BRENDA Tissue Ontology - bto

The grade for the resource as automatically determined by the criteria violations.
A full description of the resource from the resource itself, if possible.
A structured controlled vocabulary for the source of an enzyme. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
Last curated
(Optional) The ISO 8601 date of when the resource was last curated.
URL for the resource.
Source type
(Optional) How the resource relates to the data it contains. Current allowable entries are: "unknown", "repository", "source", "integrator", and "warehouse".
Curation status
Whether or not annotation is complete on this resource. Current allowable entries are: "complete", "incomplete", and "nonpublic".
The area of research for the resource.
The type of data the resource contains.
(Optional) Tags to describe the resource and its data.
enzyme sources
(Optional) Links to the resource's data.
The license that is used by the resource. We use SPDX where we can or: "inconsistent", "public domain", "unlicensed", "all rights reserved", or "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".
License location
(Optional) The link to the resource license.
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."
(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: While they are obviously attempting to be permissive by listing \"CC-BY\", this does not map onto any of the number CC-BY versions (e.g. 3.0 or 4.0), thereby, breaking the reference and meaning that we would have to contact for them for terms).
Criteria C.2: Once one knows the location of the BTO (ontology file), access is fine. However, we were unable to locate the ontology file after some searching through the main BRENDA website; most text would imply there is no free ontology file to be had.
(Optional) Further commentary on the license, possibly including the though process of the curations and things like locations of additional licenses.
• The relatively high score is due to knowing where the ontology exists and knowing to look at the header--normal use of the site seems to lead around restricted APIs webpages containing; the free ontology file is hiding in there.
• Typcial of this is: \"Use of this online version of BRENDA is free for academic research only. Commercial use or download access requires a license. See terms of use.\" (
• The \"CC-BY\" declaration in the ontology file header should be versioned or linked. Due to not knowing what version, we have marked it as a custom; obviously intended to be under very permissive terms.
(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.
(Optional) Resource contact information, link, email, or whatever is public.
(Optional) Semi-structured list of supporting grants.
This work was supported by the European Union: (FELICS: Free European Life-Science Information and Computational Services: 021902 (RII3); SLING: Serving Life-science Information for the Next Generation: 226073).

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