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Open Results from Biomedical Research Projects: Where Are They?

The following letter was submitted in response to Chelsea Wald’s article Scientists Embrace Openness.

Open Results from Biomedical Research Projects: Where Are They?
Maojo, V., Garcia-Remesal, M, Crespo, J., de la Calle, G., de la
Iglesia, D. and Kulikowski, C.

Wald has addressed scientific openness in a recent Science article (1),
including data and methods used for research. Advances in software tools
for bioinformatics search helps (2), but, just becoming aware of open
results of research projects funded by public agencies* — e.g., databases,
software, papers, e-books* — and finding them efficiently still proves
harder than it should.

In the course of producing an advanced, automatically generated on-line
inventory of bioinformatics resources (3), we analyzed results from
research projects publicly funded by the European Commission, Spanish
agencies, and the National Institutes of Health. We discovered that finding the complete set of
available information reported to have been generated by the projects
could prove quite elusive. Non-peer-reviewed summary reports were
commonplace, but specifics of electronic resources, with Web locations,
were frequently not, even when researchers mentioned their existence as
being openly available.

To enable searches with sophisticated text mining, publicly-funded
projects should provide a minimum information set including titles,
authors, funding agency, annotations with concepts from ontologies or
controlled vocabularies that characterize the functionalities of the
resources, papers reporting significant findings using these resources
*peer-reviewed quality indicators,* and their Uniform Resource
Identifiers (URIs).

Earlier suggestions for structuring abstracts of papers (4) resulted in
an experiment with disappointingly limited success (5). However, to
provide basic information resources from projects already on the Web
ought to be more straightforward. Requiring a minimum information set
like the one we propose to be available online under clearly specified
standards might help bring about more comprehensive open access, which
would promote wider reuse of resources and avoid duplication in
scientific projects, worldwide.

Agencies are increasingly requiring that
papers reporting research funded by them become publicly available. Our
proposal is that they require that other products of research, like
open electronic resources that back-up a paper’s results, should be made
equally easily accessible.

1. Wald, C. Scientists Embrace Openness. Science Issues and Perspectives.
Science. April 09, 2010
2. Dinov ID et al. iTools: a framework for classification, categorization
and integration of computational biology resources. PLoS One. 2008 May
3. de la Calle G, García-Remesal M, Chiesa S, de la Iglesia D,
Maojo V. BIRI: a new approach for automatically discovering and indexing
available public bioinformatics resources from the literature. BMC
Bioinformatics. 2009 Oct 7;10:320.
4. Gerstein M, Seringhaus M,
Fields S. Structured digital abstract makes text mining easy. Nature.
2007 May 10;447(7141):142.5.     
5. Lok C. Literature mining: Speed
reading. Nature. 2010 Jan 28;463(7280):416-8.