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BioHackathon in Tokyo

Hideaki SUGAWARA

Center for Information Biology and DNA
Data Bank of Japan (DDBJ)
National Institute of Genetics

From Web APIs for Biology(WABI) to Semantic Web APIfor Biology (SABI)

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BioHackathon in Tokyo2* [Reference] Sugawara H, Miyazaki S. Biological SOAP servers and webservices provided by the public sequence data bank. Nucleic Acids Res.
2003 Jul 1;31(13):3836-9

To improve the problem solving environment forbioinformaticians, we implemented a SOAP (SimpleObject Access Protocol) server* and Web services
that provide a programmatic interface.

It is laborious and sometimes impossible for us towrite a computer program that finds useful data
resources, sends a proper query and processes theoutput.

Motivation to develop
DDBJ Web API in 2002

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BioHackathon in Tokyo

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

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http://xml.nig.ac.jp/

BioHackathon in Tokyo

WABI provides
213 methods in26 services

http://xml.nig.ac.jp/

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http://arsa.ddbj.nig.ac.jp/
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20080211

BioHackathon in Tokyo(/ENTRY/DDBJ/feature-table/feature{/f_key=='rRNA'
AND /f_quals/qualifier{/q_name=='product' AND/q_value='16S ribosomal RNA'}})/ENTRY/DDBJ/length > 10000 AND/ENTRY/DDBJ/length < 20000/ENTRY/DDBJ/definition = '16S ribosomal RNA'e.g,• The system provides not only free keyword
search but also field search by using XML pathagainst some bio-databases.

ARSA WABI

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Entry retrieval and keyword search of morethan 20 databases
Homology search and multiple alignment
Retrieval of the secondary databases
developed by DDBJ
Retrieval of useful databases developed byother sites
An unified taxonomy by the InternationalNucleotide Sequence Database Collaboration(INSDC=DDBJ/EMBL/GenBank)

BioHackathon in Tokyo

BLAST, FASTA, ClustalW,VecScreen, Mapping

GIB, GIB-V, GIB-IS, GIBENV, GTPS, GTOP

Ensembl,NCBIGenomeAnnotation,RefSeq, GO, OMIM

TxSearch

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Description

getentry, SRS, ARSA

Service7

Categorization of WABI services

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ClustalW
BioHackathon in Tokyo

Service > Analysis > Alignment > Multiple_Sequence_Comparison

BLAST, FASTA, VecScreen, Mapping

Pairwise_Local_Aligning

Service > Analysis > Alignment > Pairwise_Sequence_Comparison >ARSA, SRS, OMIMService > Bioinformatics > Database > Searching

TxSearch , GIB, GTPS, OMIM, Ensembl etc

Service > Bioinformatics > Database > Searching > GettingText

PDB

Service > Bioinformatics > Database > Searching > GettingStructures

RefSeq (NP_ prefix etc)

GetEntry (DAD, Uniprot-TrEMBL, Uniprot-Swiss-prot, PRF, PDB)

Service > Bioinformatics > Database > Searching > GettingAminoacids

GetEntry (DDBJ), RefSeq (NM_, NC_ prefix etc)

Service > Bioinformatics > Database > Searching > GettingNucleotides

Mapping of WABI to BioMOBY’s
service ontology

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WABI workflows99

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BioHackathon in Tokyo

Genes with amino acid substitution and 3D structure
modification are also important because it causes
the disease.

Genes without the amino acid substitution areimportant for drug development.

It is to classify all of the human genes from theviewpoint of SNPs.

SNPs workflow

1010

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BioHackathon in Tokyo

10,691 genes,
14,571 amino acids

7,123 genes,
8,914 amino acids

SNPs workflow chart and result1111

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OUTREACH

Frequently posted questions and comments:
Is it useful?
Who will use?
Biologists will not use.
Neither will bioinformaticians do.
It is only for OTAKU.

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13• The term was popularized in the English speaking
world in William Gibson's 1996 novel Idoru, which has
several references to otaku. In particular, the term
was defined as 'pathological-techno-fetishist-withsocial-deficit'.
• In an April 2001 edition of The Observer, William
Gibson explained his view of the term:
The otaku, the passionate obsessive, theinformation age's embodiment of the connoisseur,more concerned with the accumulation of data thanof objects- - - Understanding otaku -hood, I think, is
one of the keys to understanding the culture of theweb.

FYI: OTAKU20080211

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WORKFLOW NAVIGATIONSYSTEM FOR OUTREACH
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http://cyclamen.ddbj.nig.ac.jp/

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Sub-categories

List of methods
BioHackathon in Tokyo

Current hierarchy

Service category

Categorization of services

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The Web interface is mechanically generated by WABI

Web interface created by WABI

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The result of the previous service

Low

Services
applicable to theresult in the left

Priority

High

Interconnection of WABIs

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The result of the previous service

This web interface
is also mechanicallygenerated

The result is mechanically given to thenext service selected20080211

SOAP
serverUser

BioHackathon in Tokyo

Web I/F
generator

Dictionaries

Metainformation

Workflow Navigation System20

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System architecture and components

20080211

BioHackathon in Tokyo– HTML tags in the web interface are defined– The HTML dictionary is referred from the input/outputdictionary.

• HTML– Each service has several input and output types.
– The input/output dictionary is used to connect services.

• Input/Output– All the services are categorized based on the service
category dictionary.

• Service category

Three dictionaries (ontology)

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20080211

BioHackathon in Tokyo• Define description, initial value and example
values which are displayed in the web interface.

• Define the web service information such as
WSDL, URL and method name to call the SOAP
with input parameters.

• Define (refer to) the category and input/outputof serviceMeta-information of a service2222

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Web interface is mechanically generated• Other information such as description, initial value, …

• WSDL: http://xml.nig.ac.jp/wsdl/GetEntry.wsdl• Output type: FASTA format (refer to in/out dictionary)• Input type: DDBJ accession (refer to in/out dictionary)(refer to category dictionary)• Category: Keyword search -> DDBJ

In the case of getFASTA_DDBJEntry(accession) method:

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Example of meta-information and dictionary20080211

Output：BLAST Result

Output：DDBJ FlatfileDDBJ accession
organismsequence

Input：Input：
DDBJ Accession

BioHackathon in TokyoDDBJ Flatfile has sequence
defined in the input/output
dictionary.

sequence

BLAST:searchSimple

getentry:getDDBJEntry“getentry” and “BLAST” is connectedby “sequence”

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20080211

BioHackathon in Tokyo<?xml version="1.0" ?><dictionary><category
name_en="Keyword search“
description_en="Keyword search service …
/><category
name_en="DDBJ"
description_en="Search and retrieve of DDBJ database."><parent name_jp=“Keyword search“ /></category>

Service category dictionary25

20080211

BioHackathon in Tokyo<?xml version="1.0" ?><dictionary><content
name=“DDBJ FlatFile“
description_en=“DDBJ Flat File”><parent name=“FlatFile” /><parser type=“LOCAL” class_name=“DDBJFFParser” /><data_list><data name=“DDBJ Accession”
method=“getAccession” /><data name=“organism”
method=“getOrganismFromFF” /><data name=“nucleotide sequence” method=“…” /><data name=“gene” method=“getGeneFromFF” /></data_list></content>…

Input/Output dictionary

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20080211

BioHackathon in Tokyo<?xml version="1.0" ?><dictionary><content
name=“text“
description_en=“The display type of text is
displayed with HTML tag input type and text”><tag_list><tag name=“text” /></tag_list></content>…

HTML dictionary

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0.00

2,000,000.00

4,000,000.00

6,000,000.00

8,000,000.00

10,000,000.00

Y2002

595,051.00
78,939.00
Y2003

2,137,074.00

Y2005

BioHackathon in Tokyo

Y2004

6,121,834.00

589,398.00

2,106,793.00
472,282.00

10,679,120.00

In&outside

14,000,000.00

12,000,000.00

Outside16,000,000.00

18,000,000.00

Y2006

778,042.00

16,301,823.00Y2007

2,435,503.00

9,499,970.00

Usage in and outside NIG

Beyond OTAKU

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0500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

Y2002

78,939
Y2003

Y2004

472,282

589,398

Y2005

BioHackathon in Tokyo

2,137,074

Usage outside NIG

Beyond OTAKU

Y2006

778,042Y2007

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2,435,503

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2002~2007

BioHackathon in Tokyo

DDBJ
ClustalW
OMIM
SRS
Gib
DDBJ
Ensembl
TxSearch
Fasta
ARSA
BlastDemo
SPS
other

GetEntry
NCBIGenomeAnnotation
RefSeqTxSearch
Blast（所外のみ）
Gtop
DDBJ
EnsemblSRS
DDBJ
ClustalW
FastaGibGO
OMIM
ARSA
BlastDemo
SPS
VecScreen
NCBIGenomeAnnotation
PML
RefSeqother
GetEntry
Mapping
Gtop
ExClustalW
Blast（所外のみ）

2007
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Plainly stated, the basic tenets of wabi-sabi are simple
is best, less is more. Leonard Koren in his book
"Wabi-Sabi: for Artists, Designers, Poets andPhilosophers (Stonebridge Press, 1995) describes it
as a beauty----From WABI to SABI

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BioHackathon in Tokyo

SABI WILL STAND FOR SEMANTICWEB API FOR BIOLOGY SOMETIME.

The common dictionaries and meta-informationwill be discussed in the BioHackathon. OTAKUs
will follow up the discussion to make programs
possible to find and interconnect Web APIs in 3years, 5years or 10years.

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Thank you very much for your sincere attention
from the beauty of WABI-SABI, an authentic teaarbor

Sabi may stand for Semantic
API for Biology.

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