Registry PubChem compound

PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.

Prefix

pubchem.compound

Alternative Prefixes

Pubchem CID DSSTox_CID PUBCHEM_CID pubchem_id PubChem_Compound_CID

Keywords

chemical chemistry epidemiology metabolite structure virology

Links

Homepage

Contact

Evan E Bolton 0000-0002-5959-6190

Pattern for Local Unique Identifiers

Local identifiers in PubChem compound should match this regular expression:
^\d+$

Example Local Unique Identifier

100101 Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from PubChem compound should match this regular expression:
^pubchem\.compound:\d+$

Example CURIE

pubchem.compound:100101

Publications

Ontology

A summary of the relations in the Semantic Farm schema can be found here.

In Collection: Synapse.org external links

Metaregistry PubChem compound

The metaregistry provides mappings between the Semantic Farm and other registries. There are 15 mappings to external registries for this resource with 12 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BioContext	`biocontext`	`PUBCHEM.COMPOUND`
Biolink	`biolink`	`CID`
Cellosaurus	`cellosaurus`	`PubChem`
CHEMINF	`cheminf`	`000140`
EDAM	`edam`	`2639`
FAIRSharing	`fairsharing`	`FAIRsharing.qt3w7z`
GO	`go`	`PubChem_Compound`
Integbio	`integbio`	`nbdc02626`
Identifiers.org	`miriam`	`pubchem.compound`
N2T	`n2t`	`pubchem.compound`
Pathguide	`pathguide`	`361`
Prefix Commons	`prefixcommons`	`pubchem.compound`
re3data	`re3data`	`r3d100010129`
TogoID	`togoid`	`PubchemCompound`
Wikidata	`wikidata`	`P662`

RDF Information

When using this resource in RDF, the following URI format should be used:

http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 100101 is used to demonstrate the providers available for PubChem compound. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Name	Metaprefix	URI
PubChem compound	`pubchem.compound`	https://pubchem.ncbi.nlm.nih.gov/compound/100101
PubChem compound (RDF)	`rdf`	http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID100101
Bioregistry	`bioregistry`	https://bioregistry.io/pubchem.compound:100101
Identifiers.org	`miriam`	https://identifiers.org/pubchem.compound:100101
Name-to-Thing	`n2t`	https://n2t.net/pubchem.compound:100101

Extra Providers

Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Code	Name	URL
`bio2rdf`	Bio2RDF	http://bio2rdf.org/pubchem.compound:100101
`scholia`	Scholia	https://scholia.toolforge.org/pubchem/100101

Normalize prefixes. This can be any capitalization or punctuation variant of the synonyms listed below.

>>> import bioregistry as br
>>> br.normalize_prefix("Pubchem")
'pubchem.compound'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("pubchem.compound")
{'Pubchem', 'CID', 'DSSTox_CID', 'PUBCHEM_CID', 'pubchem_id', 'PubChem_Compound_CID'}

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("pubchem.compound")
'PubChem compound'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("pubchem.compound")
'https://pubchem.ncbi.nlm.nih.gov/'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("pubchem.compound")
'Evan E Bolton'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("pubchem.compound")
'bolton@ncbi.nlm.nih.gov'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("pubchem.compound")
'0000-0002-5959-6190'