9 european countries 1 third country 14 research centers of excellence 5 universities 4 smes 1...

9 European Countries 9 European Countries 1 Third Country1 Third Country 14 Research Centers of Excellence14 Research Centers of Excellence 5 Universities 5 Universities 4 SMEs4 SMEs 1 Venture Capital1 Venture Capital

MUGEN OBJECTIVES

• To systematically study animal models for immune diseases

and processes through application of functional genomics

platforms.

• To integrate the research experience and capacities of each

network participant to allow the efficient application of post-

genomic approaches to generate new knowledge in immunological

diseases and processes.

• To ensure spreading of excellence, optimal use and

dissemination of the generated knowledge beyond the boundaries

of MUGEN partners, by integrating competencies to train

researchers and other key staff, to encourage knowledge transfer,

to address innovation related aspects, and to raise the public

awareness of scientific research issues.

Training and

Spreading

Integration Research

WORK-PACKAGE LIST

WP 1: Transgenesis Core

WP 2: Expression Profiling Core

WP 4: MUGEN Knowledge Environment

WP 5: Relational Databases MMMDb (MDE)

WP 22: Genotyping Core

WP 21: Phenotyping Core

Training and

Spreading

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WP 7: Innate Immune Activation

WP 8: Antigen Recognition & Acquired Imm.WP 9: Immunological Tolerance

WP 10: Intracellular Signaling Cascades

WP 11: Infectious Diseases

WP 12: Chronic Inflammation & Autoimmun.WP 13: Immune Modulation of Cancer

WP 14: Identifying Genetic Susceptibility

WP 15: MUGEN PhD Research School

WP 16: MUGEN Mobility Fellowships

WP 17: MUGEN Training Courses

WP 18: MUGEN Conference

WP 19: Management

WP 23: MUGEN Awareness & Dissemination

WP 3 (5): Bioinformatics Core

Relational Database (MMMDb - MDE)


• MMMDb is the MUGEN consortium’s very own virtual on-line mutant mouse strain repository

• It is a database whose schema was designed with postgresql and is managed with enterprise java beans (EJBs) technology

• It’s interface was developed using xml, jsp, servlets and other java classes


• MMMDb is acting as a link between MUGEN participating institutions

• Simplifies data exchange and submission for researchers

• Makes it easy for researchers to share their data with whoever might be interested by switching the dissemination level of their submitted data to Public, thus making data available to all visitors of the MMMDb


• Various dissemination levels for every single mutant’s data set plus numerous ways of categorizing data for easier sorting (i.e. research application, mutation type, gene affected etc.)

• Registered users can submit, edit and even delete their own data by themselves (…of course they cannot edit or delete data submitted by fellow MUGEN participants)

• Mutant strains, genes and references are directly linked to other databases (i.e. MGI, ENSEMBL, GENE, PUBMED)


• The MMMDb is FULLY searchable and EASY to use!

• Database can handle all kinds of files (i.e. docs or pdfs for handling and genotyping instructions and also references, images for phenotyping data)

• The schema of the database is extremely flexible allowing easy integration of differently structured datasets and adaptation of other data schemas; thus making a first step towards database interoperability and database interconnectivity

• A detailed help section for users to be able to make most out of the MMMDb!

55

137

29

Transgenic Tools

M odels of Immune Processes

M odels of Human Diseases


EMMA = 7IMSR = 2

EMMA = 4IMSR = 6

EMMA = 0IMSR = 0


Storing & handling of phenotypic data is currently under development…

• As a 1st step we adopted the MGI Mammalian Phenotype

Ontology, which has a hierarchical structure that permits a

range of detail from high-level, broadly descriptive terms to

very low-level, highly specific terms. This range is useful for

annotating phenotypic data to the level of detail known and

for searching for this information using either broad or

specific terms as search criteria.

• We have built a function to automatically load the MP OBO

file from the MGI ftp server in our database

• Thus our users can select the most appropriate MP term(s)

that suit(s) their mutant from a drop-down list


• The MMMDb is FULLY searchable and EASY to use!

• The schema of the database is extremely flexible allowing easy

integration of differently structured datasets and adaptation of

other data schemas; thus making a first step towards database

interoperability and database interconnectivity

• Database can handle all kinds of files (i.e. docs or pdfs for

handling and genotyping instructions and also references,

images for phenotyping data)

• Scheduled links to ArrayExpress (EBI), CAGE database (RIKEN)

9 European Countries 9 European Countries 1 Third Country1 Third Country 14 Research Centers of Excellence14 Research Centers of Excellence 5 Universities 5 Universities 4 SMEs4 SMEs 1 Venture Capital1 Venture Capital

9 european countries 1 third country 14 research centers of excellence 5 universities 4 smes 1...

Documents

database interoperability

mugen consortiums

mugen conferencewp

submitted data

data schemas

data available

mugen knowledge environment

mugen training courseswp