein Superfamilies<br>
 +
Patricia Babbitt, California Institute for Quantitative Biosciences (QB3), UCSF, USA<br>
 +
http://etherpad.wikimedia.org/p/isb2014-functional [[ISB2014_Babbitt]]
 +
 
 +
====Session 3 - Functional Annotations====
 +
10:00 - 12:00<br>
 +
Chaired by Iddo Friedberg<br>
 +
http://etherpad.wikimedia.org/p/isb2014-functional [[ISB2014_Session3_Functional_Annotations]]
  
 
*Hong Yu, A Robust Data-Driven Approach for Gene Ontology Annotation  
 
*Hong Yu, A Robust Data-Driven Approach for Gene Ontology Annotation  
Line 58: Line 80:
 
*Julien Gobeill, Supervised text mining for functional curation of gene products: how the data and performances have evolved in the last ten years         
 
*Julien Gobeill, Supervised text mining for functional curation of gene products: how the data and performances have evolved in the last ten years         
  
13:00 - 14:30
+
====Session 4 - Microbial informatics====
Session 4 - Microbial Informatics, Chaired by Fiona Brinkman and John Parkinson
+
13:00 - 14:30<br>
http://etherpad.wikimedia.org/p/isb2014-microbe
+
Chaired by Fiona Brinkman and John Parkinson<br>
 +
http://etherpad.wikimedia.org/p/isb2014-microbe [[ISB2014_Session4_Microbial_Informatics]]
 
*Fiona Brinkman, Microbial Informatics in 2014  
 
*Fiona Brinkman, Microbial Informatics in 2014  
 
*Nives Skunca, The importance of newly sequenced genomes and functional annotations for phylogenetic profiling  
 
*Nives Skunca, The importance of newly sequenced genomes and functional annotations for phylogenetic profiling  
Line 70: Line 93:
 
Slides: http://t.co/gfpDKRQAal  
 
Slides: http://t.co/gfpDKRQAal  
  
15.00 - 17.00
+
====Workshops====
Workshop 3 – Phenotype, Chaired by Ann-Marie Mallon & Peter D'Eustachio  
+
15.00 - 17.00<br>
Workshop 4 - Big Data Curation, Chaired by Owen White & Francis Ouellette
+
Workshop 3 – Phenotype, Chaired by Ann-Marie Mallon & Peter D'Eustachio <br>
http://etherpad.wikimedia.org/p/isb2014-bigdata
+
Workshop 4 - Big Data Curation, Chaired by Owen White & Francis Ouellette<br>
April 9
+
http://etherpad.wikimedia.org/p/isb2014-bigdata [[ISB2014_Workshop4_Big_Data_Curation]]
9:00 - 10:00
 
Will Big Data Crush Curation?
 
Lincoln Stein, OICR, Canada
 
http://etherpad.wikimedia.org/p/isb2014-data
 
  
10.00 - 12:00
+
 
Session 5 - Data Integration and Sharing, Chaired by Gary Bader and Winston Hide, Sponsored by Heidelberg Institute for Theoretical Studies  
+
===April 9===
http://etherpad.wikimedia.org/p/isb2014-data
+
====Lincoln Stein====
 +
9:00 - 10:00 <br>
 +
Will Big Data Crush Curation?<br>
 +
Lincoln Stein, OICR, Canada<br>
 +
http://etherpad.wikimedia.org/p/isb2014-data [[ISB2014_Stein]]
 +
 
 +
====Session 5 - Data Integration and Sharing
 +
10.00 - 12:00<br>
 +
Chaired by Gary Bader and Winston Hide<br>
 +
Sponsored by Heidelberg Institute for Theoretical Studies <br>
 +
http://etherpad.wikimedia.org/p/isb2014-data [[ISB2014_Session5_Data_Integration_and_Sharing]]
  
 
*Sabry Razick, The eGenVar data management system (eGDMS) - cataloguing and sharing sensitive data and meta-data for the life sciences
 
*Sabry Razick, The eGenVar data management system (eGDMS) - cataloguing and sharing sensitive data and meta-data for the life sciences
Line 91: Line 120:
 
*Eurie L. Hong , The ENCODE metadata standard to integrate diverse experimental data sets  
 
*Eurie L. Hong , The ENCODE metadata standard to integrate diverse experimental data sets  
  
13:00 - 15:00
+
====Workshops/Unworkshops====
Workshop 5 - Data Publishing and Curation, Chaired by Pascale Gaudet and David Landsman  
+
13:00 - 15:00<br>
Workshop 6 - Biological and Clinical Ontologies, Chaired by J. Michael Cherry and Chris Mungall  
+
Workshop 5 - Data Publishing and Curation, Chaired by Pascale Gaudet and David Landsman <br>
Unconference 1: Semantic Web Link Data & Publishing
+
Workshop 6 - Biological and Clinical Ontologies, Chaired by J. Michael Cherry and Chris Mungall <br>
Unconference 2: Training For the Next Generation of Biocurators
+
Unconference 1: Semantic Web Link Data & Publishing<br>
Unconference 3: Quality and Confidence Code: How Do We Advance?
+
Unconference 2: Training For the Next Generation of Biocurators<br>
Unconference 4: Getting A Community Annotation Server Up And Running In Under An Hour With Canto And GMOD In The Cloud
+
Unconference 3: Quality and Confidence Code: How Do We Advance?<br>
15:30 - 17:00
+
Unconference 4: Getting A Community Annotation Server Up And Running In Under An Hour With Canto And GMOD In The Cloud<br>
 +
 
 +
15:30 - 17:00<br>
 
Discussions, Awards and Closing Remarks
 
Discussions, Awards and Closing Remarks

Latest revision as of 19:36, 11 April 2014

Logistics

The Seventh International Biocuration Conference
Dates: April 6-9,2014
Location: Toronto, Ontario, Canada
Attendees: 
Caltech: Wen Chen, Xiaodong Wong, Karen Yook, Mary Ann Tuli
Hinxton: Paul Davis
OICR: Abby Cabunoc, Todd Harris, Scott Cain

Links

Site: ISB_meeting
Twitter feed: here, search for #isb2104
Minutes of the meeting taken by Abby and other attendees were captured in etherpad here. (Wiki pages containing copies of these notes are included next to the note links below as etherpad notes are not permanent.) ISB2014
Posters on F1000: F1000_ISB_posters

Conference Schedule and links

April 6

Tim Hubbard

18:20 - 19:20
From Genome Annotation to Genomic Medicine
Tim Hubbard, King’s College London, UK

April 7

Suzanna Lewis

09:00 - 10:00
The World of BioCuration: Optimizing Its Impact
Suzanna Lewis, Lawrence Berkeley National Laboratory, USA


Session 1 - Clinical Annotations

10:00 - 12:00
Chaired by Warren Kibbe and Mathias Brochhausen

  • Melissa Landrum, ClinVar: Archiving Variants and Their Relationship to Phenotypes
  • J. Michael Cherry, The ClinGen Portal: A new resource to provide access to expertly curated data and evidence for clinically significant genomic variants
  • Ellen Mcdonagh, Clinical Annotation of drug-gene interactions: The Pharmacogenomics Knowledge Base (PharmGKB)
  • Lynn Schriml, The Disease Ontology: an evolving tool for Disease Curation and Annotation.
  • Ben Good, Microtask crowdsourcing for disease mention annotation in Pubmed abstracts.

Slides: http://www.slideshare.net/goodb/mturk-biocuration2014-pdf

Session 2 - Systems Biology

13:00 - 14:30
Chaired by Henning Hermjakob and Fritz Roth
http://etherpad.wikimedia.org/p/isb2014-systems ISB2014_Session2_Systems_Biology

  • Robin Haw, Reactome Knowledgebase of reactions, pathways and biological processes
  • Sam Ansari, Verification of Systems Biology Research in the Age of Collaborative Competition
  • Anika Oellrich, Linking tissues to phenotypes using gene expression profiles
  • Andrew Chatr-Aryamontri, UbiGRID: a database resource for protein and genetic interactions of the ubiquitin-proteasome system
  • Selina Dwight, Yeast – why it simply has a lot to say about human disease
  • Inna Kuperstein, Visualization and analysis of data using Atlas of Cancer Signalling Networks (ACSN) and NaviCell tools for integrative systems biology of cancer

Workshops

15.00 - 17.00
Workshop 1 - BioCreative Workshop on Text Mining Applications, Chaired by Cecilia Arighi and Lynette Hirschman
Workshop 2 - Automated Function Prediction, Chaired by Iddo Friedberg and Sean Mooney

April 8

Patricia Babbitt

9:00 - 10:00
A Global Context for Prediction of Functional Trends in Protein Superfamilies
Patricia Babbitt, California Institute for Quantitative Biosciences (QB3), UCSF, USA
http://etherpad.wikimedia.org/p/isb2014-functional ISB2014_Babbitt

Session 3 - Functional Annotations

10:00 - 12:00
Chaired by Iddo Friedberg
http://etherpad.wikimedia.org/p/isb2014-functional ISB2014_Session3_Functional_Annotations

  • Hong Yu, A Robust Data-Driven Approach for Gene Ontology Annotation
  • Cedoljub Bundalovic-Torma, Enzyme Prediction and the Metabolic Reconstruction of Probiotic Bacteria
  • Sylvain Poux, Expert curation in UniProtKB: a case study in dealing with conflicting and erroneous data
  • Melanie Courtot, Effective automated classification using ontology-based annotation: experience with analysis of adverse event reports

Slides: http://www.slideshare.net/mcourtot/biocuration-2014

  • Julien Gobeill, Supervised text mining for functional curation of gene products: how the data and performances have evolved in the last ten years

Session 4 - Microbial informatics

13:00 - 14:30
Chaired by Fiona Brinkman and John Parkinson
http://etherpad.wikimedia.org/p/isb2014-microbe ISB2014_Session4_Microbial_Informatics

  • Fiona Brinkman, Microbial Informatics in 2014
  • Nives Skunca, The importance of newly sequenced genomes and functional annotations for phylogenetic profiling
  • Samantha Halliday, GIST - An ensemble approach to the taxonomic classification of metatranscriptomic reads
  • Ramona Britto, Proteomes at UniProtKB – advancements and challenges in the post-genomic era
  • Ingrid M. Keseler, Development of the EcoCyc and MetaCyc Databases and the Pathway Tools Software
  • Monica C. Munoz-Torres, Three's a crowd-source: Observations on Collaborative Genome Annotation

Slides: http://t.co/gfpDKRQAal

Workshops

15.00 - 17.00
Workshop 3 – Phenotype, Chaired by Ann-Marie Mallon & Peter D'Eustachio
Workshop 4 - Big Data Curation, Chaired by Owen White & Francis Ouellette
http://etherpad.wikimedia.org/p/isb2014-bigdata ISB2014_Workshop4_Big_Data_Curation


April 9

Lincoln Stein

9:00 - 10:00
Will Big Data Crush Curation?
Lincoln Stein, OICR, Canada
http://etherpad.wikimedia.org/p/isb2014-data ISB2014_Stein

====Session 5 - Data Integration and Sharing 10.00 - 12:00
Chaired by Gary Bader and Winston Hide
Sponsored by Heidelberg Institute for Theoretical Studies
http://etherpad.wikimedia.org/p/isb2014-data ISB2014_Session5_Data_Integration_and_Sharing

  • Sabry Razick, The eGenVar data management system (eGDMS) - cataloguing and sharing sensitive data and meta-data for the life sciences
  • Steven Jupe, A controlled vocabulary for entities and events in the Reactome database
  • Emek Demir, Pathway Commons: A public library of biological pathways
  • Claire O'Donovan, The UniRule system for data integration and sharing
  • Hardeep K. Nahal, Metadata audit between European Genome-phenome Archive and International Cancer Genome Consortium
  • Eurie L. Hong , The ENCODE metadata standard to integrate diverse experimental data sets

Workshops/Unworkshops

13:00 - 15:00
Workshop 5 - Data Publishing and Curation, Chaired by Pascale Gaudet and David Landsman
Workshop 6 - Biological and Clinical Ontologies, Chaired by J. Michael Cherry and Chris Mungall
Unconference 1: Semantic Web Link Data & Publishing
Unconference 2: Training For the Next Generation of Biocurators
Unconference 3: Quality and Confidence Code: How Do We Advance?
Unconference 4: Getting A Community Annotation Server Up And Running In Under An Hour With Canto And GMOD In The Cloud

15:30 - 17:00
Discussions, Awards and Closing Remarks