Inspired by the efforts of scientists around the world
and the game-changing efforts of projects like the
Creative Commons, the Wikipedia Foundation, and the Free
Software movement, we
hope to engage the larger community in an open and
fruitful discussion on issues concerning the use and
reuse of scientific data, including the balance of
openness and how to make ends meet in an increasingly
competitive environment.
We are not lawyers and this is not legal advice: all
institutions and groups have their own perspectives
and counsel. We are a group of scientists, engineers,
librarians, and specialists that are concerned about
the use and reuse of increasingly interconnected,
derived, and reprocessed data. We want to make sure
that data-driven scientific endeavors can work with
one another in meaningful ways without undue legal
concerns.
The (Re)usable Data Project is meant provide a
resource that looks at some of the issues
around the reuse of scientific data and open a
conversation about how to deal with them.
We also want to actively work with the community in
considering our criteria and in making sure that our
information about scientific data resources is
up-to-date and correct. If you have any questions,
concerns, or see any problems, please open a ticket on
our GitHub
tracker.
The initial driving concern of this project is the use
and reuse of biological and biomedical data. However,
this is a general problem in the scientific community
and needs to be addressed directly. For each
resource, using
our criteria, we attempt
to objectively assign zero to five stars for how well
we believe a resource's data may build upon, edited,
modified, and redistributed. Grossly speaking:
5 stars★ ★ ★ ★ ★
The license unambiguously allows the unfettered (re)use
and redistribution of the data.
4 stars★ ★ ★ ★
The license unambiguously allows (re)use and
redistribution of the data under some terms.
3 stars★ ★ ★
The license is clearly stated, unambiguous, and of
a standard type, and has clear access, but has
terms that may greatly impact the (re)use and
redistribution of the data.
2.5 or less stars★ ★ ½ - ∅
There are likely issues in definitively finding
the license, ambiguities in the license that
hamper further analysis, issues with clean data
access, or terms that require legal advice.
If you see any problems with our determinations or would
like to make corrections or clarifications, please open
a ticket for us on
our issue
tracker.
This is a short overview of the criteria that we use
when evaluating a resource's data license for use and
reuse. We have attempted to balance many needs
(credit, mutability, commercialization,
redistribution, etc.) and focused on trying to
objectively see how licenses can interact across
resources.
To learn more about how we look at resource data
licenses, please see
our criteria
and license type
pages.
Clearly stated (A)
A clearly stated, unambiguous, and hopefully
standard, license for data use is critical for any
(re)use of data: if there is no license to be
found, then rights are unclear and one needs to
assume the default: all rights reserved.
more »
Comprehensive and non-negotiated (B)
Data that is mixed under different licenses, only
partially available, or must be in some way
negotiated creates barriers to the (re)use of
data. more »
Accessible (C)
Data must be accessible in a reasonable and manner
to be useful to the broader
community. more »
Avoid restrictions on kinds of (re)use (D)
Data should be able to be copied, built upon,
edited, and modified as freely as
possible. more
»
Avoid restrictions on who may (re)use (E)
Data should should be available to as many people
as possible for their
(re)use. more
»
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data).
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.
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.
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.
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.4.155 and searches 63,959 publications for 1,507,991 protein and genetic interactions, 27,785 chemical associations and 38,559 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats.
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.
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).
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.
The Catalogue of Life is the most comprehensive and authoritative global index of species currently available. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.6 million species.
Use seems to hinge on some contact with Sp2000. For example: \"If you wish to use the Catalogue of Life content on a public portal or webpage you are required to notify the Species 2000 Secretariat, and to assist with a check that the correct credits are given.\" Check check assistance especially seems to violate B.1.
The data \"download\" is quite complicated and should not actually be considered a download (see commentary). The API as given would likely require a custom spider to obtain the data in bulk.
Distribution seems to be prohibited without negotiation; example on the main ToS: \"Commercial use of this compilation or any of the species datasets contained within...or dissemination on the Internet, requires written permission from Species 2000 and ITIS.\"
biology, biochemical, bioactive drug-like small molecules
★ ★ ★
ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).
