BioHackathon
2008
for Web Service
Feb 11-15 @ Tokyo, Japan
http://ustream.tv/channel/biohackathon-2008-tokyo
http://ustream.tv/channel/biohackathon2008
http://hackathon.dbcls.jp/

Toshiaki Katayama - organizer• KEGG lab in Tokyo branch• KEGG API (SOAP/WSDL)• KEGG DAS• ortholog clusters, regulatory pathways, ...
• BioRuby project (since 2000)• Japan Open Bio* Research Group (since 2004)• DBCLS• Integrated databases• Integrated web services

DBCLS - sponsor• Database Center for Life Science (since 2007)

MEXT

http://www.mext.go.jp/ROIS
DBCLS

NII

NIG
DDBJ

GenBank

http://www.rois.ac.jp/

EMBL

http://www.nig.ac.jp/

http://www.nii.ac.jp/:

BioHackathon #1-3
• 2002 BioHackathon #1, #2• Tucson - O'Reilly• South Africa - Electric Genetics
OBDA (Open Bio* Database Access)• 2003 BioHackathon #3• Singapore - Apple
GBrowse (Bio::Graphics), Chado, BioMOBY, ...

BioHackathon #2•Cape Town, South Africa•2002/2/24-3/1

OBDA•Open Bio* Database Access•BioRegistry•BioFlat•BioFetch•BioSQL

BioHackathon 2008 - program• 2/11 morning session - presentations••••••

From Web API for Biology (WABI) to Semantic Web API for Biology (SABI) - Hideaki Sugawara
Current status of the BioMOBY project and vision for the future directions - Mark Wilkinson
The EMBRACE project and WS-I standard - Jan Christian Bryne
Soaplab2 project to wrap up command line packages - Martin Senger
Proxying legacy applications and CGIs into BioMOBY - Paul Gordon
Generation Challenge Program effort at building interoperability - Richard Bruskiewich• 2/11 afternoon session - open space•••••••••

ServiceProvider_workgroup
OpenBio_workgroup
Workflow_workgroup
BioMOBY_workgroup
Exchangeformat_workgroup
Semanticweb_workgroup
PhyloWS_workgroup
Distributed storage - initiative (BIO.SLURP)
Distributed services - initiative (BIO.ORG.ANISM)• 2/12-15 hack, hack, hack
• We will have banquet on 2/12 18:30- @CBRC

Participants
Open Bio*
Service provider

Exchange dataformat
standardization

Client developer

BioMOBY

Favor to ask• Discussion• please speak slowly & clearly• Summary• please log to Wiki
• Be creative• ﬁnd your own goals by yourself :-)BioHackaton 2008 Open Space topics• Ontology - Richard Bruskiewich• data types, service types• standardization• Glycoinformatics - Will York• Interaction networks, DAS - Bruno Aranda• Text mining - Kano
• Phyloinformatics - Hilmar Lapp
• Async service - Jose, Fernandez• WSRF?
• Large data - Tom Oinn
• SOAP attachements• Security - Oswaldo Trelles• Description & Discovery - Mark Wilkinson• Open Bio*
• BioSQL - Mark Schreiber• Writing (creating) interoperable workﬂows - Tom Oinn, Stuart Owen
• Writing the manifesto

http://hackathon.dbcls.jp/wiki/ListOfTopics

BioHackathon2008
Meeting report - DBCLS/BioRubyToshiaki Katayama
Human Genome Center, Univ of Tokyoktym@hgc.jp

■integration {名-1} : 統合、一体化、Primary intention

統一、融合、調和、集大成• Mission of the "Database Center for Life Science"• Integration of the domestic life science databases• My proposals• Generate a template database which is really easy to deploy• Plugin for "Ruby on Rails"
Togo• Load .xls or .csv ﬁle by 1 click and build RDB• Automatically generate web interface to search• Automatically generate SOAP/WSDL APIs also
• We can also host the databases at DBCLS

DBTogoWS• Integrate large systems such as KEGG, DDBJ, PDBj via web service• Review the best way to achieve this during the BioHackathon

Togo WS - standard objects to exchange?
• BioMoby object ontology• too many similar objects• not so easy to build BioMoby server in diﬀerent language like Ruby
(only usable to Perl and Java clients)• SOAP/WSDL (complexType) - XML schema• put standard .xsd ﬁles at open-bio.org• share the same object models among Bio* projects and WSs• UML (BioUML?)• truly interoperable object models among Bio* projects• written in C
• bindings in each Bio* libraryBioMoby/MOWServ object ontology
major DB and software output
formats are under the single'text-formatted' category ﬂatly!
--> how to create workﬂows?

text-formatted

BLAST̲Text, NCBI̲BLAST̲Text,
BLAST̲XML, ...
FASTA, FASTA̲Text, FASTA̲pep, FASTA̲AA, ...
Clustalw̲Text, Newick̲Text, Phylip̲Text, ...
RefSeq̲Text, SwissProt̲Text, ...

BioMoby service ontology

Japanese
web services are biased todatabase retrieval

DDBJ, KEGG, PDBj services
Analysis
DatabaseAlignment
ConverterStructure

Far from integration• The number of programs and data types keep growing• Force them to comply our standardization eﬀort is impossible• Web service won't scale• Large data - Amount of data is increasing exponentially• Async service - Computational power is also limited• Workﬂow - Pipelining services is still hard w/o programming

Future integration• Continuous community eﬀort is required for the interoperability• Large scale services should provide interoperable APIs
• EBI, NCBI, DDBJ, KEGG, PDBj, CBRC, ...
• BioMoby• Non-standard services can also be integrated by clients and libraries• Open Bio* libraries (BioPerl, BioRuby, BioJava, BioPython)• Taverna, Seahawk, MOWServ, jORCA, ...
• In Japan, DBCLS will develop TogoWS to integrate domestic services• Provide "shim" services: parsers and converters for various db/app• Provide WS-I proxy for the BioMoby services?

Remaining issues• Number of problems are represented• Standard data types and workﬂow• Large data
• Async service• Security• Error handling• .....
• Publication• Manifesto• Journal article• Meeting• BOSC session for web service• annual BioHackathon

Slide by Prof. Trelles (INB/MOWServ)

BioRuby group - hackathon results• BioMoby client is newly developed• access to BioMoby central to ﬁnd services and execute• Bio::Sequence class is extended to be generic• inport/export interface for major sequence data formats• Bio::SQL is enhanced and tested consistency• based on ActiveRecord (Ruby on Rails)• Some bug ﬁxes
• Web site migration• open-bio.org - Nice new top page + Media Wiki
• rubyforge.org - gem distribution, bug trackers• Details -> http://hackathon.dbcls.jp/wiki/BioRuby