InterMine is an

open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

data warehouse system, licensed under the LGPL 2.1. InterMine is used to create databases of biological data accessed by sophisticated web query tools. InterMine can be used to create databases from a single data set or can integrate multiple sources of data. Support is provided for several common biological formats and there is a framework for adding other data. InterMine includes a user-friendly web interface that works 'out of the box' and can be easily customised. InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the

sequence ontology The Sequence Ontology (SO) is an ontology In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped int ...

and supports several biological data formats, allowing sysadmins to configure which organisms or data files are required. It is easy to extend the data model and integrate other data, with a web service API, clients in seven different languages, and an

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. T ...

format to help import custom data. As an active open source project, InterMine maintains
developer mailing list
and thoroug
developer
an
user documentation

Supported data formats

Chado The Japanese tea ceremony (known as or ) is a Japanese cultural activity involving the ceremonial preparation and presentation of , powdered green tea, the procedure of which is called . While in the West it is known as "tea ceremony", it is sel ...

GFF3 In bioinformatics, the general feature format (gene-finding format, generic feature format, GFF) is a file format used for describing genes and other features of DNA, RNA and protein sequences. GFF Versions The following versions of GFF exist: ...

FASTA FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...

* GO & gene association files *

UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from ...

XML * PSI XML (protein interactions,

Protein Structure Initiative The Protein Structure Initiative (PSI) was a USA based project that aimed at accelerating discovery in structural genomics and contribute to understanding biological function. Funded by the U.S. National Institute of General Medical Sciences (NIGMS ...

) * InParanoid orthologs *

Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...

Clients

Web clients allow users to access the data programatically with minimal effort, and are available fo
perlpythonrubyjavascriptJava
an
R
Data can also be queried via
native Android app

Web application

The InterMine web application allows creation of custom bioinformatics queries, includes template queries (web forms to run 'canned' queries). Users can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded.

Current projects (not exhaustive list)

An up-to-date list of projects can be viewed at th
InterMine Registry
*

Generic Model Organism Database The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the Unit ...

modENCODE

FlyMine

HumanMine

RatMine

YeastMine

TargetMine

MitoMiner

MouseMine

ZebrafishMine

WormMine

INDIGO

ThaleMine

TargetMine

PhytoMine

MedicMine

BovineMine

HymenopteraMine

SoyMine

BeanMine

ChickpeaMine

LegumeMine

PeanutMine

Shaare

Wheat3Bmine

PlanMine

GrapeMine

RepetDB

XenMine

CHOMine

References

{{Reflist

External links

InterMine

Department of Genetics, University of Cambridge

Wellcome Trust

InterMine API Documentation
Bioinformatics software Biological databases Data warehousing products Genetics in the United Kingdom Science and technology in Cambridgeshire South Cambridgeshire District