A Web Resource for Exploring the CORD-19 Dataset Using Root- and Rule-Based Phrases.

This short paper describes a web resource-the NIST CORD-19 Web Resource-for community explorations of the COVID-19 Open Research Dataset (CORD-19). The tools for exploration in the web resource make use of the NIST-developed Root- and Rule-based method, which exploits underlying linguistic structures to create terms that represent phrases in a corpus. The method allows for auto-suggesting-related terms to discover terms to refine the search of a COVID-19 heterogenous document base.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive.

New concepts for building vocabulary for cell image ontologies.

Background: There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms.

Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry.

Unlabelled: The Thermodynamics of Enzyme-catalyzed Reactions Database (TECRDB) is a comprehensive collection of thermodynamic data on enzyme-catalyzed reactions. The data, which consist of apparent equilibrium constants and calorimetrically determined molar enthalpies of reaction, are the primary experimental results obtained from thermodynamic studies of biochemical reactions. The results from approximately 1000 published papers containing data on approximately 400 different enzyme-catalyzed reactions constitute the essential information in the database.