Difference between revisions of "InterMine"

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m (adding interactions)
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{{Tool data
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|name=InterMine
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|status=mature
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|dev=active
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|support=active
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|type=Database tools
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|platform=web
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|about=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.
 +
|open source=Yes
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|licence=[http://opensource.org/licenses/LGPL-3.0 LGPL]
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|input=Chado, [[GFF3]], [[FASTA]], GO ontology files, GO gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, Uniprot, and many others. Custom formats can be supported through the data-source framework.
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|output=Flat files (tsv, csv), JSON, XML, GFF3, BED, FASTA
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|language=Java
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|release date=2002/01/01
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|logo=InterMineLogo.png
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|papers=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
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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
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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
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|dl tracking=We record download statistics through github
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|contact email=[alex@intermine.org Alex Kalderimis], [info@intermine.org General InterMine contact]
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|dev status=
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}}
 
[[File:InterMineLogo.png|center|InterMine]]
 
[[File:InterMineLogo.png|center|InterMine]]
  
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The [[:Image:InterMineLogo.png|InterMine logo]] was created by Sean O'Connell, a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linn-benton.edu Linn-Benton Community College].
 
The [[:Image:InterMineLogo.png|InterMine logo]] was created by Sean O'Connell, a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linn-benton.edu Linn-Benton Community College].
  
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{{Tool data
 
−
|name=InterMine
 
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|full name=
 
−
|status=mature
 
−
|dev=active
 
−
|support=active
 
−
|type=Database tools
 
−
|platform=web
 
−
|about=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.
 
−
|release date=2002
 
−
|open source=Yes
 
−
|licence=[http://opensource.org/licenses/LGPL-3.0 LGPL]
 
−
|language=Java
 
−
|input=Chado, [[GFF3]], [[FASTA]], GO ontology files, GO gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl, Uniprot, and many others. Custom formats can be supported through the data-source framework.
 
−
|output=Flat files (tsv, csv), JSON, XML, GFF3, BED, FASTA
 
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|audience=
 
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|logo=InterMineLogo.png
 
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|screenshot=
 
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|mail=
 
−
|contact email=[alex@intermine.org Alex Kalderimis], [info@intermine.org General InterMine contact]
 
−
|papers=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
 
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|presentations=
 
−
|tutorials=
 
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|getting started preamble=
 
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|req=
 
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|install=
 
−
|config=
 
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|doc=
 
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|dev ppl=
 
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|dev status=
 
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|dl tracking=We record download statistics through github
 
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|logo info=
 
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|see also=
 
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|extra=
 
−
}}
 
  
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[[Category:Database Tools]]
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[[Category:InterMine]]
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[[Category:GMOD Components]]
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[[Category:Java]]
 +
[[Category:GMOD Component]]
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=https://github.com/intermine/intermine.git
 
|linkurl=https://github.com/intermine/intermine.git
 +
|linktitle=InterMine source at GitHub
 
|linktype=download
 
|linktype=download
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|linktitle=InterMine source at GitHub
 
 
|linkdesc=InterMine should always be checked out in source code form
 
|linkdesc=InterMine should always be checked out in source code form
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=https://github.com/intermine/intermine.git
 
|linkurl=https://github.com/intermine/intermine.git
 
|linktype=source code
 
|linktype=source code
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://www.intermine.org
 
|linkurl=http://www.intermine.org
 
|linktype=website
 
|linktype=website
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://www.flymine.org
 
|linkurl=http://www.flymine.org
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|linktype=wild URL
 
 
|linktitle=FlyMine
 
|linktitle=FlyMine
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|linktype=wild URL
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://yeastmine.yeastgenome.org/
 
|linkurl=http://yeastmine.yeastgenome.org/
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|linktitle=YeastMine
 
|linktype=wild URL
 
|linktype=wild URL
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|linktitle=YeastMine
 
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://www.mousemine.org/
 
|linkurl=http://www.mousemine.org/
 +
|linktitle=MouseMine
 
|linktype=wild URL
 
|linktype=wild URL
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|linktitle=MouseMine
 
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://ratmine.mcw.edu/
 
|linkurl=http://ratmine.mcw.edu/
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|linktype=wild URL
 
 
|linktitle=RatMine
 
|linktitle=RatMine
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|linktype=wild URL
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://zmine.zfin.org/
 
|linkurl=http://zmine.zfin.org/
 +
|linktitle=ZMine
 
|linktype=wild URL
 
|linktype=wild URL
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|linktitle=ZMine
 
 
}}
 
}}
−
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://www.wormbase.org/tools/wormmine
 
|linkurl=http://www.wormbase.org/tools/wormmine
 +
|linktitle=WormMine
 
|linktype=wild URL
 
|linktype=wild URL
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|linktitle=WormMine
 
 
}}
 
}}
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{{InteroperableComponent
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[[Category:Database Tools]]
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|relationship=consumes data from
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[[Category:InterMine]]
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|object=Chado
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[[Category:GMOD Components]]
+
}}
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[[Category:Java]]
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{{InteroperableComponent
−
[[Category:GMOD Component]]
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|relationship=can provide data for
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|object=JBrowse
 +
}}
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{{InteroperableComponent
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|relationship=can provide data for
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|object=GBrowse
 +
}}
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{{InteroperableComponent
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|relationship=can provide data for
 +
|object=Galaxy
 +
}}
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{{InteroperableComponent
 +
|relationship=uses library for processing and loading data
 +
|object=Pathway Tools
 +
}}

Revision as of 23:43, 15 October 2013

InterMine


Status
  • Mature release
  • Active development
  • Active support
Resources

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.

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

Contact

Mailing List Link Description Archive(s)
InterMine dev InterMine support and development list. InterMine, Nabble (2010/05+)

Some Interesting Email Threads

Downloads

All code is released under the LGPL license and is available in subversion.

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.

Retrieved from "http://gmod.org/mediawiki/index.php?title=InterMine&oldid=24714"
Facts about "InterMine"RDF feed
Available on platformweb +
Has URLhttps://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 descriptionInterMine 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 statusactive +
Has input formatChado +, 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 licenceLGPL +
Has logoInterMineLogo.png +
Has output formatFlat files (tsv +, csv) +, JSON +, XML +, GFF3 +, BED + and FASTA +
Has software maturity statusmature +
Has support statusactive +
Has titleInterMine source at GitHub +, FlyMine +, YeastMine +, MouseMine +, RatMine +, ZMine + and WormMine +
Has topicInterMine +
Interaction typeconsumes data from +, can provide data for + and uses library for processing and loading data +
InteractorInterMine +
Interacts withChado +, JBrowse +, GBrowse +, Galaxy + and Pathway Tools +
Is open sourceYes +
Link typedownload +, source code +, website + and wild URL +
Release date1 January 2002 +
Tool functionality or classificationDatabase tools +
Written in languageJava +
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 +