NOTE: We are working on migrating this site away from MediaWiki, so editing pages will be disabled for now.
InterMine
- Mature release
- Development: active
- Support: active
Contents
About InterMine
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.
Visit the InterMine website.
Downloads
Publications, Tutorials, and Presentations
Publications on or mentioning InterMine
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics. 2012 Dec 1;28(23):3163-5. doi: 10.1093/bioinformatics/bts577. Epub 2012 Sep 27. PubMed PMID: 23023984; PubMed Central PMCID: PMC3516146.
Sullivan J, Karra K, Moxon SA, Vallejos A, Motenko H, Wong JD, Aleksic J, Balakrishnan R, Binkley G, Harris T, Hitz B, Jayaraman P, Lyne R, Neuhauser S, Pich C, Smith RN, Trinh Q, Cherry JM, Richardson J, Stein L, Twigger S, Westerfield M, Worthey E, Micklem G. InterMOD: integrated data and tools for the unification of model organism research. Sci Rep. 2013;3:1802. doi: 10.1038/srep01802. PubMed PMID: 23652793; PubMed Central PMCID: PMC3647165.
Nucleic Acids Res. 2012 January; 40(D1): D1082–D1088. Published online 2011 November 12. doi: 10.1093/nar/gkr921 PMCID: PMC3245176 modMine: flexible access to modENCODE data Sergio Contrino, Richard N. Smith, Daniela Butano, Adrian Carr, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Alex Kalderimis, Julie Sullivan, Seth Carbon, Ellen T. Kephart, Paul Lloyd, E. O. Stinson, Nicole L. Washington, Marc D. Perry, Peter Ruzanov, Zheng Zha, Suzanna E. Lewis, Lincoln D. Stein and Gos Micklem
Contacts and Mailing Lists
InterMine in the wild
Public installations of InterMine:
More on InterMine
| 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 +, Python + and JavaScript + |
| 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 + |
