PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem

By Sunghwan Kim, Paul A. Thiessen, Evan E. Bolton, Stephen H. Bryant. 2015

99 citations recorded by the source corpus.

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, developed and maintained by the US National Institutes of Health (NIH). PubChem contains more than 180 million depositor-provided chemical substance descriptions, 60 million unique chemical structures and 225 million bioactivity assay results, covering more than 9000 unique protein target sequences. As an information resource for the chemical biology research community, it routinely receives more than 1 million requests per day from an estimated more than 1 million unique users per month. Programmatic access to this vast amount of data is provided by several different systems, including the US National Center for Biotechnology Information (NCBI)'s Entrez Utilities (E-Utilities or E-Utils) and the PubChem Power User Gateway (PUG)—a common gateway interface (CGI) that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides two additional general purpose web services: PUG-SOAP, which uses the simple object access protocol (SOAP) and PUG-REST, which is a Representational State Transfer (REST)-style interface. These interfaces can be harnessed in combination to access the data contained in PubChem, which is integrated with the more than thirty databases available within the NCBI Entrez system.

Subfields: Molecular Biology, Pharmacology

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Citations in the corpus

PubChem Substance and Compound databases (2015, methodology): “PUG-REST is the simplest programmatic access tool to use and learn because it does not require the overhead of XML and SOAP envelopes.”
PubChem 2019 update: improved access to chemical data (2018, background): “Our previous papers (27,28) describe multiple programmatic access routes to PubChem data, including Entrez Utilities (E-Utilities), Power User Gateway (PUG), PUGSOAP and PUG-REST (see Table 1).”
PubChem in 2021: new data content and improved web interfaces (2020, methodology): “In addition, these data are not only available through the web interfaces but also programmatically through PUG-REST (23,24) and PUG-View (25).”
PubChem BioAssay: 2017 update (2016, background): “html) (38), which provide great flexibility for retrieving AID specific metadata and assay result, database links and bioactivity data across multiple assays for a compound or target; (iv) Daily updated PubChem BioAssay FTP at ftp://ftp.”