Table 1.

Content and feature comparison between ChemBank v2.0 and PubChem

Database content/feature	ChemBank v2.0	PubChem
Chemical structure	>1.2 million unique	>10 million unique
Molecule names/synonyms	IUPAC and manually curated names/synonyms	IUPAC and depositor-supplied synonyms
Molecular descriptors	36 searchable plus >300 displayed calculated properties and descriptors per molecule	18 calculated chemical properties, atom types and stereochemistry flags per molecule
Literature annotations	Manually curated; connected to controlled vocabularies	Extensive linking to Entrez databases
Metadata describing screens	Extensive field-based metadata collected (some displayed); standardized terms connected to controlled vocabularies	Depositor-supplied comments; primarily free-text, no standard controlled vocabularies for assay components
Biological assay data	Raw data required with plate locations (except legacy ChemBank v1. × data sets); standard data-analysis model	∼15% of assays display raw data; no standardized analysis performed beyond submitter interpretations
Screening assay analysis and visualization tools	Plate-map, histogram, scatterplot and multi-assay heat-map visualizations	Structure-activity relationship analyses; clustering visualizations
Public data submission	Required for Broad Institute screening center; limited external submissions	Required for Molecular Libraries Screening Centers; others may submit voluntarily