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. 2014 Jul;42(Web Server issue):W468-72.
doi: 10.1093/nar/gku301. Epub 2014 Apr 21.

InterMine: extensive web services for modern biology

Alex Kalderimis  1 , Rachel Lyne  1 , Daniela Butano  1 , Sergio Contrino  1 , Mike Lyne  1 , Joshua Heimbach  1 , Fengyuan Hu  1 , Richard Smith  1 , Radek Stěpán  1 , Julie Sullivan  1 , Gos Micklem  2
Affiliations

InterMine: extensive web services for modern biology

Alex Kalderimis et al. Nucleic Acids Res. 2014 Jul.

Abstract

InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that underpin the web interface and can be re-used in many other applications: to find and filter data; export it in a flexible and structured way; to upload, use, manipulate and analyze lists; to provide services for flexible retrieval of sequence segments, and for other statistical and analysis tools. Here we describe these features and discuss how they can be used separately or in combinations to support integrative and comparative analysis.

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Figures

Figure 1.
Figure 1.
Summary of web services available through InterMine.
Listing A:
Listing A:
Truncated results in JSON format when searching for the keyword ‘eve’. The header of the results of a keyword search includes the facets. ‘Category’ is the summary of the types of data returned and, for each, the number of matching records. In this specific search, no pathways were found so that section is empty. The last facet lists the relevant organisms found.
Listing B:
Listing B:
A. Python code illustrating how a search can be made for features (in this case Introns and Exons) mapped to a defined chromosomal region (in this case Chromosome 2L: 14614843..14619614 from FlyMine). B. Output from the python code (full results are not shown) showing two exons (FBgn0000055:1 Adh:1 and FBgn0000055:4 Adh:4) and two introns from the Adh gene.
Listing C:
Listing C:
A. Python code calculating enrichment statistics for MEDIC (10) ontology terms on a public list of 321 mouse DNA repair genes. The full gene list (Mouse DNA repair genes 6 January 2013) can be viewed at http://www.mousemine.org/mousemine/bag.do?subtab=view. B. The output from the code in (A): MEDIC is a merging of OMIM disease identifiers onto the MeSH disease ontology, thus the output includes MeSH and OMIM terms. Each line displays the MeSH/OMIM ontology term, the ontology ID and the calculated P-value.
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References

    1. Smith R.N, Aleksic J., Butano D., Carr A., Contrino S., Hu F., Lyne M, Lyne R, Kalderimis A, Rutherford K, et al. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics. 2012;28:3163–3165. - PMC - PubMed
    1. Lyne R., Smith R., Rutherford K., Wakeling M., Varley A., Guillier F., Janssens H., Ji W., Mclaren P., North P., et al. FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol. 2007;8:R129. - PMC - PubMed
    1. Balakrishnan R., Park J., Karra K., Hitz B.C., Binkley G., Hong E.L., Sullivan J., Micklem G., Cherry J.M. YeastMine–an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford) 2012:bar062. - PMC - PubMed
    1. Contrino S., Smith R.N., Butano D., Carr A., Hu F., Lyne R., Rutherford K., Kalderimis A., Sullivan J., Carbon S., et al. modMine: flexible access to modENCODE data. Nucleic Acids Res. 2012;40(Database issue):D1082–D1088. - PMC - PubMed
    1. Lyne M., Smith R.N., Lyne R., Aleksic J., Hu F., Kalderimis A., Stepan R., Micklem G. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. Database (Oxford) 2013:bat060. - PMC - PubMed

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