Biocuration 2012
The Conference of the International Society for Biocuration
April 2-4, 2012 Washington DC, USA
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BioCreative Satellite Workshop

Biocuration 2012 Conference Agenda

Sunday April 1st 2012

 

2.00-5.00 Registration

Monday April 2nd 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 DEustachio 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 ODonovan 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 DEustachio 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 3rd 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 ODonovan and UniProt Consortium

Rule-based annotation in UniProtKB

Duration: 15 m + 5 m (for questions)

 

Claire ODonovan

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 4th Thursday April 5th 2012, Washington DC, USA:

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

 

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

GMOD Community Meeting



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