EPICO / BLUEPRINT Data Analysis Portal REST API

This API is needed by EPICO / BLUEPRINT Data Analysis Portal version 1.0 and later.

Installation procedures (dependencies, Apache setup, etc...) are available at INSTALL.md.

Endpoints

• GET / It returns the ids of available domains, along with a brief description

• GET /{domain} It returns the domain information, if it could be instantiated

• GET /{domain}/model It returns the model, in JSON format (if applicable)

• GET /{domain}/model/CV It returns the list of controlled vocabularies related to the model.

• POST /{domain}/model/CV/terms It returns all the terms from the controlled vocabularies, filtered by input terms. If the input is empty, it returns an empty array.

• GET /{domain}/model/CV/{cv_id} It returns a brief description of this controlled vocabulary

• GET /{domain}/model/CV/{cv_id}/terms It returns the terms for given CV id (disease,tissue,cell)

• POST /{domain}/model/CV/{cv_id}/terms It returns the terms for given CV id (disease,tissue,cell), filtered by input terms

• GET /{domain}/model/CV/{conceptDomain}/{concept}/{column} It returns all the controlled vocabularies associated to the column

• GET /{domain}/model/CV/{conceptDomain}/{concept}/{column}/terms It returns all the terms from the controlled vocabularies associated to the column

• POST /{domain}/model/CV/{conceptDomain}/{concept}/{column}/terms It returns all the terms from the controlled vocabularies associated to the column, filtered by input terms

• GET /{domain}/sdata It returns the identifiers of all the donors, specimens, samples and experiments registered in the database.

• GET /{domain}/sdata/_all It returns all the donors, specimens, samples and experiments registered in the database.

• GET /{domain}/sdata/donor It returns the identifiers of all the registered donors.

• GET /{domain}/sdata/donor/{donor_id} It returns the donor whose donor id is this. Special '_all' donor id returns all the donors.

• GET /{domain}/sdata/specimen It returns the identifiers of all the registered specimens.

• GET /{domain}/sdata/specimen/{specimen_id} It returns the specimen whose specimen id is this. Special '_all' specimen id returns all the specimens.

• GET /{domain}/sdata/sample It returns the identifiers of all the registered samples.

• GET /{domain}/sdata/sample/{sample_id} It returns the sample whose sample id is this. Special '_all' sample id returns all the samples.

• GET /{domain}/sdata/experiment It returns the identifiers of all the registered experiments.

• GET /{domain}/sdata/experiment/{experiment_id} It returns the experiment whose experiment id is this. Special '_all' experiment id returns all the experiments.

• GET /{domain}/analysis/metadata It returns the identifiers of all the registered analysis.

• GET /{domain}/analysis/metadata/{analysis_id} It returns the analysis metadata whose analysis id is this. Special '_all' analysis id returns all the analysis.

• GET /{domain}/analysis/data/{chromosome}/{chromosome_start}/{chromosome_end}

• GET /{domain}/analysis/data/{chromosome}:{chromosome_start}-{chromosome_end} It returns the results which are in this range

• GET /{domain}/analysis/data/{chromosome}/{chromosome_start}/{chromosome_end}/stream

• GET /{domain}/analysis/data/{chromosome}:{chromosome_start}-{chromosome_end}/stream It returns a handler to fetch results chunk by chunk

• POST /{domain}/analysis/data/fetchStream Sending the handler receive with previous call, you are fetching the results chunk by chunk

• GET /{domain}/analysis/data/{chromosome}/{chromosome_start}/{chromosome_end}/count

• GET /{domain}/analysis/data/{chromosome}:{chromosome_start}-{chromosome_end}/count It counts the number of related results per analysis

• GET /{domain}/analysis/data/{chromosome}/{chromosome_start}/{chromosome_end}/stats

• GET /{domain}/analysis/data/{chromosome}:{chromosome_start}-{chromosome_end}/stats It gives detailed stats (only for BLUEPRINT)

• GET /{domain}/genomic_layout/{chromosome}/{chromosome_start}/{chromosome_end}

• GET /{domain}/genomic_layout/{chromosome}:{chromosome_start}-{chromosome_end} It returns the genomic layout features found in the range

• GET /{domain}/features?q= It returns the features, their types and their coordinates matching the input query (which can be an identifier, for instance)

• GET /{domain}/features/suggest?q= It returns the features suggested by the input prefix query (useful for autocompletion)

Next methods expect a tabular input, and return tables. They can be called from command line like this:

curl -X POST -T 'identifiers.txt' -o results.txt http://localhost:5000/EPICO:2016-08/analysis/query/gene_expression/byAnalyses

• POST /{domain}/analysis/query/gene_expression/byDonors

• GET /{domain}/analysis/query/gene_expression/byDonors/{donor_id}

• POST /{domain}/analysis/query/gene_expression/bySamples

• GET /{domain}/analysis/query/gene_expression/bySamples/{sample_id}

• POST /{domain}/analysis/query/gene_expression/byExperiments

• GET /{domain}/analysis/query/gene_expression/byExperiments/{experiment_id}

• POST /{domain}/analysis/query/gene_expression/byAnalyses

• GET /{domain}/analysis/query/gene_expression/byAnalyses/{analysis_id}

• POST /{domain}/analysis/query/regulatory_regions/byDonors

• GET /{domain}/analysis/query/regulatory_regions/byDonors/{donor_id}

• POST /{domain}/analysis/query/regulatory_regions/bySamples

• GET /{domain}/analysis/query/regulatory_regions/bySamples/{sample_id}

• POST /{domain}/analysis/query/regulatory_regions/byExperiments

• GET /{domain}/analysis/query/regulatory_regions/byExperiments/{experiment_id}

• POST /{domain}/analysis/query/regulatory_regions/byAnalyses

• GET /{domain}/analysis/query/regulatory_regions/byAnalyses/{analysis_id}