shivanigangadharan / InterMine-Data-Browser-Tool

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

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 InterMine

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

DEPLOYMENT

Try it out with the Heroku deployment here (automatic deployment, may have some delay)

GETTING STARTED

Please visit Getting Started

DEPENDENCIES

Check package.json file

DOCUMENTATION

Apart from the in-line comments in the code, documentation generated with documentation.js can be accessed here. 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 GUIDELINES

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 repository.

3. Create your new feature branch.

   git checkout -b my-new-feature

4. Commit your changes.

   git commit -am 'Add some feature

5. Push to the newly created feature branch.

   git push origin my-new-feature

6. Create a new Pull Request

CONTACT

You can contact the developers by opening a new issue in this repository here.

SCREENSHOTS

Searching in HumanMine (Release 1.1.0)

Searching in HumanMine for Alzheimer disease (Release 1.1.0)

Searching in FlyMine (Release 1.1.0)

Searching in HymenopteraMine (Release 1.1.0)