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Microbiological Common Language (MCL) project: overview

MCL is a data exchange standard for microbiological information. In short, MCL defines terms which can be used to reference and describe microorganisms. It is designed to form a simple and generic framework leveraging the electronical exchange of information about microorganisms. MCL is loosely coupled from its actual representation technologies and is currently used to structure XML and RDF files (see examples).

An introduction to the background of the standard and its use cases can be found in:
Verslyppe, B., Kottmann, R., De Smet, W., De Baets, B., De Vos, P., and Dawyndt, P. (2010). Microbiological Common Language (MCL): a standard for electronic information exchange in the Microbial Commons. Research in Microbiology 161(6), 439-445. doi:10.1016/j.resmic.2010.02.005

Although the standard was set up by StrainInfo, it is intended as a common ground for the whole microbiological community. Therefore, it is open to community feedback and extension. We are glad to receive your remarks or suggestions.

Contact: Bert.Verslyppe@UGent.be or the StrainInfo team (see contact)

Examples

This is a simple example of the MCL represenation of the E. coli type strain (XML file):

<mcl:Strain xmlns:mcl="http://www.straininfo.net/ns/mcl/2.0/">
   <mcl:strainNumber>ATCC 11775</mcl:strainNumber>
   <mcl:strainNumber>CIP 54.8</mcl:strainNumber>
   <mcl:strainNumber>DSM 30083</mcl:strainNumber>

   <mcl:speciesName>Escherichia coli</mcl:speciesName>
   <mcl:typeStrainOf>Escherichia coli</mcl:typeStrainOf>

   <mcl:Sample>
      <mcl:sampleLocationCountry>Denmark</mcl:sampleLocationCountry>
      <mcl:sampleHabitat>Urine</mcl:sampleHabitat>
   </mcl:Sample>

   <mcl:isolationDate>1952</mcl:isolationDate>
</mcl:Strain>

Strain passports are also available in MCL format. The XML file corresponding with a strain passport can be downloaded by appending ".xml" to the strain passport URL. For example, the MCL file for the Bacillus smithii type strain can be found at http://www.straininfo.net/strains/29804.xml.

Advanced search results can also be represented in MCL format (see exports overview)

Another example can be found in the description of the StrainInfo catalog schema.

MCL reference

The authorative definition of all terms in MCL can be found in the MCL reference.

MCL schemas

Schemas define the way MCL files need to be formatted and allow automatic validation of MCL files. A specific XML schema is available for each important distinct use case. RDF users can use the generic RDF schema.