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Citations per year

Number of citations per year for the bioinformatics software tool InterMine
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Protocols

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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Versioning


No version available

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 citations

 (76)
library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] zome, 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, th […]

library_books

JAMI: a Java library for molecular interactions and data interoperability

2018
BMC Bioinformatics
PMCID: 5896107
PMID: 29642846
DOI: 10.1186/s12859-018-2119-0

[…] JSON modules for exporting publications, experiments, interactions and complexes in the relevant formats. This application integrates the ComplexViewer described in the previous section, and like the InterMine use case, it is fed by the JAMI-JSON module. Using JAMI-UNIPROT and JAMI-CHEBI, the editor can import proteins from UniProtKB and small molecules from ChEBI. Similarly, the use of a publicat […]

library_books

Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome

2018
PLoS Comput Biol
PMCID: 5825174
PMID: 29432412
DOI: 10.1371/journal.pcbi.1005989

[…] /ONTOLOGY/anatomy_association.WS256.wb). 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, S […]

library_books

Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

2018
Genome Biol
PMCID: 5784609
PMID: 29368663
DOI: 10.1186/s13059-017-1369-x

[…] able 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 (https://www.ncbi.nlm.ni […]

call_split

Chromatin state changes during neural development revealed by in vivo cell type specific profiling

2017
Nat Commun
PMCID: 5741632
PMID: 29273756
DOI: 10.1038/s41467-017-02385-4
call_split See protocol

[…] es 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 are H […]

library_books

Update notifications for the BioCyc collection of databases

2017
PMCID: 5691348
PMID: 29220477
DOI: 10.1093/database/bax086

[…] imilar issues. They typically issue news announcements when notable or significant data updates are available, but these announcements are not targeted to individual user interests. MODs that use the InterMine platform () enable users to save searches and lists of objects of interest to facilitate regular checks, but they still rely on the user returning to re-execute searches and to check for new […]


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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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