Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons

Anamika Chatterjee*, Tsjalling Swierstra, Martin Kuiper

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Current research of gene regulatory mechanisms is increasingly dependent on the availability of high-quality information from manually curated databases. Biocurators undertake the task of extracting knowledge claims from scholarly publications, organizing these claims in a meaningful format and making them computable. In doing so, they enhance the value of existing scientific knowledge by making it accessible to the users of their databases. In this capacity, biocurators are well positioned to identify and weed out information that is of insufficient quality. The criteria that define information quality are typically outlined in curation guidelines developed by biocurators. These guidelines have been prudently developed to reflect the needs of the user community the database caters to. The guidelines depict the standard evidence that this community recognizes as sufficient justification for trustworthy data. Additionally, these guidelines determine the process by which data should be organized and maintained to be valuable to users. Following these guidelines, biocurators assess the quality, reliability, and validity of the information they encounter. In this article we explore to what extent different use cases agree with the inclusion criteria that define positive and negative data, implemented by the database. What are the drawbacks to users who have queries that would be well served by results that fall just short of the criteria used by a database? Finally, how can databases (and biocurators) accommodate the needs of such more explorative use cases?

Original languageEnglish
Article number194779
Number of pages9
JournalBiochimica et Biophysica Acta-Gene Regulatory Mechanisms
Issue number1
Early online date28 Dec 2021
Publication statusPublished - Jan 2022


  • Biocuration
  • Database
  • Pollution

Cite this