5 papers · ranked by Valyu relevance
Michael Statt, Kristopher Brown, Santosh Suram, Linda Hung + 3 more
In this work, we present DBgen, a Python library that provides a framework for defining extract-transform-load (ETL) pipelines to create and populate SQL databases. DBgen is most useful when the underlying data has complex relationships, requires multi-step analysis, is large-scale, and the type of data being collected…
Tiqing Liu, Linda Hwang, Stephen K Burley, Carmen I Nitsche + 3 more
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models, and computational chemistry…
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In recent years, the development of large language models (LLMs) has revolutionized various fields of natural science, yet their application in molecular data processing remains constrained due to the reliance on single-modality inputs and outputs. To bridge the gap between experimenters and computational tools, we…
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Mass spectrometry (MS) generates large datasets that are stored in increasingly optimized and complex file types, demanding technical expertise to extract information rapidly and easily. We wondered whether a simple structured query language (SQL) database could hold raw MS data and allow for easily readable queries…
Michael Statt, Brian Rohr, Dan Guevarra, Ja'Nya Breeden + 2 more
Materials knowledge is inherently hierarchical. While high-level descriptors such as composition and structure are valuable for contextualizing materials data, the data must ultimately be considered in the context of its low-level acquisition details. Graph databases offer an opportunity to represent hierarchical…