# DSMZ Plasmid Catalogue - Information file
# Version 2023.02.16.1
# Last Updated February 16, 2023
# Author: Domenico Marra & Francesca Piersigilli & Paolo Romano
# (c) CABRI 1999-2023

$DSMZ_PLASMID_RES=$Resource:[
  description:
    |<p>
    |This is the DSMZ Plasmid database.
  contact:
    |<ADDRESS>
    |Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH,<br> 
    |Inhoffenstr. 7B,<br>
    |D-38124 BRAUNSCHWEIG,<br>
    |Germany.<br>
    |</ADDRESS><P>
  www:
    |Web: <a href="http://www.dsmz.de/">http://www.dsmz.de/</a><br>
    |Email: Dr Christine Rohde <a href=mailto:christine.rohde@dsmz.de>christine.rohde@dsmz.de</a>
  email: 
    |<a href=mailto:help@dsmz.de>help@dsmz.de</a>
  fields: { 
     Name: 
         |Name of the element<br>
         |<b>Input process</b>: name given by the depositor or as published<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: /.-<br>
         |<b>Not indexed characters</b>: )(+%$"\&'?!|#@<<br>
     Collection_number:
         |Number of the element in the own collection under
         |which it is distributed<br>
         |<b>Input process</b>: Collection acronym followed by a number 
         |separated by space<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Unique element<br>
         |<b>Skipped characters</b>: ,;:.+*<br>
         |<b>Not indexed characters</b>: +$"\&'?!|#@<br>
     Type:
         |Element type<br>
         |<b>Input process</b>: Reference list: plasmid, phasmid, cosmid, 
         |shuttle vector, transposon, minitransposon, IS element<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Class:
         |Origin of the element<br>
         |<b>Input process</b>: Reference list: non-recombinant, recombinant<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Other_culture_collection_numbers:
         |Numbers of the element under which it is distributed by other 
         |culture<br>
         |collections, incl. non-CABRI numbers if possible 
         |(e.g. ATCC, NCTC, etc.)<br>
         |<b>Input process</b>: 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.<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Host_for_distribution:
         |Taxonomic designation and strain designation of the host organism in 
         |which the element is distributed<br>
         |<b>Input process</b>: e.g. Escherichia coli K12 MC1061. 
         |Reference list: CABRI in house agreed list<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Medium:
         |Name or collection number of the medium on which the host organism is 
         |preferably grown<br>
         |<b>Input process</b>: Free text which may be linked to a text file 
         |describing the recipe for the medium<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!|#@<br>
     Restricted_distribution:
         |Restrictions for distribution of the element (hazard group, "for
         |research purposes only", patent info, import/export regulations, 
         |etc.)<br>
         |<b>Input process</b>: Free text: "No" or the description of the 
         |appropriate restrictions<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Literature:
         |Original publication in which the element is described<br>
         |<b>Input process</b>: Free text<br> <u>New entry</u>: Author, Title 
         |Year';'Volume(iusse)':'beginning page#'-'ending page#<br>
         |The title of the journal is abbreviated following international 
         |standard rules; the abbreviations are without dot 
         |The title of the article is not mentioned<br>
         |<u>Existing entries</u>: Conversion by SRS following 
         |CABRI agreed standard<br>     
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters skipped</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     History_of_deposit:
         |History of the element from author to depositor, in reverse order<br>
         |<b>Input process</b>: Free text. The name of the depositor must be 
         |entered obligatory; history when known<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Selectable_phenotype:
         |Feature encoded by the element enforcing its host strain 
         |to maintain the 
         |element in order to survive under 
         |appropriate cultivation conditions<br>
         |<b>Input process</b>: Reference list: CABRI in house agreed list<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Replicon:
         |Names of replicon elements<br>
         |<b>Input process</b>: Reference list: CABRI in house agreed list<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Host_range:
         |Hosts in which the element can be propagated and/or used and, when
         |applicable, the peculiar features that are necessary for making use of
         |the special characteristics of the element<br>
         |<b>Input process</b>: Free text based on the VECAP3 list in 
         |Vicente et al., World J. Microbiol. and Biotechnol. 
         |8 (1992), 519-526<br>
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@<br>
     Properties_and_applications:
         |Description of the properties of the element, as well as its 
         |application possibilities<br> 
         |<b>Input process</b>: Reference list: CABRI in house agreed list 
         |based on the VECAP4, VECAP5 and VECAP6 lists in Vicente et al., 
         |World J. Microbiol. and Biotechnol. 8 (1992), 519-526)<br> 
         |<b>Required for</b>: Minimum Data SETo (MDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"\'?!=|#@&<br>
     Cloned_gene:
         |Description of the genetic markers inserted<br> 
         |<b>Input process</b>: Free text<br> 
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
     Promoter:
         |Type of promoters present on the plasmid. 
         |The promoters controlling expression of the prokaryotic 
         |antibiotic resistance genes are not indicated<br>
         |<b>Input process</b>: Free text<br>
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
     Ribosome_binding_site:
         |Type of ribosome binding sites present on the plasmid. 
         |The ribosome binding sites upstream of the prokaryotic antibiotic 
         |resistance genes are not indicated<br>
         |<b>Input process</b>: Free text<br>
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
    Terminator:
         |Type of transcription terminators present on the plasmid<br>
         |<b>Input process</b>: Free text<br>
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
    Further_information:
         |Description of peculiar features and special functions which are 
         |not easily fitted into the other sections.<br>
         |Remarks on the history, other names and queries about the fine 
         |structure of the plasmid are also mentioned here<br>
         |<b>Input process</b>: Free text<br>
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
    Restriction_sites:
         |The restriction sites are obtained from REBASE version 611 
         |(Dr R.J. Roberts Enzyme Database; New England Biolabs).<br>
         |They are indicated as U-sites (really unique sites) or as E-sites 
         |(expression sites). In case the expression site is not unique, 
         |this is mentioned in the field 'Further information'<br>
         |<b>Input process</b>: Free text<br>
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
    Sequence_detail:
         |Part of the nucleotide sequence of the plasmid (e.g. a multiple 
         |cloning site, the result of a mutagenesis) is described in detail<br>
         |<b>Input process</b>: Free text<br>
         |<b>Required for</b>: Full Data SETo (FDS)<br>
         |<b>Indexed by</b>: Single words<br>
         |<b>Skipped characters</b>: Blank space<br>
         |<b>Not indexed characters</b>: )(+$"'?!=|#@<br>
     } 
]