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Revision 1.14 - (download) (as text) (annotate)
Tue Feb 27 19:22:29 2007 UTC (12 years, 9 months ago) by bartels
Branch: MAIN
Changes since 1.13: +1 -0 lines
added 16S data

<?xml version="1.0" encoding="UTF-8"?>

<project_space label="GBBergeyDB" superspace="GenDB">

<object label="Domain">
  <scalar label="name" type="CHAR(250)" />
</object>

<object label="Phyla">
  <scalar label="name" type="CHAR(250)" />
  <object label="Domain" type="Domain" />
</object>
 
<object label="Class">
  <scalar label="name" type="CHAR(250)" />
  <object label="Phyla" type="Phyla" />
</object>

<object label="GOrder">
  <scalar label="name" type="CHAR(250)" />
  <object label="Class" type="Class" />
</object>

<object label="Family">
  <scalar label="name" type="CHAR(250)" />
  <object label="GOrder" type="GOrder" />
</object>

<object label="Genus">
  <scalar label="name" type="CHAR(250)" />
  <object label="Family" type="Family" />
  <scalar label="form" type="INT"/>
</object>

<object label="Species">
  <scalar label="name" type="CHAR(250)" />
  <object label="Genus" type="Genus" />
  <object label="ScientificSpecies" type="Species" />
  <scalar label="userflag1" type="INT" />
  <scalar label="userflag2" type="INT" />
  <scalar label="userflag3" type="INT" />
  <scalar label="userflag4" type="INT" />
  <scalar label="computedscore" type="INT" />
  <scalar label="score" type="INT" />
  <scalar label="taxid" type="INT" />
</object>

<object label="Note">
  <scalar label="user" type="CHAR(250)" />
  <scalar label="description" type="CHAR(250)" />
  <scalar label="timestamp" type="INT" />
  <scalar label="voting" type="INT" />
  <scalar label="confidence" type="INT" />
  <object label="Strain" type="Genome" />
  <object label="Species" type="Species" />
</object>

<object label="STScluster">
  <scalar label="number" type="INT" />
  <scalar label="seqrepresentation" type="INT" />
</object>

<object label="Genome">
  <scalar label="name" type="CHAR(250)" />
  <object label="STScluster" type="STScluster" />
  <scalar label="STSvalue" type="FLOAT" />
  <object label="Species" type="Species" />
  <scalar label="typeStrain" type="INT" />
  <scalar label="sixTeenS" type="TEXT" />
  <array>
    <scalar label="strainAliases" type="CHAR(250)" />
  </array>
  <scalar label="gramStain" type="CHAR(125)" />
  <scalar label="taxid" type="CHAR(16)" />
  <scalar label="figid" type="CHAR(16)" />
  <scalar label="ncNumber" type="CHAR(125)" />
  <scalar label="ncbiNumber" type="INT" />
  <scalar label="CMRAlias" type="CHAR(125)" />
  <scalar label="CMRID" type="INT" />
  <scalar label="goldstamp" type="CHAR(125)" />
  <scalar label="carbon" type="CHAR(250)" />
  <scalar label="chromosomeType" type="CHAR(250)" />
  <scalar label="desease" type="INT" />
  <scalar label="energy" type="CHAR(250)" />
  <scalar label="oxygen" type="CHAR(250)" />
  <scalar label="obligate" type="CHAR(125)" />
  <scalar label="doubleTimeMins" type="INT" />
  <scalar label="pH" type="FLOAT" />
  <scalar label="temperature" type="INT" />
  <scalar label="habitat" type="CHAR(250)" />
  <scalar label="extremophile" type="CHAR(250)" />
  <scalar label="shape" type="CHAR(125)" />
  <scalar label="width" type="FLOAT" />
  <scalar label="motile" type="CHAR(125)" />
  <scalar label="numberChromosomes" type="INT" />
  <scalar label="totalReplicons" type="INT" />
  <scalar label="hxh" type="INT" />
  <scalar label="sequencingStatus" type="CHAR(250)" />
  <scalar label="orderOfPublication" type="INT" />
  <scalar label="InBergey" type="INT" />
  <scalar label="InGOLD" type="INT" />
  <scalar label="InNCBI" type="INT" />
  <scalar label="InDSMZ" type="INT" />
  <scalar label="InCCUG" type="INT" />
  <scalar label="InSEED" type="INT" />
  <scalar label="InGenomeData" type="INT" />
  <scalar label="InSTS" type="INT" />
  <!-- added from andi's schema from now on -->
  <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!--  (describing translation and use of start codons) -->
  <scalar label="estiGenomeSize" type="INT" />
  <scalar label="cultivationStatus" type="CHAR(255)" /> <!-- Flag for the procedure of cultivating an organism, it can be e.g. easy, hard, mediumm, slow ... --> <!-- Flags have to be discussed --> 
  <array>
    <scalar label="addFeatures" type="CHAR(250)" />
  </array>
</object>

<object label="GenomeSequence">
    <object label="Genome" type="Genome" mandatory="1" /> <!--  Organism a sequence belongs to -->
    <scalar label="version" type="int" /> <!-- Version number of the sequence -->
    <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
    <object label="Contact" type="Contact" />
    <array>
      <object label="FundingOrganisation" type="Institution" />
    </array>
    <array>
      <object label="GenomeDatabase" type="GenomeDatabase" />
    </array>
    <array>
      <object label="Institution" type="Institution" />
    </array>
    <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
    <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
    <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
    <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
    <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file  -->
    <scalar label="sequenceChecksum" type="int"/>
    <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
    <scalar label="lastUpdate" type="char(255)"/>
    <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
    <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
    <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
    <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
    <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
    <scalar label="seedStatus" type="CHAR(50)"/> <!-- Status of the genome sequence describing the relation to the SEED, e.g. is new, is in seed or rejected, ... -->
    <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
    <scalar label="noORFs" type="INT" />
    <object label="Publication" type="Publication" />
</object>


<object label="GenomeAlias">
  <scalar label="name" type="CHAR(250)" />
  <scalar label="scientificName" type="CHAR(250)" />
  <scalar label="taxid" type="INT" />
  <scalar label="ident" type="INT" />
  <scalar label="aliasType" type="CHAR(250)" />
</object>

<object label="Publication">
  <scalar label="pubmed" type="INT" />
  <scalar label="url" type="CHAR(250)" />
  <scalar label="year" type="INT" />
  <scalar label="journal" type="CHAR(250)" />
  <scalar label="number" type="INT" />
  <scalar label="pages" type="CHAR(250)" />
</object>

<object label="Institution">
  <scalar label="name" type="CHAR(250)" />
  <scalar label="url" type="CHAR(250)" />
</object>

<object label="GenomeDatabase">
  <scalar label="name" type="CHAR(250)" />
  <scalar label="url" type="CHAR(250)" />
</object>

<object label="Contact">
  <scalar label="name" type="CHAR(250)" />
  <scalar label="url" type="CHAR(250)" />
  <scalar label="email" type="CHAR(250)" />
</object>

<object label="GenomeFeatures">
  <scalar label="name" type="CHAR(250)" />
  <scalar label="value" type="CHAR(250)" />
</object>

<object label="SOP">
  <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
  <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
  <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
  <scalar label="note" type="TEXT"/>
  <index>
      <attribute label="name"/>
      <attribute label="date"/>
  </index>
</object>

<object label="SequenceLog">
  <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
  <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
  <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
  <scalar label="date" type="int"/> <!-- Date of the event -->
  <object label="organism" type="GenomesDB::Organism"/>
</object>

<object label="File">
  <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
  <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
  <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
  <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
  <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
  <scalar label="uid" type="text" /> <!-- User id of the file -->
  <index>
    <attribute label="name" />
    <attribute label="path" />
    <attribute label="creation_time"/>
  </index>
</object>

</project_space>

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