The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Abstract

BackgroundBioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research.ResultsThe theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization.ConclusionWe provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Community and Code: Nine Lessons from Nine NESCent Hackathons

“…However, we found it to be too limiting as a general strategy: choosing participants from an open pool is important if one of the goals of the hackathon is to grow the community, whereas invitation-only hackathons (e.g. the BioHackathons [23][24][25][26] organized by DBCLS, Japan) have a danger of ossifying patterns of inclusion and exclusion.…”

“…Indeed, hackathons vary in many ways, even within the broad categories of corporate, community, and internal hackathons 13 . They may be one-off events 29 , or a series that repeats yearly [23][24][25][26] or even more frequently 15 . The event may last a single day (e.g., 12), an entire week 9 , or longer 18 .…”

“…professional networking. For example, participants of the BioHackathon series of events [23][24][25][26] are strongly encouraged by the organizers to connect with each other on social networks, such as LinkedIn.…”

EMBnet.journal 19 Suppl. B

“…The first years of the BioHackathon meetings in Japan focused on Web services and interoperability (Katayama et al, 2010;Katayama et al 2011) and later moved to improving life science data integration with Semantic Web technologies (Katayama et al, 2013), reflecting the perceived needs of the biomedical community to move from work flows towards integration of data resources, ontology, semantics and reasoning.…”

“…This is short for "biologically motivated code hacking marathons". This initiative evolved into the annual BioHackathons in Japan, organised every year since 2008 with Japanese and key foreign Open Source developers attending (Katayama et al, 2010;Katayama et al, 2011;Katayama et al, 2013).…”