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Chemical Markup Language

Abbreviation: CML

General Information

CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. CML covers most mainstream chemistry and especially molecules, reactions, solid-state, computation and spectroscopy as well as a wide range of chemical properties, parameters and experimental observation. It is particularly concerned with the communication between machines and humans, and machines to machines.

Homepage http://www.xml-cml.org/spec/

Countries that developed this resource United Kingdom

Created in 1995

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: CML; Chemical Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.3mdt9n; Last edited: June 22, 2021, 2:23 p.m.; Last accessed: Dec 06 2021 9:23 p.m.

Record updated: June 22, 2021, 2:03 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.3mdt9n' by 'The FAIRsharing Team' at 14:03, 22 Jun 2021 (approved):

	'onto_domains' has been modified:
		Before:
			Mathematical model
			Reaction data
			Structure
			molecular entity
			spectroscopy
		After:
			Mathematical model
			Reaction data
			Structure
			modeling and simulation objective
			molecular entity
			spectroscopy
		Added:
			modeling and simulation objective
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Edits to 'https://fairsharing.org/FAIRsharing.3mdt9n' by 'The FAIRsharing Team' at 13:30, 11 May 2021 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.xml-cml.org/documentation/FAQ.html
			help|http://www.xml-cml.org/documentation/index.html
			mailing list|cml-discuss@lists.sourceforge.net
			schema file|http://www.xml-cml.org/schema/schema24/
			schema file|http://www.xml-cml.org/schema/schema3/
			training|http://www.xml-cml.org/tutorial/
		After:
			FAQ|http://www.xml-cml.org/documentation/FAQ.html
			help|http://www.xml-cml.org/documentation/index.html
			mailing list|cml-discuss@lists.sourceforge.net
			training|http://www.xml-cml.org/tutorial/
		Added:
		Removed:
			schema file|http://www.xml-cml.org/schema/schema24/
			schema file|http://www.xml-cml.org/schema/schema3/

	'dataProcesses' has been modified:
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		After:
			Download Specification, data release, http://www.xml-cml.org/schema/schema24/
			Download Specification, data release, http://www.xml-cml.org/schema/schema3/
		Added:
			Download Specification, data release, http://www.xml-cml.org/schema/schema24/
			Download Specification, data release, http://www.xml-cml.org/schema/schema3/
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.3mdt9n' by 'The FAIRsharing Team' at 16:01, 06 May 2021 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.xml-cml.org/documentation/FAQ.html
			help|http://www.xml-cml.org/documentation/index.html
			mailing list|cml-discuss@lists.sourceforge.net
			schema file|http://www.xml-cml.org/schema/schema24/
			training|http://www.xml-cml.org/tutorial/
		After:
			FAQ|http://www.xml-cml.org/documentation/FAQ.html
			help|http://www.xml-cml.org/documentation/index.html
			mailing list|cml-discuss@lists.sourceforge.net
			schema file|http://www.xml-cml.org/schema/schema24/
			schema file|http://www.xml-cml.org/schema/schema3/
			training|http://www.xml-cml.org/tutorial/
		Added:
			schema file|http://www.xml-cml.org/schema/schema3/
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.3mdt9n' by 'The FAIRsharing Team' at 10:26, 15 Mar 2018 (approved):

	'related_standards' has been modified:
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			bsg-s001143|Extensible Markup Language
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			bsg-s001143|Extensible Markup Language
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Edits to 'https://fairsharing.org/FAIRsharing.3mdt9n' by 'The FAIRsharing Team' at 10:26, 15 Mar 2018 (approved):

	'miriam_url' has been modified:
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Edits to 'https://fairsharing.org/FAIRsharing.3mdt9n' by 'The FAIRsharing Team' at 22:00, 27 Nov 2016 (approved):

'description' has been modified:
Before: CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. CML covers most mainstream chemistry and especially molecules, reactions, solid-state, computation and spectroscopy. Since it has a special flexible approach to numeric science it also covers a very wide range of chemical properties, parameters and experimental observation. It is particularly concerned with the communication between machines and humans, and machines to machines. It has been heavily informed by the current chemical scholarly literature and chemical databases. XML is a mainstream approach providing semantics for science, such as MathML, SBML/BIOPAX (biology), GML and KML (geo) SVG (graphics) and NLM-DTD, ODT and OOXML (documents). CML provides support for most chemistry, especially molecules, compounds, reactions, spectra, crystals and computational chemistry (compchem). CML has been developed by Peter Murray-Rust and Henry Rzepa since 1995. It is the de facto XML for chemistry, accepted by publishers and with more than 1 million lines of Open Source code supporting it. CML can be validated and built into authoring tools (for example the Chemistry Add-in for Microsoft Word). A list of CML-compliant and CML-aware software can be found on the software page. The infrastructure includes legacy converters, dictionaries and conventions, Semantic Web and Linked Open Data. There are several versions of the CML schema. The most recent schema is schema 3. This essentially relaxes many of the constraints imposed in the previous stable release (schema 2.4), allowing users to put together the elements and attributes in a more flexible manner to fit the data that they want to represent more easily.
After: CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. CML covers most mainstream chemistry and especially molecules, reactions, solid-state, computation and spectroscopy as well as a wide range of chemical properties, parameters and experimental observation. It is particularly concerned with the communication between machines and humans, and machines to machines. Domain list has changed: Previous values: Biochemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100610 Chemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100618 Computational modeling|process| Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367 Molecular structure|information content entity|http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Chemical.owl#CHEBI_24431 Reaction|| Spectroscopy|| New values: Biochemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100610 Chemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100618 Computational modeling|process| Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367 Molecular structure|information content entity|http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Chemical.owl#CHEBI_24431 Reaction|| Spectroscopy|| Life Science|domain| Publication List has changed: Previous values: Chemical markup|XML|and the World Wide Web. 4. CML schema. New values: Chemical markup|XML|and the World Wide Web. 4. CML schema Organisations have changed: Previous values: CML authors Peter Murray-Rust and Henry Rzepa New values: CML Administrators Cambridge University Support links have changed: Previous values: http://www.xml-cml.org/documentation/FAQ.html http://www.xml-cml.org/documentation/index.html cml-discuss[at]lists.sourceforge.net http://www.xml-cml.org/schema/schema24/ New values: http://www.xml-cml.org/documentation/FAQ.html http://www.xml-cml.org/documentation/index.html cml-discuss[at]lists.sourceforge.net http://www.xml-cml.org/schema/schema24/ http://www.xml-cml.org/tutorial/

In Collections

Chemistry

Support

General

FAQ	http://www.xml-cml.org/documentation/FAQ ...
help	http://www.xml-cml.org/documentation/ind ...
Mailing List	CML Mailing list
training	http://www.xml-cml.org/tutorial/

Additional Information

Contact

Peter Murray-Rust ORCID

Tools

CML aware tools

http://www.xml-cml.org/tools/software.html

Schemas

Name: CML
Version: 3.0

Download

Name: CML
Version: 2.4

Download

Access / Retrieve Data

Conditions of Use

Data Release

Download Specification	http://www.xml-cml.org/schema/schema24/
Download Specification	http://www.xml-cml.org/schema/schema3/

Publications

Chemical markup, XML, and the World Wide Web. 4. CML schema

Murray-Rust P, Rzepa HS
J Chem Inf Comput Sci 2003

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Extensible Markup Language

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (3)

Rhea
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.

Chemical Component Dictionary
The Chemical Component Dictionary is an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.

eCrystals
eCrystals is the archive for Crystal Structures generated by the Southampton Chemical Crystallography Group and the EPSRC UK National Crystallography Service. It contains all the fundamental and derived data resulting from a single crystal X-ray structure determination, but excluding the raw images.

Implementing Policies

This record is not implemented by any policy.

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Record Maintainer

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Maintains

Chemical Markup Language (CML) Administrators (Consortium)
Cambridge University, Cambridge, UK (University)

Chemical Markup Language

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