Difference between revisions of "InterMine"
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− | = | + | <div style="float:right; padding:0.5em">{{#icon: InterMine.png|InterMine||http://www.intermine.org}}</div> |
− | 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: | + | [http://www.intermine.org/ 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 [Glossary#XML 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 | * [[Chado]], GFF3, FASTA, GO & gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl | ||
− | 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. | + | 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. |
− | 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 [http://www.modencode.org/ modENCODE] project to import genome annotation from FlyBase and WormBase [[Chado]] databases. More information: http://www.intermine.org/wiki/ChadoDBSource | + | 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 [http://www.modencode.org/ modENCODE] project to import genome annotation from [[:Category:FlyBase FlyBase]] and [[:Category:WormBase WormBase]] [[Chado]] databases. More information: http://www.intermine.org/wiki/ChadoDBSource |
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[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
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Revision as of 22:32, 13 October 2008
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 [Glossary#XML 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
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.
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 Category:FlyBase FlyBase and Category:WormBase 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'.
Contact
If you have any questions about using InterMine, contact the FlyMine/InterMine team by e-mail: dev[at]flymine.org
Downloads
All code is released under the LGPL license and is available in subversion.