Micklem Lab

University of Cambridge

Resources

InterMine

An open source data warehouse system, produced by the Micklem Lab. Created specifically with the challenges of large scale biological data integration in mind, InterMine offers an easily extensible data model, optimised flexible querying, a user-friendly web interface and web service APIs for programmatic data access, as well as statistical analysis tools. Find out more at www.intermine.org, or get the code on GitHub.

FlyMine

A data warehouse of integrated fruit fly and other insect genetic, genomic and proteomic data, developed by the Micklem Lab using the InterMine data warehouse framework. It provides access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists. The datasets range from gene and protein annotations to pathways, homology, interactions, a range of ontologies, gene expression, regulation and diseases among others.

metabolicMine

A data warehouse targeted at the metabolic disease community. Developed by the Micklem Lab in collaboration with leading UK metabolic disease groups, metabolicMine integrates disease datasets from a range of experiments and model organisms alongside tools for exploring them, enabling the metabolic research community to search across domains of biological knowledge. The current version brings together information covering genes, proteins, orthologues, interactions, expression, pathways, ontologies, diseases, GWAS and SNPs. While the emphasis is on human data, key datasets from mouse and rat are included.

mitoMiner

A data warehouse of mitochondrial proteomics data for a range of organisms, developed by Alan Robinson's group at the MRC Mitochondrial Biology Unit based on the InterMine framework. The purpose of this data warehouse is to facilitate storage and analysis of mitochondrial proteomics data gathered from publications of mass spectrometry and green fluorescent protein tagging studies. In MitoMiner, these data are integrated with data from UniProt, Gene Ontology, Online Mendelian Inheritance in Man, HomoloGene, Kyoto Encyclopaedia of Genes and Genomes and PubMed.

modMine

The modENCODE project data warehouse, developed by the Micklem Lab as part of the modENCODE Data Coordination Centre. The aim of the modENCODE project was to characterise functional elements in the genomes of the model organisms Drosophila and C. elegans. modMine provides users with access to tools for data browsing and basic analysis, and a range of datasets generated by modENCODE can be downloaded from there. These include a wide range of genomics experiments such as ChIP-seq and gene expression profiling, as well as studies focusing on gene and chromatin structure, replication and copy number variation.

MouseMine

An integrated data warehouse of mouse genomic data. This data warehouse has been developed by Joel Richardson's group at the mouse model organism database MGI, as part of the InterMOD project – an initiative to set up InterMine databases which can interoperate for a number of major model organisms, including nematode worm, budding yeast, fruit fly, rat, mouse, zebrafish and human.

RatMine

An integrated data warehouse of rat genomic data. This data warehouse has been developed first by Simon Twigger's group, and now by Liz Worthey's group at the model organism database RGD. It is part of the InterMOD project – an initiative to set up interoperability links between datasets from a number of major model organisms, including nematode worm, budding yeast, fruit fly, rat, mouse, zebrafish and human.

TargetMine

A data warehouse for candidate gene prioritisation and drug target discovery. This data warehouse has been developed by Kenji Mizuguchi's lab at NIBIO, Japan, in order to facilitate a more efficient prioritisation of candidate genes for further exploration in biomedical studies, based on an integrated data approach. TargetMine utilises the InterMine framework, with new data models such as protein-DNA interactions integrated in a novel way. It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data.

WormMine

An integrated data warehouse of yeast genomic data. This data warehouse has been developed by Lincoln Stein's group/WormBase as part of the InterMOD project, an initiative to set up interoperation between datasets from a number of major model organisms, including nematode worm, budding yeast, fruit fly, rat, mouse, zebrafish and human.

YeastMine

An integrated data warehouse of yeast genomic data. This data warehouse has been developed by the Cherry group at the model organism database Saccharomyces Genome Database, as part of the InterMOD project, an initiative to set up interoperation between datasets from a number of major model organisms, including nematode worm, budding yeast, fruit fly, rat, mouse, zebrafish and human. YeastMine is also available as an iPhone app, Yeast Genome.