Vocabulary for Chemical Species Identification

Markup with HTML microdata attributes annotates domain-specific items on web pages. The following vocabulary defines properties (values of the attribute itemprop) to index HTML5-based web pages and snippets associated with items such as chemical elements and chemical compounds. By annotating chemical species on your web page(s), you will support web crawlers, search engines and future applications to better understand your page content. Microdata wrapping of chemical identifiers promotes successful integration of your information on molecules and materials with the chemical web. See an HTML5 annotation and markup example.

Basic identifiers

AtomSymb Atomic symbol to specify a chemical element
CompName Name of a chemical compound
ElemName Name of a chemical element
ShortName Short name such as an abbreviation or short-term designation
StrucName Name of a structure or substructure including ions, radicals and formal groups
SystName Systematic name derived by application of chemical nomenclature rules
TradeName Trademark name of a chemical product
TrivialName Trivial name of a chemical product

Service-related identifiers

BRN Beilstein registry number assigned by Beilstein Information System
CASRN Chemical Abstract Service registry number assigned by CAS registry system, also see Wikipedia
ChEBI ChEBI ID assigned by database service ChEBI (Chemical Entities of Biological Interest), see ChEBI User Manual
ChEMBL ChEMBL ID assigned by ChEMBLB database of bioactive drug-like small molecules, see blog post on ChEMBL Identifiers
ChemSpider ChemSpider ID assigned by the free chemical database ChemSpider
DrugBank DrugBank ID assigned by DrugBank
EINECS EINECS number of the European Commission (also known as EC number or EC# for short), see registered substances and Wikipedia
KEGG KEGG number assigned by Kyoto Encyclopedia of Genes and Genomes
PubChem PubChem ID assigned PubChem database of chemical molecules and their activities against biological assays (see PubChem Search and PubChem Download Facility Help)
RTECS RTECS number used within the Registry of Toxic Effects of Chemical Substances data compendium
UNII Unique Ingredient Identifier of the U.S. Food and Drug Administration (FDA), see Substance Registration System and Wikipedia

Compositional and structural notations

CurlySMILES Notation based on CurlySMILES language defined in publication and updated at CurlySMILES Project site
Formula Chemical formula in the format used for emprical and molecular formulae, formed by juxtaposition of atomic symbols with appropiate integer subscripts (but without subscript markup); for inclusion of isotopic labels and/or formal charges, the SFN attribute is employable
FormulaSub Chemical formula: same as Formula, but with subscript markup using sub tag
InChI International chemical identifier (format explained at Wikipedia)
SFN Stoichiometric formula notation of the CurlySMILES language (see SFN)
SLN SYBYL line notation (see introduction of SLN Language, Applications and Wikipedia)
SMILES Simplified molecular input line entry specification (see original publication, Daylight SMILES Tutorial , Wikipedia and SMILES ambiguities)

Vocabulary author: Axel Drefahl
Last update: December 19, 2014
Axel at ResearchGate

Custom Search