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ChemBank: a small-molecule screening and cheminformatics resource database.

Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA - Nucleic Acids Res. (2007)

Bottom Line: ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules.Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied.The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

View Article: PubMed Central - PubMed

Affiliation: Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.

ABSTRACT
ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

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Conceptual summary of ChemBank schema. Logical illustration of ChemBank data model, in which 95 tables are organized into groups representing components of the chemical biology research enterprise. Each box represents several actual database tables, as indicated, and pseudocardinality relationships between boxes are meant to convey conceptual relationships, rather than the more complex cardinality relationships that relate the actual tables.
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Figure 1: Conceptual summary of ChemBank schema. Logical illustration of ChemBank data model, in which 95 tables are organized into groups representing components of the chemical biology research enterprise. Each box represents several actual database tables, as indicated, and pseudocardinality relationships between boxes are meant to convey conceptual relationships, rather than the more complex cardinality relationships that relate the actual tables.

Mentions: The ChemBank database consists of 95 tables segmented into seven logical groups representing compound information, molecular descriptors, assay results, assay metadata, biological findings, ontological associations and user information (Figure 1). Data from over 2500 high-throughput biological assays from 188 screening projects currently reside in ChemBank, with new assays loaded quarterly. ChemBank houses information on 1.7 million compound samples, representing more than 1.2 million unique small-molecule structures, with over 300 calculated molecular descriptor values for each molecule. Over 1000 proteins, 500 cell lines and 70 species are associated with the assays. ChemBank data are stored and searched using an Oracle 10g (Oracle Corporation; Redwood Shores, CA, USA) relational database extended with the DayCart Oracle cartridge (Daylight Chemical Information Systems; Aliso Viejo, CA, USA), which is used for molecule substructure and similarity searches.Figure 1.


ChemBank: a small-molecule screening and cheminformatics resource database.

Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA - Nucleic Acids Res. (2007)

Conceptual summary of ChemBank schema. Logical illustration of ChemBank data model, in which 95 tables are organized into groups representing components of the chemical biology research enterprise. Each box represents several actual database tables, as indicated, and pseudocardinality relationships between boxes are meant to convey conceptual relationships, rather than the more complex cardinality relationships that relate the actual tables.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238881&req=5

Figure 1: Conceptual summary of ChemBank schema. Logical illustration of ChemBank data model, in which 95 tables are organized into groups representing components of the chemical biology research enterprise. Each box represents several actual database tables, as indicated, and pseudocardinality relationships between boxes are meant to convey conceptual relationships, rather than the more complex cardinality relationships that relate the actual tables.
Mentions: The ChemBank database consists of 95 tables segmented into seven logical groups representing compound information, molecular descriptors, assay results, assay metadata, biological findings, ontological associations and user information (Figure 1). Data from over 2500 high-throughput biological assays from 188 screening projects currently reside in ChemBank, with new assays loaded quarterly. ChemBank houses information on 1.7 million compound samples, representing more than 1.2 million unique small-molecule structures, with over 300 calculated molecular descriptor values for each molecule. Over 1000 proteins, 500 cell lines and 70 species are associated with the assays. ChemBank data are stored and searched using an Oracle 10g (Oracle Corporation; Redwood Shores, CA, USA) relational database extended with the DayCart Oracle cartridge (Daylight Chemical Information Systems; Aliso Viejo, CA, USA), which is used for molecule substructure and similarity searches.Figure 1.

Bottom Line: ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules.Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied.The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

View Article: PubMed Central - PubMed

Affiliation: Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.

ABSTRACT
ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Show MeSH