Sunday April 1^st 2012

2.00-5.00 Registration

Monday April 2^nd 2012

7.30-8.45 Breakfast

8.45-9.00 Welcome

                        Cathy Wu and Elliott Crooke

Session 1

9.00-10.40 Community annotation

                       Chairs: Alex Bateman and Robert Finn  

#69 Qinghua Wang et al.

Community annotation and bioinformatics workforce development in concert ─ Little skate genome annotation

workshops and jamborees

Duration: 15 m + 5 m (for questions)

#22 Gillian Millburn et al.

Directly e-mailing authors of newly published papers encourages community curation

Duration: 15 m + 5 m (for questions)

#49 Antonia Lock et al.

PomBase Community Curation: A Fast Track to Capture Expert Knowledge

Duration: 15 m + 5 m (for questions)

#158 Nicholas Stover et al.

Tetrahymena Genome Database Wiki: A community-maintained model organism database

Duration: 15 m + 5 m (for questions)

#14 Andrew Su et al.

The Gene Wiki: Crowdsourcing human gene annotation

Duration: 15 m + 5 m (for questions)

10.40-11.00 Break

Session 2

11.00-12.30 Functional annotation and pathways

                         Chairs: Peter D’Eustachio and Renate Kania  

#1 Alexander Shearer et al.

Biocuration Has an Essential Role in Systems Biology

Duration: 15 m + 5 m (for questions)

#3 Constance Jeffery

Moonlighting proteins

Duration: 15 m + 5 m (for questions)

#50 Robert Finn et al.

Protein similarity web searches and services using HMMER

Duration: 10 m + 5 m

#90 Marco Punta et al.

Value of manual curation: the case of Pfam family-specific inclusion thresholds

Duration: 10 m + 5 m

#140 Eugenio Belda et al.

From bacterial genome annotation to metabolic pathway curation

Duration: 15 m + 5 m (for questions)

12.30-1.30 Lunch

1.30-2.45 Workshop 1

Databases & Journals – How to have a sustainable long term plan for journals and databases

Chairs: Francis Ouellette and Mike Cherry  

2.45-4.00 Workshop 2

Careers in biocuration

Chairs: Ilene Mizrachi and Monica Munoz-Torres

Sarah Burge

Duration: 10 m +

Phoebe Roberts, Pfizer

Duration: 5 m +

Jignesh Bhate, Molecular Connections

Duration: 5 m +

Parthiban Srinivasan, Parthys Reverse Informatics

Duration: 5 m +

Sam Ansari, Philip Morris International

Duration: 5 m +   

Beverly Underwood, NCBI

Duration: 5 m +

Questions & Discussion

Duration: + 40 m

4.00-4.30 Break

Session 3

4.30-6.30 Curation workflows and tools

                        Chairs: Claire O’Donovan and Kim Pruitt  

#126 Ed Lee et al.

WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation

Duration: 15 m + 5 m (for questions)

#171 Attila Csordas et al.

PRIDE: Quality control in a proteomics data repository

Duration: 15 m + 5 m (for questions)

#159 Julie Park et al.

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations

Duration: 15 m + 5 m (for questions)

#154 Darryl Gietzen and Anne Sarver

From published finding to biological interpretation, the importance of biological context in applying literature-based

curation to molecular data analysis and biological interpretation

Duration: 15 m + 5 m (for questions)

#118 Peter D’Eustachio et al.

How Do You Get A Gaggle Of Independent Curators To Work Together: Reactome Curation Management Practices

And Tools

Duration: 15 m + 5 m (for questions)

6.30-8.30 Oxford University Press-sponsored Reception and Poster Session 1

Tuesday April 3^rd 2012

7.30-9.00 Breakfast

9.00-10.00 Plenary session 1

                       Mark Yandell (Bio, title, and abstract)

                       Introduction: Susanna Lewis  

10.00-10.30 Break

Session 4

10.30-12.30 Genomics, metagenomics, comparative genomics

                         Chairs: Michelle Giglio and Granger Sutton  

#101 Will Mckerrow et al.

ENIGMA: comparative, consensus gene structure annotation  

Duration: 15 m + 5 m (for questions)

#15 Igor Grigoriev

Genomics data integration, analysis, and curation using MycoCosm, a genomics hub for community of fungal biologists

Duration: 15 m + 5 m (for questions)

#71 Jennifer Harrow et al.

Integrating RNA-seq and mass spectrometry data to identify novel protein-coding loci and thousands of IncRNA loci in

the human genome

Duration: 15 m + 5 m (for questions)

#77 Patrick Masson et al.

Viralzone: a web resource dedicated to viruses

Duration: 15 m + 5 m (for questions)

#122 L. Aravind et al.

Comparative genomic analysis finds a new widespread bacterial polymorphic toxin system

Duration: 15 m + 5 m (for questions)

#109 Raja Mazumder et al.

Representative Proteomes and Genomes: A standardized, stable and unbiased set of proteomes/genomes ideal for

use in genome annotation, metagenomic efforts and analyzing taxonomic nomenclature biases

Duration: 15 m + 5 m (for questions)

12.30-1.30 Lunch

1.30-3.30 Workshop 3

Quality information in support of annotations

Chairs: Frederic Bastian and Marc Robinson-Rechavi

Panlists/speakers:

Marcus Chibucos and Michelle Giglio, ECO

Sylvain Poux, Swiss-Prot

Sandra Orchard, IntAct

Verena Weiss, RegulonDB

Marc Robinson-Rechavi, Bgee

Nives Skunca, OMA

1.30-3.30 Workshop 4

Classification of Diseases for Curation of Animal Models

Chairs: Judith Blake and Paul Schofield

Panlists include:

Judy Blake: Issues and Minimal Requirements

Allen Davis: Integrating OMIM and MeSH

Paul Schofield: HUPO and disease classification

Lindsay Cowell: Infectious Disease Ontology

Oliveir Bodenreider: MeSH

1.30-4.00 Workshop 5

NCBI and UniProt curation and tools

Chairs: Bill Klimke and Maria Jesus Martin

10-minutes Lightning Talks:

Ilene Mizrachi: Primary Submission/Genomes

Melissa Landrum: Refseq: Eukaryotic Genome Annotation

William Klimke: Refseq: Prokaryotic Genomes/Clusters

Rodney Brister: Refseq: Viruses

Tatiana Tatusova: Annotation Standards

Questions & Discussion

#75 Sylvain Poux , Ioannis Xenarios and UniProt Consortium

Manual biocuration of proteins in UniProtKB/Swiss-Prot

Duration: 20 m + 5 m (for questions)

#47 Klemens Pichler, Diego Poggioli, Claire O’Donovan and UniProt Consortium

Rule-based annotation in UniProtKB

Duration: 15 m + 5 m (for questions)

Claire O’Donovan

UniProt: Coordinating annotation with other database resources

Duration: 10 m + 5 m (for questions)

Maria Martin

UniProt: Proteome representation

Duration: 10 m + 5 m (for questions)

4.00-4.30 Break

Session 5

4.30-6.30 Protein structure, complexes, interactions

                        Chairs: Sona Vasudevan and Jasmine Young  

#147 Torsten Schwede et al.

The Protein Model Portal – Towards Continuous Automated Homology Model EvaluatiOn (CAMEO)

Duration: 15 m + 5 m (for questions)

#63 Phoebe Roberts et al.

Targeted literature curation of therapeutic drug-induced toxic events

Duration: 15 m + 5 m (for questions)

#52 Marina Zhuravleva et al.

Assessment of Structure-Model Quality and Validation of Macromolecular Structures at the Protein Data Bank

Duration: 15 m + 5 m (for questions)

#82 Jyoti Khadake et al.

IntAct editor – an effective Interaction curation tool

Duration: 15 m + 5 m (for questions)

#102 Benjamin Shoemaker et al.

Deciphering human protein interactome using Inferred Biomolecular Interaction Server

Duration: 15 m + 5 m (for questions)

#150 Jose Cruz-Toledo et al.

Aptamer Base: A collaborative knowledge base to describe aptamers and SELEX experiments

Duration: 15 m + 5 m (for questions)

6.30-8.30 Oxford University Press-sponsored Reception and Poster Session 2

Wednesday April 4th 2012

7.30-9.00 Breakfast

9.00-10.00 Plenary session 2

                       Fritz Roth(Bio, title, and abstract)

                       Introduction: Mike Cherry  

10.00-10.30 Break

Session 6

10.30-12.30 Integrating text mining into biocuration workflows

                         Chairs: Lynette Hirschman and Cecilia Arighi  

#155 Goran Nenadic et al.

Towards semi-automated curation: using text mining to recreate the HIV1-human protein interaction database

Duration: 15 m + 5 m (for questions)  

#134 Maximilian Haeussler and David Haussler

Annotating genomes with data from fulltext articles

Duration: 15 m + 5 m (for questions)

#152 Lynette Hirschman et al.

Text Mining for the BioCuration Workflow

Duration: 15 m + 5 m (for questions)

#117 Fabio Rinaldi et al.

Using ODIN for a PharmGKB re-validation experiment

Duration: 15 m + 5 m (for questions)

#104 Kimberly Van Auken et al.

Natural Language Processing (NLP) and Gene Ontology (GO) Curation: Using the Textpresso Information System,

Support Vector Machines (SVMs), and Hidden Markov Models (HMMs) to Improve Efficiency of Manual GO Curation

Duration: 15 m + 5 m (for questions)

12.30-1.30 Lunch

Session 7

1.30-3.30 Ontologies and standards

                        Chairs: Darren Natale and Marc Robinson-Rechavi  

#113 Marcus Chibucos et al.

The Evidence Ontology (ECO): a standardized representation of evidence to support database annotations  

Duration: 15 m + 5 m (for questions)

#18 Allan Davis et al.

MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database

Duration: 15 m + 5 m (for questions)

#41 Adrienne Zweifel et al.

Developing an Ontology for Microbial Phenotypes

Duration: 15 m + 5 m (for questions)

#139 Tobias Wittkop et al.

STOP Using Just GO: A Multi-Ontology Hypothesis Generation Tool for High Throughput Experimentation

Duration: 15 m + 5 m (for questions)

#168 Rachel Harte et al.

Tracking and coordinating an international curation effort for the CCDS Project

Duration: 15 m + 5 m (for questions)

#137 Alexander D. Diehl et al.

The Neurological Disease Ontology

Duration: 7 m + 3 m (for questions)

#53 John Anderson et al.

NCBI BioSample database: capture and storage of sample metadata

Duration: 7 m + 3 m (for questions)

3.30-4.00 Break

4.00-5.00 Plenary session 3

                        Rich Roberts(Bio, title, and abstract)

                        Introduction: Cathy Wu  

5.00-5.30 Poster awards announcements and Closing remarks

                        Pascale Gaudet

Wednesday April 4^th – Thursday April 5^th 2012, Washington DC, USA:

Biocreative-2012 Workshop: Interactive Text Mining in the Biocuration Workflow

Thursday April 5^th – Thursday April 6^th 2012, Washington DC, USA:

GMOD Community Meeting