PubChem is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). It provides a BioAssay database containing biological test results for over 700,000 compounds. The goal of PubChem is to make this information accessible to biomedical researchers. The article presents web-based tools to facilitate and optimize the use of biological activity information within PubChem. These tools include data retrieval, integration, comparison of screening results, exploratory structure-activity analysis, and target selectivity examination. The BioAssay Summary service provides a detailed overview of deposited bioassay records, including data attribution, assay description, experimental protocol, and screening outcome. It also allows users to review the update history of a bioassay deposition and access biological test results for active compounds. The BioActivity Summary tool allows users to aggregate all available screening results and examine and compare biological outcomes across multiple assays for one or more tested compounds. It provides a comprehensive overview of the biological profile for tested small molecules using up-to-date screening results. The Structure-Activity Analysis tool enables exploratory analysis by clustering compound and assay information using a single linkage clustering methodology. It allows users to compare and contrast screening results by bioactivity profile or assay target similarity, or analyze the activity of compound analog series in a panel of assays to identify SAR. The Data Table tool supports rapid search and retrieval of test results for a single or multiple assay records. It is integrated with the BioActivity Summary and Structure-Activity Analysis services. The Test Result Select tool allows users to search and select assay readouts, filter chemical substances/compounds by bioactivity outcome, bioactivity score or active concentration. The Histogram and Scatter Plot tools enable preliminary data analysis using numerical readouts from one assay. The BLAST search tool allows users to search assay targets and link to the biological test results contained in PubChem. PubChem provides a set of web servers for accessing, retrieving and analyzing biological test results archived in PubChem databases. These tools will be further enhanced towards two directions: develop additional methods to support data analysis and scale up the system for efficient management of the growth of information content and diversity.PubChem is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). It provides a BioAssay database containing biological test results for over 700,000 compounds. The goal of PubChem is to make this information accessible to biomedical researchers. The article presents web-based tools to facilitate and optimize the use of biological activity information within PubChem. These tools include data retrieval, integration, comparison of screening results, exploratory structure-activity analysis, and target selectivity examination. The BioAssay Summary service provides a detailed overview of deposited bioassay records, including data attribution, assay description, experimental protocol, and screening outcome. It also allows users to review the update history of a bioassay deposition and access biological test results for active compounds. The BioActivity Summary tool allows users to aggregate all available screening results and examine and compare biological outcomes across multiple assays for one or more tested compounds. It provides a comprehensive overview of the biological profile for tested small molecules using up-to-date screening results. The Structure-Activity Analysis tool enables exploratory analysis by clustering compound and assay information using a single linkage clustering methodology. It allows users to compare and contrast screening results by bioactivity profile or assay target similarity, or analyze the activity of compound analog series in a panel of assays to identify SAR. The Data Table tool supports rapid search and retrieval of test results for a single or multiple assay records. It is integrated with the BioActivity Summary and Structure-Activity Analysis services. The Test Result Select tool allows users to search and select assay readouts, filter chemical substances/compounds by bioactivity outcome, bioactivity score or active concentration. The Histogram and Scatter Plot tools enable preliminary data analysis using numerical readouts from one assay. The BLAST search tool allows users to search assay targets and link to the biological test results contained in PubChem. PubChem provides a set of web servers for accessing, retrieving and analyzing biological test results archived in PubChem databases. These tools will be further enhanced towards two directions: develop additional methods to support data analysis and scale up the system for efficient management of the growth of information content and diversity.