GTEx - gtex

Grade: The grade for the resource as automatically determined by the criteria violations.; 2.5
Description: A full description of the resource from the resource itself, if possible.; The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs.
Last curated: (Optional) The ISO 8601 date of when the resource was last curated.; Unknown
Location: URL for the resource.; http://www.gtexportal.org
Source type: (Optional) How the resource relates to the data it contains. Current allowable entries are: "unknown", "repository", "source", "integrator", and "warehouse".; TBD
Curation status: Whether or not annotation is complete on this resource. Current allowable entries are: "complete", "incomplete", and "nonpublic".; complete
Field: The area of research for the resource.; biology
Type: The type of data the resource contains.; human
Categories: (Optional) Tags to describe the resource and its data.; gene expression
Access: (Optional) Links to the resource's data.; download
License: The license that is used by the resource. We use SPDX where we can or: "inconsistent", "public domain", "unlicensed", "all rights reserved", or "custom".; custom
License type: The type of license that is being used. This will be to define compatible data pools in the future; we only use the grossest terms now. If it is not known "unknown" is used. Current possible values are: "unknown", "unlicensed", "copyleft", "permissive", "public domain", "copyright", "restrictive", or "private pool".; permissive
License location: (Optional) The link to the resource license.; https://www.gtexportal.org/home/documentationPage
Focused curation: (Optional) Setting this flag to true indicates that the licensing was combinatorially complicated enough (as is the case in some commercial licenses) that the curator chose to wear a single "hat" during the process. From the site text: "While we try to cover as much of the licensing possibilities of a data resource that we can, in a few cases we may choose a particular "hat" to wear while evaluating to prevent a combinatorial explosion, which may also reduce the clarity of our curations for the community. In these cases, we may take on the role of a (1) non-commercial (2) academic (3) group that is (4) based in the US and trying to (5) create an aggregating resource, noting that other entities may have different results in the license commentary."; false
Issues: (Optional) Structured issues with the license. For every issue discovered with a resource, there should be a corresponding item in the license-issues field that marks the /exact/ violation, along with any comments. This field can be used by resources as the first step to improvement, as well as clarify any surrounding circumstances. Any issues or thoughts about a resource that do not slot into one of the criteria violations can go into the license-commentary field.; Criteria A.2.2: Custom license based on the various datasets and NIH Genomic Data Sharing Policy.
Criteria C.1: No API or URL to access all data groupings with single action.
Criteria C.2: No API or URL and therefore no reasonable and transparent access.
Criteria D.1.1: As stated copyright may be interpreted by non-legal professional that the contents may be reused/remixed for research/scientific purposes.
Criteria E.1.1: As stated copyright may be interpreted by non-legal professional that the contents may be reused/remixed research/scientific purposes.
Commentary: (Optional) Further commentary on the license, possibly including the though process of the curations and things like locations of additional licenses.; • Protected Data and Raw Data in the portal has not included in evaluation of this resource. See the dbGaP file for score.
• The data not under the exceptions listed are under the NIH GDS (https://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-124.html).
• Pilot data set (phs000424.v3.p1) - acceptance of the "Ft. Lauderdale" principles of rapid, pre-publication data release (see Sharing Data from Large-Scale Biological Research Projects: A System of Tripartite Responsibility, 2003). The continued success of rapid pre-publication data release relies on the scientific community to respect the data producer’s interest to publish a full analysis of their data first. Secondary users are asked to refrain from submitting manuscripts describing comprehensive analyses until the Consortium has published their analysis.
• May 8, 2015 - No restrictions - main manuscript published.
• phs000424.v4.p1 - the dataset is subject to 9 months publication restriction starting from the date of the release; no restrictions after Jan 4, 2015.
• All datasets from phs00424.v5.p1 forward will follow the NIH GDS policy. This means that once released through dbGaP, there are no restrictions on use or publication. This document and an accompanying table of dataset releases can be found at http://www.gtexportal.org/home/documentationPage.
• https://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-124.html
Controversial: (Optional) Marker noting that there was some extended internal discussion or controversy about the evaluation of the licensing terms. If this is marked at "true", the controversy, or a link to a permanent archive of the controversy, must be sufficiently contained in the "license-commentary" to reconstruct the issues.; false
Contacts: (Optional) Resource contact information, link, email, or whatever is public.; http://www.gtexportal.org/home/contact
Grants: (Optional) Semi-structured list of supporting grants.; TBD