A Java API for working with PubChem datasets

PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Powe...

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Veröffentlicht in:Bioinformatics (Oxford, England) Jg. 27; H. 5; S. 741 - 742
Hauptverfasser: Southern, Mark R., Griffin, Patrick R.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Oxford Oxford University Press 01.03.2011
Schlagworte:
Applications Note
Biological and medical sciences
Computational Biology - methods
Databases, Factual
Fundamental and applied biological sciences. Psychology
General aspects
Information Storage and Retrieval - methods
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Programming Languages
Software
Java
Asia
Indonesia
JAVA language
ISSN:1367-4803, 1367-4811, 1367-4811
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Zusammenfassung:PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability:  http://code.google.com/p/pubchemdb Contact:  southern@scripps.edu
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SourceType-Scholarly Journals-1
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Associate Editor: Martin Bishop
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btq715