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InterMine Data Browser: a tool for exploring semi-homogeneous biological datasets
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README.md

InterMine Data Browser

Build Status (Travis CI):

The goal of this project, is to implement a faceted search tool to display the data from InterMine database, allowing the users to search easily within the different mines available around InterMine. without the requirement of having an extensive knowledge of the data model.

For the project organization, please refer to https://github.com/intermine

Please note that development is very early on and the project is not ready to use yet.

DEPLOYMENT

Try it out with the Heroku deployment (automatic deployment, may have some delay): http://im-browser-prototype.herokuapp.com/

DEPENDENCIES

Check package.json

BUILDING

See BUILD.md

DOCUMENTATION

Apart from the in-line comments in the code, documentation generated with documentation.js is available in https://adrianbzg.github.io/InterMine-Data-Browser-Tool/. To update the documentation, the 'gulp documentation' is available.

REQUIRED ONTOLOGY CONCEPTS (PER MINE) FOR EACH FILTER

Filter Ontology concepts
GO Annotation goAnnotation.ontologyTerm.name
Dataset Name dataSets.name
Pathway Name pathways.name
Organism short name Gene.organism.shortName
Location locations.start + locations.end + locations.locatedOn.primaryIdentifier
Diseases (OMIM) diseases.name
ClinVar alleles.clinicalSignificance + alleles.type
Protein Localisation proteinAtlasExpression.cellType + proteinAtlasExpression.tissue.name + proteinAtlasExpression.expressionType + proteinAtlasExpression.level + proteinAtlasExpression.reliability
Protein Domain Name proteins.proteinDomainRegions.proteinDomain.name
Interactions interactions.participant2.symbol + interactions.details.type + interactions.details.dataSets.name
Expression atlasExpression.pValue + atlasExpression.tStatistic + atlasExpression.expression + atlasExpression.dataSets.name

CONTRIBUTING

  1. Find a thing to fix/implement in Issues or come up with your own idea, create a discussion issue for it and get a feedback.
  2. Fork the repo
  3. Create your feature branch (git checkout -b my-new-feature)
  4. Commit your changes (git commit -am 'Add some feature')
  5. Push to the branch (git push origin my-new-feature)
  6. Create new Pull Request

CONTACT

You can contact the developers by opening an issue in this repo.

SCREENSHOTS

Searching in HumanMine (Release 1.0.8)

Searching in HumanMine for Alzheimer disease (Release 1.0.8)

Searching in FlyMine (Release 1.0.8)

Searching in HymenopteraMine (Release 1.0.8)

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