Saccharomyces Genome Database (SGD) - sgd

Grade: The grade for the resource as automatically determined by the criteria violations.; 4.5
Description: A full description of the resource from the resource itself, if possible.; The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.
Last curated: (Optional) The ISO 8601 date of when the resource was last curated.; 2019-03-01
Location: URL for the resource.; https://yeastgenome.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.; MOD
Categories: (Optional) Tags to describe the resource and its data.; genotype-phenotype association
disease-model association
gene expression
Access: (Optional) Links to the resource's data.; download
api
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".; CC-BY-4.0
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://sites.google.com/view/yeastgenome-help/about
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 B.2.1: While the downloadable data seems quite clearly CC-BY-4.0, the API footer has terms that indicate that all data may not be covered under the same license (see comments).
Criteria B.2.2: The API does not seem to be any easy way to differentiate the \"clean\" CC-BY-4.0 data from other licenses.
Commentary: (Optional) Further commentary on the license, possibly including the though process of the curations and things like locations of additional licenses.; • The license information found in the "About SGD" paragraph on the SGD Help page at https://sites.google.com/view/yeastgenome-help/about
• SGD operates under the Creative Commons Attribution 4.0 International license (CC BY 4.0).
• However, the license information for the API is much less clear, reading: "Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts."
• The API did not seem to offer any way of filter out things with other licenses.
• Without ascending, noting that various upstream for the SGD API could have other terms: https://yeastmine.yeastgenome.org/yeastmine/dataCategories.do
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.; https://www.yeastgenome.org/suggestion
sgd-helpdesk@lists.stanford.edu
Grants: (Optional) Semi-structured list of supporting grants.; The SGD is funded by the US National Institutes of Health, National Human Genome Research Institute (NHGRI), [U41HG001315]. Our efforts are also supported via the Gene Ontology Consortium (GOC) funded by the NHGRI [U41HG002273] and the Alliance of Genome Resources supplement via WormBase [U41HG02223-17S1].