Biology subjects

Imker, H. J.

Publications and source records attributed to Imker, H. J..

4 recordsLinked to original sources

bioRxiv2025

Sustainability During Instability: Long-Lived Life Science Databases and Science Funding Outlook in the United States

For decades, life science researchers have had cost-free, unrestricted access to data through online databases. However, the sustainability of even well-established resources was already tenuous, and abrupt changes in science funding in the United States seems poised to exacerbate these challenges. This study employed a multiple mini case study approach, triangulating semi-structured interviews with supplemental documentation to investigate 9 diverse, long-standing databases that had previously received support from U.S. federal agencies. The research explored each databases purpose and use, examined current and emerging funding strategies, and considered the potential consequences if any of these databases were forced to shut down. Participating databases include: 1) BHL: Biodiversity Heritage Library, 2) MorphoBank, 3) OMIM: Online Mendelian Inheritance in Man, 4) ORDB: Olfactory Receptor Database, 5) rrnDB: ribosomal RNA operon copy number database, 6) VEuPathDB: Eukaryotic Pathogen, Vector, and Host Informatics Resources, 7) WormAtlas, and 8-9) two databases that wished to remain anonymous. Findings revealed anticipation of higher barriers to data access and reuse, loss of subject matter expertise now and into the future, and lost or interrupted opportunities. Additionally, real impacts have already begun through redirection of energy, abrupt reductions in support, and increased competition for funding. Sustainability models in light of the current funding outlook in the US are discussed.

bioinformatics↗

bioRxiv2025

Analyzing the Naming Conventions of Life Science Data Resources to Inform Human and Computational Findability

This study aimed to evaluate the names of life science data resources and consider the impacts on findability, a core feature of the FAIR (Findability, Accessibility, Interoperability, and Reusability) Principles. Utilizing a previously published list of unique data resources, we identified and validated data resources with both common and full names available (n = 1153). From this set, we analyzed characteristics of resource names to identify if any naming conventions have emerged organically. Additionally, since common names are often used in the absence of a resources full name, we performed a test to evaluate our ability to infer any meaning from common names. Our results highlight suboptimal naming practices and a wide-spread opaqueness in common names, which poses challenges to resource identification and retrieval by both human-and computationally-centric methods. These results are informative for those who establish and promote data resources as well as for those who search for data to use in individual research projects, develop data discovery systems, analyze the scientific literature, or assess research infrastructure. The findings underscore the value of findability in the FAIR Principles and the current efforts to develop infrastructure that supports more efficient communication and global connectedness.

bioinformatics↗

bioRxiv2019

Who Bears the Burden of Long-Lived Molecular Biology Databases?

In the early 1990s the life sciences quickly adopted online databases to facilitate wide-spread dissemination and use of scientific data. From 1991, the journal Nucleic Acids Research has published an annual Database Issue dedicated to articles describing molecular biology databases. Analysis of these articles reveals a set of long-lived databases which have now remained available for more than 15 years. Given the pervasive challenge of sustaining community resources, these databases provide an opportunity to examine what factors contribute to persistence by addressing two questions 1) which organizations fund these long-lived databases? and 2) which organizations maintain these long-lived databases? Funding and operating organizations for 67 databases were determined through review of Database Issue articles. The results reveal a diverse set of contributing organizations with financial and operational support spread across six categories: academic, consortium/collective, government, industry, philanthropic, and society/association. The majority of databases reported support from more than one funding organization, of which government organizations were most common source of funds. Operational responsibilities were more distributed, with academic organizations serving as the most common hosts. Although overall there is evidence of diversification, the most acknowledged funding and operating organizations contribute to disproportionately large percentages of the long-lived databases investigated here.

scientific communication and education↗

bioRxiv2018

25 Years of Molecular Biology Databases: A Study of Proliferation, Impact, and Maintenance

Online resources enable unfettered access to and analysis of scientific data and are considered crucial for the advancement of modern science. Despite the clear power of online data resources, including web-available databases, proliferation can be problematic due to challenges in sustainability and long-term persistence. As areas of research become increasingly dependent on access to collections of data, an understanding of the scientific communitys capacity to develop and maintain such resources is needed.\n\nThe advent of the Internet coincided with expanding adoption of database technologies in the early 1990s, and the molecular biology community was at the forefront of using online databases to broadly disseminate data. The journal Nucleic Acids Research has long published articles dedicated to the description of online databases, as either debut or update articles. Snapshots throughout the entire history of online databases can be found in the pages of Nucleic Acids Research s \"Database Issue.\" Given the prominence of the Database Issue in the molecular biology and bioinformatics communities and the relative rarity of consistent historical documentation, database articles published in Database Issues provide a particularly unique opportunity for longitudinal analysis.\n\nTo take advantage of this opportunity, the study presented here first identifies each unique database described in 3055 Nucleic Acids Research Database Issue articles published between 1991-2016 to gather a rich dataset of databases debuted during this time frame, regardless of current availability. In total, 1727 unique databases were identified and associated descriptive statistics were gathered for each, including year debuted in a Database Issue and the number of all associated Database Issue publications and accompanying citation counts. Additionally, each database identified was assessed for current availability through testing of all associated URLs published. Finally, to assess maintenance, database websites were inspected to determine the last recorded update. The resulting work allows for an examination of the overall historical trends, such as the rate of database proliferation and attrition as well as an evaluation of citation metrics and on-going database maintenance.

molecular biology↗