Uniform resolution of compact identifiers for biomedical data

Authors: Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael Jimenez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone & Tim Clark

Abstract: Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such “compact identifiers” have been widely used in biomedical informatics to support global resource identification with local identifier assignment. We report here on our project to provide robust support for machine-resolvable, persistent compact identifiers in biomedical data citation, by harmonizing the Identifiers.org and N2T.net (Name-To-Thing) meta-resolvers and extending their capabilities. Identifiers.org services hosted at the European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), and N2T.net services hosted at the California Digital Library (CDL), can now resolve any given identifier from over 600 source databases to its original source on the Web, using a common registry of prefix-based redirection rules. We believe these services will be of significant help to publishers and others implementing persistent, machine-resolvable citation of research data.

Citation: Sarala M. Wimalaratne et al. Uniform resolution of compact identifiers for biomedical data. Sci. Data. 5:180029 doi: 10.1038/sdata.2018.29

Source: Scientific Data

Assessing Stewardship Maturity of the Global Historical Climatology Network-Monthly (GHCN-M) Dataset: Use Case Study and Lessons Learned

Authors: Ge Peng, Jay Lawrimore, Valerie Toner, Christina Lief, Richard Baldwin, Nancy Ritchey, Danny Brinegar, Stephen A. Del Greco


Abstract: Assessing stewardship maturity — the current state of how datasets are documented, preserved, stewarded, and made accessible publicly — is a critical step towards meeting U.S. federal regulations, organizational requirements, and user needs. The scientific data stewardship maturity matrix (DSMM), developed in partnership with NOAA’s National Centers of Environmental Information (NCEI) and the Cooperative Institute for Climate and Satellites-North Carolina (CICS-NC), provides a consistent framework for assessing stewardship maturity of individual Earth Science datasets and capturing justifications for transparency. The consolidated stewardship maturity information will allow users and decision-makers to make informed use decisions based on their unique data needs. This DSMM was applied to a widely utilized monthly-land-surface-temperature dataset derived from the Global Historical Climatology Network (GHCN-M). This paper describes the stewardship maturity ratings of GHCN-M version 3 and provides actionable recommendations for improving the maturity of the dataset. The results from the use case study show that an application of DSMM like this one is useful to people who produce or care for digital environmental datasets. Assessments can identify the strengths and weaknesses of an individual dataset or organization’s preservation and stewardship practices, including how information about the dataset is integrated into different systems.


Citation: Peng, G., Lawrimore, J., Toner, V., Lief, C., Baldwin, R., Ritchey, N., . . . Greco, S. A. (2016). Assessing Stewardship Maturity of the Global Historical Climatology Network-Monthly (GHCN-M) Dataset: Use Case Study and Lessons Learned. D-Lib Magazine, 22(11/12). doi.org/10.1045/november2016-peng




A Data Citation Roadmap for Scholarly Data Repositories

Authors: Martin Fennera, Merce Crosasb, Jeffrey S. Grethec, David Kennedy, Henning Hermjakobe, Phillippe Rocca-Serraf, Robin Berjong, Sebastian Karcherh, Maryann Martonei, Tim Clark


Abstract: This article presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles (Data Citation Synthesis Group, 2014), a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Early Adopters Expert Group, part of the Data Citation Implementation Pilot (DCIP) project (FORCE11, 2015), an initiative of FORCE11.org and the NIH BioCADDIE (2016) program. The roadmap makes 11 specific recommendations, grouped into three phases of implementation: a) required steps needed to support the Joint Declaration of Data Citation Principles, b) recommended steps that facilitate article/data publication workflows, and c) optional steps that further improve data citation support provided by data repositories.


Citation: Fenner, M., Crosas, M., Grethe, J., Kennedy, D., Hermjakob, H., Rocca-Serra, P., … Clark, T. (2016). A Data Citation Roadmap for Scholarly Data Repositories. bioRxiv. https://doi.org/10.1101/097196