Identifying research resources in biomedical literature should be easy
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1
The University of California, San Diego, Center for Research in Biological Systems, United States
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2
OHSU, Libraries, United States
The published literature is where researchers go to build upon previous work; however, the reproducibility of this research has recently been scrutinized in the scientific community and even the popular media. A central tenet of reproducibility is a clear and unambiguous description of the data, methods, and material resources in publications. While research resource identification is an important step towards promoting reproducible and efficient science, we recently attempted to identify research resources (model organisms, antibodies, knockdown reagents, constructs, and cell lines) in the biomedical literature. The results showed that only 54% of resources were uniquely identifiable, regardless of domain, journal impact factor, or reporting requirements (Vasilevsky et al., 2013; https://peerj.com/articles/148/). This was largely due to a lack of unique identifiers such as a catalog numbers in the publications.
To address this issue, the Resource Identification Initiative (RII) was formed by a dedicated group of academics, government and non-government institute officials, publishers and commercial antibody companies. This initiative aims to enable resource identification within the biomedical literature through a pilot study promoting the use of unique Research Resource Identifiers (RRIDs). In the pilot study, authors are asked to include RRIDs in their manuscripts prior to publication for three resource types: antibodies, model organisms and tools (including software and databases). RRIDs meet key criteria: they are unique, they are machine readable, free to generate and access, and are consistent across publishers and journals. The intention is to provide a central resource for journal submission systems to access shared resource identifiers and conversely link to the various nomenclature and data authorities.
To facilitate access to the RRIDs, we aggregated data for the three resource types into the Resource Identification Portal (http://scicrunch.com/resources). The portal pulls data from antibody catalogs from over 200 vendors, transgenic organisms from sources such as MGI, IMSR, ZFIN, ZIRC, CGC, WormBase, and RGD; and additionally, the portal contains the NIF Resource Catalog, which contains over 3,700 software tools and over 3,300 academic databases. Accessibility from a single portal, with integrated help features and a “cite this” button enables researchers to quickly find their resources and include the RRID in the methods section or as a keyword in their publications.
The pilot study included 25 participating journals over a 3-month time span, and had a stated goal to determine if authors could improve the way they identify their resources. While the pilot study is still underway, the preliminary data shows authors are using the Research Identification Portal (as of 4/11/2014 there were 10,878 sessions on the portal from 8,822 unique users, more than 100 user help requests, and 73 databases/software tool and 186 antibody registration requests were documented). An initial search for RRIDs in the literature indexed in PubMed showed there were 3 papers that had been indexed into PubMed that contained a total of 7 unique identifiers, 6 for software tools, 1 antibody, while google scholar shows 19 papers that contain at least one RRID. We anticipate the numbers of RRIDs in the literature will increase over the upcoming months as the papers continue to be published.
Acknowledgements
We would like to thank the INCF, and NIH for hosting meetings, antibodies-online and compare networks for participating and putting forward both programming and advertising, the group of edits for participating, and a large group of volunteers for running the web site and answering questions.
References
Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA.
On the reproducibility of science: unique identification of research resources in the biomedical literature.
PeerJ. 2013 Sep 5;1:e148. doi: 10.7717/peerj.148. eCollection 2013.
Keywords:
RII,
Neuroscience Information Framework,
infrastructure,
Publishing,
IDENTIFICATION
Conference:
Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014.
Presentation Type:
Poster, to be considered for oral presentation
Topic:
General neuroinformatics
Citation:
Bandrowski
A,
Martone
M,
Vasilevsky
N,
Brush
M and
Haendel
M
(2014). Identifying research resources in biomedical literature should be easy.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2014.
doi: 10.3389/conf.fninf.2014.18.00080
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Received:
28 Apr 2014;
Published Online:
04 Jun 2014.
*
Correspondence:
Dr. Anita Bandrowski, The University of California, San Diego, Center for Research in Biological Systems, San Diego, United States, abandrowski@ucsd.edu