Maryann Martone, PhD and Anita Bandrowski, PhD
University of California, San Diego
A central tenet in support of research reproducibility is the ability to identify research resources, i.e., the reagents, tools, and materials that underlie the findings of any study. However, current reporting practices for research resources are out of date, and not designed to allow either humans or algorithms to identify the exact resources that are reported. Because of the lack of identifiability, we cannot easily answer even basic questions from the literature such as: “What other studies used resource X?” Without this basic capability, we cannot easily aggregate data on an individual genetically modified mouse, for example, report errors that might arise as these resources are used, or track the impact of funding decisions by determining how resources like databases and tools are used.
To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers. The project was run out of FORCE11.org, the Future of Research Communications and e-Scholarship, a grassroots effort designed to encourage scholarly communications to adapt to new possibilities enabled by web technology. The pilot initially engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials to participate, largely from the neurosciences. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource.
To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal. RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014. To date, RRIDs appear in over 500 papers from 70+ journals. In this presentation, we will present an overview of the pilot project, its outcomes to date and plans for future expansion and governance of the RRID system.
Dr. Martone received her BA from Wellesley College in biological psychology and her PhD in neuroscience in 1990 from the University of California, San Diego, where she just retired as a Professor in the Department of Neuroscience. Her background is in neuroanatomy, particularly light and electron microscopy, but she spends most of her time now in the field of neuroinformatics. Dr. Martone is the principal investigator of the Neuroinformatics Framework project, a national project to establish a uniform resource description framework for neuroscience. Her recent work has focused on building ontologies for neuroscience for data integration. She just completed her tenure as the US scientific representative to the International Neuroinformatics Coordinating Facility (INCF), where she still heads the program on ontologies. She is finishing up her tenure as president of FORCE11, an organization dedicated to advancing scholarly communication and e-scholarship, on December 31, 2015. Dr. Martone remains a professor emeritus at UCSD and has recently joined Hypothes.is, a non-profit dedicated to developing an annotation layer over the web, as Director of Biosciences.
Dr. Bandrowski’s background is bench neuroscience, electrophysiology, where she worked to examine the G-protein signaling in the auditory cortex, then moved to somatosensory cortex physiology and epileptic phenomena under the direction of Drs. Prince and Huguenard. Dr. Bandrowski started working in informatics when employed by with Celera corp. as a scientific curator for the human genome project. Working primarily in signaling molecules and protein representation, but soon moving toward algorithms. Dr. Bandrowski works as the scientific curator and project lead for the Neuroscience Information Framework (NIF), a large informatics project, whose goal is to represent neuroscience knowledge in a computable fashion, making it more findable and understandable to both humans and machines. Dr. Bandrowski currently works collaboratively with computer scientists, programmers and curation staff to build information systems for biologists.