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MUGEN MICE DATABASE (MMdb) (mugen-noe/database/) - PowerPoint PPT Presentation

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MUGEN MICE DATABASE (MMdb) ( What is the MMdb. MMdb is the MUGEN consortium’s 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

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What is the MMdb

  • MMdb is the MUGEN consortium’s 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

Serving Purposes

  • MMdb is acting as a link between MUGEN participating institutions

  • Simplifies data exchange and submission for researchers

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

Key features
Key Features

  • Numerous ways of categorizing data for every single mutant’s dataset, 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/delete data submitted by fellow MUGEN participants)

  • Mutant strains, genes and references are directlylinked to other databases (i.e.EMMA, JAX, MGI, ENSEMBL, ENTREZ, ARRAYEXPRESS, EUREXPRESS, PUBMED)

Even more key features
Even More Key Features

  • The MMdb is FULLY searchable and EASY to use!

  • Database can handleall kinds of files ( 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 interconnectivity

Sorting the list
Sorting the List

The mutant list can be sorted according to research application, affected gene, institution, mutation type and dissemination level by simply selecting a value from the drop down menu

A mutant s detailed information page
A Mutant’s Detailed Information Page

Each tab represents a different category of data relevant to a mutant

Each category can be easily edited as long as the user has the right to

User’s comments (user may post comment on particular mutant mouse)

Creating editing a mutant
Creating/Editing A Mutant

Basic data creation/editing of mutant

Line name entered, research application chosen from drop-down list, contact person selected, comments inserted and desired dissemination level chosen

NOTE – the desired dissemination level is different from the actual dissemination level. The actual dissemination can be switched to public only by the MMdb administration and only after the data have been thoroughly checked for their correctness and integrity.

Adding availability for a mutant
Adding Availability for A Mutant

  • This is an example of how to add availability information to a mutant

  • Repository, genetic background, strain type and state selected from the relevant drop-down lists

  • Available repository and genetic background lists may also be enriched by clicking on the appropriate links

Other mutant information
Other Mutant Information

Apart from general & availability information, one can also add

  • Genetic Background Information

    (DNA origin, targeted, host and backcrossing background and of course number of backcrosses)

  • Mutation type and allele information

    (you can pick a mutation type from a drop-down list, add the allele’s name and symbol, its MGI id etc.)

  • A list of affected genes

    (one can either choose from a list or provide a new gene)

  • Handling and genotyping info in the form of documents or hyperlinks

  • References again in the form of hyperlinks or documents

Creating editing a gene
Creating/Editing A Gene

Similar to mutant mouse data entry/editing, GENE submission is also available

Gene information
Gene Information

Apart from obvious gene information such as gene name, gene symbol and chromosome one can be redirected to other on-line databases, notably MGI, ENTREZ, ENSEMBL, ARRAYEXPRESS and EUREXPRESS II

A gene’s page – lists all the related MUGEN mutant mice


The MMdb search engine is looking for the provided keyword in every possible field in the database.

Just type in a little keyword and press search.

For this example we are looking for ‘cre’


…50 hits!

The cre search resulted in a list of 50 mutants & genes

The list contains the name of the entity that contained the keyword, its entity type and some comments (if available)

Help section
Help Section

All major functionalities (a.k.a. workflows) of the MMdb are split into 3 categories each represented by a tab

To see all the detailed steps of a workflow – just click on the tab

The public view
The Public View

The public view is more or less the same as the registered user’s view….

But (at least for now) less mice are enlisted, since less mice are registered as public…

A mutants public detail page
A Mutants Public Detail Page

Public mice offer the same amount of information for registered and unregistered users

The biggest difference though is that public users have absolutely no write permission on any sort of data

Other features
Other Features

  • Have also developed phenotype data handling

  • Complete storage and handling of phenotypic data and most importantly end up with a widely acceptable data structure

Connection to other databases
Connection to other Databases

We have browsed through MMdb and considered the abilities that this database has

Icons on the right hand side of the MMdb page

Will lead directly to IMSR’s, EMMA’s, MGI’s, EurExpress’s, ArrayExpress’s or Ensembl’s search pages

Interoperability future plans
Interoperability? Future Plans?

  • Having adopted the IMSR data format for our database schema, we could claim to have made a significant step towards defining a minimum information dataset for the mouse model

  • Our aim is to describe the ideal mouse using a comprehensive and well-structured dataset*

    • Use other online resources

    • Implement/adopt web services (i.e. BioMart etc)

    • Use standard ontologies – already using MP terminology and look forward to using any new or updated ontology terms that may make mouse model description better

  • Ultimate goal - Combine phenotypic and genotypic data so as to draw conclusions

    *The Mouse Phenotype Database Intergration Consortium (2007) Integration of mouse phenome data resources.Mamm Genome18(3):157-163

Interoperability future plans1
Interoperability? Future Plans?

B.S.R.C. Fleming Institute

34 Fleming Str., Vari, 16672, Greece

Vassilis Aidinis

Menelaos Manoloukos

Christina Chandras

Michalis Zouberakis

George Kollias