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Microbiological Common Language (MCL) reference

Title: Microbiological Common Language (MCL) reference
Version: 2.1 (revision 4cd9fd59ebe233bdcb322e43f5af9b83f7)
Replaces old version: 2.0 r2078
Creator: Bert Verslyppe (Bert.Verslyppe@UGent.be)

Introduction

This document specifies terms in the Microbiological Common Language (MCL). This is the authorative document for term definitions. This document does not define how MCL files should be formatted or used. For general information or example MCL files, refer to the MCL project homepage.

MCL was heavily influenced by MINE and CABRI projects. To allow an easier mapping from these standards, deprecated "legacy" terms were added to the language. If possible, try to avoid the use of these deprecated terms in new applications. If possible, mappings to MINE are included in the term definitions.

For some terms, MCL strongly recommends the use of a controlled vocabulary. This enables other users to interpret values in the intended way. Terms with a recommended vocabulary list the recommended values in a table that is included with the term definition. Please use the canonical value as the effective value of the term. The alternative notations and comments columns help you to create mappings from other data formats.

Namespaces

All MCL terms are defined in the default MCL namespace, which is by convention abbreviated by "mcl:". Terms from other namespaces are also used in MCL. This is an overview of all namespaces used by MCL:

PrefixNamespace
mcl:http://www.straininfo.net/ns/mcl/2.0/
dc:http://purl.org/dc/elements/1.1/
dcterms:http://purl.org/dc/terms/
prism:http://prismstandard.org/namespaces/basic/2.0
wgs84_pos:http://www.w3.org/2003/01/geo/wgs84_pos#

Overview

MCL defines the following entities:

MCL defines the following properties: mcl:strainNumber, mcl:otherStrainNumber, mcl:otherStrainNumbers, mcl:catalogURL, mcl:cultureURI, mcl:speciesName, mcl:qualifiedSpeciesName, mcl:id, mcl:typeStrainOf, mcl:typeStrainOfSpecies, mcl:typeStrainOfGenus, mcl:history, mcl:isolationDate, mcl:isolator, mcl:isolatorInstitute, mcl:isolationMethod, mcl:growthTemperature, mcl:noGrowthTemperature, mcl:minimalGrowthTemperature, mcl:optimalGrowthTemperature, mcl:maximalGrowthTemperature, mcl:oxygenRelationship, mcl:recommendMedium, mcl:hasSample, mcl:isolatedFromSample, mcl:hasCulture, mcl:publication, mcl:nomenclaturalPublication, mcl:taxonomicPublication, mcl:historyPublication, mcl:environmentPublication, mcl:preservationPublication, dcterms:bibliographicCitation, dc:title, dc:creator, prism:publicationName, prism:volume, prism:number, prism:startingPage, prism:pageRange, dcterms:issued, mcl:mediumNumber, mcl:mediumName, mcl:mediumURL, mcl:mediumDescription, mcl:sampleDescription, mcl:sampleDate, mcl:sampleLocationDescription, mcl:sampleLocationCountry, mcl:sampleLocationPlace, wgs84_pos:alt, wgs84_pos:lat, wgs84_pos:long, mcl:sampleCultureStrainNumber, mcl:sampleCulture, mcl:sampleHabitat, mcl:sampleCollector, mcl:sampleCollectorInstitute, mcl:comments, mcl:originatingStrainNumber, mcl:resultingStrainNumber, mcl:originatingCulture, mcl:resultingCulture, mcl:depositor, mcl:depositorInstitute, mcl:depositDate, mcl:catalogVersion, mcl:catalogLastUpdateDate, dcterms:created, mcl:cultureLastUpdateDate, mcl:cellGcContent, mcl:cellLength, mcl:cellWidth, mcl:cellSize, mcl:cellShape, mcl:motile, mcl:sporeForming, mcl:motileBy, mcl:maximumGrowthNACL, mcl:optimalGrowthNACL, mcl:minimumGrowthNACL, mcl:noGrowthNACL, mcl:maximumGrowthPH, mcl:optimalGrowthPH, mcl:minimumGrowthPH, mcl:growthPH, mcl:noGrowthPH, mcl:colonyShape, mcl:alkalinePhosphataseReaction, mcl:betaGalactosidaseReaction, mcl:catalaseReaction, mcl:cytochromeOxidaseReaction, mcl:gramReaction, mcl:oxidaseReaction, mcl:ureaseReaction, mcl:indoleReaction, mcl:significantFattyAcid, mcl:significantPolarLipid, mcl:inhibitedBy, mcl:notInhibitedBy, mcl:significantQuinone, mcl:utilizes, mcl:notUtilizes

Classes

mcl:Culture - An instance of a strain, held at a given place and time.
In domain of: mcl:strainNumber mcl:otherStrainNumber mcl:otherStrainNumbers mcl:catalogURL mcl:cultureURI mcl:speciesName mcl:qualifiedSpeciesName mcl:id mcl:typeStrainOf mcl:typeStrainOfSpecies mcl:typeStrainOfGenus mcl:history mcl:growthTemperature mcl:noGrowthTemperature mcl:minimalGrowthTemperature mcl:optimalGrowthTemperature mcl:maximalGrowthTemperature mcl:oxygenRelationship mcl:recommendMedium mcl:hasSample mcl:publication mcl:nomenclaturalPublication mcl:taxonomicPublication mcl:historyPublication mcl:environmentPublication mcl:preservationPublication mcl:comments mcl:cultureLastUpdateDate mcl:cellGcContent mcl:cellLength mcl:cellWidth mcl:cellSize mcl:cellShape mcl:motile mcl:sporeForming mcl:motileBy mcl:maximumGrowthNACL mcl:optimalGrowthNACL mcl:minimumGrowthNACL mcl:noGrowthNACL mcl:maximumGrowthPH mcl:optimalGrowthPH mcl:minimumGrowthPH mcl:growthPH mcl:noGrowthPH mcl:colonyShape mcl:alkalinePhosphataseReaction mcl:betaGalactosidaseReaction mcl:catalaseReaction mcl:cytochromeOxidaseReaction mcl:gramReaction mcl:oxidaseReaction mcl:ureaseReaction mcl:indoleReaction mcl:significantFattyAcid mcl:significantPolarLipid mcl:inhibitedBy mcl:notInhibitedBy mcl:significantQuinone mcl:utilizes mcl:notUtilizes
In range of: mcl:hasCulture mcl:sampleCulture mcl:originatingCulture mcl:resultingCulture
Description:

According to the definition of Staley and Krieg, a bacterial culture is seen as a population of bacterial cells of a strain, instantiated in a given place during a given time, e.g. in a test tube, on an agar plate or in a cryopreserved or lyophilized state intended for long preservation. In practice, a mcl:Culture is associated with a strain number. Each issue of a new strain number yields a new culture.

Reference: J.T. Staley and N.R. Krieg. Classification of procaryotic organisms: Bergeys Manual of Systematic Bacteriology, pages 1-4, 1984.

mcl:Strain - The result of the StrainInfo integration of cultures.
In domain of: mcl:strainNumber mcl:catalogURL mcl:speciesName mcl:qualifiedSpeciesName mcl:typeStrainOf mcl:typeStrainOfSpecies mcl:typeStrainOfGenus mcl:history mcl:growthTemperature mcl:noGrowthTemperature mcl:minimalGrowthTemperature mcl:optimalGrowthTemperature mcl:maximalGrowthTemperature mcl:oxygenRelationship mcl:recommendMedium mcl:hasSample mcl:hasCulture mcl:publication mcl:nomenclaturalPublication mcl:taxonomicPublication mcl:historyPublication mcl:environmentPublication mcl:preservationPublication mcl:comments mcl:cellGcContent mcl:cellLength mcl:cellWidth mcl:cellSize mcl:cellShape mcl:motile mcl:sporeForming mcl:motileBy mcl:maximumGrowthNACL mcl:optimalGrowthNACL mcl:minimumGrowthNACL mcl:noGrowthNACL mcl:maximumGrowthPH mcl:optimalGrowthPH mcl:minimumGrowthPH mcl:growthPH mcl:noGrowthPH mcl:colonyShape mcl:alkalinePhosphataseReaction mcl:betaGalactosidaseReaction mcl:catalaseReaction mcl:cytochromeOxidaseReaction mcl:gramReaction mcl:oxidaseReaction mcl:ureaseReaction mcl:indoleReaction mcl:significantFattyAcid mcl:significantPolarLipid mcl:inhibitedBy mcl:notInhibitedBy mcl:significantQuinone mcl:utilizes mcl:notUtilizes
In range of:
Description:

Staley and Krieg define a strain as the descendants of a single isolation in pure culture, usually a succession of cultures ultimately derived from a single colony. As a result, strain is associated with the integration results of StrainInfo.

Reference: J.T. Staley and N.R. Krieg. Classification of procaryotic organisms: Bergeys Manual of Systematic Bacteriology, pages 1-4, 1984.

mcl:Sample - Sample from which a microorganism was isolated.
In domain of: mcl:sampleDescription mcl:sampleDate mcl:sampleLocationDescription mcl:sampleLocationCountry mcl:sampleLocationPlace wgs84_pos:alt wgs84_pos:lat wgs84_pos:long mcl:sampleCultureStrainNumber mcl:sampleCulture mcl:sampleHabitat mcl:sampleCollector mcl:sampleCollectorInstitute mcl:comments
In range of: mcl:hasSample mcl:isolatedFromSample
Description:

The environmental sample from which a microorganism was isolated. Multiple cultures can be isolated from the same Sample.

mcl:Isolation - The process of isolating a pure culture from an environmental sample.
In domain of: mcl:isolationDate mcl:isolator mcl:isolatorInstitute mcl:isolationMethod mcl:isolatedFromSample mcl:comments
In range of:
Description:

The process of isolating a pure culture from an environmental sample. If multiple cultures have been isolated from a sample, each isolate corresponds to one Isolation entity.

mcl:Medium - A culture medium.
In domain of: mcl:mediumNumber mcl:mediumName mcl:mediumURL mcl:mediumDescription mcl:comments
In range of: mcl:recommendMedium
Description:

Culture medium used to grow cultures.

mcl:Publication - A scientific publication.
In domain of: dcterms:bibliographicCitation dc:title dc:creator prism:publicationName prism:volume prism:number prism:startingPage prism:pageRange dcterms:issued
In range of: mcl:publication mcl:nomenclaturalPublication mcl:taxonomicPublication mcl:historyPublication mcl:environmentPublication mcl:preservationPublication
Description:

Describes a scientific publication.

The term dcterms:bibliographicCitation is obligatory when describing publications. It contains a human-readable citation of the work, containing enough information to enable the user to find the intended publication. If the components of the citation are available separately (or if the citation can be easily split into components), it is recommended to include the separate components. The dc:creator field must be repeated for each individual author.

mcl:Deposit - The transition of one culture to another.
In domain of: mcl:comments mcl:originatingStrainNumber mcl:resultingStrainNumber mcl:originatingCulture mcl:resultingCulture mcl:depositor mcl:depositorInstitute mcl:depositDate
In range of:
Description:

When a BRC transfers a culture to another BRC, a new culture originates: this process is characterized by the assignment of a new strain number. The process of deposit and assignment of new strain numbers results in a strain with an exchange history. StrainInfo visualises this exchange history as the Histri of the strain.

The mcl:Deposit entity is used to model one transfer, along with meta-information, of the exchange history.

mcl:CatalogDescription - Metadata of a BRC catalog.
In domain of: dc:creator
In range of:
Description:

Metadata of a BRC catalog exported using the MCL 'catalog' XML schema.

mcl:BRC - Description of a BRC.
In domain of: mcl:catalogVersion mcl:catalogLastUpdateDate dcterms:created
In range of:
Description:

Used as part of the mcl:CatalogDescription element to describe a BRC (in the 'catalog' XML schema).

mcl:StrainInfo - Root element used in XML files.
In domain of:
In range of:
Description:

This element is used by StrainInfo in XML files, as the root element of for example exports.

Properties

mcl:strainNumber - A strain number.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

A strainNumber identifies a culture. As a result, this field is obligatory for each mcl:Culture. Describing equivalent strain numbers can be done using the mcl:otherStrainNumber term. Acronyms must be included in the strain number as this field is taken as is, and no extra context is assumed when processing this field.

Note that mcl:Strain corresponds to the equivalence integration result of multiple cultures, and by consequence, this term occurs once for each culture in the strain.

Other standards: Bacterial and Fungal MINE: STN, ACCN
mcl:otherStrainNumber - Other, equivalent strain number.
Domain: mcl:Culture
Range: none (literal value)
Description:

Individual equivalent strain numbers can be given using this term. If multiple equivalent strain numbers are known, the term must be used for each individual equivalent strain number. Acronyms must be included in the strain number as this field is taken as is, and no extra context is assumed when processing this field.

Note that mcl:Strain does not accept this property as all strain numbers are regarded as mcl:strainNumber of the given strain.

Other standards: Bacterial and Fungal MINE: see mcl:otherStrainNumbers
mcl:otherStrainNumbers - A list of other, equivalent strain numbers.
Domain: mcl:Culture
Range: none (literal value)
Description:

Multiple equivalent strain numbers can be listed using this term. Only ; and = are accepted as delimiters, but can not be mixed. Whitespace before and after the delimiter is discarded.

This property is deprecated. Use mcl:otherStrainNumber if possible; this field is provided for compatibility with legacy BRC catalogs.

Other standards: Bacterial and Fungal MINE: OCC
mcl:catalogURL - URL of corresponding online catalog entry.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Is functional: True.
Description:

URL containing a direct link to the online BRC catalog entry.

If this term is used by StrainInfo, it will contain the URL of the BRC catalog entry in the strain browser.

If this term is used by BRCs, it may contain a direct link to the BRC catalog entry. If such link does not exist, a link to an indermediary page can be given (e.g. an overview of a species) instead. However, this is disadvantageous as this can decrease the number of users reaching the correct catalog entry. Make sure that the URL does not resolve to an error page.

mcl:cultureURI - Culture URI.
Domain: mcl:Culture
Range: none (literal value)
Is functional: True.
Description:

Culture URI of a mcl:Culture. When using RDF, the culture URI is explicitly used to refer to mcl:Culture resources. This term can be used to explicitly include the culture URI in XML files.

mcl:speciesName - The species name.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Is functional: True.
Description:

The species name of a culture or strain. Species name contains genus and species epithet, and if applicable, the subspecies epithet. Author names are not included, but can be referred to using the mcl:nomenclaturalPublication property.

Other standards: Bacterial and Fungal MINE: SP (partial). SPP is also included in this term.
mcl:qualifiedSpeciesName - The qualified species name (including authors).
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Is functional: True.
Description:

Species name, containing authors. Species name contains genus and species epithet, and if applicable, the subspecies epithet. Formatting follows rules of Bacterial and Fungal MINE.

Since: MCL 2.1
Other standards: Bacterial and Fungal MINE: SP. SPP is also included in this term.
mcl:id - Culture id.
Domain: mcl:Culture
Range: none (literal value)
Is functional: True.
Description:

This term can be used to explicitly refer to the cultureId of a culture. Note that the cultureId is included as part of the culture URI (see mcl:cultureURI), which can be resolved and dereferenced. Therefore, the latter is the preferred identifier.

mcl:typeStrainOf - Name of taxon if type strain.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Is functional: True.
Description:

If a strain is a type strain (or if a culture belongs to a type strain), the corresponding taxonomic name can be described using the typeStrainOf property. If the strain is type strain of multiple taxa, these names must be listed using multiple mcl:typeStrainOf statements.

Other standards: Related to Bacterial MINE: STAT
mcl:typeStrainOfSpecies - Species name if type strain.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
More general form: mcl:typeStrainOf
Is functional: True.
Description:

If a strain is a type strain (or if a culture belongs to a type strain), the corresponding species can be described using the mcl:typeStrainOfSpecies property. If the strain is type strain of multiple species, these species are listed using multiple mcl:typeStrainOfSpecies statements.

Other standards: Related to Bacterial MINE: STAT
mcl:typeStrainOfGenus - Genus name if type strain of genus.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
More general form: mcl:typeStrainOf
Is functional: True.
Description:

If a strain is a type strain (or if a culture belongs to a type strain), the corresponding genus can be described using the mcl:typeStrainOfGenus property. If the strain is type strain of multiple genera, all names must be listed using multiple statements.

Other standards: Related to Bacterial MINE: STAT
mcl:history - Textual description of exchange history.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Is functional: True.
Description:

Textual description of exchange history of a culture, as often found in BRC catalogs. There are no strict formatting rules for this field as this field accepts the legacy descriptions found in BRC catalogs. Possibly contains extra annotations regarding date of deposit and depositors; and generally consists of arrows pointing left ('<--'), dates, and strain numbers.

Other standards: Bacterial and Fungal MINE: HIS (Bacterial MINE uses delimiter '<', Fungal MINE uses delimiter '>' and reverse order)
mcl:isolationDate - Date of isolation.
Domain: mcl:Isolation
Range: none (literal value)
Is functional: True.
Description:

Date of isolation. If unknown, month and/or day can be omitted.

Other standards: Bacterial and Fungal MINE: ISOL, third subfield (delimited by ',')
mcl:isolator - Person responsible for isolation.
Domain: mcl:Isolation
Range: none (literal value)
Is functional: True.
Description:

Full name of person responsible for isolation from environmental sample (isolator).

Other standards: Bacterial and Fungal MINE: ISOL
mcl:isolatorInstitute - Institute of isolator.
Domain: mcl:Isolation
Range: none (literal value)
Is functional: True.
Description:

Institute of isolator at time of isolation. There is no mapping from MINE.

mcl:isolationMethod - Isolation method used.
Domain: mcl:Isolation
Range: none (literal value)
Is functional: True.
Description:

Method used to isolate the environmental sample into a pure culture.

This term uses the same recommended vocabulary as Bacterial MINE.

Recommended values:
Canonical value Alternative notations Comment
DP dilution plate; -
ES endospores; -
CC continuous culture; -
CY cysts; -
DI direct plating; -
EM enrichment method; -
PAST pasteurisation; -
Other standards: Bacterial MINE: ISOM
mcl:growthTemperature - Growth temperature.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Temperature at which growth can be observed. This field can be used when the given temperature is not neccessary or not known to be optimal, but certainly yields growth when used for incubation. Unit is omitted.

Other standards: Related to Bacterial and Fungal MINE: TEGR
mcl:noGrowthTemperature - Temperature at which no growth can be observed.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Temperature at which no growth can be observed. Unit is omitted.

Other standards: Related to Bacterial and Fungal MINE: TEGR
mcl:minimalGrowthTemperature - Minimal growth temperature.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
More general form: mcl:growthTemperature
Is functional: True.
Description:

Minimal temperature (degree Celsius, do not include unit) neccessary to observe growth on culture medium.

Other standards: Bacterial and Fungal MINE: TEGR, first subfield (Bacterial MINE: delimited by ';', Fungal MINE: delimited by '/')
mcl:optimalGrowthTemperature - Optimal growth temperature.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
More general form: mcl:growthTemperature
Is functional: True.
Description:

Temperature (degree Celsius, do not include unit) at which optimal growth on culture medium can be observed.

Other standards: Bacterial MINE: TEGR, second subfield (Bacterial MINE: delimited by ';', Fungal MINE: delimited by '/')
mcl:maximalGrowthTemperature - Maximal growth temperature.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
More general form: mcl:growthTemperature
Is functional: True.
Description:

Maximal temperature (degree Celsius, do not include unit) at which growth on culture medium can be observed.

Other standards: Bacterial MINE: TEGR, third subfield (Bacterial MINE: delimited by ';', Fungal MINE: delimited by '/')
mcl:oxygenRelationship - Oxygen relationship of organism.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Is functional: True.
Description:

Oxygen requirements of organism, i.e. aerobicity. Uses the same values as Bacterial MINE.

Recommended values:
Canonical value Alternative notations Comment
AE aerobic; strictly aerobic; 100% air
MA microaerophilic; 5% air
FAN facultative aerobic; facultatively anaerobic; -
AT aerotolerant; prefers anaerobic conditions for good growth, but tolerates aerobic condtions
MAT microaerotolerant; anaerobic bacteria tolerating microaerophilic conditions
AN anaerobic; anaerobe; obligately anaerobic; strictly anaerobic; -
Other standards: Bacterial MINE: OXR
mcl:recommendMedium - Medium recommended for cultivation.
Domain: mcl:Culture mcl:Strain
Range: mcl:Medium
Description:

Recommended medium for cultivation of a culture; medium on which the culture will yield growth.

mcl:hasSample - Environmental sample from which the microorganism was isolated.
Domain: mcl:Culture mcl:Strain
Range: mcl:Sample
Description:

Links a mcl:Culture to the mcl:Sample from which it was isolated. It therefore skips the intermediate step mcl:Isolation, which makes handling legacy BRC catalogs easier. Multiple cultures can be isolated from the same sample.

This property is deprecated. Since MCL 2.1, it is recommended to use mcl:isolatedFromSample instead. This field is retained to ensure compatibility with MCL 2.0.

mcl:isolatedFromSample - Isolation process from sample.
Domain: mcl:Isolation
Range: mcl:Sample
Description:

Isolation process from sample. Multiple isolations can be performed on the same Sample, but these are modelled using different Isolation entities using separate mcl:isolatedFromSample statements.

Since: MCL 2.1
mcl:hasCulture - References a particular culture of a strain.
Domain: mcl:Strain
Range: mcl:Culture
Description:

Links cultures to a strain. This field is only to be used by StrainInfo as this corresponds to the equivalence integration, integrating cultures into strains.

mcl:publication - General publiciation.
Domain: mcl:Culture mcl:Strain
Range: mcl:Publication
Description:

Used to refer to a publication. When more information is known about the type of publication (e.g. nomenclatural publication, taxonomic publication, etc.), use one of the more precise terms.

mcl:nomenclaturalPublication - A publication on nomenclature.
Domain: mcl:Culture mcl:Strain
Range: mcl:Publication
More general form: mcl:publication
Description:

References the publication in which the species name was introduced. This citation is also part of the mcl:qualifiedSpeciesName.

mcl:taxonomicPublication - A publication on taxonomy.
Domain: mcl:Culture mcl:Strain
Range: mcl:Publication
More general form: mcl:publication
Description:

References the publication in which the taxonomy of the strain (or the species it belongs to) is described.

Other standards: Bacterial MINE: TAXLIT
mcl:historyPublication - A publication on the (exchange) history of the microorganism.
Domain: mcl:Culture mcl:Strain
Range: mcl:Publication
More general form: mcl:publication
Description:

References a publication in which strain history is described.

Other standards: Related to Bacterial MINE: ENHISLIT
mcl:environmentPublication - A publication on isolation environment.
Domain: mcl:Culture mcl:Strain
Range: mcl:Publication
More general form: mcl:publication
Description:

References a publication in which the original sample environment is described.

Other standards: Related to Bacterial MINE: ENHISLIT
mcl:preservationPublication - A publication on the preservation of the microorganism.
Domain: mcl:Culture mcl:Strain
Range: mcl:Publication
More general form: mcl:publication
Description:

References a publication in which preservation methods (applicable to the culture or strain) are described.

Other standards: Bacterial MINE: PRELIT
dcterms:bibliographicCitation - Full bibliographic citation of publication.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Each publication must be described using a bibliographic citation. The citation must contain enough information to fully identify the publication. However, the format of the citation is not defined. If components such as publication title, authors or journal are available separately, these are preferably also listed separately using the terms dc:title, dc:creator, prism:publicationName, prism:volume, prism:number, prism:startingPage, prism:pageRange and dcterms:issued

Other standards: Part of the DCMI Metadata Terms, see DCMI Metadata Terms, term dcterms:bibliographicCitation for more information.
dc:title - Article title.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Title of publication.

Other standards: Part of the DCMI Metadata Terms, see DCMI Metadata Terms, term dc:title for more information.
dc:creator - Author.
Domain: mcl:Publication mcl:CatalogDescription
Range: none (literal value)
Is functional: True.
Description:

Author of article or BRC catalog MCL XML export.

Other standards: Part of the DCMI Metadata Terms, see DCMI Metadata Terms, term dc:creator for more information.
prism:publicationName - Name of journal or book.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Name of journal or book where article was published.

Other standards: Part of the Publishing Requirements for Industry Standard Metadata (PRISM) standard, see specifications for more information.
prism:volume - Volume number.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Volume number of article.

Other standards: Part of the Publishing Requirements for Industry Standard Metadata (PRISM) standard, see specifications for more information.
prism:number - Issue number.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Issue number of article.

Other standards: Part of the Publishing Requirements for Industry Standard Metadata (PRISM) standard, see specifications for more information.
prism:startingPage - First page number of publication.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

First page number of publication. Can be used when last page number is not known.

Other standards: Part of the Publishing Requirements for Industry Standard Metadata (PRISM) standard, see specifications for more information.
prism:pageRange - Page range of publication.
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Page range of publication. When last page number is not known, prism:startingPage can be used. Field must contain two numbers, delimited by '--'. Example: "450--455"

Other standards: Part of the Publishing Requirements for Industry Standard Metadata (PRISM) standard, see specifications for more information.
dcterms:issued - Year of issue
Domain: mcl:Publication
Range: none (literal value)
Is functional: True.
Description:

Date (year) when publication was issued.

Other standards: Part of the DCMI Metadata Terms, see DCMI Metadata Terms, term dcterms:issued for more information.
mcl:mediumNumber - 'Strain number' of a culture medium.
Domain: mcl:Medium
Range: none (literal value)
Is functional: True.
Description:

Medium identifier consisting of BRC acronym, the word 'Medium' and the internal BRC medium number/identifier.

Example: 'LMG Medium 1'

mcl:mediumName - Common name of medium.
Domain: mcl:Medium
Range: none (literal value)
Is functional: True.
Description:

Common name of culture medium.

Example: 'TSA', 'Columbia Agar'

mcl:mediumURL - URL at which a description of the medium can be found.
Domain: mcl:Medium
Range: none (literal value)
Is functional: True.
Description:

URL of the description of the culture medium in the online catalog. In cases where there is no separate medium page available, and the medium is listed directly on the culture catalog entry, an URL template needs to be provided. The following fields can be used and will be replaced depending on the particular context (i.e. current culture):

  • %STRAIN_NUMBER: replaced by the complete strain number
  • %STRAIN_NUMBER_NUMBER: replaced by the number portion of the strain number

mcl:mediumDescription - Full description of culture medium preparation.
Domain: mcl:Medium
Range: none (literal value)
Is functional: True.
Description:

Full description (including list of ingredients and procedure) of culture medium preparation.

mcl:sampleDescription - Full textual description of sample.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

Full textual description of habitat and geographical location where sample was taken; may contain dates, collector names and a description of the sampling process.

mcl:sampleDate - Date of sampling.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

Date of sampling. If unknown, month and/or day can be omitted.

Other standards: Bacterial and Fungal MINE: COLL, third subfield (delimited by ',')
mcl:sampleLocationDescription - Geographic location where sample was taken.
Domain: mcl:Sample
Range: none (literal value)
More general form: mcl:sampleDescription
Is functional: True.
Description:

Full description of geographic location where sample was taken. This includes, but is not limited to, names of countries, administrative areas, places, mountains, rivers, oceans and seas. Textual names and GeoNames URIs (preferred) are valid values for this term.

Other standards: Bacterial and Fungal MINE: LOC
mcl:sampleLocationCountry - Country where sample was taken.
Domain: mcl:Sample
Range: none (literal value)
More general form: mcl:sampleLocationDescription
Is functional: True.
Description:

Country where the sample was taken. This can be done textually or using a GeoNames URI (preferred). For practical reasons, states, oceans and continents are also valid for inclusion in this term.

Other standards: Bacterial and Fungal MINE: LOC, first subfield (delimited by ';')
mcl:sampleLocationPlace - Place where sample was taken.
Domain: mcl:Sample
Range: none (literal value)
More general form: mcl:sampleLocationDescription
Is functional: True.
Description:

Description of the place where the sample was taken. This is the geographical location inside the country. Therefore, the country must not be included. The value can be text or a GeoNames URI (preferred). When using the latter, mcl:sampleLocationCountry can be omitted as it is redundant.

Other standards: Bacterial and Fungal MINE: LOC, second subfield (delimited by ';')
wgs84_pos:alt - Altitude at which sample was taken.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

Altitude is measured in metric meters, and the unit is omitted. Depth (e.g. for samples taken in caves, mines or oceans) is considered a negative altitude (and is measured relative to the elevation).

Since: MCL 2.1 (replaces mcl:sampleAlt)
Other standards: Part of WGS84 Geo Positioning RDF vocabulary. Related Bacterial and Fungal MINE: LOC, second subfield (delimited by ';')
wgs84_pos:lat - Latitude at which sample was taken.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

The WGS84 latitude at which the sample was taken (decimal degrees).

Since: MCL 2.1 (replaces mcl:sampleLat)
Other standards: Part of WGS84 Geo Positioning RDF vocabulary
wgs84_pos:long - Longitude at which sample was taken.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

The WGS84 longitude at which the sample was taken (decimal degrees).

Since: MCL 2.1 (replaces mcl:sampleLong)
Other standards: Part of WGS84 Geo Positioning RDF vocabulary
mcl:sampleCultureStrainNumber - Culture derived from other culture.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

This term can be used when the microorganism was derived from another microorganism. A change in the genome sequence as the result of deliberate methods or actions is necessary to be able to use this term.

Historic relations between cultures (i.e. the Histri) are expressed using the mcl:Deposit entity.

mcl:sampleCulture - Culture derived from other culture.
Domain: mcl:Sample
Range: mcl:Culture
Is functional: True.
Description:

This is the resolved form of mcl:sampleCultureStrainNumber, explicitly pointing to the culture.

mcl:sampleHabitat - Habitat where sample was taken.
Domain: mcl:Sample
Range: none (literal value)
More general form: mcl:sampleDescription
Is functional: True.
Description:

Description of habitat where sample was taken. This can be fully textual, but it is recommended to use terms from ontologies such as EnvO.

Note that this term is related to, but different from, Bacterial MINE: HABI and Fungal MINE: HAB. Those terms are used on a higher (species) level and document a known generality.

Other standards: Bacterial MINE: ISOFR; Fungal MINE: SSTR
mcl:sampleCollector - Name of sample collector.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

Full name of sample collector: responsible for the physical act of retrieving the Sample from the environment.

Other standards: Bacterial and Fungal MINE: COLL
mcl:sampleCollectorInstitute - Institute of sample collector.
Domain: mcl:Sample
Range: none (literal value)
Is functional: True.
Description:

Institute of sample collector at time of sample collection.

mcl:comments - Various comments and notes.
Domain: mcl:Culture mcl:Strain mcl:Medium mcl:Sample mcl:Deposit mcl:Isolation
Range: none (literal value)
Is functional: True.
Description:

To be used to attach various comments or notes.

This property is deprecated. This term is intended as a 'last resort' if data does not fit other terms.

mcl:originatingStrainNumber - Original strain number of culture, before being deposited in other BRC.
Domain: mcl:Deposit
Range: none (literal value)
Is functional: True.
Description:

Original strain number of culture, before it is deposited into another BRC. This corresponds to the ancestor of the culture in the Histri.

mcl:resultingStrainNumber - Newly assigned strain number after culture is deposited in BRC.
Domain: mcl:Deposit
Range: none (literal value)
Is functional: True.
Description:

Strain number of the culture in the receiving BRC. The latter appoints the strain number as part of the accession.

mcl:originatingCulture - Original culture, before being deposited into another BRC.
Domain: mcl:Deposit
Range: mcl:Culture
Is functional: True.
Description:

Culture that will be deposited in another BRC.

This field can only be used after resolving mcl:originatingStrainNumber to a culture.

mcl:resultingCulture - New culture after deposit in BRC.
Domain: mcl:Deposit
Range: mcl:Culture
Is functional: True.
Description:

Strain number of the culture in the receiving BRC. The latter appoints the strain number as part of the accession.

This field can only be used after resolving mcl:resultingStrainNumber to a culture.

mcl:depositor - Person depositing culture to other BRC.
Domain: mcl:Deposit
Range: none (literal value)
Is functional: True.
Description:

Full name of person responsible for transferring the culture to a or another BRC.

Other standards: Bacterial and Fungal MINE: DEP
mcl:depositorInstitute - Institute depositing culture to a BRC.
Domain: mcl:Deposit
Range: none (literal value)
Is functional: True.
Description:

Institute transferring the culture to a BRC. This is applicable for both the first deposit and subsequent deposits between BRCs.

Other standards: Bacterial and Fungal MINE: DEP
mcl:depositDate - Date of deposit.
Domain: mcl:Deposit
Range: none (literal value)
Is functional: True.
Description:

Date at which culture was deposited into other BRC. If unknown, month and/or day can be omitted.

As opposed to MINE, MCL does not discriminate between date of receipt and date of accession. If both dates are known, but significantly different from each other, the earliest date (date of receipt) is preferred.

Other standards: Bacterial and Fungal MINE: EDR and EDA
mcl:catalogVersion - Version of BRC catalog.
Domain: mcl:BRC
Range: none (literal value)
Is functional: True.
Description:

Text field which can be used by BRCs that have an internal catalog version number, for example associated with printed catalog releases. There are no requirements on the form or the included information and can be omitted if no internal version number is used.

mcl:catalogLastUpdateDate - Timestamp of the last change to the BRC catalog.
Domain: mcl:BRC
Range: none (literal value)
Is functional: True.
Description:

Date and time of the last change to the BRC catalog, formatted as a ISO 8601 xsd:dateTime

dcterms:created - Creation timestamp.
Domain: mcl:BRC
Range: none (literal value)
Is functional: True.
Description:

Creation date and time.

Other standards: Part of the DCMI Metadata Terms, see DCMI Metadata Terms, term dc:created for more information.
mcl:cultureLastUpdateDate - Timestamp of the last change to a culture.
Domain: mcl:Culture
Range: none (literal value)
Is functional: True.
Description:

Date and time of the last change to the BRC catalog entry or record of a culture, formatted as a ISO 8601 xsd:dateTime.

Other standards: Bacterial and Fungal MINE: EDM
mcl:cellGcContent - GC content.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Guanine-cytosine (GC) content of the cell DNA/RNA, expressed as a percentage (without "%").

Since: MCL 2.1
Other standards: Bacterial and Fungal MINE: GC
mcl:cellLength - Average length of the cell, measured in µm.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Average length of the cell, measured in micrometer under standard conditions. The value can be one number or a range, unit is omitted.

Since: MCL 2.1
Other standards: MINE: see mcl:cellShape
mcl:cellWidth - Average width of the cell, measured in µm.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Average width of the cell, measured in micrometer under standard conditions. The value can be one number or a range, unit is omitted. The mcl:cellWidth needs to be less (or equal) than the mcl:cellLength.

Since: MCL 2.1
Other standards: MINE: see mcl:cellShape
mcl:cellSize - Average size of a cell, measured in µm.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Average size of a cell, measured in micrometer under standard conditions. The value contains both the average width and length (possibly as a range), separated by 'x'. Unit is omitted.

Examples: 0.3–0.6x0.8–3.5
0.4x4.9

This property is deprecated. Use mcl:cellLength and mcl:cellWidth if possible.

Since: MCL 2.1
Other standards: Bacterial and Fungal MINE: CELL, third subfield
mcl:cellShape - Shape of cells.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Shape of cells as measured under standard conditions.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
rod rods; rod-shaped; Bacterial MINE: 'R'
coc coccus; cocci; Bacterial MINE: 'C'
spiral spirillum; Bacterial MINE: 'S'
vibrio - Bacterial MINE: 'V'
Other standards: Bacterial MINE: CELL, first subfield
mcl:motile - Cells are motile.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Indicates if cells are motile or non-motile. If cells are motile, the mechanism can be indicated with mcl:motileBy.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
true motile; weakly motile; -
false non-motile; not motile; -
Other standards: Bacterial MINE: MOT, first subfield (delimited by ';')
mcl:sporeForming - Cells are spore forming.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Indicates whether cells form spores.

Recommended values:
Canonical value Alternative notations Comment
true spore-forming; spores are formed; -
false non-spore-forming; -
Other standards: Related to Bacterial MINE: RESTST
mcl:motileBy - Motility mechanism used.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Motility mechanism used. If organism is not motile, this term is omitted. Recommended values correspond to Bacterial MINE.

Recommended values:
Canonical value Alternative notations Comment
gliding - -
peritrigus flagella - -
polar flagella - -
bipolar flagella - -
twitching - -
Other standards: Bacterial MINE: MOT, second subfield (delimited by ';')
mcl:maximumGrowthNACL - Maximal NaCl concentration for growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Maximal NaCl concentration at which growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Related to Bacterial MINE: SALR and SALC
mcl:optimalGrowthNACL - NaCl concentration for optimal growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

NaCl concentration at which optimal growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Related to Bacterial MINE: SALR and SALC
mcl:minimumGrowthNACL - Minimum NaCl concentration for growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Minimum NaCl concentration at which growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Related to Bacterial MINE: SALR and SALC
mcl:noGrowthNACL - NaCl concentration yielding no growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

NaCl concentration at which no growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Related to Bacterial MINE: SALR and SALC
mcl:maximumGrowthPH - Highest pH for growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Highest pH level at which growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Bacterial MINE: PHC, third subfield (delimited by ';')
mcl:optimalGrowthPH - pH for optimal growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Optimal pH level at which optimal growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Bacterial MINE: PHC, second subfield (delimited by ';')
mcl:minimumGrowthPH - Minimum pH for growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Minimum pH level at which growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Bacterial MINE: PHC, first subfield (delimited by ';')
mcl:growthPH - pH level yielding growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

pH level at which growth can be observed. This field can be used when the given pH level is not neccessary or not known to be optimal, but certainly yields growth when used for incubation. Unit is omitted.

Since: MCL 2.1
Other standards: Related to Bacterial MINE: PHR and PHC
mcl:noGrowthPH - pH level yielding no growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

pH level at which no growth can be observed. Unit is omitted.

Since: MCL 2.1
Other standards: Related to Bacterial MINE: PHR and PHC
mcl:colonyShape - Colony shape.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Typical shape of colonies.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
convex - -
concave - -
mcl:alkalinePhosphataseReaction - Alkaline phosphatase reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of an alkaline phosphatase reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive - -
negative - -
variable - -
unknown - -
mcl:betaGalactosidaseReaction - Beta-galactosidase reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of a beta-galactosidase reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive - -
negative - -
variable - -
unknown - -
mcl:catalaseReaction - Catalase reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of a catalase reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive catalase-positive; -
negative catalase-negative; -
variable - -
unknown - -
mcl:cytochromeOxidaseReaction - Cytochrome oxidase reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of a cytochrome oxidase reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive - -
negative - -
variable - -
unknown - -
mcl:gramReaction - Gram reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of a Gram staining reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive gram-staining-positive; gram-stain-positive; gram-positive; -
negative gram-staining-negative; gram-stain-negative; gram-negative; -
variable gram-variable; -
unknown - -
Other standards: Bacterial MINE: GRAM
mcl:oxidaseReaction - Oxidase reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of an oxidase reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive oxidase-positive; -
negative oxidase-negative; -
variable - -
unknown - -
mcl:ureaseReaction - Urease reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of an urease reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive urease-positive; -
negative urease-negative; -
variable - -
unknown - -
mcl:indoleReaction - Indole reaction.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Results of an indole reaction: positive, negative, variable or unknown.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
positive indole-positive; -
negative indole-negative; -
variable - -
unknown - -
mcl:significantFattyAcid - Major fatty acid in cells
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Major fatty acid found in cells. List only one fatty acid per term: use multiple statements to indicate multiple major fatty acids.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
14 : 0 C14 : 0; -
14 : 0 iso i14 : 0; iso-C14 : 0; -
15 : 0 C15 : 0; -
15 : 0 anteiso anteiso-C15 : 0; ai-C15 : 0; -
15 : 0 iso i15 : 0; iso-C15 : 0; -
15 : 0 iso 2-OH i15 : 0 2-OH; iso-C15 : 0 2-OH; 15 : 0 2-OH; -
15 : 0 iso 3-OH i15 : 0 3-OH; -
15 : 1 i15 : 1; -
15 : 1 iso i15 : 1; iso-C15 : 1; -
15 : 1 anteiso anteiso-C15 : 1; ai-C15 : 1; -
16 : 0 C16 : 0; -
16 : 0 iso i16 : 0; iso-C16 : 0; -
16 : 0 3-OH - -
16 : 0 iso 3-OH - -
16 : 1 C16 : 1; -
16 : 1{omega}5c - -
16 : 1{omega}7 - -
16 : 1{omega}7c - -
16 : 1{omega}7t - -
17 : 0 C17 : 0; -
17 : 0 iso i17 : 0; iso-C17 : 0; -
17 : 0 iso 3-OH iso-C17 : 0 3-OH; iso-C17 3-OH; -
17 : 0 anteiso anteiso-C17 : 0; ai-C17 : 0; -
17 : 1 i17 : 1; -
17 : 1 anteiso anteiso-C17 : 1; -
C18 : 0 - -
C18 : 1{omega}7c - -
11-methyl C18 : 1{omega}7c - -
mcl:significantPolarLipid - Major polar lipid of cells
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Major polar lipid found in cells. List only one polar lipid per term: use multiple statements to indicate multiple polar lipids.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
diphosphatidylglycerol - -
phosphatidylcholine - -
phosphatidylethanolamine - -
phosphatidylglycerol - -
phosphatidylinositol - -
mcl:inhibitedBy - Growth inhibitor.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Chemical (antibiotic) known to inhibit growth. List only one antibiotic per term: use multiple statements to indicate multiple antibiotics.

See also inverse term mcl:notInhibitedBy.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
anisomycin - -
bacitracin - -
colistin sulfate - -
cyclohexamine - -
cycloheximide - -
mycostatin - -
nalidixic acid - -
penicillin - -
polymixin - -
rifampicin - -
simvastatin - -
vancomycin - -
http://www.chemspider.com/Chemical-Structure.6013 ampicillin; -
http://www.chemspider.com/Chemical-Structure.5693 benzylpenicillin; penicillin G; -
http://www.chemspider.com/Chemical-Structure.19599 carbenicillin; -
http://www.chemspider.com/Chemical-Structure.5802 cephalothin; cephalotin; -
http://www.chemspider.com/Chemical-Structure.5744 chloramphenicol; -
http://www.chemspider.com/Chemical-Structure.10482106 doxycycline; -
http://www.chemspider.com/Chemical-Structure.12041 erythromycin; -
http://www.chemspider.com/Chemical-Structure.390067 gentamicin; -
http://www.chemspider.com/Chemical-Structure.5810 kanamycin; -
http://www.chemspider.com/Chemical-Structure.2272112 lincomycin; -
http://www.chemspider.com/Chemical-Structure.8075 neomycin; -
http://www.chemspider.com/Chemical-Structure.10226117 novobiocin; -
http://www.chemspider.com/Chemical-Structure.4447646 oleandomycin; -
polymyxin B - -
http://www.chemspider.com/Chemical-Structure.18508 streptomycin; -
http://www.chemspider.com/Chemical-Structure.10257122 tetracycline; -
Other standards: Related to Bacterial MINE: TOL
mcl:notInhibitedBy - Chemical not inhibiting growth.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Chemical (antibiotic) known to not inhibit growth, i.e. for which a culture or strain is resistant. Inverse of mcl:inhibitedBy. List only one antibiotic per term: use multiple statements to indicate multiple antibiotics.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
anisomycin - -
bacitracin - -
colistin sulfate - -
cyclohexamine - -
cycloheximide - -
mycostatin - -
nalidixic acid - -
penicillin - -
polymixin - -
rifampicin - -
simvastatin - -
vancomycin - -
http://www.chemspider.com/Chemical-Structure.6013 ampicillin; -
http://www.chemspider.com/Chemical-Structure.5693 benzylpenicillin; penicillin G; -
http://www.chemspider.com/Chemical-Structure.19599 carbenicillin; -
http://www.chemspider.com/Chemical-Structure.5802 cephalothin; cephalotin; -
http://www.chemspider.com/Chemical-Structure.5744 chloramphenicol; -
http://www.chemspider.com/Chemical-Structure.10482106 doxycycline; -
http://www.chemspider.com/Chemical-Structure.12041 erythromycin; -
http://www.chemspider.com/Chemical-Structure.390067 gentamicin; -
http://www.chemspider.com/Chemical-Structure.5810 kanamycin; -
http://www.chemspider.com/Chemical-Structure.2272112 lincomycin; -
http://www.chemspider.com/Chemical-Structure.8075 neomycin; -
http://www.chemspider.com/Chemical-Structure.10226117 novobiocin; -
http://www.chemspider.com/Chemical-Structure.4447646 oleandomycin; -
polymyxin B - -
http://www.chemspider.com/Chemical-Structure.18508 streptomycin; -
http://www.chemspider.com/Chemical-Structure.10257122 tetracycline; -
Other standards: Related to Bacterial MINE: TOL
mcl:significantQuinone - Significant quinones.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

A significant ubi, isoprenoid or mena quinone.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
http://www.chemspider.com/Chemical-Structure.4446660.html MK-6; -
http://www.chemspider.com/Chemical-Structure.4449904.html MK-7; -
http://www.chemspider.com/Chemical-Structure.4952805.html MK-10; -
MK-9(H4) DMK-9(H4); -
MK-10(H4) - -
MK-11 - -
MK-12 - -
MK-13 - -
Q-7 - -
Q-8 - -
http://www.chemspider.com/RecordView.aspx?rid=8987155d-56a1-4377-bf88-982d5b3a2062 Coenzyme Q9; Q-9; ubiquinone 9; -
http://www.chemspider.com/Chemical-Structure.4445197.html Q-10; -
mcl:utilizes - Organic compound utilized by cell metabolism.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Organic compound utilized by cell metabolism. List only one organic compound per term: use multiple statements to indicate multiple organic compounds.

See also inverse property mcl:notUtilizes.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
2,3-butanediol - -
2'-deoxyadenosine - -
2-oxoglutarate - -
3-methyl D-glucose - -
acetate - -
acetic acid - -
acid phosphatase - -
adenosine - -
adenosine 5'-monophosphate - -
adipate - -
adonitol - -
alanine - -
alanyl-phenylalanyl-proline arylamidase - -
alkaline phosphatase - -
amygdalin - -
amylose - -
arabinose - -
arabitol - -
arbutin - -
arginine - -
arginine arylamidase - -
aspartate - -
azelate - -
benzoate - -
betaine - -
butane-2,3-diol - -
butanol - -
butyrate - -
cellobiose - -
cis-aconitate - -
citrate - -
D- and L-alanine - -
D-arabinose - -
dextrin - -
D-fructose - -
D-fructose 6-phosphate - -
D-galactose - -
D-galacturonate - -
D-galacturonic acid - -
D-gluconate - -
D-gluconic acid - -
D-glucosamine - -
-D-glucose - -
-D-glucose 1-phosphate - -
D-glucose 6-phosphate - -
DL-3-hydroxybenzoate - -
DL-3-hydroxybutyrate - -
DL-4-hydroxybenzoate - -
D-lactic acid methyl ester - -
DL--glycerol phosphate - -
DL-lactate - -
D-malic acid - -
D-mannitol - -
D-mannose - -
D-psicose - -
D-ribose - -
D-sorbitol - -
D-tagatose - -
dulcitol - -
D-xylose - -
erythritol - -
esterase - -
esterase lipase - -
ethanol - -
formate - -
fructose - -
fumarate - -
galactitol - -
galactose - -
galacturonate - -
gentiobiose - -
gluconuronate - -
glucose - -
glutarate - -
http://www.chemspider.com/Chemical-Structure.733.html glycerol; -
glycine - -
glycine arylamidase - -
glycogen - -
glycolate - -
glycyl L-glutamic acid - -
glycyl-tryptophan arylamidase - -
hexadecane - -
hippuric acid - -
histidine arylamidase - -
inosine - -
inositol - -
inulin - -
itaconate - -
lactamide - -
lactate - -
-lactose - -
lactose - -
lactulose - -
L-alaninamide - -
L-alanine - -
L-alanyl glycine - -
L-arabinitol - -
L-arabinose - -
L-asparagine - -
L-cysteine - -
leucine - -
leucine arylamidase - -
leucyl glycine arylamidase - -
L-fucose - -
L-glutamate - -
L-glutamic acid - -
L-proline - -
L-histidine - -
L-lactic acid - -
L-leucine - -
L-malic acid - -
L-ornithine - -
L-phenylacetate - -
L-phenylalanine - -
L-proline - -
L-pyroglutamic acid - -
L-rhamnose - -
L-serine - -
L-sorbose - -
L-tryptophan - -
lysine - -
malate - -
malonate - -
maltitol - -
maltose - -
maltotriose - -
mannan - -
mannitol - -
mannose - -
melezitose - -
melibiose - -
mesaconate - -
methanol - -
methyl -D-galactoside - -
methyl -D-glucoside - -
methyl D-glucoside - -
methyl -D-mannoside - -
methyl β-D-galactoside - -
methyl β-D-glucoside - -
myo-inositol - -
N-acetyl-D-galactosamine - -
N-acetyl-D-glucosamine - -
N-acetyl-L-glutamic acid - -
N-acetyl-β-D-mannosamine - -
naphthol-AS-BI-phosphohydrolase - -
palatinose - -
p-arbutin - -
phenylalanine arylamidase - -
p-hydroxyphenylacetic acid - -
p-ketoglutaric acid - -
p-ketovaleric acid - -
proline arylamidase - -
propanol - -
propionate - -
propionic acid - -
putrescine - -
pyroglutamic acid arylamidase - -
pyrrolidonyl arylamidase - -
pyruvate - -
pyruvic acid - -
pyruvic acid methyl ester - -
quinate - -
raffinose - -
rhamnose - -
ribitol - -
ribose - -
saccharate - -
salicin - -
sedoheptulosan - -
serine - -
serine arylamidase - -
sorbitol - -
stachyose - -
suberate - -
succinamic acid - -
succinate - -
succinic acid - -
succinic acid monomethyl ester - -
sucrose - -
thymidine - -
thymidine 5'-monophosphate - -
trans-aconitate - -
trehalose - -
trypsin - -
turanose - -
tween 40 - -
tween 80 - -
tyrosine arylamidase - -
urease - -
uridine - -
uridine 5'-monophosphate - -
xylan - -
xylitol - -
xylose - -
β-alanine - -
β-and -hydroxybutyric acids - -
β-cyclodextrin - -
mcl:notUtilizes - Organic compound not utilized by cell metabolism.
Domain: mcl:Culture mcl:Strain
Range: none (literal value)
Description:

Organic compound not utilized by cell metabolism. Inverse of mcl:utilizes: explicitly states that organic compound is not utilized by the cell metabolism. List only one organic compound per term: use multiple statements to indicate multiple organic compounds.

Since: MCL 2.1
Recommended values:
Canonical value Alternative notations Comment
2,3-butanediol - -
2'-deoxyadenosine - -
2-oxoglutarate - -
3-methyl D-glucose - -
acetate - -
acetic acid - -
acid phosphatase - -
adenosine - -
adenosine 5'-monophosphate - -
adipate - -
adonitol - -
alanine - -
alanyl-phenylalanyl-proline arylamidase - -
alkaline phosphatase - -
amygdalin - -
amylose - -
arabinose - -
arabitol - -
arbutin - -
arginine - -
arginine arylamidase - -
aspartate - -
azelate - -
benzoate - -
betaine - -
butane-2,3-diol - -
butanol - -
butyrate - -
cellobiose - -
cis-aconitate - -
citrate - -
D- and L-alanine - -
D-arabinose - -
dextrin - -
D-fructose - -
D-fructose 6-phosphate - -
D-galactose - -
D-galacturonate - -
D-galacturonic acid - -
D-gluconate - -
D-gluconic acid - -
D-glucosamine - -
-D-glucose - -
-D-glucose 1-phosphate - -
D-glucose 6-phosphate - -
DL-3-hydroxybenzoate - -
DL-3-hydroxybutyrate - -
DL-4-hydroxybenzoate - -
D-lactic acid methyl ester - -
DL--glycerol phosphate - -
DL-lactate - -
D-malic acid - -
D-mannitol - -
D-mannose - -
D-psicose - -
D-ribose - -
D-sorbitol - -
D-tagatose - -
dulcitol - -
D-xylose - -
erythritol - -
esterase - -
esterase lipase - -
ethanol - -
formate - -
fructose - -
fumarate - -
galactitol - -
galactose - -
galacturonate - -
gentiobiose - -
gluconuronate - -
glucose - -
glutarate - -
http://www.chemspider.com/Chemical-Structure.733.html glycerol; -
glycine - -
glycine arylamidase - -
glycogen - -
glycolate - -
glycyl L-glutamic acid - -
glycyl-tryptophan arylamidase - -
hexadecane - -
hippuric acid - -
histidine arylamidase - -
inosine - -
inositol - -
inulin - -
itaconate - -
lactamide - -
lactate - -
-lactose - -
lactose - -
lactulose - -
L-alaninamide - -
L-alanine - -
L-alanyl glycine - -
L-arabinitol - -
L-arabinose - -
L-asparagine - -
L-cysteine - -
leucine - -
leucine arylamidase - -
leucyl glycine arylamidase - -
L-fucose - -
L-glutamate - -
L-glutamic acid - -
L-proline - -
L-histidine - -
L-lactic acid - -
L-leucine - -
L-malic acid - -
L-ornithine - -
L-phenylacetate - -
L-phenylalanine - -
L-proline - -
L-pyroglutamic acid - -
L-rhamnose - -
L-serine - -
L-sorbose - -
L-tryptophan - -
lysine - -
malate - -
malonate - -
maltitol - -
maltose - -
maltotriose - -
mannan - -
mannitol - -
mannose - -
melezitose - -
melibiose - -
mesaconate - -
methanol - -
methyl -D-galactoside - -
methyl -D-glucoside - -
methyl D-glucoside - -
methyl -D-mannoside - -
methyl β-D-galactoside - -
methyl β-D-glucoside - -
myo-inositol - -
N-acetyl-D-galactosamine - -
N-acetyl-D-glucosamine - -
N-acetyl-L-glutamic acid - -
N-acetyl-β-D-mannosamine - -
naphthol-AS-BI-phosphohydrolase - -
palatinose - -
p-arbutin - -
phenylalanine arylamidase - -
p-hydroxyphenylacetic acid - -
p-ketoglutaric acid - -
p-ketovaleric acid - -
proline arylamidase - -
propanol - -
propionate - -
propionic acid - -
putrescine - -
pyroglutamic acid arylamidase - -
pyrrolidonyl arylamidase - -
pyruvate - -
pyruvic acid - -
pyruvic acid methyl ester - -
quinate - -
raffinose - -
rhamnose - -
ribitol - -
ribose - -
saccharate - -
salicin - -
sedoheptulosan - -
serine - -
serine arylamidase - -
sorbitol - -
stachyose - -
suberate - -
succinamic acid - -
succinate - -
succinic acid - -
succinic acid monomethyl ester - -
sucrose - -
thymidine - -
thymidine 5'-monophosphate - -
trans-aconitate - -
trehalose - -
trypsin - -
turanose - -
tween 40 - -
tween 80 - -
tyrosine arylamidase - -
urease - -
uridine - -
uridine 5'-monophosphate - -
xylan - -
xylitol - -
xylose - -
β-alanine - -
β-and -hydroxybutyric acids - -
β-cyclodextrin - -