InterMine
- Mature release
- Active development
- Active support
InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the Sequence Ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Currently supported formats include Chado, GFF3, FASTA, GO & gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, Uniprot, and many others.
A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded.
Contents
Chado Integration
We are developing a parser to load data from the GMOD Chado database schema into a companion InterMine warehouse. This will provide a web environment to perform rapid, complex queries on imported Chado data with minimal development effort. The eventual aim is to allow import of any Chado database with some configuration, the parser is currently used in FlyMine and the modENCODE project to import genome annotation from FlyBase and WormBase Chado databases. More information: http://www.intermine.org/wiki/ChadoDBSource
Demo
FlyMine is an example of InterMine in use.
Requirements
InterMine is written in Java and uses the PostgreSQL database. The web application requires Apache Tomcat. For more details on requirements see: http://www.intermine.org/wiki/Prerequisites
Documentation
Documentation is available at: http://www.intermine.org/
For a quick tour of the web application features go to FlyMine and click 'Take a tour'.
Presentations
- InterMine and Chado by Richard Smith at the July 2008 GMOD Meeting.
- Presentation on InterMine by Gos Micklem at the GMOD Middleware meeting that happened at the January 2007 GMOD Meeting. This presentation is also available as a wiki page.
Contact
| Mailing List Link | Description | Archive(s) | |
|---|---|---|---|
| InterMine | dev | InterMine support and development list. | InterMine, Nabble (2010/05+) |
Some Interesting Email Threads
- Status of BioMart integration - 2010/09, Josh Goodman, Richard Smith
Downloads
All code is released under the LGPL license and is available in subversion.
Logo
The InterMine logo was created by Sean O'Connell, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.
| Available on platform | web + |
| Has URL | https://github.com/intermine/intermine.git +, http://www.intermine.org +, http://www.flymine.org +, http://yeastmine.yeastgenome.org/ +, http://www.mousemine.org/ +, http://ratmine.mcw.edu/ +, http://zmine.zfin.org/ + and http://www.wormbase.org/tools/wormmine + |
| Has description | InterMine makes it easy to integrate multi … InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the Sequence Ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Currently supported formats include Chado, GFF3, FASTA, GO and gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, UniProt, and many others. A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded.the web app can be configured and branded. + and InterMine should always be checked out in source code form + |
| Has development status | active + |
| Has input format | Chado +, GFF3 +, FASTA +, GO ontology files +, GO gene association files +, UniProt XML +, PSI XML (protein interactions) +, InParanoid orthologs +, Ensembl +, Uniprot + and and many others. Custom formats can be supported through the data-source framework. + |
| Has licence | LGPL + |
| Has logo | InterMineLogo.png + |
| Has output format | Flat files (tsv +, csv) +, JSON +, XML +, GFF3 +, BED + and FASTA + |
| Has software maturity status | mature + |
| Has support status | active + |
| Has title | InterMine source at GitHub +, FlyMine +, YeastMine +, MouseMine +, RatMine +, ZMine + and WormMine + |
| Has topic | InterMine + |
| Interaction type | consumes data from +, can provide data for + and uses library for processing and loading data + |
| Interactor | InterMine + |
| Interacts with | Chado +, JBrowse +, GBrowse +, Galaxy + and Pathway Tools + |
| Is open source | Yes + |
| Link type | download +, source code +, website + and wild URL + |
| Release date | 1 January 2002 + |
| Tool functionality or classification | Database tools + |
| Written in language | Java + |
| Has subobjectThis property is a special property in this wiki. | InterMine#https://github.com/intermine/intermine.git +, InterMine#http://www.intermine.org +, InterMine#http://www.flymine.org +, InterMine#http://yeastmine.yeastgenome.org/ +, InterMine#http://www.mousemine.org/ +, InterMine#http://ratmine.mcw.edu/ +, InterMine#http://zmine.zfin.org/ +, InterMine#http://www.wormbase.org/tools/wormmine +, InterMine +, InterMine +, InterMine +, InterMine + and InterMine + |
