PUG View

PUG View is a REST-style web service that provides information content that is not directly contained within the primary PubChem Substance, Compound, or BioAssay records. Its purpose is primarily to drive the PubChem database summary record web pages, but can also be used independently as a programmatic web service.

 

PUG View is mainly designed to provide complete summary reports on individual PubChem records. Users may also be interested in PUG REST (https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest-tutorial), a different style of service that gives smaller bits of information about one or more PubChem records.

 

An overview of PUG View can be found in the following paper:

 

Kim S, Thiessen PA, Cheng T, Zhang J, Gindulyte A, Bolton EE. PUG-View: programmatic access to chemical annotations integrated in PubChem. J Cheminform. 2019 Aug 9; 11:56. doi:10.1186/s13321-019-0375-2.
[PubMed PMID: 31399858] [PubMed Central PMCID: PMC6688265] [Free Full Text]
USAGE POLICY: Please note that PUG View is not designed for very large volumes (millions) of requests. We ask that any script or application not make more than 5 requests per second, in order to avoid overloading the PubChem servers. To check additional request volume limitations, please read this document. If you have a large data set that you need to compute with, please contact us for help on optimizing your task, as there are likely more efficient ways to approach such bulk queries.
 

Contents:

 

Formats

Record Summaries

Full Records

By Specific Heading

Compounds

Substances

BioAssays

Patents

Genes

Proteins

Pathways

Taxonomies

Cell Lines

Special Reports

Annotations

Source Categories

Neighbors

Literature

Biologics

QR

Linkout

PDB/MMDB Structures

Annotation Attachments

Limitations

 

 

Formats

 

PUG View provides structured information in a variety of formats, specified at the end of the URL path. Most results can be formatted as JSON(P), XML, or ASN.1 as text (ASNT) or base64-encoded binary (ASNB). For example, these all contain exactly the same information, just in different formats:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/JSON

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/JSONP?callback=func

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/XML

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/ASNT

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/ASNB

 

An XML schema is available here. Note that the JSON and ASN.1 formats follow the same content model.

 

https://pubchem.ncbi.nlm.nih.gov/pug_view/pug_view.xsd

 

 

Record Summaries

 

Full Records and Indexes

 

PUG View provides record summaries for the three primary PubChem databases - Compounds, Substances, and BioAssays - as well as patents and targets. Each of these can be accessed as an index, providing a listing of what information is present, but without the entire data content; essentially a table of contents for that record:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/index/compound/1234/JSON

 

Or the complete data can be retrieved:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/JSON

 

This choice of index or full data is applicable to all the primary record types.

 

 

Specific Heading

 

If only a subcategory of information is desired, a heading can be used to restrict the data returned. Note that the index as above is a convenient way to see what headings are present for a given record, as not all records will have all possible headings present. For example, to get just the experimental property section:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/2244/JSON?heading=Experimental+Properties

 

Or even just a single value type, like melting point:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/2244/JSON?heading=Melting+Point

 

Section headings that can be used in PUG-View data retrieval can be found in the PubChem Compound TOC tree (using the PubChem Classification Browswers).

 

https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72
 

 

Compounds

 

Compounds records are accessed by CID number. Note that PUG View provides textual and third-party information associated with the compound, but not the chemical structure, which is handled by other PubChem services.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1234/JSON

 

 

Substances

 

Substances records are accessed by SID number. Information on substances is fairly minimal; in particular, no third party annotation is associated with substances. Again, chemical structure is not part of PUG View’s results.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/substance/1/JSON

 

 

BioAssays

 

BioAssays are accessed by AID number.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/assay/1/JSON

 

 

Patents

 

Patents can be accessed by an identifier string. For USPTO patent grants, this is 'US' followed by a 7-digit number. For applications, it is 'US' followed by a 4-digit year, followed by a 6-digit number.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/patent/US5837728/JSON

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/patent/US2015000048/XML

 

 

Genes

Gene information can be retrieved by NCBI Gene ID:

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/gene/1/JSON

 

 

 Proteins

Protein information can be retrieved by NCBI Protein Accession:

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/protein/P00533/JSON

 

 

 Pathways

Pathway information can be retrieved by Source:ExternalID:

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/pathway/Reactome:R-HSA-70171/JSON/

 

 

 Taxonomies

Taxonomy information can be retrieved by NCBI Taxonomy ID:

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/taxonomy/9606/JSON/

 

 

 Cell Lines

Taxonomy information can be retrieved by Cell Line name (case-insensitive):

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/cell/HeLa/JSON/

 

 

Special Reports

The following are not primary PubChem records, but rather extra information of various sorts that is attached to PubChem records. These reports contain information not present in the main record data described above.

 

Annotations

 

PUG View can provide information of a specific type across all of PubChem’s primary databases. For example, if you are interested in all of the experimental viscosity measurements contained within PubChem and its associated third-party annotations, you can request this by heading:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/Viscosity/JSON

 

Or equivalently (useful if the heading contains special characters not compatible with URL syntax):

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/JSON?heading=Viscosity

 

This will include PubChem identifiers – CIDs in this example – for each data value, along with attribution detailing exactly where each bit of information was obtained.

 

Note that in the new data model, a heading may refer to different types of PubChem records, making it necessary to specify which one is intended:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/Boiling%20Point/XML?heading_type=Compound

 

Also keep in mind that some headings have more data than others, and retrieval is limited. There will be "Page" and "TotalPages" values at the end of the request data, that will indicate the given page number and whether there is more data than shown in the given request (that is, whether TotalPages is greater than one). By default, page #1 is returned, but subsequent pages (up to the TotalPages limit) can be accessed by adding a page argument: 

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/CAS/JSON?page=10

 

Lastly, it is possible to get a complete list of all annotation headings (and their types) for which PubChem has any data, and that can be used in URLs such as the above:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug/annotations/headings/JSON

 

Source Categories

 

PUG View can list all PubChem depositors and their SIDs for a given compound, including a categorization of each source – such as chemical vendor, research and development, journal publishers, etc.:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/categories/compound/1234/JSON

 

 

Neighbors

 

If a given compound has neighbors – other compounds with similar chemical structure – that have useful information like bioactivities or patents, etc., this will give a listing of such neighbors, grouped by information type:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/neighbors/compound/1234/JSON

 

 

Literature

 

This will give URLs into PubMed for literature associated with a compound, organized by subheading:

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/literature/compound/1234/JSON

 

 

Biologics

 

This is used do display biologic images associated with compounds. The integer here is an internal identifier, which will be present in the primary compound record.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/image/biologic/243577/SVG

 

 

QR

 

This is a specialized image generator for QR codes that link to the LCSS page for a compound, intended for safety and hazard labelling.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/qr/short/compound/1234/SVG

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/qr/long/compound/1234/SVG

 

 

Linkout

 

This gives a listing of all the NCBI LinkOut records present for a substance, compound, or assay.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/linkout/compound/1234/JSON

 

 

PDB/MMDB Structures

 

This gives a listing of 3D protein structures associated with a compound. 

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/structure/compound/2244/JSON

 

 

Annotation Attachments

 

This is another specialized retrieval for attachments associated with some records, such as spectral images, etc. This key value will be present in the main record.

 

https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/key/804945_1

 

Limitations

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