Biocuration 2016

The Ninth International Biocuration Conference will be held in the hometown of the Swiss-Prot Database, Geneva, Switzerland, from April 10-14, 2016.

Scientific Program

Monday 11 April
08:45-9:00 Welcome
09:00-10:00 Keynote lecture:  Edward Marcotte
Evolution and the proteome: Insights into protein function from deeply conserved gene modules
10:00-11:00 Data integration, data visualization
Chairs: Marc Robinson-Rechavi and Ilene Karsch-Mizrachi
10:00-10:15 Cecilia Arighi
iPTMnet: An Integrated Resource for Protein Post-Translational Modification Network Analysis
10:15-10:30 Andrew Nightingale
Knowledge driven research by combining large-scale genomic data and functional annotations in UniProt.
10:30-10:45 Frédéric Bastian
TopAnat: GO-like enrichment of anatomical terms mapped to genes by expression patterns
10:45-11:00 Jean-Philippe Gourdine
Using glycobiology in the evaluation of undiagnosed diseases
11:00-11:30 Coffee break
11:30-13:10 Data standards and ontologies
Chairs: Pascale Gaudet and Paul Thomas
11:30-11:50 Amos Bairoch
The Cellosaurus, a wealth of information on cell lines
11:50-12:10 Jinmeng Jia
PAM: A standards-based database for integrating and exchanging pediatrics-specified information from multitude of biomedical resources
12:10-12:30 Lynn Schriml
The OBO Foundry in 2016
12:30-12:50 Valerie Hinard
ICEPO: the Ion Channel ElectroPhysiology Ontology
12:50-13:10 Marie-Angelique Laporte
Comparison of ontology mapping techniques to map traits
13:10-13:15 Launch of the Giga-Curation Challenge, Chris Hunter
13:15-14:30 Lunch
14:30-15:30 Keynote lecture:  Theodora Bloom
Publishing articles and making linked data available: steps towards seamless research reporting
15:30-17:40 Functional Annotation
Chairs: Sylvain Poux and Frédérique Lisacek
15:30-15:50 Matthew Campbell
How to make glycomics more accessible to the life science community?
15:50-16:10 Judith Blake
'What does this gene do': Strategies for Summary Data Presentation in MODs
16:10-16:40 Coffee break
16:40-17:00 Lucila Aimo
The SwissLipids knowledge resource for lipid biology
17:00-17:20 Paul D. Thomas
LEGO: expressing complex biological models using the Gene Ontology
17:20-17:35 Philippe Le Mercier
Human immunodeficiency virus life cycle and host interaction resource at Viralzone
17:40-19:00 Poster session
Tuesday 12 April
09:00-10:00 Keynote lecture:  Donna Maglott (will be presented by Kim Pruitt)
From paper to the cloud: the mechanics of biocuration may change but not the logic
10:00-11:00 Crowd/community curation
Chair: Alex Bateman
10:00-10:15 Ellen M. McDonagh
Curation in the 100,000 Genomes Project
10:15-10:30 Alba Gutierrez Sacristan
Leveraging text mining, expert curation and data integration to develop a database on psychiatric diseases and their genes
10:30-10:45 Andra Waagmeester
Leveraging Wikidata for crowd curation
10:45-11:00 Aleksandra Shypitsyna
The Gene Ontology Annotation project: community curation standards and best practices
11:00-11:30 Coffee break
11:30-13:10 Curation standards and best practice; inference from evidence; data and annotation quality
Chairs: Kim Pruitt and Sandra Orchard
11:30-11:50 Ivan Erill
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
11:50-12:10 Raul Rodriguez-Esteban
Biocuration with insufficient resources and fixed timelines
12:10-12:30 Cricket Sloan
Principles of metadata organization at the ENCODE Data Coordination Center
12:30-12:50 Steven Vercruysse
SciCura: a new tool for intuitive annotation
12:50-13:10 Kent Shefchek
Creating a Standard Schema for Evidence and Provenance in Data Sharing
13:10-14:30 Lunch
14:30-15:30 Text mining
Chairs: Patrick Ruch and Cecilia Arighi
14:30-14:45 Tonia Korves
Exploring human-machine cooperative curation
14:45-15:00 Jiao Li
A text-mining method for identifying a scientific program generated data use
15:00-15:15 Zhiyong Lu
Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine
15:15-15:30 Kimberly Van Auken
TextpressoCentral: A System for Integrating Full Text Literature Curation with Diverse Curation Platforms including the Gene Ontology Consortium’s Common Annotation Framework
15:30-17:40 DATABASE Virtual Issue session
15:30-15:45 Lionel Breuza
The UniProtKB guide to the human proteome
15:45-16:00 Amaia Sangrador
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations
16:00-16:30 Coffee break
16:30-16:45 Stacia Engel
From one to many: Expanding the Saccharomyces cerevisiae reference genome panel
16:45-17:00 Zhiyong Lu
Discovering Biomedical Semantic Relations in PubMed Queries for Database Curation and Literature Retrieval
17:00-17:15 Timothy Putman
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes
17:15-17:30 Tanya Berardini
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model
17:40-19:00 Poster session
Wednesday 13 April
Thursday 14 April
09:00-10:00 Keynote lecture:  Melissa Haendel
Why the world needs phenopacketeers, and how to be one
10:00-11:00 Large scale and predictive annotation
Chairs: Alan Bridge and Monica Muñoz-Torres
10:00-10:15 Gemma Holliday
David meets Goliath: Using curated data to infer functional boundaries in large datasets
10:15-10:30 Ivo Pedruzzi
HAMAP – leveraging Swiss-Prot curation for the annotation of uncharacterized proteins
10:30-10:45 Marco Pagni
MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
10:45-11:00 Betina Porcel
The gene repertoire of eukaryotes: a focus on the missing knowledge of current genome annotations
11:00-11:30 Coffee break
11:30-12:30 Big data
Chairs: Zhang Zhang and Ioannis Xenarios
11:30-11:45 Michael Baudis
Harvesting cancer genome data - Current opportunities and future challenges
11:45-12:00 Zhang Zhang
The BIG Data Center: from deposition to integration to translation
12:00-12:15 Anna I Guyer
Compendium of gene-expression data sets to facilitate machine-learning benchmarks
12:15-12:30 Markus Muller
Mining Large Scale Proteomics LC-MS/MS Data for Protein Modifications
12:30-13:30 International Society of Biocuration General Meeting
ISB General Meeting
Next conference announcement
Announcement of the ISB award laureate
Poster prize sponsored by Genomics, Proteomics & Bioinformatics and f1000
Closing remarks
13:30-14:30 Lunch