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
Inte
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tio
nR
ese
arc
h
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)
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
Relational Database (MMMDb - MDE)
• 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
Relational Database (MMMDb - MDE)
• 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)
Relational Database (MMMDb - MDE)
• 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
Relational Database (MMMDb - MDE)
EMMA = 7IMSR = 2
EMMA = 4IMSR = 6
EMMA = 0IMSR = 0
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
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
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
Relational Database (MMMDb - MDE)
• 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