d3b-center/diseasexpress-rest-api

Rest API for disease express

d3b-disease-express-rest-api

Rest API for disease express

Build and Deploy(after clone)

1. docker build -t disease-express:latest .
2. docker run -p 80:80 --e MONGO_URI=<mongo_uri> --e MONGO_DATABASE=<database> --name disease-express disease-express

example docker run -p 8080:80 -e JAVA_OPTS="-Xms1g" --e MONGO_URI=mongodb://host.docker.internal:27017 --e MONGO_DATABASE=disease_express --name disease-express disease-express

Queries

1. Give me all sample annotation & RSEM value data where symbol is GPC2

   This is done in two api calls

   • curl -X GET 'http://disease-express.dev.cavatica-dns.org/api/v1/samples' -H 'accept: application/json'
   • curl -X GET 'http://disease-express.dev.cavatica-dns.org/api/v1/data/genes/symbols/GPC2/normalizations/rsem' -H 'accept: text/tab-separated-values'

2. Give me all TPM data where transcript_id is ENST00000292377.3 for samples that have disease is ALL

   • curl -X POST 'http://disease-express.dev.cavatica-dns.org/api/v1/tags/data/transcripts/ids/ENST00000292377.3/normalizations/sample_abundance,sample_rsem_isoform' -H 'accept: text/tab-separated-values' -H "Content-Type: application/json" -d '{"$eq":{"disease": "ALL"}}'

3. Give me all sample annotation & TPM & FPKM value data for a subset of genes (gene symbol is in GPC2, MYCN, ALK) in study TARGET that have mycn_status is amplified?

   This is done in two api calls

   • curl -X GET 'http://disease-express.dev.cavatica-dns.org/api/v1/samples' -H 'accept: application/json'
   • curl -X POST 'http://disease-express.dev.cavatica-dns.org/api/v1/tags/data/genes/symbols/GPC2,MYCN,ALK/normalizations/rsem,sample_abundance,sample_rsem_isoform?projection=summary' -H 'accept: text/tab-separated-values' -H 'Content-Type: application/json' -d '{"$and":[{"$eq":{"study":"TARGET"}},{"$eq":{"mycn_status":"amplified"}}]}'

4. Give me all sample annotation and RSEM value for all genes where study is ‘TCGA’ AND disease is ‘THCA’ AND disease_subtype is ‘Papillary Thyroid Cancer’ AND definition is ‘Primary Solid Tumor’ AND extrathyroid_invasion_stage is T4a.

   This is done in two api calls

   • curl -X GET 'http://disease-express.dev.cavatica-dns.org/api/v1/samples' -H 'accept: application/json'
   • curl -X POST 'http://disease-express.dev.cavatica-dns.org/api/v1/data/normalizations/rsem?projection=summary' -H 'accept: text/tab-separated-values' -H 'Content-Type: application/json' -d '{"$and":[{"$eq":{"study":"TCGA"}},{"$eq":{"disease":"THCA"}},{"$eq":{"disease_subtype":"Papillary Thyroid Cancer"}},{"$eq":{"definition":"Primary Solid Tumor"}},{"$eq":{"extrathyroid_invasion_stage":"T4a"}}]}'

5. Give me all samples where mycn_status is amplified AND risk is high.

   • curl -X POST 'http://disease-express.dev.cavatica-dns.org/api/v1/data/normalizations/rsem,sample_abundance,sample_rsem_isoform?projection=summary' -H 'accept: text/tab-separated-values' -H 'Content-Type: application/json' -d '{"$and":[{"$eq":{"risk":"high"}},{"$eq":{"mycn_status":"amplified"}}]}'

6. I would like to get all data where disease is ALL AND gender is male AND cns_status is 2.

   • curl -X POST 'http://disease-express.dev.cavatica-dns.org/api/v1/data/normalizations/rsem,sample_abundance,sample_rsem_isoform?projection=summary' -H 'accept: text/tab-separated-values' -H 'Content-Type: application/json' -d '{"$and":[{"$eq":{"disease":"ALL"}},{"$eq":{"gender":"male"}}, {"$eq":{"cns_status":2}}]}'

7. Give me sample, clinical annotation and RSEM value for all genes where study in [‘TCGA’, ‘TARGET’] AND rsem > 50 AND gender is female.

   • TODO

8. Give me all FPKM data for all genes where disease is NBL AND definition is Primary Solid Tumor AND mycn_status is amplified.

   • curl -X POST 'http://disease-express.dev.cavatica-dns.org/api/v1/data/normalizations/rsem?projection=summary' -H 'accept: text/tab-separated-values' -H 'Content-Type: application/json' -d '{"$and":[{"$eq":{"disease":"NBL"}},{"$eq":{"definition":"Primary Solid Tumor"}}, {"$eq":{"mycn_status":"amplified"}}]}'

Note: Check Notes.md for additional information about disease-express

diseasexpress-rest-api's Issues

Get sample Source file from config properties

diseaseXpress-rest-api/app/de/dao/SamplesDAO.scala

Line 30 in 7313db0

Source

Add search api for gene symbol

Normalize "Definition" clinical attribute

Support pagination and sorting