<?xml version="1.0" encoding="ISO-8859-1" ?>
<mlst>
<system
 longcode="nm_isolates"
 webroot="/neisseria" 
 indexpage=""  
 dbprof="nm_profiles" 
 profhome="/cgi-bin/mlstdbnet/mlstdbnet.pl?file=pub-nm_profiles.xml" 
 noshow="other_name,Z_number,region"
 view="isolates" 
 fieldgroup1="identifier fields:id,strain,other_name,Z_number"
 dbtype="st"
 description="Neisseria PubMLST">Neisseria PubMLST</system>
<author>Martin Maiden</author>
<author>Dominique Caugant</author>
<author>Ian Feavers</author>
<author>Mark Achtman</author>
<author>Brian Spratt</author>
<reference>Maiden et al 1997</reference>
<doclink>http://neisseria.mlst.net</doclink>

<!-- CURATORS -->
<curator>Keith Jolley</curator>
<curator>Rachel Urwin</curator>

<!-- LOCI -->
<locus fullname="ABC transporter" length="433">abcZ</locus>
<locus fullname="adenylate kinase" length="465">adk_</locus>
<locus fullname="shikimate dehydrogenase" length="490" orf="2">aroE</locus>
<locus fullname="fumarate hydratase" length="465">fumC</locus>
<locus fullname="glucose-6-phosphate dehydrogenase" length="501">gdh_</locus>
<locus fullname="pyruvate dehydrogenase subunit" length="480">pdhC</locus>
<locus fullname="phosphoglucomutase" length="450">pgm_</locus>
<!-- PROFILES FIELDS -->
<field type="int" length="5" userupdate="no" comments="primary key">id</field>
<field type="text" length="20" comments="Original strain name as supplied by sender">strain</field>
<field type="text" required="no" maindisplay="no" length="20"
  comments="Other name of strain, if there are more than two names, please put others in comments fields">other_name</field>
<field type="int" length="5" comments="sequence type">ST</field>
<field type="text" length="30" 
  comments="Country where strain was isolated,use name of country at time of isolation">country</field>
<field type="text" required="no" maindisplay="no" length="30" comments="Region/city etc inside country">region</field>
<field type="int" length="4" comments="year of isolation">year</field>
<field type="int" required="no" maindisplay="no" comments="age in years">age_yr</field>
<field type="int" required="no" maindisplay="no" comments="month part of age 1-12">age_mth</field>

<field type="text" maindisplay="no" length="12" optlist="yes">sex
<optlist>
<option>unspecified</option>
<option>male</option>
<option>female</option>
</optlist>
</field>

<field type="text" length="40" optlist="yes"
  comments="please put other diseases in comments field">disease
<optlist>
<option>unspecified</option>
<option>carrier</option>
<option>meningitis</option>
<option>septicaemia</option>
<option>meningitis and septicaemia</option>
<option>invasive (unspecified/other)</option>
<option>other</option>
</optlist>
</field>

<field type="text" maindisplay="no" length="40" optlist="yes">source
<optlist>
<option>unspecified</option>
<option>blood</option>
<option>CSF</option>
<option>throat swab</option>
<option>other</option>
</optlist>
</field>
<field type="text" maindisplay="no" length="40" optlist="yes">epidemiology
<optlist>
<option>unspecified</option>
<option>carrier</option>
<option>healthy contact</option>
<option>sporadic case</option>
<option>endemic</option>
<option>epidemic</option>
<option>pandemic</option>
</optlist>
</field>
<field type="text" length="40" optlist="yes" default="Neisseria meningitidis" 
  comments="Species name in multiple species databases where permitted">species
<optlist>
<option>Neisseria meningitidis</option>
<option>Neisseria lactamica</option>
<option>Neisseria gonorrhoeae</option>
<option>Neisseria cinerea</option>
<option>Neisseria mucosa</option>
<option>Neisseria flava</option>
<option>Neisseria flavescens</option>
<option>Neisseria perflava</option>
<option>Neisseria polysacchareae</option>
<option>Neisseria sicca</option>
<option>Neisseria subflava</option>
<option>Neisseria elongata</option>
<option>Neisseria dentrificans</option>
</optlist>
</field>


  <!--Species specific typing fields(part of profiles fields-->
<field type="text" length="20" optlist="yes">serogroup
<optlist>
<option>unspecified</option>
<option>A</option>
<option>B</option>
<option>C</option>
<option>X</option>
<option>Y</option>
<option>Z</option>
<option>W-135</option>
<option>29E</option>
<option>H</option>
<option>J</option>
<option>K</option>
<option>L</option>
<option>Non-groupable</option>
<option>other</option>
</optlist>
</field>
<field type="text" maindisplay="no" length="40" optlist="yes">MLEE_designation
<optlist>
<option>unspecified</option>
<option>A4 Cluster</option>
<option>ET-37 Complex</option>
<option>ET-5 Complex</option>
<option>Lineage 3</option>
<option>Lineage IV</option>
<option>Subgroup I</option>
<option>Subgroup II</option>
<option>Subgroup III</option>
<option>Subgroup IV-I</option>
<option>Subgroup IV-II</option>
<option>Subgroup V</option>
<option>Subgroup VI</option>
<option>Subgroup VII</option>
<option>Subgroup VIII</option>
<option>Subgroup IX</option>
<option>Subgroup X</option>
<option>other</option>
</optlist>
</field>
<!-- <field type="text" required="no" maindisplay="no" length="40" regex="/[A|B|C|W-135|X|Y|NT]\:[0-9]+\:P[0-9]+\.[0-9]+/"
  comments="serogroup , serosubtype etc">phenotype</field>-->
<field type="text" required="no" maindisplay="no" length="10">serotype</field>
<field type="text" required="no" maindisplay="no" length="10">porB_allele</field>
<field type="text" required="no" maindisplay="no" length="10">sero_subtype</field>
<field type="text" required="no" maindisplay="no" length="10" comments="porA variable region 1" host="phoenix.medawar.ox.ac.uk" port="5432" user="remote" pass="remote" dbpep="poravr" table="vr1" qryname="id" seq="pep_seq" web="http://neisseria.org/cgi-bin/agdbnet/agdbnet.pl?file=poravr.xml&amp;page=seqinfo&amp;locus=VR1_p&amp;id=\?">VR1</field>
<field type="text" required="no" maindisplay="no" length="10" comments="porA variable region 2" host="phoenix.medawar.ox.ac.uk" port="5432" user="remote" pass="remote" dbpep="poravr" table="vr2" qryname="id" seq="pep_seq" web="http://neisseria.org/cgi-bin/agdbnet/agdbnet.pl?file=poravr.xml&amp;page=seqinfo&amp;locus=VR2_p&amp;id=\?">VR2</field>
<field type="text" required="no" maindisplay="no" length="10" comments="porA allele number" host="phoenix.medawar.ox.ac.uk" port="5432" user="remote" pass="remote" dbnuc="pora_alleles" table="pora" qryname="id" seq="seq">porA_allele</field>

<field type="text" required="no" maindisplay="no" length="10">ET_no</field>
<field type="int" required="no" maindisplay="no" length="4">Z_number</field>

  <!--Antibiotics(part of profiles fields-->

<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">penicillin</field>
<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">sulphonamide</field>
<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">ceftriaxone</field>
<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">chloramphenicol</field>
<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">cefotaxime</field>
<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">rifampicin</field>
<field type="text" required="no" maindisplay="no" length="20" comments="MIC in mg/l">ciprifloxacin</field>

<field type="int" required="no" maindisplay="no" length="10" comments="Medline number if published">reference1</field>
<field type="int" required="no" maindisplay="no" length="10" comments="Medline number if published">reference2</field>
<field type="int" required="no" maindisplay="no" length="10" comments="Medline number if published">reference3</field>
<field type="int" required="no" maindisplay="no" length="10" comments="Medline number if published">reference4</field>
<field type="int" required="no" maindisplay="no" length="10" comments="Medline number if published">reference5</field>

<field type="text" required="no" maindisplay="no" length="1000" comments="any other comments">comments</field>
<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
<field type="int" maindisplay="no" userupdate="no" length="4" comments="curator who entered data,link to users">curator</field>
<field type="DATE" maindisplay="no" length="10" comments="date first entered">date_entered</field>
<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date last modified">datestamp</field>
</mlst>


