CABRI: Catalogue production guidelines: plasmids: data input

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 plasmids

Data Sets

Data entry and validation

Name
Collection number
Type
Class

Other culture collection numbers
Host for distribution
Medium
Restricted distribution

Literature
History of deposit
Selectable phenotype
Replicon

Host range
Properties and applications

Name

Field	Name
Description	Name of the element
Input process	Name given by the depositor or as published
Required for	MDS

Collection number

Field	Collection number
Description	Number of the element in the own collection under which it is distributed
Input process	Collection acronym followed by a number separated by space
Required for	MDS

Type

Field	Type
Description	Element Type
Input process	Reference list: plasmid phasmid cosmid shuttle vector transposon minitransposon IS element
Required for	MDS

Class

Field	Class
Description	Origin of the element
Input process	Reference list: non-recombinant, recombinant
Required for	MDS

Other culture collection numbers (*)

Field	Other culture collection numbers
Description	Numbers of the element under which it is distributed by other culture collections.
Input process	This field is automatically generated. (*) If the content of this field cannot automatically be generated at the main site it will be removed from the MDS for plasmids. This field does not apply to all strains.
Required for	MDS

Host for distribution

Field	Host for distribution
Description	Taxonomic designation and strain designation of the host organism in which the element is distributed
Input process	e.g. Escherichia coli K-12 MC1061 Reference list: CABRI agreed list
Required for	MDS

Medium

Field	Medium
Description	Name or collection number of the medium on which the host organism is preferably grown
Input process	Free text which may be linked to a text file describing the recipe for the medium
Required for	MDS

Restricted distribution

Field	Restricted distribution
Description	Restrictions for distribution of the element
Input process	Restrictions for distribution of the element (hazard group, "for research purposes only", patent info., import/export regulations, etc.
Required for	MDS

Literature

Field	Literature
Description	Original publication in which the element is described.
Input process	new entry: Author, JournalTitle Year; Volume (issue): beginning page#-ending page# The journal title is abbreviated following international standard rules. The abbreviations are without dot. Title of the article is not mentioned. existing entries: conversion by SRS following CABRI agreed standard. This field does not apply to all strains. 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	MDS

History of deposit

Field	History of deposit
Description	History of the element from author to depositor, in reverse chronology (depositor< … < author).
Input process	The name of the depositor must be entered obligatory; history when known. This field does not apply to all strains: for plasmids deposited before december 1993 (cfr. CBD convention), this field may lack information.
Required for	MDS

Selectable phenotype

Field	Selectable phenotype
Description	Feature encoded by the element enforcing its host strain to maintain the element in order to survive under appropriate cultivation conditions
Input process	Reference list: CABRI agreed list
Required for	MDS

Replicon

Field	Replicon
Description	Names of replicon elements
Input process	Reference list: CABRI agreed list This field does not apply to all strains.
Required for	MDS

Host range

Field	Host range
Description	Host in which the element can be propagated and/or used and, when appicable, the peculiar features that are necessary for making use of the special characteristics of the element.
Input process	Free text based on the reference list VECAP3 list in Vicente et al., World J Microbiol Biotechnol 1992;8:519-526 Ex.: Escherichia coli preferably containing the lacI^q gene This field does not apply to all strains.
Required for	MDS

Properties and applications

Field	Properties and applications
Description	Description of the properties of the element, as well as its application possibilities
Input process	Reference list: CABRI agreed list based on the VECAP4, VECAP5 and VECAP6 list in Vicente et al., World J Microbiol Biotechnol 1992;8:519-526
Required for	MDS

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