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bioRxiv · 10.1101/2021.06.25.449966

DatumKB: A Database of Biological Experimental Results

Knapp, M.·McCarthy, T.·Talcott, C.
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Abstract

1.DatumKB is a freely accessible database of experimental results involving the function and regulation of human proteins in cultured cells. The results are manually curated from biological research literature using a shorthand language and stored as datums. Datums were originally designed to be used as evidence for rules in a Pathway Logic model of intracellular signal transduction (STM8, http://pl.csl.sri.com/online.html) (1). They are independent units that can be understood by biologists, traced back to their source, and have enough structure to be interrogated computationally. The information is expressed using a controlled vocabulary with links to well known databases such as HUGO Gene Nomenclature Committee (HGNC), UniProt, PubChem, and Cellosaurus. DatumKB can be searched using a query interface and the results can be downloaded in the original datum format, a simplified text format, or a JSON file. Links to detailed documentation of datum structure and a tutorial for the search engine are provided. Database URLhttps://datum.csl.sri.com

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Knapp, M., McCarthy, T., Talcott, C.. 2021-06-26. DatumKB: A Database of Biological Experimental Results. https://doi.org/10.1101/2021.06.25.449966

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