Abstract
PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies.
Highlights
PubChem [1–3] is a chemical data repository and open chemistry database that aims to provide comprehensive information on various chemical entities, including small molecules, siRNAs, miRNAs, carbohydrates, lipids, peptides, and chemically modified macromolecules
To get annotations corresponding to non-Compound ID (CID) identifiers, they need to be converted to CIDs first and those CIDs should be used in Power User Gateway (PUG)-View requests
The JavaScript Object Notation (JSON)/eXtensible Markup Language [10] (XML) file returned from a PUG-View request for such data usually have nodes called “ExternalTableName” and “ExternalTableNumRows”, as exemplified in the output returned from the following request: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/60823/JSON?heading=Depositor+Provided+PubMed+Citations
Summary
PubChem (https://pubchem.ncbi.nlm.nih.gov) [1–3] is a chemical data repository and open chemistry database that aims to provide comprehensive information on various chemical entities, including small molecules, siRNAs, miRNAs, carbohydrates, lipids, peptides, and chemically modified macromolecules. Available (sub)headings (“indices”) for CID 1983 https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/ index/compound/1983/JSON This request returns the Table of Contents for the Summary page of CID 1983, without the entire data content of the record. The data presented can be retrieved using the following PUG-View request URL: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/categories/compound/24/JSON. The data content presented may be retrieved through PUG-View, using the following request URL: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/ neighbors/compound/60823/JSON. Note that this request returns only the neighbors with pre-defined types of annotations. The following URL retrieves papers about the synthesis of CID 2244 (aspirin), presented in the “Synthesis Reference” section: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/2244/JSON?heading=Synthesis+References. Each spectral image on this page has a unique key, which can be found in the annotation data returned from the following PUG-View request: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/7510/JSON?heading=Mass+Spectrometry. PUG-View can be used to retrieve a list of all the NCBI LinkOut data available for a compound record, as shown in this example (for CID 2244): https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/linkout/compound/2244/JSON
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