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CABRI Guidelines for Catalogue Production

Guidelines prepared for CABRI by BCCM, CBS, CERDIC, DSMZ, ECACC, HGMP, INRC, MSDN
Page layout by CERDIC


Data input & authentication Flat file preparation Flat file submission


Data input & authentication for bacteria & archaea

Data Sets

Data entry and validation

Accession number
Other culture collection numbers
Restrictions
Organism type
Name
Infrasubspecific names
Status
Other names
History of deposit
Conditions for growth
Form of supply
Serovar
Isolated from
Geographic origin
Mutant
Genotype
Literature

  1. Accession number
  2. Field

    Accession number
    Description collections’ own accession number of the strain
    Input process consists of collection acronym followed by a number or alphanumeric identifier separated with a blank

    Make sure unique number is given to each strain

    Required for MDS

  3. Other culture collection numbers
  4. Field Other culture collection numbers
    Description accession numbers of the strain in other collections
    Input process New strain: as given by depositor

    Existing strain: if strain is sent to another collection, get and add accession number used in that collection. It can not be given if the strain is unique in the collection.

    numbers from individual researchers are also allowed

    Collection acronyms: CABRI agreed list

    Numbers are separated by semicolon

    Required for MDS

  5. Restrictions
  6. Field Restrictions
    Description value "no", or a text field describing the appropriate restrictions: hazard group, import/export regulations
    Input process Enter ‘No’, or actual restrictions, which may be linked to a file for conditions of delivery

    The text may contain codes which refer to text files explaining the restrictions in more detail.

    Required for MDS

  7. Organism type
  8. Field Organism type
    Description contain value "Bacteria" or "Archaea".
    Input process Enter "B" or "A"
    Required for MDS

  9. Name
  10. Field Name
    Description full scientific and most recent name of the strain:

    - Genus name and species epithet
    - Subspecies *
    - Pathovar *
    - Authors of the name
    - Year of valid publication or validation
    - Approbation of the name

    Input process Enter full scientific name as given by depositor and confirmed (or changed) by collection. Names of authors of the name, year of valid publication or validation and approbation are included after a comma.

    Values for approbation:

    AL = approved list, c.f.r. IJSB 1980
    VL = validation list, in IJSB after 1980
    VP = validly published, paper in IJSB after 1980

    Reference list: DSMZ list of bacterial names

    Required for MDS

  11. Infrasubspecific names
  12. Field Infrasubspecific names
    Description variety designation, epithet, authors and reference.

    Does not apply to all strains

    Input process Enter type and epithet of the variety as given by depositor and confirmed (or changed) by collection. Names of authors and reference are included.
    This field excludes the pathovar name and the serovar name, which are both infrasubspecific names but are to be netered int the NAME field

    Format: see MINE format
    Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852

    Required for MDS

  13. Status
  14. Field Status
    Description nomenclatural status of the strain (like "type", "neotype", etc.)

    Does not apply to all strains

    Input process Enter information on type and scientific name of organism, for which material from which strain was isolated is type material.

    Format: see MINE format
    Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852

    Required for MDS

  15. Other names
  16. Field Other names
    Description names used for the strain in the past (not synonyms) that may still be in use. Same format as Name field.

    Does not apply to all strains.

    Input process Enter previous names used for the strain if they are no synonyms of the current name.

    Same format as Name field.

    Required for RDS

  17. History of deposit
  18. Field History of deposit
    Description history of the element from depositor to isolator.

    - Name of depositor
    - Institute of depositor
    - Name of isolator
    - Institute of isolator
    - Names and institutes in between

    Input process Enter information as given by depositor

    Format: see MINE format< br>Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852

    Required for MDS

  19. Conditions for growth
  20. Field Conditions for growth
    Description Culture medium
    Atmospheric and light conditions
    Temperature conditions
    Input process Each collection has to provide its own list of culture media and recipes, medium provided for strain is linked to medium in this file.
    (http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/list-of-media-for-microorganisms.html)

    Atmospheric and light conditions should only be given if they are special.

    Additional remarks on the cultivation like 'freshly prepared medium is necessary' or 'extended incubation time…' if necessary'

    Required for MDS

  21. Form of supply
  22. Field Form of supply
    Description form in which the strain will be sent to the customer
    Input process Values: 'Active', 'Dried', 'Dried ice'
    Required for MDS

  23. Serovar
  24. Field Serovar
    Description serovar name and author.

    Required for some medically important species.

    Does not apply to all strains

    Input process Format: see MINE format
    Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852
    Required for RDS

  25. Isolated from
  26. Field Isolated from
    Description name of substrate or host from which the strain was isolated.
    Input process Enter information as given by depositor or as retrieved from public information sources

    Format: see MINE format
    Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852

    Required for RDS

  27. Geographic origin
  28. Field Geographic origin
    Description name of country where strain originated from, followed by details on location.
    Input process Enter information as given by depositor or as retrieved from public information sources
    Format: see MINE format
    Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852

    CABRI agreed list for country: name based on country code file retrieved from: ftp://ftp.ripe.net/iso3166-countrycodes.txt updated by the RIPE Network Co-ordination Centre, in co-ordination with the ISO 3166 Maintenance Agency at DIN Berlin.

    Exception for UK, USA, USSR, Netherlands, North Korea

    Required for RDS

  29. Mutant
  30. Field Mutant
    Description type and parent of mutant if strain is a mutant strain.

    Applies only to a small number of strains.

    Input process Free text: enter information as given by depositor or as retrieved from public information sources
    Required for RDS

  31. Genotype
  32. Field Genotype
    Description names of chromosomal markers of the strain. Especially recommended for strains of species for which many genetically modified strains exist.

    Does not apply to all strains

    Input process Format: see MINE format
    Stalpers et al., Systematic Applied Microbiol 1990;13:92-103
    DOI: 10.1016/S0723-2020(11)80185-2
    http://www.sciencedirect.com/science/article/pii/S0723202011801852
    Required for RDS

  33. Literature
  34. Field Literature
    Description reference to publication in which the strain is described.

    Especially recommended for type strains

    Input process new entry: Journal Title Year;Volume(issue):beginning page#-ending page#
    The journal title is abbreviated following international standard rules (ISSN abbreviations).
    The abbreviations are without dot. Authors and title of the article are not mentioned.

    existing catalogues: conversion by SRS following CABRI agreed standard

    This reference can be followed by the Pubmed ID enclosed within square brackets as follows:
    [PMID: 1234567], where '1234567' is the Pubmed ID of the paper

    Required for RDS
 
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