[Bio] / GBBergeyDB / GBBergeyDB.xml Repository:
ViewVC logotype

Diff of /GBBergeyDB/GBBergeyDB.xml

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.2, Wed Jan 17 13:42:44 2007 UTC revision 1.3, Thu Jan 18 15:46:58 2007 UTC
# Line 1  Line 1 
1  <?xml version="1.0" encoding="UTF-8"?>  <?xml version="1.0" encoding="UTF-8"?>
2    
3  <project_space label="GBBergeyDB" superspace="GenDB">  <project_space label="GBergeyDB" superspace="GenDB">
4    
5  <object label="Domain">  <object label="Domain">
6    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
# Line 50  Line 50 
50      <scalar label="CMRID" type="INT" />      <scalar label="CMRID" type="INT" />
51      <scalar label="carbon" type="CHAR(250)" />      <scalar label="carbon" type="CHAR(250)" />
52      <scalar label="chromosomeType" type="CHAR(250)" />      <scalar label="chromosomeType" type="CHAR(250)" />
53    <!--
54      <object label="Contact" type="Contact" />      <object label="Contact" type="Contact" />
55      <array>      <array>
56        <object label="FundingOrganisation" type="Institution" />        <object label="FundingOrganisation" type="Institution" />
# Line 60  Line 61 
61      <array>      <array>
62        <object label="Institution" type="Institution" />        <object label="Institution" type="Institution" />
63      </array>      </array>
64    -->
65      <scalar label="desease" type="INT" />      <scalar label="desease" type="INT" />
66      <scalar label="energy" type="CHAR(250)" />      <scalar label="energy" type="CHAR(250)" />
67      <scalar label="oxygen" type="CHAR(250)" />      <scalar label="oxygen" type="CHAR(250)" />
# Line 71  Line 73 
73      <scalar label="extremophile" type="CHAR(250)" />      <scalar label="extremophile" type="CHAR(250)" />
74      <scalar label="shape" type="CHAR(125)" />      <scalar label="shape" type="CHAR(125)" />
75      <scalar label="width" type="FLOAT" />      <scalar label="width" type="FLOAT" />
76      <scalar label="genomeSize" type="INT" />  <!--    <scalar label="genomeSize" type="INT" /> -->
77      <scalar label="noORFs" type="INT" />  <!--    <scalar label="noORFs" type="INT" /> -->
78      <scalar label="motile" type="CHAR(125)" />      <scalar label="motile" type="CHAR(125)" />
79      <scalar label="numberChromosomes" type="INT" />      <scalar label="numberChromosomes" type="INT" />
80      <scalar label="totalReplicons" type="INT" />      <scalar label="totalReplicons" type="INT" />
81      <scalar label="hxh" type="INT" />      <scalar label="hxh" type="INT" />
82      <scalar label="sequencingStatus" type="CHAR(250)" />      <scalar label="sequencingStatus" type="CHAR(250)" />
83      <scalar label="orderOfPublication" type="INT" />      <scalar label="orderOfPublication" type="INT" />
84      <object label="Publication" type="Publication" />  <!--    <object label="Publication" type="Publication" /> -->
85      <array>      <array>
86        <scalar label="addFeatures" type="CHAR(250)" />        <scalar label="addFeatures" type="CHAR(250)" />
87      </array>      </array>
88    <!-- added from andi's schema from now on -->
89        <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!--  (describing translation and use of start codons) -->
90        <scalar label="estiGenomeSize" type="INT" />
91        <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 -->
92      </object>
93    
94    
95    <object label="GenomeSequence">
96        <object label="Genome" type="Genome" mandatory="1" /> <!--  Organism a sequence belongs to -->
97        <scalar label="version" type="int" /> <!-- Version number of the sequence -->
98        <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
99        <object label="Contact" type="Contact" />
100        <array>
101          <object label="FundingOrganisation" type="Institution" />
102        </array>
103        <array>
104          <object label="GenomeDatabase" type="GenomeDatabase" />
105        </array>
106        <array>
107          <object label="Institution" type="Institution" />
108        </array>
109        <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
110        <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
111        <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
112        <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
113        <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file  -->
114        <scalar label="sequenceChecksum" type="int"/>
115        <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
116        <scalar label="lastUpdate" type="char(255)"/>
117        <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
118        <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
119        <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
120        <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
121        <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
122        <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, ... -->
123        <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
124        <scalar label="noORFs" type="INT" />
125        <object label="Publication" type="Publication" />
126    </object>    </object>
127    
128    
129  <object label="Publication">  <object label="Publication">
130    <scalar label="pubmed" type="INT" />    <scalar label="pubmed" type="INT" />
131    <scalar label="url" type="CHAR(250)" />    <scalar label="url" type="CHAR(250)" />
# Line 115  Line 156 
156    <scalar label="value" type="CHAR(250)" />    <scalar label="value" type="CHAR(250)" />
157  </object>  </object>
158    
159    <object label="SOP">
160      <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
161      <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
162      <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
163      <scalar label="note" type="TEXT"/>
164      <index>
165          <attribute label="name"/>
166          <attribute label="date"/>
167      </index>
168    </object>
169    
170    <object label="SequenceLog">
171      <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
172      <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
173      <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
174      <scalar label="date" type="int"/> <!-- Date of the event -->
175      <object label="organism" type="GenomesDB::Organism"/>
176    </object>
177    
178    <object label="File">
179      <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
180      <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
181      <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
182      <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
183      <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
184      <scalar label="uid" type="text" /> <!-- User id of the file -->
185      <index>
186        <attribute label="name" />
187        <attribute label="path" />
188        <attribute label="creation_time"/>
189      </index>
190    </object>
191    
192  </project_space>  </project_space>

Legend:
Removed from v.1.2  
changed lines
  Added in v.1.3

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3