ClinVar - clinvar

Grade
The grade for the resource as automatically determined by the criteria violations.
4
Description
A full description of the resource from the resource itself, if possible.
ClinVar archives and aggregates information about relationships among variation and human health. ClinVar collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data.
Last curated
(Optional) The ISO 8601 date of when the resource was last curated.
2017-12-07
Location
URL for the resource.
https://www.ncbi.nlm.nih.gov/clinvar/
Source type
(Optional) How the resource relates to the data it contains. Current allowable entries are: "unknown", "repository", and "source", and "integrator".
integrator
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.
biomedical
Type
The type of data the resource contains.
human
Categories
(Optional) Tags to describe the resource and its data.
disease-gene association
variant-disease association
variant definitions
Access
(Optional) Links to the resource's data.
download
License
The license that is used by the resource. We use SPDX where we can (https://spdx.org/licenses/) or: "unknown", "public domain", "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 "TODO" is used. Current possible values are: "unknown", "copyleft", "permissive", "public domain", "copyright", "restrictive", or "closed pool".
public domain
License location
(Optional) The link to the resource license.
http://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/
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: Public domain declaration
Criteria B.2.1: The license page section \"Molecular Data Usage\" states that all data may not be covered under the public domain (see comments).
Criteria B.2.2: There does not seem to be any easy way to differentiate the \"clean\" data.
Commentary
(Optional) Further commentary on the license, possibly including the though process of the curations and things like locations of additional licenses.
• We turned on the \"controversial\" flag for this resource due to the unclear nature of sumbitted data. While the stated intent seems to have the data available as PD, ClinVar does not require a copyright reassignment and explicitly states that they cannot vouch for submitted data, which rather undermines any PD-style statement. We were intitially intending on adding a B.1 violation as ClinVar would be acting more like a directory than a unified resource, possibly requiring negotiation with upstream resources.
• While an API is offered through E-Utilities, we will evaluate the more concrete downloads given their ease.
• Custom PD declaration.
• The license page section \"Molecular Data Usage\" states that\: \"NCBI is not in a position to assess the validity of such claims and since there is no transfer of rights from submitters to NCBI, NCBI has no rights to transfer to a third party. Therefore, NCBI cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the molecular databases.\"
• We also considered the wording at https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/ , but decided that the one we chose above was mostly likely indended and correct.
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.
true
Contacts
(Optional) Resource contact information, link, email, or whatever is public.
info@ncbi.nlm.nih.gov
Grants
(Optional) Semi-structured list of supporting grants.
TBD

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