Integration of Data and Publications - Alliance for Permanent Access

Report on Integration of Data and Publications Grant Agreement no.: 261530
with current best practice in their discipline for the sharing of data via databases:
for example, deposition of microarray data in ArrayExpress or GEO; deposition of
gene sequences in GenBank or EMBL; and deposition of ecological data in
DRYAD. We encourage all authors to comply with available field-specific
standards for the preparation and recording of data.
A similar policy encouraging authors to deposit their data in ‘approved databases’ is
followed by the journal Science. Their instructions say 39 :
Science supports the efforts of databases that aggregate published data for the
use of the scientific community. Therefore, appropriate data sets (including
microarray data, protein or DNA sequences, atomic coordinates or electron
microscopy maps for macromolecular structures, and climate data) must be
deposited in an approved database, and an accession number or a specific access
address must be included in the published paper.
For those cases where such an approved appropriate repository does not exist, Science
wishes to have the datasets on its own website as supplementary material or at least
hold the material in escrow if the files are hosted on a institutional website by the
author.
Further reading of the instructions seems to indicate that Science is also struggling with
certain types of supplementary material in a careful balance to avoid having to absorb
too much and still ensure that the underlying material can be examined by its readers.
The journal asks authors to follow special procedures for making large or complex
datasets available. See their special instructions for complex supporting data at their
website.
While these well known titles are rather specific in their support for community
endorsed databases, it has become an established custom in many areas for publishers to
collaborate with the main data archives. Typical author instructions for data deposits in
public archives, linked to the publications, are (source Elsevier 29 ):
If your article contains relevant unique identifiers or accession numbers
(bioinformatics) linking to information on entities (genes, proteins, diseases, etc.)
or structures deposited in public databases, then please indicate those entities
according to the standard explained below.
Authors should explicitly mention the database abbreviation (as mentioned
below) together with the actual database number, bearing in mind that an error
in a letter or number can result in a dead link in the online version of the article.
Please use the following format: Database ID: xxxx
And most publishers will specify the databases that allow links from (and increasingly
to) the article:
39 Science: see http://www.sciencemag.org/site/feature/contribinfo/prep/gen_info.xhtml#dataavail
and http://www.sciencemag.org/site/feature/contribinfo/prep/prep_online.dtl and
http://www.sciencemag.org/site/feature/contribinfo/prep/prep_online_special.xhtml
Opportunities for Data Exchange (ODE) –www.ode-project.eu 50