Opening Remarks
Database Center forLife Science
Prof. Takagi
Director of DBCLS

BioHackathon 2010 Symposium>80 participants!
32 invited
33 domestic
15 organizers

Hackathon Basics
BioHackathon= bio + hack + marathon= bioinformatics coding camp!

‣ One unique style of the international workshop‣ Face-to-face meeting of the geeks‣ Addressing issues by intensive software development‣ Originated from free software culture‣ History‣ Open Bio* Hackathon (2002, 2003)‣ Phyloinformatics Hackathon (2006-)‣ Systems Biology Super Hackathon (2008)‣ DBCLS Hackathon (2008-)

Evolution of DBCLS BioHackathons
Mission of the DBCLS= integration of life science resources(standardization / interoperability)
The 1st DBCLS BioHackathon (2008)
Towards interoperable web services inlife science with Open Bio * libraries
The 2nd DBCLS BioHackathon (2009)
Integration of web services inbioinformatics applications
The 3rd DBCLS BioHackathon (2010)
Interpretation of biological knowledge
with Semantic Web technologies

Goals of the BioHackathon 2010
Learn the Semantic Web technology
What is the RDF, OWL, SPARQL, ... #@&*%$ ?!
Is it promising?
Will it give better answer than existing systems?
Survey the current status and develop some software
Linked Data
What kind of biological data is currently available?
Triple Stores
Which implementation to use? pros/cons? Scalability?
Semantic Web Tools in Open Bio*
Generic tools to manipulate RDF graph
Interface to acess SPARQL endpoints

BH10 schedule: Day 1
Session
Talk
Talk
Talk
Talk
Talk
Lunch
Talk
Talk
Talk
Talk
Poster
Open space
Banquet

Time
10:10
10:40
11:00
11:20
11:40
12:00
13:30
13:50
14:10
14:30
15:00
16:30
18:00

Presented by / Participants
Erick Antezana
Matthias Samwald
Thomas Kappler and Jerven Bolleman
François Belleau
Heiko Horn
Tetsuro Toyoda
Mark Wilkinson
Andrea Splendiani
Mitsuteru Nakao and Toshiaki Katayama
Invited participants +α
All participants
Registered participantsBH10 schedule: Day 2-5DaySession

TimeParticipants / Activities

2/9

Hack

9:00 - 18:00

Invited & domestic participants

2/10

Hack

9:00 - 18:00

Invited & domestic participants

2/11

Hack

9:00 - 18:00

Invited & domestic participants

2/12

Hack

9:00 - 16:00

Invited & domestic participants

2/12

Talk

16:00 - 18:00

Summary session

2/12

Drink18:00 - 21:00

Farewell party :-)2/13-15

Write

10:00 - 18:00

Writing a meeting report with volunteers

10:10-10:40

Erick Antezana

Belgium

AFFILIATION
Genomics Data Platform
BioInformation Management
Bayer CropScience

PROJECTS
Semantic Systems Biology
http://www.semantic-systems-biology.org

Cell Cycle Ontology

http://www.cellcycleontology.org

Towards a Semantic Systems Biology:
Biological Knowledge Management Using
Semantic Web Technologies

10:45-11:05

Austria

Matthias Samwald
AFFILIATIONDERI Galway (Ireland) andthe Konrad Lorenz Institute (Austria)

PROJECTS
Concept Web Alliance
http://conceptweblog.wordpress.com/<a>Tag

http://hcls.deri.org/atag/generator/

High-level knowledge representation on the Semantic Web:
the Concept Web Alliance and related efforts

11:05-11:25

Switzerland

Thomas Kappler / Jerven Bolleman

AFFILIATION
UniProt in RDF

UniProt ConsortiumUniProt Consortium
Swiss Institute of Bioinformatics
http://uniprot.org

11:25-11:45

François Belleau

Canada

AFFILIATION
Laval University

PROJECTS
Bio2RDF
http://www.bio2rdf.org

Semantic web atlas of
postgenomic knowledge

Bio2RDF cognoscope : A killer app for the life science11:50-12:10

Heiko HornDenmark

AFFILIATIONNNF Center for Protein Research
Faculty of Health Sciences
University of Copenhagen

PROJECTS
Reflect
http://www.reflect.ws

NetworKIN

http://networkin.info

Reflect - text mining in Semantic Web

13:35-14:05

Tetsuro Toyoda

Japan

AFFILIATION
Bioinformatics and Systems
Engineering division,
RIKEN

PROJECTS
SciNeS
http://omicspace.riken.jp/base/index.html#6

RIKEN SciNeS

14:05-14:25

Mark Wilkinson

Canada

AFFILIATION
Dept. of Medical Genetics,
University of British Columbia,
Heart + Lung Institute at
St. Paul's Hospital

PROJECTS
BioMoby

http://www.biomoby.org

SADI

http://sadiframework.org

Cardio SHARE

http://biordf.net/cardioSHARE

SADI - semantic web service

14:25-14:45

Andrea Splendiani

UK

AFFILIATION
Centre for Mathematical andComputational Biology
Rothamsted Research

PROJECTS
RDFScape
http://bioinformatics.org/rdfscapeOndex

http://www.ondex.org

BioPAX

http://www.biopax.org

Visualization and analysis of biologicalnetworks on the Semantic Web

Beat

http://beat.sourceforge.net

SWAT4LS

http://www.swat4ls.org

Extending TogoWS andOpen Bio* libraries forLinked Data
Mitsuteru Nakao (DBCLS)
Toshiaki Katayama (HGC, Univ. of Tokyo)
Personal Semantic Web--- If you have data, export it as Linked Data ---http://hackathon3.dbcls.jp/

BH10 Preliminar y Objectives
Queries

Datasets

Targeted biological queries tobe resolved by the Semantic
Web technologies.

List currently available
and/or still missing datasets(as Linked Data / RDF) toresolve the queries.

Develop our own or survey
existing extensible storage
systems for RDF triples andfunctional query interfaces.

Develop common APIs among
Open Bio* projects for RDF
stores and SPARQL endpoints.

StoresTools

Current effor ts in DBCLS
Queries

Datasets
Text search:
AllieinMeXes

Original data:
Life Science DBs
in JapanTogoDB

Sandbox:4storeVirtuoso
SesameStores

TogoWS
Open Bio*Tools

SemWeb for everybody
TogoDB

deploy your DB in 5minYour data in CSV

configureuploadTogoWS

integrated REST/SOAP ser vices

endpoint
Can beaccessed with REST
API as Linked Data
http://togows.dbcls.jp/entry/togodb-foobardb/123.rdf

deployAny databaserecord by the user
http://togodb.dbcls.jp/foobardb/show/123

As a RDF/SPARQL provider* Appropriate parameters* Entry cache* Built-in parsers* Status monitor

NCBITSRESOAPREST
Resource

TogoWSUserAnalysis

TODO:
RDF export
SPARQL endpoint

RESTSOAPSO
AP

SOAP

TogoDB

DDBJ

EBI
PDBj
KEGG

LinkedData...
TogoWS

TogoDB

Open Bio* ?

http://friendfeed.com/the-life-scientists/188942c1/bioinformaticians-which-is-bioinformatics

What's come out?

What kind of achievements will emerge from the cloud?
Nobody knows. Let's look again after one week. :-)Poster session 15:00Poster presentation← Organizers will pin up the cover sheet on the wall

← Please hang your slides under the cover sheet
Self-introduction
Look around freely
Talk to each otherFind your collaborators for BH10
If you forget to bring your printed poster,
ask organizers nearby. We have printers.

Open space session 16:30Open space discussion= Sort of brainstorming
in self-organized discussion groups

Biological
LinkedDataOpen
Procedure / Rules
Bio* RDF
1. Raise candidate discussion topics
tools
2. Select some discussion groups
3. Start discussion in group
Text
4. Look around some discussions
mining
5. You can switch group at any time
6. You can create additional group at any time
7. Finally join at least one group
SPARQL
endpoint /8. Sort out issues
Visualization
queries
9. What will you challange during BH10?

Open space session 16:3016:50-17:20
UseCases!

Arakawa

KawajiNextGen
Seq

Network/ interaction

Visualization

Andrea17:25-17:55
Implementation
bootcamp

Rutger
How toproperly use
OWL
JervenFrancois
Biological
LinkedData
SPARQL
endpoint /queries

Katayama
AlbertoTextmining

Open Bio*RDF tools
Ruby/Python

ioningsrev:rvideDB pro SID?
LBH2010
SummarySession
12 Feb 16:00-

Before BH10

What kind of achievements will emerge from the cloud?
Nobody knows. Let's look again after one week. :-)After BH10

Now we have brain-washed with RDF and SPARQL! :-)Geek++

What we made/learned actually?

#1
Clique of the world-top-level
developers in bioinformatics.
Now we know each other.
Keep in touch.
Have good collaborations.

What we made/learned actually?

Name spaceTools
Hosting#2
Database providers now understandpotential of SemWeb (RDF/SPARQL)
technologies

What we made/learned actually?

#3
Different tastes

SemWeb for everybody
TogoDB

deploy your DB in 5minYour data in CSV

configureupload

TogoWS

integrated REST/SOAP ser vices

endpoint
Can beaccessed with REST
API as Linked Data
http://togows.dbcls.jp/entry/togodb-foobardb/123.rdf

deployAny databaserecord by the user
http://togodb.dbcls.jp/foobardb/show/123

DEMO
Expose user's data to
the Semantic Web world
http://togodb.dbcls.jp/dbname/show/1

http://togows.dbcls.jp/entry/togodb-dbname/1.xml

http://togows.dbcls.jp/entry/togodb-dbname/1.ttl

As a RDF/SPARQL provider* Appropriate parameters* Entry cache* Built-in parsers* Status monitor

NCBI

TS
RESOAPRESTResource

TogoWS

UserAnalysis

DONE:
RDF exportTODO:
SPARQL endpoint

RESTSOAPSOAP

SOAPTogoDB

DDBJ

EBIPDBj
KEGG

BIOHACKATHON 2010 GROUP PHOTO

GROUP PHOTOTSUKIJI FISH MARKET TOURASAKUSA TOUR

Special Thanks to
Keiko Sakuma, Eiji Ueda, Toshihisa Takagi and DBCLS staff
Keiko Nemoto, Kiyoshi Asai and CBRC staff
Alan Ruttenberg (NeuroCommons) through ML discussions
Organizers
Mitsuteru Nakao, Shuichi Kawashima,Shinobu Okamoto, Shin Kawano
Yasunori Yamamoto, Atsuko Yamaguchi