ISB2014 group notes

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


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.


Session 2 - Systems Biology

13:00 - 14:30
Chaired by Henning Hermjakob and Fritz Roth 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


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 ISB2014_Babbitt

Session 3 - Functional Annotations

10:00 - 12:00
Chaired by Iddo Friedberg 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


  • 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 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



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 ISB2014_Workshop4_Big_Data_Curation

April 9

Lincoln Stein

9:00 - 10:00
Will Big Data Crush Curation?
Lincoln Stein, OICR, Canada 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 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


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