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Unit Leader

Technology and Development Unit for Knowledge Base of Mouse Phenotype

Tech

nology and Development Unit

for Knowledge Base of MousePheno

type

Goal

Activities

Large amounts of worldwide genetic resources about mice

have fuelled international effort toward the completion of

a functional annotation of the whole mouse genome, which

will furnish systems for viewing mammalian biological

networks and determining the causes of diseases. Under these

circumstances, the development of information technology for

integrating phenotypic data has presented new challenges in

the biomedical field. The overall goal of the Technology and

Development Unit for knowledge base of mouse phenotypes

is to establish an intelligence infrastructure for formulating

phenotypic variations in mice with which the relationship of

mouse phenotype with human diseases can be determined,

thereby contributing to the development of a worldwide

Development of methodology for integration of

phenotype information.

Establishment of worldwide standard from phenotype

data produced by Japan Mouse Clinic and the

Experimental Animal Division.

MembersUnit Leader

Hiroshi MASUYA, Ph.D. (2008.4 ～ )

Research & Development Scientist

Nobuhiko TANAKA, Ph.D. (2008.4 ～ )

Technical Staff I

Kazunori WAKI (2008.4 ～ )

Agency Staff

Kiyota TOGUCHI (2008.4 ～ ) Yukiyo IRISAWA (2008.4 ～ )

Tetsu MIYAGI (2008.4 ～ )

1.

2.

standard data format and ensuring a broad sharing of detailed

phenotypic data of mice. This includes the establishment of

the compatibility of the phenotypic data of the Japan Mouse

Clinic system developed by the Technology and Development

Team for Mouse Phenotype Analysis and the environmental

data of Experimental Animal Division with a worldwide

standard. We also aim to determine the association between

mouse phenotypes and human diseases using data integration

technology. The advanced mouse resource information

that can be accumulated through these goals will increase

the availability of mouse resources for use in research and

contribute to the establishment of the world’s highest level of

bioresource quality in BRC.

Representation of phenotype-disease association.3.

Hiroshi MASUYA, Ph.D.

[2008.4~]

[~2008.3: Shiroishi Research Collaborative Group]

Technology and Development Unit for Knowledge Base of Mouse PhenotypeRIKEN BRC Annual Report 2005 ～ 2007

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Miyagi, Toguchi, IrisawaTanaka, Masuya, Waki

Specific Aims

1. Development of fundamental infrastructure for representing universal data framework for experimental genetics workflow

We have developed a fundamenta l f ramework for

representing generic logic of experimental genetics named

Genetics Ontology (GXO). Using this basic technology, we

developed a logical methodology for constructing basic data

structures of various items and their relationships. GXO

provides fundamental data structures of basic components in

experimental genetics such as genes, alleles, loci, molecules,

biological processes, anatomical structures, cells, cellular

components, phenotypes, phenotyping analyses, and data

produced from analysis, experimental procedures and other

experimental conditions.

2. Establishment of worldwide standard data format for mouse phenotypic data and experimental procedure

We participate in an international consortium, namely,

the Mouse Phenotype Database Integration Consortium

(InterPhenome) with the aim of integrating, as much as

possible, current and future mouse phenotype resources, and

promoting a process of developing standards for describing

phenotypes. The InterPhenome consortium have identified

three major priority requirements for meeting standards

for describing phenotyping procedures, data exchange

technologies and phenotype ontologies. In cooperation with

the Bioinformatics Laboratory of Medical Research Council

(MRC) Harwell, we develop a minimal information standard

associated with data formats, such as XML schemas, that

will allow data reuse and analysis as well as data interchange

between public repositories. The InterPhenome consortium is

now discussing a draft version of MIMPP for standardization

(http://www.interphenome.org/ppxml/ppml_v1_3.html). One

of the activities of MIMPP is to cooperate with the Minimum

Information for Biological and Biomedical Investigations

(MIBBI) consortium for a broad coordination in the

biomedical community.

3. Development of website for representing standardized operation procedures (SOPs) of Japan Mouse Clinic system.

We developed a website for standardized operation procedures

Technology and Development Unit for Knowledge Base of Mouse PhenotypeRIKEN BRC Annual Report 2005 ～ 2007

― 164 ―

(SOPs) to be used by Japan Mouse Clinic, using SOP

documents provided by the Technology and Development

Team for Mouse Phenotypic Analysis (http://www.brc.

riken.go.jp/lab/bpmp/SOPs/). We are converting such

SOP documents into EMPReSS-style XML format (http://

empress.har.mrc.ac.uk/). In parallel, we are developing a

detailed representation of the procedure content named the

Standardized Description of Operation Procedure (SDOP)

website, where we show detailed information on behavioral

experimental procedures, reproduction technologies and

animal husbandry procedures of multiple institutes (SDOP

website: http://www.brc.riken.go.jp/lab/gsc/mouse/SDOP/).

We have recently introduced modifications to the function of

the SDOP website to show different procedures by column

coloring. We are now planning to develop an MIMPP

standardized form of the SDOP contents.

Figure 1. Objectives and workflow of Technology and development unit for knowledge base of mouse phenotype

Figure 2. Screenshot of SOPs website

Technology and Development Unit for Knowledge Base of Mouse PhenotypeRIKEN BRC Annual Report 2005 ～ 2007

― 165 ―

Figure 3. Screen shot of new SDOP website

Publications【Original Papers】 (*Peer reviewed journals)

Taylor C.F., Field D., Sansone S-A., Aerts J., Apweiler R.,

Ashburner M., Ball C.A., Binz P-A., Bogue M., Booth

T., Brazma A., Brinkman R.R., Clark A.M., Deutsch

E.W., Fiehn O., Fostel J., Ghazal P., Gibson F., Gray T.,

Grimes G., Hancock J.M., Hardy N.W., Hermjakob H.,

Julian R.K.Jr., Kane M., Kettner C., Kinsinger C., Kolker

E., Kuiper M., Novère N., Leebens-Mack J., Lewis

S.E., Lord P., Mallon A-M., Marthandan N., Masuya

H., McNally R., Mehrle A., Morrison N., Orchard S.,

Quackenbush J., Reecy J.M., Robertson D.G., Rocca-

Serra P., Rodriguez H., Rosenfelder H., Santoyo-Lopez

J., Scheuermann R.H., Schober D., Smith B., Snape J.,

Stoeckert C.J.Jr., Tipton K., Sterk P., Untergasser A.,

Vandesompele J., Wiemann S.: “Promoting Coherent

Minimum Reporting Requirements for Biological and

Biomedical Investigations: The MIBBI Project.” Nature

Biotechnology, 26:889-896 (2008).*

Gondo Y., Wakana S., Masuya H.: “Trend in the large-

scale mouse mutagenesis projects in the world.”

Jikkennigaku 26, 2130-2135 (2008) in Japanese.

Kaminuma E., Masuya H., Miura I., Motegi H.,

Takahashi K., Nakazawa M., Matsui M., Gondo Y.,

Noda T., Shiroishi T., Wakana S., Toyoda T.: “Objective

evaluation measures of marker selection in large-

scale SNP genotyping.” Journal of Bioinformatics and

Computational Biology, 6:905-917 (2008).*

Sakuraba Y., Kimura T., Masuya H., Noguchi H., Sezutsu

H., Takahasi K.R., Toyoda A., Fukumura R., Murata T.,

Sakaki Y., Yamamura M., Wakana S., Noda T., Shiroishi

T., Gondo Y.: “Identification and characterization of new

long conserved noncoding sequences in vertebrates.”

Mammalian Genome (in press).*

Technology and Development Unit for Knowledge Base of Mouse PhenotypeRIKEN BRC Annual Report 2005 ～ 2007

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Oral Presentations

Masuya H.: “Development of an ontological framework

to describe experimental procedures, experimental results

and phenotypes.” CASIMIR/Interphenome Workshop on

Describing and Reporting Phenotypes, Cambridge, UK,

Sep. (2008).

Furuse T., Wada Y., Hattori K., Yamada I.,, Kushida

T., Shibukawa Y., Masuya H., Kaneda H., Miura I.,

Kobayashi K., Shiroishi T., Yuasa S., Wakana S.:

“Genetic and phenotypic analyses of an ENU-induced

mouse mutant that shows AD/HD-like behavior.” 22nd

International Mammalian Genome Conference, Prague,

Czech Republic, Nov. (2008).

Masuya H., Tanaka N., Waki K., Kobayashi N., Toyoda

T., Shiroishi T., Wakana S., Mizoguchi R.: “Statistical

inference for mammalian omic data integration on the

Semantic Web.” 22nd International Mammalian Genome

Conference, Prague, Czech Republic, Nov. (2008).

Tanaka N., Waki K., Mizoguchi R., Kobayashi N.,

Toyoda T., Shibukawa Y., Kushida T., Yamada I., Furuse

T., Wakana S., Masuya H.: “Development of interigent

infrastructure for description of experimental protocols

with Semantic Web technology.” 22nd International

Mammalian Genome Conference, Prague, Czech

Republic, Nov. (2008).

Wakana S., Suzuki T., Masuya H., Miura I., Kobayashi

K., Kaneda H., Furuse T., Yamada I., Motegi H., Toki

H., Inoue M., Minowa O., Tanaka N., Noda T., Shiroishi

T., Obata Y.: “A plan of Japanese Mouse Clinic in

RIKEN BRC.” 22nd International Mammalian Genome

Conference, Prague, Czech Republic, Nov. (2008).

Suzuki T., Sato H., Ikeda K., Masuya H., Yokoyama

H., Nishimura S., Kaneda H., Miura I., Kobayashi K.,

Toki H., Minowa O., Kurihara Y., Shiroishi T., Wakana

S.: “Genetic analyses of inherited retinal degeneration

model mouse in ENU mutagenesis.” 22nd International

Mammalian Genome Conference, Prague, Czech

Republic, Nov. (2008).

【International Conferences】 【Domestic Conference】　Total　23