Accessing and using data in GTR
Disclaimer and data use policy
Copyright Status Information that is created by or for the US government on this site is within the public domain. Public domain information on the National Library of Medicine (NLM) Web pages may be freely distributed and copied. However, it is requested that in any subsequent use of this work, NLM be given appropriate acknowledgment. More information about NCBI's copyright and disclaimer policy is available.
If you distribute or copy data from the NIH Genetic Testing Registry, we ask that you provide attribution to GTR as a data source in publications and websites:
- Link to the GTR website: http://www.ncbi.nlm.nih.gov/gtr/
- Cite this publication: http://nar.oxfordjournals.org/content/41/D1/D925.full
- PubMed ID: 23193275
- PubMed Central ID: PMC3531155
IMPORTANT NOTE: NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in the GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.
Methods to access the data
Web access
The data in GTR's web site are updated daily.
There are multiple ways to identify information in GTR using direct queries to the GTR site. Our help documents provide detailed instructions about constructing queries to identify registered tests. There are other sites at NCBI, however, that provide links to GTR based on common content, and thus can be considered as portals to information in the GTR. These include:
| Resource | Basis of the link | Where the link appears |
|---|---|---|
| ClinVar | Submitters detailing the test used to identify variants | In the Evidence tab, under Details of each submission, as Method |
| GeneReviews | Genes (by gene symbol) or Conditions (name used by GTR) |
Tests in GTR by Gene Tests in GTR by Condition |
| NCBI Gene | Human genes in for which testing is registered in GTR |
GTR link under Related Information Find tests for this gene in the NIH Genetic Testing Registry (GTR) link at the top of the Phenotypes section Compare labs link in the Associated conditions table per disorder |
| MedGen | Conditions with tests registered in GTR |
Link to GTR under the disorder name in the search Results page Genetic Testing Registry section in the right sidebar of a detailed report |
Data for download
GTR provides files in several formats and with different degrees of coverage. These files, with the update cycles, are detailed in Table 2.
| Format and scope | Path | Coverage | Update cycle |
|---|---|---|---|
|
XML: Complete public data set TXT and XLSX: Reports about labs, tests, methods, genes, and conditions |
https://ftp.ncbi.nlm.nih.gov/pub/GTR/data/_README.html | comprehensive | weekly |
| TSV: disease names and gene-disease relationships | https://ftp.ncbi.nlm.nih.gov/pub/clinvar/ | comprehensive | daily |
Application programming interface (API)
Data from GTR can be retrieved programmatically via several application programming interfaces (API). These include:
E-utilities and Entrez Direct
As part of NCBI's Entrez system, GTR can be accessed by E-utilities, both via web services and a UNIX command line as Entrez Direct. The subset of functions GTR currently supports are esearch and esummary.
| Function | Retrieves | Example |
|---|---|---|
| einfo | Fields in GTR | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gtr |
| esearch | Unique identifiers (UIDs) of test records | http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gtr&term=%22FGFR3[gene]%22&retmax=500 |
| esummary | Document summary (or set) of the UID(s) retrieved in the previous query / or specified in the query | http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gtr&id=[identifier here] |
| efetch | Document summary (or set) of the UID(s) retrieved in the previous query / or specified in the query | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gtr&id=[identifier here] |
| elink | UID(s) for records linked to the GTR record
Links to Gene, MedGen, OMIM, orgtrack (organization data, i.e., labs) are supported |
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gtr&db=gene&id=[identifier here]
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gtr&db=medgen&id=[identifier here] |
- The identifier returned by esearch is the identifier for the test. That identifier corresponds to the accession of the test, when padded to 9 numerals. Thus, test id 7406 corresponds to test accession GTR000007406.
- The data for esummary are returned as XML. The contents summarize
- the name of the test (<TestName>)
- the type of the test (<TestType>, e.g. Clinical or Research)
- the names, acronyms, and MedGen CUI of up to 3 of the condition(s) being tested (<ConditionList>)
- the names, identifiers, and cytogenetic locations of the analytes being tested (<Analytes>),
- information about the laboratory offering the test and its staff (<Offerer>, <OffererLocation>, <OffererID>, <DirectorList>)
- methods used <Method>
- analytical validity (<AnalyticalValidity>)
- target population (<TargetPopulation>)
- certifications (<Certifications>)
- study description (<StudyDesc>)
- a partial list of test targets (used for display) (<TestTargetList>),
- the number of conditions for which the test is appropriate (<ConditionCount>),
- the number of test targets (<TestTargetCount>)
- Please note that the esummary result cannot be used to obtain a full list of conditions being tested in a test. Those data are best obtained from https://ftp.ncbi.nlm.nih.gov/pub/GTR/data/test_condition_gene.txt