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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
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(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
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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
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