mugen mice database (mmdb) (

MUGEN MICE

DATABASE (MMdb)(www.mugen-noe.org/database/)

• 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

What is the MMdb

• 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

Serving Purposes

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 directly linked to other databases (i.e. EMMA, JAX, MGI, ENSEMBL, ENTREZ, ARRAYEXPRESS, EUREXPRESS, PUBMED)

Even More Key Features

• The MMdb 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 interconnectivity

MUGEN Mutant Mouse 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

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

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

• 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

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

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

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

Searching…

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’

Results

…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

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 Help Section (Details of a Workflow)

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

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

• 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

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?

• 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 Genome 18(3):157-163

Interoperability? Future Plans?

B.S.R.C. Fleming Institute34 Fleming Str., Vari, 16672, Greece

Vassilis AidinisMenelaos Manoloukos

Christina ChandrasMichalis Zouberakis

George Kollias