Microbiological Common Language (MCL) reference

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.

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.

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

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.

Culture medium used to grow cultures.

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.

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.

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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

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

This term uses the same recommended vocabulary as Bacterial MINE.

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.

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

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

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

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

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

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

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.

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.

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.

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.

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

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

References a publication in which strain history is described.

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

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

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

Title of publication.

Author of article or BRC catalog MCL XML export.

Name of journal or book where article was published.

Volume number of article.

Issue number of article.

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

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"

Date (year) when publication was issued.

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

Example: 'LMG Medium 1'

Common name of culture medium.

Example: 'TSA', 'Columbia Agar'

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

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

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

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

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.

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.

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.

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).

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

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

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.

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

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.

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

Institute of sample collector at time of sample collection.

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.

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

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

Culture that will be deposited in another BRC.

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

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.

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

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

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.

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.

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

Creation date and time.

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

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

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

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.

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.

Shape of cells as measured under standard conditions.

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

Indicates whether cells form spores.

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

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

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

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

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

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

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

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

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.

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

Typical shape of colonies.

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

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

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

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

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

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

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

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

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

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

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.

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.

A significant ubi, isoprenoid or mena quinone.

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.

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.