ISB2014 group notes

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The Seventh International Biocuration Conference
Toronto, Canada
April 6-9, 2014
ISB2014 Posters on F1000:

   http://f1000.com/posters/browse?conferenceId=259713564

Schedule and links:

April 6
18:20 - 19:20
From Genome Annotation to Genomic Medicine
Tim Hubbard, King’s College London, UK<br.

April 7
09:00 - 10:00
The World of BioCuration: Optimizing Its Impact
Suzanna Lewis, Lawrence Berkeley National Laboratory, USA

10:00 - 12:00
Session 1 - Clinical Annotations, 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

13:00 - 14:30
Session 2 - Systems Biology, Chaired by Henning Hermjakob and Fritz Roth
http://etherpad.wikimedia.org/p/isb2014-systems

  • 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

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
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
Session 3 - Functional Annotations, Chaired by Iddo Friedberg
http://etherpad.wikimedia.org/p/isb2014-functional

  • 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

13:00 - 14:30
Session 4 - Microbial Informatics, Chaired by Fiona Brinkman and John Parkinson
http://etherpad.wikimedia.org/p/isb2014-microbe

  • 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

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


April 9
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
http://etherpad.wikimedia.org/p/isb2014-data

  • 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

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