Difference between revisions of "ISB2014 group notes"
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| − | The Seventh International Biocuration Conference | + | The Seventh International Biocuration Conference<br> |
| − | Toronto, Canada | + | Toronto, Canada<br> |
| − | April 6-9, 2014 | + | April 6-9, 2014<br> |
ISB2014 Posters on F1000: | ISB2014 Posters on F1000: | ||
http://f1000.com/posters/browse?conferenceId=259713564 | http://f1000.com/posters/browse?conferenceId=259713564 | ||
| + | |||
Schedule and links: | Schedule and links: | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | April 7 | + | April 6<br> |
| − | 09:00 - 10:00 | + | 18:20 - 19:20<br> |
| − | The World of BioCuration: Optimizing Its Impact | + | From Genome Annotation to Genomic Medicine<br> |
| + | Tim Hubbard, King’s College London, UK<br. | ||
| + | |||
| + | April 7<br> | ||
| + | 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 | + | 10:00 - 12:00<br> |
| − | Session 1 - Clinical Annotations, Chaired by Warren Kibbe and Mathias Brochhausen | + | Session 1 - Clinical Annotations, 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 27: | ||
Slides: http://www.slideshare.net/goodb/mturk-biocuration2014-pdf | Slides: http://www.slideshare.net/goodb/mturk-biocuration2014-pdf | ||
| − | 13:00 - 14:30 | + | 13:00 - 14:30<br> |
| − | Session 2 - Systems Biology, Chaired by Henning Hermjakob and Fritz Roth | + | Session 2 - Systems Biology, Chaired by Henning Hermjakob and Fritz Roth<br> |
http://etherpad.wikimedia.org/p/isb2014-systems | http://etherpad.wikimedia.org/p/isb2014-systems | ||
| Line 36: | Line 38: | ||
*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 | + | 15.00 - 17.00<br> |
| − | Workshop 1 - BioCreative Workshop on Text Mining Applications, Chaired by Cecilia Arighi and Lynette Hirschman | + | 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 | + | April 8<br> |
| − | A Global Context for Prediction of Functional Trends in Protein Superfamilies | + | 9:00 - 10:00<br> |
| − | Patricia Babbitt, California Institute for Quantitative Biosciences (QB3), UCSF, USA | + | 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 | http://etherpad.wikimedia.org/p/isb2014-functional | ||
| − | 10:00 - 12:00 | + | 10:00 - 12:00<br> |
| − | Session 3 - Functional Annotations, Chaired by Iddo Friedberg | + | Session 3 - Functional Annotations, Chaired by Iddo Friedberg<br> |
http://etherpad.wikimedia.org/p/isb2014-functional | http://etherpad.wikimedia.org/p/isb2014-functional | ||
| Line 58: | Line 61: | ||
*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 | + | 13:00 - 14:30<br> |
| − | Session 4 - Microbial Informatics, Chaired by Fiona Brinkman and John Parkinson | + | Session 4 - Microbial Informatics, Chaired by Fiona Brinkman and John Parkinson<br> |
http://etherpad.wikimedia.org/p/isb2014-microbe | http://etherpad.wikimedia.org/p/isb2014-microbe | ||
*Fiona Brinkman, Microbial Informatics in 2014 | *Fiona Brinkman, Microbial Informatics in 2014 | ||
| Line 70: | Line 73: | ||
Slides: http://t.co/gfpDKRQAal | Slides: http://t.co/gfpDKRQAal | ||
| − | 15.00 - 17.00 | + | 15.00 - 17.00<br> |
| − | Workshop 3 – Phenotype, Chaired by Ann-Marie Mallon & Peter D'Eustachio | + | Workshop 3 – Phenotype, Chaired by Ann-Marie Mallon & Peter D'Eustachio <br> |
| − | Workshop 4 - Big Data Curation, Chaired by Owen White & Francis Ouellette | + | Workshop 4 - Big Data Curation, Chaired by Owen White & Francis Ouellette<br> |
http://etherpad.wikimedia.org/p/isb2014-bigdata | http://etherpad.wikimedia.org/p/isb2014-bigdata | ||
| − | April 9 | + | |
| − | 9:00 - 10:00 | + | |
| − | Will Big Data Crush Curation? | + | April 9<br> |
| − | Lincoln Stein, OICR, Canada | + | 9:00 - 10:00 <br> |
| + | Will Big Data Crush Curation?<br> | ||
| + | Lincoln Stein, OICR, Canada<br> | ||
http://etherpad.wikimedia.org/p/isb2014-data | http://etherpad.wikimedia.org/p/isb2014-data | ||
| − | 10.00 - 12:00 | + | 10.00 - 12:00<br> |
| − | Session 5 - Data Integration and Sharing, Chaired by Gary Bader and Winston Hide | + | Session 5 - Data Integration and Sharing, Chaired by Gary Bader and Winston Hide<br> |
| + | Sponsored by Heidelberg Institute for Theoretical Studies <br> | ||
http://etherpad.wikimedia.org/p/isb2014-data | http://etherpad.wikimedia.org/p/isb2014-data | ||
| Line 91: | Line 97: | ||
*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 | + | 13:00 - 15:00<br> |
| − | Workshop 5 - Data Publishing and Curation, Chaired by Pascale Gaudet and David Landsman | + | Workshop 5 - Data Publishing and Curation, Chaired by Pascale Gaudet and David Landsman <br> |
| − | Workshop 6 - Biological and Clinical Ontologies, Chaired by J. Michael Cherry and Chris Mungall | + | Workshop 6 - Biological and Clinical Ontologies, Chaired by J. Michael Cherry and Chris Mungall <br> |
| − | Unconference 1: Semantic Web Link Data & Publishing | + | Unconference 1: Semantic Web Link Data & Publishing<br> |
| − | Unconference 2: Training For the Next Generation of Biocurators | + | Unconference 2: Training For the Next Generation of Biocurators<br> |
| − | Unconference 3: Quality and Confidence Code: How Do We Advance? | + | Unconference 3: Quality and Confidence Code: How Do We Advance?<br> |
| − | Unconference 4: Getting A Community Annotation Server Up And Running In Under An Hour With Canto And GMOD In The Cloud | + | 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 | + | |
| + | 15:30 - 17:00<br> | ||
Discussions, Awards and Closing Remarks | Discussions, Awards and Closing Remarks | ||
Revision as of 19:02, 11 April 2014
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
