Search

Text Color

Margin Size

Font Type

Enable Dyslexic Font

1.7: Accessing PubChem through a Web Interface

Last updated

Jul 26, 2022
Save as PDF
- 1.6: Installing Mathematica
- 1.8: Programmatic Access to the PubChem Database

$\newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}}$

$\newcommand{\id}{\mathrm{id}}$ $\newcommand{\Span}{\mathrm{span}}$

( \newcommand{\kernel}{\mathrm{null}\,}\) $\newcommand{\range}{\mathrm{range}\,}$

$\newcommand{\RealPart}{\mathrm{Re}}$ $\newcommand{\ImaginaryPart}{\mathrm{Im}}$

$\newcommand{\Argument}{\mathrm{Arg}}$ $\newcommand{\norm}[1]{\| #1 \|}$

$\newcommand{\inner}[2]{\langle #1, #2 \rangle}$

$\newcommand{\Span}{\mathrm{span}}$

$\newcommand{\id}{\mathrm{id}}$

$\newcommand{\Span}{\mathrm{span}}$

$\newcommand{\kernel}{\mathrm{null}\,}$

$\newcommand{\range}{\mathrm{range}\,}$

$\newcommand{\RealPart}{\mathrm{Re}}$

$\newcommand{\ImaginaryPart}{\mathrm{Im}}$

$\newcommand{\Argument}{\mathrm{Arg}}$

$\newcommand{\norm}[1]{\| #1 \|}$

$\newcommand{\inner}[2]{\langle #1, #2 \rangle}$

$\newcommand{\Span}{\mathrm{span}}$ $\newcommand{\AA}{\unicode[.8,0]{x212B}}$

$\newcommand{\vectorA}[1]{\vec{#1}} % arrow$

$\newcommand{\vectorAt}[1]{\vec{\text{#1}}} % arrow$

$\newcommand{\vectorB}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vectorC}[1]{\textbf{#1}}$

$\newcommand{\vectorD}[1]{\overrightarrow{#1}}$

$\newcommand{\vectorDt}[1]{\overrightarrow{\text{#1}}}$

$\newcommand{\vectE}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash{\mathbf {#1}}}}$

$\newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}}$

$\newcommand{\avec}{\mathbf a}$

$\newcommand{\bvec}{\mathbf b}$

$\newcommand{\cvec}{\mathbf c}$

$\newcommand{\dvec}{\mathbf d}$

$\newcommand{\dtil}{\widetilde{\mathbf d}}$

$\newcommand{\evec}{\mathbf e}$

$\newcommand{\fvec}{\mathbf f}$

$\newcommand{\nvec}{\mathbf n}$

$\newcommand{\pvec}{\mathbf p}$

$\newcommand{\qvec}{\mathbf q}$

$\newcommand{\svec}{\mathbf s}$

$\newcommand{\tvec}{\mathbf t}$

$\newcommand{\uvec}{\mathbf u}$

$\newcommand{\vvec}{\mathbf v}$

$\newcommand{\wvec}{\mathbf w}$

$\newcommand{\xvec}{\mathbf x}$

$\newcommand{\yvec}{\mathbf y}$

$\newcommand{\zvec}{\mathbf z}$

$\newcommand{\rvec}{\mathbf r}$

$\newcommand{\mvec}{\mathbf m}$

$\newcommand{\zerovec}{\mathbf 0}$

$\newcommand{\onevec}{\mathbf 1}$

$\newcommand{\real}{\mathbb R}$

$\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}$

$\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}$

$\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}$

$\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}$

$\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}$

$\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}$

$\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}$

$\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}$

$\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}$

$\newcommand{\laspan}[1]{\text{Span}\{#1\}}$

$\newcommand{\bcal}{\cal B}$

$\newcommand{\ccal}{\cal C}$

$\newcommand{\scal}{\cal S}$

$\newcommand{\wcal}{\cal W}$

$\newcommand{\ecal}{\cal E}$

$\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}$

$\newcommand{\gray}[1]{\color{gray}{#1}}$

$\newcommand{\lgray}[1]{\color{lightgray}{#1}}$

$\newcommand{\rank}{\operatorname{rank}}$

$\newcommand{\row}{\text{Row}}$

$\newcommand{\col}{\text{Col}}$

$\renewcommand{\row}{\text{Row}}$

$\newcommand{\nul}{\text{Nul}}$

$\newcommand{\var}{\text{Var}}$

$\newcommand{\corr}{\text{corr}}$

$\newcommand{\len}[1]{\left|#1\right|}$

$\newcommand{\bbar}{\overline{\bvec}}$

$\newcommand{\bhat}{\widehat{\bvec}}$

$\newcommand{\bperp}{\bvec^\perp}$

$\newcommand{\xhat}{\widehat{\xvec}}$

$\newcommand{\vhat}{\widehat{\vvec}}$

$\newcommand{\uhat}{\widehat{\uvec}}$

$\newcommand{\what}{\widehat{\wvec}}$

$\newcommand{\Sighat}{\widehat{\Sigma}}$

$\newcommand{\lt}{<}$

$\newcommand{\gt}{>}$

$\newcommand{\amp}{&}$

$\definecolor{fillinmathshade}{gray}{0.9}$

PUG

PUG stands for Power User Gateway and is an Application Program Interface (API) service PubChem offers that allows users to access data programmatically. Access to this data is done through a REST or SOAP. REST is a web service type of architecture and uses web URIs (Uniform Resource identifiers). A URI is similar to the common web URL (Uniform Resource Locater) that browsers use to find web pages, but is associated with an object that may, or may not be a webpage (a URL is a type of URI). REST can provide data in many file formats, like text, html and jpeg. SOAP (Simple Object Access Protocol) is actually a protocol that works with XML files and is typically used for organizations that need higher levels of security. Although PUG works with both SOAP and REST, this course will focus on the use of REST interfaces.

REST Architecture

REST = Representational State Transfer is a way for computers to communicate over the web, where one computer may be a database server and the other is the client. One advantage to REST interfaces is that they are built upon the internet's Hypertext Transfer Protocol (http) that web browsers use, and which most people are familiar with. In essence, they are a special type of URL that interacts with specific objects with a database. A REST request is analogous to a sentence where the noun is the object and the verb is the action. Here are some typical REST verbs

GET - retrieve a resource/object
POST - upload a resource/object
PUT - update a resource/object
DELETE - remove a resource/object

In PubChem data is stored of essentially three types, each with its own identifier; compound (CID), substance (SID) and BioAssay (AID). The following figure shows the general process where you input a name, that gets converted to an identifier, and you then perform an operation to produce the type of object you are seeking and then returns an output of the file type that you are seeking.

Figure $\PageIndex{1}$ : Flow chart for a REST request in PubChem (Image Credit: PubChem)

The PUG REST request is based on http (or https) and we can consider the URL to consist of four parts; the prolog, input, operation and output

https://pubchem.ncbi.nlm.nih.gov/rest/pug	/compound/name/aspirin	/property/InChI	/TXT
prolog	input	operation	output

Prolog

The prolog essentially identifies the API service being used in the request.

Input

There are a variety of input methods supported

By Identifier

/substance/sid/[insert: substance ID]

/compound/cid/[insert: compound ID]

/assay/aid/[insert: Assay ID]

Examples

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/999/synonyms/txt

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/15/png

For a list of properties

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/1,2,3,4,5/property/MolecularFormula,MolecularWeight,CanonicalSMILES/CSV

For a summary of assay 999

https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/999/summary/JSON

By Name

/compound/name/[insert: name of chemical]

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/glucose/PNG

By Structure

If you have a structural drawing software you can convert you image to a SMILES string or InChI Key and search with that

/compound/smiles/[insert: smiles string here]/[output]/file type

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/CC(=O)C/property/IUPACName/txt

Operation

There is a variety of data available.

Images

Images are available for all types of structure input, just finish with png

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/THC/PNG

Synonyms

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/THC/synonyms/txt

Compound Properties

Note, these are computed properties. Actual experimental values are not available because there can be more than one value for the same property.

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/THC/property/MolecularWeight/txt

The following properties can be obtained through the REST architecture

Property	Notes
MolecularFormula	Molecular formula.
MolecularWeight	The molecular weight is the sum of all atomic weights of the constituent atoms in a compound, measured in g/mol. In the absence of explicit isotope labelling, averaged natural abundance is assumed. If an atom bears an explicit isotope label, 100% isotopic purity is assumed at this location.
CanonicalSMILES	Canonical SMILES (Simplified Molecular Input Line Entry System) string. It is a unique SMILES string of a compound, generated by a “canonicalization” algorithm.
IsomericSMILES	Isomeric SMILES string. It is a SMILES string with stereochemical and isotopic specifications.
InChI	Standard IUPAC International Chemical Identifier (InChI). It does not allow for user selectable options in dealing with the stereochemistry and tautomer layers of the InChI string.
InChIKey	Hashed version of the full standard InChI, consisting of 27 characters.
IUPACName	Chemical name systematically determined according to the IUPAC nomenclatures.
XLogP	Computationally generated octanol-water partition coefficient or distribution coefficient. XLogP is used as a measure of hydrophilicity or hydrophobicity of a molecule.
ExactMass	The mass of the most likely isotopic composition for a single molecule, corresponding to the most intense ion/molecule peak in a mass spectrum.
MonoisotopicMass	The mass of a molecule, calculated using the mass of the most abundant isotope of each element.
TPSA	Topological polar surface area, computed by the algorithm described in the paper by Ertl et al.
Complexity	The molecular complexity rating of a compound, computed using the Bertz/Hendrickson/Ihlenfeldt formula.
Charge	The total (or net) charge of a molecule.
HBondDonorCount	Number of hydrogen-bond donors in the structure.
HBondAcceptorCount	Number of hydrogen-bond acceptors in the structure.
RotatableBondCount	Number of rotatable bonds.
HeavyAtomCount	Number of non-hydrogen atoms.
IsotopeAtomCount	Number of atoms with enriched isotope(s)
AtomStereoCount	Total number of atoms with tetrahedral (sp3) stereo [e.g., (R)- or (S)-configuration]
DefinedAtomStereoCount	Number of atoms with defined tetrahedral (sp3) stereo.
UndefinedAtomStereoCount	Number of atoms with undefined tetrahedral (sp3) stereo.
BondStereoCount	Total number of bonds with planar (sp2) stereo [e.g., (E)- or (Z)-configuration].
DefinedBondStereoCount	Number of atoms with defined planar (sp2) stereo.
UndefinedBondStereoCount	Number of atoms with undefined planar (sp2) stereo.
CovalentUnitCount	Number of covalently bound units.
Volume3D	Analytic volume of the first diverse conformer (default conformer) for a compound.
XStericQuadrupole3D	The x component of the quadrupole moment (Qx) of the first diverse conformer (default conformer) for a compound.
YStericQuadrupole3D	The y component of the quadrupole moment (Qy) of the first diverse conformer (default conformer) for a compound.
ZStericQuadrupole3D	The z component of the quadrupole moment (Qz) of the first diverse conformer (default conformer) for a compound.
FeatureCount3D	Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
FeatureAcceptorCount3D	Number of hydrogen-bond acceptors of a conformer.
FeatureDonorCount3D	Number of hydrogen-bond donors of a conformer.
FeatureAnionCount3D	Number of anionic centers (at pH 7) of a conformer.
FeatureCationCount3D	Number of cationic centers (at pH 7) of a conformer.
FeatureRingCount3D	Number of rings of a conformer.
FeatureHydrophobeCount3D	Number of hydrophobes of a conformer.
ConformerModelRMSD3D	Conformer sampling RMSD in Å.
EffectiveRotorCount3D	Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)
ConformerCount3D	The number of conformers in the conformer model for a compound.
Fingerprint2D	Base64-encoded PubChem Substructure Fingerprint of a molecule.

Output

The following output formats are supported

Output Format	Description
XML	standard XML, for which a schema is available
JSON	JSON, JavaScript Object Notation
JSONP	JSONP, like JSON but wrapped in a callback function
ASNB	standard binary ASN.1, NCBI’s native format in many cases
ASNT	NCBI’s human-readable text flavor of ASN.1
SDF	chemical structure data
CSV	comma-separated values, spreadsheet compatible
PNG	standard PNG image data
TXT	plain text

Sources

PUG REST Tutorial https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest-tutorial

PUG