Wednesday, 29 October 2014

What is BioHackathon 2014?

In a week BioHackathon 2014 will start ( It will be my first time ins this kind of "meeting". I will give a talk about PRIDE and ProteomeXchange and future developments of both platforms (below the complete list of talks).

But first, a quick introduction of BioHackathon. National Bioscience Database Center (NBDC) and Database Center for Life Science (DBCLS) have been organizing annual BioHackathon since 2008, mainly focusing on standardization (ontologies, controlled vocabularies, metadata) and interoperability of bioinformatics data and web services for improving integration (semantic web, web services, data integration), preservation and utilization of databases in life sciences. This year, we will focus on the standardization and utilization of human genome information with Semantic Web technologies in addition to our previous efforts on semantic interoperability and standardization of bioinformatics data and Web services.

BioHackathon 2014 will be focus in these topics:

In addition to the efforts in the past BioHackathons including development of tools, ontologies, RDF data and accumulation of best practices, we will focus on the standardization and utilization of human genome information:

  • Topics may cover the following domains, but are not limited to:
  • Standardization of RDF data and development of tools/ontologies
  • Human genome/variation and medical information
  • Animal, plant and microbial genomes
  • Ortholog/phylogenomic databases
  • Proteomics, metabolomics, glycomics etc.
  • Text-mining and ontology mapping
  • Documentation and visualization of RDF model
  • URI transformation and mapping for interlinking resources
  • Quality assessment of SPARQL endpoints
  • Applications based on Linked Open Data
  • Natural language processing and QA system
  • Utilization of TogoStanza, TogoTable etc.

Biohackaton Symosium:

  8:30 Meet up at the hotel lobby
  9:00 Registration opens
10:00 Introduction from organizers
10:00-10:05 Welcome address
10:05-10:20 Introduction to the NBDC/DBCLS BioHackathon 2014 (Toshiaki Katayama)
10:20-10:40 Introduction to the Tohoku Medical Megabank Organization (Masao Nagasaki Tohoku Medical Megabank Organization)
10:40-11:00 Integrated database and triplestore in prospective cohort study at the Tokyo Medical Megabank Project (Soichi Ogishima Tohoku Medical Megabank Organization, Japan)
11:00 Coffee break
11:20 Invited talks
11:20-11:40 Embracing Semantic Web Technologies at the European Bioinformatics Institute (Simon Jupp European Bioinformatics Institute, UK)
11:40-12:00 new services to support the Semantic Web community (Sarala Wimalaratne European Bioinformatics Institute, UK)
12:00-12:20 Introduction to BioJS (Leyla Jael Garcia Castro European Bioinformatics Institute, UK)
12:20 Lunch
13:30 Invited talks
13:30-13:45 Construction of ortholog database using the Semantic Web technology (Hirokazu Chiba National Institute for Basic Biology, Japan)
13:45-14:00 Semantic integration of orthology resources: beyond the OGO experience (Jesualdo Thomas Fernandez Breis University of Murcia, Spain)
14:00-14:20 Text mining for ontology learning and matching (Jung-Jae Kim Nanyang Technological University, Singapore)
14:20 Coffee break
14:40 Invited talks
14:40-15:00 Rhea: a reactions database linking biology and chemistry (Thierry Lombardot Swiss Institute of Bioinformatics, Switzerland)
15:00-15:20 PRIDE and ProteomeXchange – Making proteomics data accessible and reusable (Yasset Perez-Riverol European Bioinformatics Institute, UK)
15:20-15:40 PubChemRDF: Towards a semantic (web) description of PubChem (Evan Bolton National Center for Biotechnology Information, US)
15:40-16:00 Challenges and Solutions for Data Integrity in Linked Data Systems (Robert Buels Foundation Medicine, US)
16:00 Group photo
16:30 ToMMo tour
17:00 Bus to the hackathon venue
19:00 Reception party