BioCyc Database Collection (BioCyc, public) - biocyc-open

Grade
The grade for the resource as automatically determined by the criteria violations.
3
Description
A full description of the resource from the resource itself, if possible.
BioCyc is a collection of 20,028 Pathway/Genome Databases (PGDBs) for model eukaryotes and for thousands of microbes, plus software tools for exploring them. BioCyc is an encyclopedic reference that contains curated data from 130,000 publications.
Last curated
(Optional) The ISO 8601 date of when the resource was last curated.
2023-03-08
Location
URL for the resource.
https://www.biocyc.org/
Source type
(Optional) How the resource relates to the data it contains. Current allowable entries are: "unknown", "repository", "source", "integrator", and "warehouse".
source
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.
genomic resource
Categories
(Optional) Tags to describe the resource and its data.
sequence
gene structure
pathways
reactions
functional annotation
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".
restrictive
License location
(Optional) The link to the resource license.
http://biocyc.org/all-reg.shtml
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: Non-standard/custom license.
Criteria B.1: One term of the license is that you must "Notify SRI that you are making BIOCYC DATABASES available in this manner"; this, combined with somewhat bulky access (see comments), I believe rises to a barrier to reuse as a manual step invloving people has been added.
Criteria D.1.2: The license specifically notes that it is being licensed to you and you do not have rights betond that; I believe that this puts second-hand reuse in question: you may remix, but a downstream party from you would have to register and comply directly with BioCyc.
Commentary
(Optional) Further commentary on the license, possibly including the though process of the curations and things like locations of additional licenses.
• This curation is for the post two-year embargo window data, excluding EcoCyc and MetaCyc which are current and supported by the NIH; data within that window is available with a subscription.
• All data access to the downloads is mediated by an individual URL/password/login combination that is obtained by filling out a form and waiting for a response. The curator waited a little over two business days for their response. I do not believe this constitutes a violation of C.2 by itself.
• The core of the license seems to be essentially: "...you may use, modify and redistribute the BIOCYC DATABASES on a royalty-free basis, worldwide, and for any purpose; provided that[...]" changes are identified and BioCyc is credited in a couple of specific ways, including branding.
• The terms are very interesting. I believe the D.1.2 violation could also be interpreted as a D.1.1 violation.
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.
biocyc-support@sri.com
https://www.biocyc.org/contact.shtml
Grants
(Optional) Semi-structured list of supporting grants.
TBD

All copyrightable materials on this site are © 2019 the (Re)usable Data Project under the CC-BY 4.0 license.
The (Re)usable Data Project is funded by the National Center for Advancing Translational Sciences (NCATS) OT3 TR002019 as part of the Biomedical Data Translator project and U24TR002306 as part of the CTSA Program National Center for Data to Health (CD2H).
The (Re)usable Data Project would like to acknowledge the assistance of many more people than can be listed here. Please visit the about page for the full list.