InterMine: extensive web services for modern biology.

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

modMine: flexible access to modENCODE data.

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine

Forever in Bluegenes: BlueGenes / InterMine Poster for BOSC 2017

<p>The plight of the computational biologist, or indeed any data scientist, often boils down to data: data may be badly formatted, missing information, hard to access and hard to integrate with other sources. Similarly, user interfaces designed for data analysis may not be easy to use, hindering scientific analysis rather than assisting it.</p><p>BlueGenes is designed to facilitate biological data discovery and analysis in a user-friendly and enjoyable way, without requiring that scientists write code or wrangle multiple datasets themselves. Designed as a modern replacement for InterMine’s[1] JSP-powered interface, which traces its origin as far back as 2003, BlueGenes focuses on enhancing user experience using in-page updates, colour-coded data types, and mobile / touch friendliness where possible. Iterative user testing and community feedback is used to enhance usability.</p><p>The data available in BlueGenes is sourced via web services from individual InterMine instances, which are typically comprised of multiple high-quality integrated datasets. Using InterMine as a data source allows BlueGenes to source genomic and proteomic data from the array of biological databases worldwide that run InterMine instances, including model organisms such as the mouse, rat, budding yeast, fruit fly, nematode worm, and thale cress as well as cattle, chinese hamster ovary cells, and many plants.</p><p>BlueGenes is browser-based and runs client-side. The decoupled architecture separates the user interface from the data server, allowing the same front-end instance to seamlessly switch between InterMine data sources. Whilst the core of BlueGenes is programmed in ClojureScript for rapid iterative prototyping purposes, a plugin architecture is currently under development that will allow data analysis and visualisation tools to be seamlessly integrated in native JavaScript. BlueGenes runs on Re-Frame[2], a ClojureScript library based on React.js.</p><p>[1]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. 28(23):3163-5 (2012)</p><p>[2]Thompson, M. Re-Frame: A Reagent Framework For Writing SPAs, in Clojurescript. Zenodo. <a href="http://doi.org/10.5281/zenodo.801613">http://doi.org/10.5281/zenodo.801613</a> (2015)</p><div><br></div

HumanMine: advanced data searching, analysis and cross-species comparison.

HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration and analysis of data compiled from experimental, computational and curated data sources. Built using the InterMine data integration platform, HumanMine includes genes, proteins, pathways, expression levels, Single nucleotide polymorphism (SNP), diseases and more, integrated into a single searchable database. HumanMine promotes integrative analysis, a powerful approach in modern biology that allows many sources of evidence to be analysed together. The data can be accessed through a user-friendly web interface as well as a powerful, scriptable web service Application programming interface (API) to allow programmatic access to data. The web interface includes a useful identifier resolution system, sophisticated query options and interactive results tables that enable powerful exploration of data, including data summaries, filtering, browsing and export. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other biological entities. HumanMine can be used for integrative multistaged analysis that can lead to new insights and uncover previously unknown relationships. Database URL: https://www.humanmine.org

InterMine: extensive web services for modern biology

InterMine (www.intermine.org) is a biological data warehousing system providing extensive automati-cally generated and configurable RESTful web ser-vices that underpin the web interface and can be re-used in many other applications: to find and fil-ter 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 inte-grative and comparative analysis

Making Linked Data SPARQL with the InterMine Biological Data Warehouse

Abstract. InterMine is a system for integrating, analysing, and republishing biological data from multiple sources. It provides access to these data via a web user interface and programmatic web services. However, the precise invocation of services and subsequent exploration of returned data require substantial expertise on the structure of the underlying database. Here, we describe an approach that uses Semantic Web technologies to make InterMine data more broadly accessible and reusable, in accordance with the FAIR principles. We describe a pipeline to extract, transform, and load a Linked Data representation of the InterMine store. We use Docker to bring together SPARQL-aware applications to search, browse, explore, and query the InterMine-based data. Our work therefore extends interoperability of the InterMine platform, and supports new query functionality across InterMine installations and the network of open Linked Data

Cross-organism analysis using InterMine.

InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community