InterMine statistics

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InterMine specifications

Information


Unique identifier OMICS_03840
Name InterMine
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Javascript, Perl, Other
License GNU Lesser General Public License version 2.1
Computer skills Medium
Version 1.8.3
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/InterMine

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Documentation


Maintainers


  • person_outline Gos Micklem <>
  • person_outline InterMine Team <>

Additional information


Tuto: http://intermine.readthedocs.io/en/latest/get-started/tutorial/

Publication for InterMine

InterMine in publications

 (45)
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] plaza), gene/chromosome synteny (coge, pgdd, phytozome, plaza, pgsb), protein domains (plantgdb, phytozome, ensemblplant), gene expression (phytozome, pgsb), biomart (phytozome, ensemblplants), intermine (phytozome), go annotation (phytozome, ensemblplants, plaza, pgsb), alternative splicing (ensemblplants, plantgdb)., although these comprehensive databases contain a large array of species, […]

PMCID: 5829562
PMID: 29688362
DOI: 10.1093/database/bay007

[…] as dna binding site motifs and protein domains. as with other data types at sgd, all regulatory relationships and accompanying data are available through yeastmine, sgd’s data warehouse based on intermine., database url: http://www.yeastgenome.org, the saccharomyces genome database (sgd; http://www.yeastgenome.org) collects and organizes scientific information regarding the genes, proteins […]

PMCID: 5825174
PMID: 29432412
DOI: 10.1371/journal.pcbi.1005989

[…] these annotations were assigned to individual neurons using the anatomical hierarchy defined in wormbase, which we retrieved using the wormbase api (wormmine: intermine.wormbase.org) [], propagating each term down the hierarchy to individual neurons. we manually corrected the assignment of twelve head neurons (ala, avfl, avfr, avg, rifl, rifr, rigl, rigr, […]

PMCID: 5784609
PMID: 29368663
DOI: 10.1186/s13059-017-1369-x

[…] s1 (10.15252/embj.201488769); differential gene expression data for cgh-1 mutant [], additional file 2: table s1 (10.1371/journal.pgen.1002742.s008); previous c. elegans 3′utr studies [] (http://intermine.modencode.org/release-33/experiment.do?experiment=encyclopedia%20of%20c.%20elegans%203%27utrs%20and%20their%20regulatory%20elements), and [], supplementary dataset 2 […]

PMCID: 5741632
PMID: 29273756
DOI: 10.1038/s41467-017-02385-4

[…] encoding transcription factors were determined via a previously published list of all predicted and annotated drosophila transcription factors. all gene ontogeny analysis was carried out using the intermine perl api. lists of all genes annotated with a go term and associated child terms were obtained from the ebi quickgo site (http://www.ebi.ac.uk/quickgo/)., all p-values listed in the text […]


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InterMine institution(s)
Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK; Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK
InterMine funding source(s)
Supported by Wellcome Trust [099133, 090297]; National Human Genome Research Institute [R01HG004834, U41HG004269].

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