Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract modMine is an integrated database of genomic, expression and protein data for Drosophila, and C. elegans.

Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.

modMine Quick Search --

Enter any identifier or symbol in the search box on the modMine home page to access summary pages and integrated tools.

Some examples are:

1) For the Drosophila gene zen, enter: FBgn0004053, CG1046, zen or any of its synonyms.

2) For C. elegans genes, use the Worm Base identifiers or symbols (e.g. M117.2, WBGene00003920, par-5).

3) For proteins use UniProt identifiers or primary accessions (e.g. 18C_DROME, P16909).

modMine Browse Data Categories --

modMine presents data in categories, with each providing information on a particular type of data (for example ‘Gene Expression’ or ‘Protein Interactions’).

Use the icons in the Data box on the modMine home page to run a predefined template query or to build your own query.

Certain template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category.

modMine Run Template Queries --

A number of specific queries have been predefined. These template queries range from fairly simple queries to retrieve a particular type of data to more complex queries that span the different types of data available in modMine.

More template queries will be added as modMine develops and the manufacturers welcome suggestions.

Find lists of predefined template queries in each data category or use the templates page to search through them.

modMine QueryBuilder --

Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries.

modMine Operate on Lists --

All queries in modMine can be performed on lists of data. Lists can be created by typing or pasting in identifiers, or uploading a file.

Data from previous queries can also be saved into a list using the boxes displayed underneath the query results.

Saved lists of data can be used to constrain new queries, perform logical operations and can be analyzed on a page that shows graphs, summary tables and statistics.

modMine now includes a number of public lists that the manufacturer's create and make available from published sources.

modMine MyMine --

You can save your lists, queries and templates between sessions by creating an account using the ‘Log in’ link in the header of every page.

modMine Perl Application Programming Interface (API) --

modMine provides ‘RESTful web services’ enabling execution of queries directly from programs you write.

All Template Queries can be executed from the command line or a script, click the ‘Embed’ link on a Template Query form for more details.

The manufacturers also provide a ‘Perl client API’ that makes it easy to run templates and create custom queries from simple Perl programs.

The download contains some sample code that will connect to modMine and run queries too, for example, fetch details of antibodies and to find modENCODE features located near to gene(s) of interest.

modMine now integrates Cytoscape Web --

In any of the gene or protein report page(s), modMine shows the interaction network of the gene displayed by Cytoscape Web: nodes (genes) and edges (interactions) are both active links to the relevant modMine pages, and the sources of an interaction are displayed as the pointer is hovered over an edge.

Different colors of edges are for different interaction types, and the network can be rendered by interaction type. Exporting the network to SIF and XGMML formats is supported.

Cytoscape Web - Cytoscape Web is a web-based network visualization tool, modeled after Cytoscape - (see G6G Abstract Number 20092), that is open source, interactive, customizable, and easily integrated into websites.

Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF.

Availability and Implementation:

Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available.

System Requirements

Contact manufacturer.


Manufacturer Web Site modMine

Price Contact manufacturer.

G6G Abstract Number 20689

G6G Manufacturer Number 104264