dbgap

dbGaP to bioCADDIE metadata conversion utilities

Introduction

This package contains a general utility that allows you to:

Download study metadata from the dbGaP ftp site by study id.
Convert the study metadata from XML into JSON
Transform the dbGaP JSON into a structure that is compatible with the bioCADDIE study schema, dataset schema and dimension schema
Transform the bioCADDIE compatible JSON into RDF for use in mapping functions.
Transform RDF into bioCADDIE compatible JSON

Installation

Make sure you have a running image of python 3
Enter the appropriate virtual environment

> . myenv/bin/activate
(myenv) >

3a. Install dbgap from github

(myenv) > git clone https://github.com/crDDI/dbgap
(myenv) > cd dbgap
(myenv) > python setup.py install

3b. Install dbgap from PyPi

(myenv) > pip install dbgap

4 . Run download_study

(myenv) > download_study
usage: download_study [-h] [-i [INFILE [INFILE ...]]] [-id INDIR]
                      [-o [OUTFILE [OUTFILE ...]]] [-od OUTDIR] [-f] [-s]
                      [-v VERSION] [-p PVALUE] [--ftproot FTPROOT] [-r RDFDIR]
                      [--logfile LOGFILE]
                      [--loglevel {DEBUG,INFO,WARNING,ERROR}] [--port PORT]
                      [-c CONTEXT]
                      studyid [{d,j,r,a} [{d,j,r,a} ...]]
download_study: error: the following arguments are required: studyid

Use

Transformation description

Downloading XML files

The utility allows any version of any study to be downloaded in XML from the dbGaP XML server

The default download directory is data/<studyid>/xml.

As an example,

(myenv) > download_study 979 d

Creates a data/phs000979/xml directory with the following files:

(myenv) > ls xml
StudyDescription.xml
phs000979.v1.pht005193.v1.Mental_Disorders_Postmortem_Subject.data_dict.xml
phs000979.v1.pht005194.v1.Mental_Disorders_Postmortem_Sample.data_dict.xml
phs000979.v1.pht005195.v1.Mental_Disorders_Postmortem_Subject_Phenotypes.data_dict.xml
phs000979.v1.pht005196.v1.Mental_Disorders_Postmortem_Sample_Attributes.data_dict.xml

Where StudyDescription.xml was downloaded from ftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000979/phs000979.v1.p1/GapExchange_phs000979.v1.p1.xml

and the four data_dict files from ftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000979/phs000979.v1.p1/pheno_variable_summaries/

Converting XML to JSON

This utility uses the Object Management Group (OMG) XML to JSON conversion specification, as implemented in the pyjxslt utility, and loads the result as a first-class python object using the jsonasobj utility. The following transformations are performed on the input data:

Study transformations

The transformations in the table below are implemented by the biocaddie_json method in https://github.com/crDDI/dbgap/blob/master/dbgap/dbgap_study_information.py, and generate bioCADDIE compatible output from a dbGaP Study record:

key	value	Notes
@type	"biocaddie:Study"	This is necessary to establish the type of the entire document
@id	"dbgap:"<study>".v"<version>	This is necessary establish the subject of the entire document
identifierInfo	identifier= "dbgap:"<study>".v"<version>	The bioCaddie schema calls for an identifier/scheme pair -- although, curiously, the identifier is specified to be a URI
	identifierScheme = "dbGaP"
title	GapExchange.Studies.Study[0].Configuration.StudyNameEntrez	ISSUE: We need to determine what an entry with more than one study looks like
description	GapExchange.Studies.Study[0].Configuration.StudyNameReportPage
studyType	GapExchange.Studies.Study[0].Configuration.StudyTypes.StudyType[0]	ISSUE: The alignment between dbGaP study type(s) and bioCaddie StudyType is not obvious. Mapping may be required or this may not be a valid field.
keywords	GapExchange.Studies.Study[0].Configuration.Diseases.Disease (prefixed with "MESH - ") ISSUE: There are no keywords in the latest bioCaddie schema.	Is there somewhere else this would work better? -- perhaps `isAboutBiologicalProcess`
resultsIn	(this is a list of the identifiers of all of the datasets)

The transformations in the table below are implemented by the xform_dbgap_dataset method in https://github.com/crDDI/dbgap/blob/master/dbgap/xform_dbgap.py, and generate bioCADDIE compatible output from a dbGaP DataSet record:

key	value	Notes
@type	''biocaddie:Dataset"
@id	"biocaddie:"data_table.study_id
identifierInfo	identifier="dbgap:"data_table.study_id
	identifierScheme=dbgap
date_info	date=data_table.date_created
	dateType="dct:created"	Dublin core seemed to be a reasonable source for date_info
context	"fhir:Observation"	if dataset is "Subject Phenotypes"
	"fhir:Specimen"	if dataset is "Sample Attributes"
hasPartDimension	"dbgap:"v.id	for each data_table.variable
*	*	All other dbgap elements are copied as is.

The transformations in the table below are implemented by the xform_dbgap_dimension method in https://github.com/crDDI/dbgap/blob/master/dbgap/xform_dbgap.py, and generate bioCADDIE compatible output from a dbGaP dataset variable:

key	value	Notes
@type	''biocaddie:Dimension"
@id	"biocaddie:"variable.id
identifierInfo	identifier="dbgap:"variable.id
	identifierScheme="dbgap"
dimensionType	"xsd:string"	if variable.type == "string'. Note: We need to decide whether this is the correct use of type and whether datatypes even belong in bioCaddie
*	*	All other dbgap elements are copied as is.

The JSON images of the XML are stored in the data/<studyid>/json directory.

Study Transformation Example

(myenv) > download_study 979 j
(myenv) > ls data/phs000979/json
StudyDescription.biocaddie.json
StudyDescription.json
phs000979.v1.pht005193.v1.Mental_Disorders_Postmortem_Subject.data_dict.json
phs000979.v1.pht005194.v1.Mental_Disorders_Postmortem_Sample.data_dict.json
phs000979.v1.pht005195.v1.Mental_Disorders_Postmortem_Subject_Phenotypes.data_dict.json
phs000979.v1.pht005196.v1.Mental_Disorders_Postmortem_Sample_Attributes.data_dict.json

Where StudyDescription.json is the direct JSON image of ../xml/StudyDescription.xml and StudyDescription.biocaddie.json has been mapped according to the rules above.

StudyDescription in XML

Mapped StudyDescription in JSON

{
   "resultsIn": [
      "dbgap:pht005193.v1",
      "dbgap:pht005194.v1",
      "dbgap:pht005195.v1",
      "dbgap:pht005196.v1"
   ],
   "description": "Gene Expression in Postmortem DLPFC and Hippocampus from Schizophrenia and Mood Disorders",
   "studyType": "Case-Control",
   "identifierInfo": [
      {
         "identifierScheme": "dbGaP",
         "identifier": "dbgap:phs000979.v1"
      }
   ],
   "@type": "biocaddie:Study",
   "title": "Gene Expression in Postmortem DLPFC and Hippocampus from Schizophrenia and Mood Disorders",
   "@id": "dbgap:phs000979.v1",
   "keywords": "MESH - Schizophrenia, Schizophrenia,Bipolar Disorder,Major Depressive Disorder"
}

data_dict in XML

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="./datadict_v2.xsl"?>
<data_table id="pht005196.v1" study_id="phs000979.v1" participant_set="1" date_created="Wed Dec  9 12:55:00 2015">
    <description/>
    <variable id="phv00258279.v1">
        <name>SAMPLE_ID</name>
        <description>De-identified Sample ID</description>
        <type>string</type>
    </variable>
    <variable id="phv00258280.v1">
        <name>BODY_SITE</name>
        <description>Body site where sample was collected</description>
        <type>string</type>
    </variable>
    <variable id="phv00258281.v1">
        <name>ANALYTE_TYPE</name>
        <description>Analyte Type</description>
        <type>string</type>
    </variable>
    <variable id="phv00258282.v1">
        <name>IS_TUMOR</name>
        <description>Tumor status</description>
        <type>encoded values</type>
        <value code="N">Is not a tumor</value>
        <value code="Y">Is Tumor</value>
    </variable>
    <variable id="phv00258283.v1">
        <name>HISTOLOGICAL_TYPE</name>
        <description>Cell or tissue type or subtype of sample</description>
        <type>string</type>
    </variable>
    <variable id="phv00258284.v1">
        <name>RIN</name>
        <description>RNA integrity number</description>
        <type/>
    </variable>
    <variable id="phv00258285.v1">
        <name>BATCH</name>
        <description>Sample batch number</description>
        <type/>
    </variable>
</data_table>

Mapped data_dict in JSON

{
   "data_table": {
      "study_id": "phs000979.v1",
      "participant_set": "1",
      "description": "",
      "date_created": "Wed Dec  9 12:55:02 2015",
      "id": "pht005193.v1",
      "identifierInfo": [
         {
            "identifierScheme": "dbgap",
            "identifier": "dbgap:phs000979.v1"
         }
      ],
      "variable": [
         {
            "name": "SUBJECT_ID",
            "identifierInfo": [
               {
                  "identifierScheme": "dbgap",
                  "identifier": "dbgap:phv00258253.v1"
               }
            ],
            "description": "Subject ID",
            "@type": "biocaddie:Dimension",
            "dimensionType": "xsd:string",
            "id": "phv00258253.v1",
            "@id": "dbgap:phv00258253.v1"
         },
         {
            "name": "CONSENT",
            "value": {
               "code": "1",
               "_content": "General Research Use (GRU)"
            },
            "identifierInfo": [
               {
                  "identifierScheme": "dbgap",
                  "identifier": "dbgap:phv00258254.v1"
               }
            ],
            "description": "Consent group as determined by DAC",
            "@type": "biocaddie:Dimension",
            "type": "encoded value",
            "id": "phv00258254.v1",
            "@id": "dbgap:phv00258254.v1"
         }
      ],
      "date_info": [
         {
            "dateType": "dct:created",
            "date": "Wed Dec  9 12:55:02 2015"
         }
      ],
      "hasPartDimension": [
         "dbgap:phv00258253.v1",
         "dbgap:phv00258254.v1"
      ],
      "@type": "biocaddie:Dataset",
      "@id": "dbgap:phs000979.v1"
   }
}

Converting JSON to RDF

The JSON to RDF conversion uses the PyLD JSON-LD library to convert the JSON generated in the previous step into RDF. It uses the output schema_to_context converter, which has been applied to the JSON Schema's in the bioCaddie Working Group 3 Repository. It adds one additional context:

{
     "@context": {
         "dbgap": "http://www.ncbi.nlm.nih.gov/gap/mms#",
         "@vocab": "http://www.ncbi.nlm.nih.gov/gap/mms#"
      }
}

which assigns a prefix and URI for tags that are specifically identified as being part of dbGaP as well as assigning the default tag.

Sample conversion

(myenv) > download_study 979 r -c http://localhost:8080/json-ld

Resulting Study in RDF Turtle

@prefix biocaddie: <http://biocaddie.org/mms#> .
@prefix dbgap: <http://www.ncbi.nlm.nih.gov/gap/mms#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix fhir: <http://hl7.org/fhir/mms#> .
@prefix mms: <http://rdf.cdisc.org/mms#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

dbgap:phs000979.v1 a biocaddie:Study ;
    biocaddie:description "Gene Expression in Postmortem DLPFC and Hippocampus from Schizophrenia and Mood Disorders" ;
    biocaddie:identifierInfo ( [ biocaddie:identifier dbgap:phs000979.v1 ;
                                             biocaddie:identifierScheme "dbGaP" ] ) ;    
    biocaddie:resultsIn ( "dbgap:pht005193.v1" "dbgap:pht005194.v1" "dbgap:pht005195.v1" "dbgap:pht005196.v1" ) ;
    biocaddie:title "Gene Expression in Postmortem DLPFC and Hippocampus from Schizophrenia and Mood Disorders" ;
    dbgap:keywords "MESH - Schizophrenia, Schizophrenia,Bipolar Disorder,Major Depressive Disorder" .

Resulting Dataset in RDF Turtle

@prefix biocaddie: <http://biocaddie.org/mms#> .
@prefix dbgap: <http://www.ncbi.nlm.nih.gov/gap/mms#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix fhir: <http://hl7.org/fhir/mms#> .
@prefix mms: <http://rdf.cdisc.org/mms#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

dbgap:phs000979.v1 a biocaddie:Dataset ;
    biocaddie:date_info ( [ biocaddie:date "Wed Dec  9 12:55:00 2015"^^<xsd:dateTime> ;
                biocaddie:dateType <dct:created> ] ) ;
    biocaddie:description "" ;
    biocaddie:hasPartDimension ( "dbgap:phv00258279.v1" "dbgap:phv00258280.v1" "dbgap:phv00258281.v1" "dbgap:phv00258282.v1" "dbgap:phv00258283.v1" "dbgap:phv00258284.v1" "dbgap:phv00258285.v1" ) ;
    biocaddie:identifierInfo ( [ biocaddie:identifier dbgap:phs000979.v1 ;
                biocaddie:identifierScheme "dbgap" ] ) ;
    dbgap:context "fhir:Specimen" ;
    dbgap:date_created "Wed Dec  9 12:55:00 2015" ;
    dbgap:id "pht005196.v1" ;
    dbgap:participant_set "1" ;
    dbgap:study_id "phs000979.v1" ;
    dbgap:variable dbgap:phv00258279.v1,
        dbgap:phv00258280.v1,
        dbgap:phv00258281.v1,
        dbgap:phv00258282.v1,
        dbgap:phv00258283.v1,
        dbgap:phv00258284.v1,
        dbgap:phv00258285.v1 .

Sample Dimension Entry in RDF Turtle

@prefix biocaddie: <http://biocaddie.org/mms#> .
@prefix dbgap: <http://www.ncbi.nlm.nih.gov/gap/mms#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix fhir: <http://hl7.org/fhir/mms#> .
@prefix mms: <http://rdf.cdisc.org/mms#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

dbgap:phv00258282.v1 a biocaddie:Dimension ;
    biocaddie:description "Tumor status" ;
    biocaddie:identifierInfo ( [ biocaddie:identifier dbgap:phv00258282.v1 ;
                biocaddie:identifierScheme "dbgap" ] ) ;
    biocaddie:name "IS_TUMOR" ;
    dbgap:id "phv00258282.v1" ;
    dbgap:type "encoded values" ;
    dbgap:value [ dbgap:_content "Is Tumor" ;
            dbgap:code "Y" ],
        [ dbgap:_content "Is not a tumor" ;
            dbgap:code "N" ] .

Name		Name	Last commit message	Last commit date
Latest commit History 13 Commits
dbgap		dbgap
images		images
scripts		scripts
static/json-ld		static/json-ld
tests		tests
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
setup.py		setup.py

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dbgap

Introduction

Installation

Use

Transformation description

Downloading XML files

Converting XML to JSON

Study transformations

Study Transformation Example

StudyDescription in XML

Mapped StudyDescription in JSON

data_dict in XML

Mapped data_dict in JSON

Converting JSON to RDF

Sample conversion

Resulting Study in RDF Turtle

Resulting Dataset in RDF Turtle

Sample Dimension Entry in RDF Turtle

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crDDI/dbgap

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dbgap

Introduction

Installation

Use

Transformation description

Downloading XML files

Converting XML to JSON

Study transformations

Study Transformation Example

StudyDescription in XML

Mapped StudyDescription in JSON

data_dict in XML

Mapped data_dict in JSON

Converting JSON to RDF

Sample conversion

Resulting Study in RDF Turtle

Resulting Dataset in RDF Turtle

Sample Dimension Entry in RDF Turtle

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