ISB2014 group notes
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 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
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
10:00 - 12:00
Session 3 - Functional Annotations, 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
13:00 - 14:30
Session 4 - Microbial Informatics, 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
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
9:00 - 10:00
Will Big Data Crush Curation?
Lincoln Stein, OICR, Canada
http://etherpad.wikimedia.org/p/isb2014-data ISB2014_Stein
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 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