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revision 1.2, Wed Jan 17 13:42:44 2007 UTC revision 1.12, Wed Feb 21 15:30:51 2007 UTC
# Line 35  Line 35 
35  <object label="Species">  <object label="Species">
36    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
37    <object label="Genus" type="Genus" />    <object label="Genus" type="Genus" />
38      <object label="ScientificSpecies" type="Species" />
39      <scalar label="userflag1" type="INT" />
40      <scalar label="userflag2" type="INT" />
41      <scalar label="userflag3" type="INT" />
42      <scalar label="userflag4" type="INT" />
43      <scalar label="computedscore" type="INT" />
44      <scalar label="score" type="INT" />
45      <scalar label="taxid" type="INT" />
46    </object>
47    
48    <object label="Note">
49      <scalar label="user" type="CHAR(250)" />
50      <scalar label="description" type="CHAR(250)" />
51      <scalar label="timestamp" type="INT" />
52      <scalar label="voting" type="INT" />
53      <scalar label="confidence" type="INT" />
54      <object label="Strain" type="Genome" />
55      <object label="Species" type="Species" />
56    </object>
57    
58    <object label="STScluster">
59      <scalar label="number" type="INT" />
60      <scalar label="seqrepresentation" type="INT" />
61  </object>  </object>
62    
63    <object label="Genome">    <object label="Genome">
64      <scalar label="name" type="CHAR(250)" />      <scalar label="name" type="CHAR(250)" />
65      <object label="Genus" type="Genus" />  es->  <object label="STScluster" type="STScluster" />
66      <scalar label="STSvalue" type="FLOAT" />
67      <object label="Species" type="Species" />      <object label="Species" type="Species" />
68      <scalar label="strain" type="CHAR(125)" />    <scalar label="typeStrain" type="INT" />
69      <array>
70        <scalar label="strainAliases" type="CHAR(250)" />
71      </array>
72      <scalar label="gramStain" type="CHAR(125)" />      <scalar label="gramStain" type="CHAR(125)" />
73      <scalar label="taxid" type="CHAR(16)" />      <scalar label="taxid" type="CHAR(16)" />
74      <scalar label="ncNumber" type="CHAR(125)" />      <scalar label="ncNumber" type="CHAR(125)" />
75      <scalar label="ncbiNumber" type="INT" />      <scalar label="ncbiNumber" type="INT" />
76      <scalar label="CMRAlias" type="CHAR(125)" />      <scalar label="CMRAlias" type="CHAR(125)" />
77      <scalar label="CMRID" type="INT" />      <scalar label="CMRID" type="INT" />
78      <scalar label="goldstamp" type="CHAR(125)" />
79      <scalar label="carbon" type="CHAR(250)" />      <scalar label="carbon" type="CHAR(250)" />
80      <scalar label="chromosomeType" type="CHAR(250)" />      <scalar label="chromosomeType" type="CHAR(250)" />
     <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>  
81      <scalar label="desease" type="INT" />      <scalar label="desease" type="INT" />
82      <scalar label="energy" type="CHAR(250)" />      <scalar label="energy" type="CHAR(250)" />
83      <scalar label="oxygen" type="CHAR(250)" />      <scalar label="oxygen" type="CHAR(250)" />
# Line 71  Line 89 
89      <scalar label="extremophile" type="CHAR(250)" />      <scalar label="extremophile" type="CHAR(250)" />
90      <scalar label="shape" type="CHAR(125)" />      <scalar label="shape" type="CHAR(125)" />
91      <scalar label="width" type="FLOAT" />      <scalar label="width" type="FLOAT" />
     <scalar label="genomeSize" type="INT" />  
     <scalar label="noORFs" type="INT" />  
92      <scalar label="motile" type="CHAR(125)" />      <scalar label="motile" type="CHAR(125)" />
93      <scalar label="numberChromosomes" type="INT" />      <scalar label="numberChromosomes" type="INT" />
94      <scalar label="totalReplicons" type="INT" />      <scalar label="totalReplicons" type="INT" />
95      <scalar label="hxh" type="INT" />      <scalar label="hxh" type="INT" />
96      <scalar label="sequencingStatus" type="CHAR(250)" />      <scalar label="sequencingStatus" type="CHAR(250)" />
97      <scalar label="orderOfPublication" type="INT" />      <scalar label="orderOfPublication" type="INT" />
98      <object label="Publication" type="Publication" />    <scalar label="InBergey" type="INT" />
99      <scalar label="InGOLD" type="INT" />
100      <scalar label="InNCBI" type="INT" />
101      <scalar label="InDSMZ" type="INT" />
102      <scalar label="InCCUG" type="INT" />
103      <scalar label="InSEED" type="INT" />
104      <scalar label="InGenomeData" type="INT" />
105      <scalar label="InSTS" type="INT" />
106      <!-- added from andi's schema from now on -->
107      <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!--  (describing translation and use of start codons) -->
108      <scalar label="estiGenomeSize" type="INT" />
109      <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 -->
110      <array>      <array>
111        <scalar label="addFeatures" type="CHAR(250)" />        <scalar label="addFeatures" type="CHAR(250)" />
112      </array>      </array>
113    </object>    </object>
114    
115    <object label="GenomeSequence">
116        <object label="Genome" type="Genome" mandatory="1" /> <!--  Organism a sequence belongs to -->
117        <scalar label="version" type="int" /> <!-- Version number of the sequence -->
118        <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
119        <object label="Contact" type="Contact" />
120        <array>
121          <object label="FundingOrganisation" type="Institution" />
122        </array>
123        <array>
124          <object label="GenomeDatabase" type="GenomeDatabase" />
125        </array>
126        <array>
127          <object label="Institution" type="Institution" />
128        </array>
129        <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
130        <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
131        <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
132        <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
133        <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file  -->
134        <scalar label="sequenceChecksum" type="int"/>
135        <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
136        <scalar label="lastUpdate" type="char(255)"/>
137        <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
138        <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
139        <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
140        <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
141        <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
142        <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, ... -->
143        <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
144        <scalar label="noORFs" type="INT" />
145        <object label="Publication" type="Publication" />
146    </object>
147    
148    
149    <object label="GenomeAlias">
150      <scalar label="name" type="CHAR(250)" />
151      <scalar label="scientificName" type="CHAR(250)" />
152      <scalar label="taxid" type="INT" />
153      <scalar label="ident" type="INT" />
154      <scalar label="aliasType" type="CHAR(250)" />
155    </object>
156    
157  <object label="Publication">  <object label="Publication">
158    <scalar label="pubmed" type="INT" />    <scalar label="pubmed" type="INT" />
159    <scalar label="url" type="CHAR(250)" />    <scalar label="url" type="CHAR(250)" />
# Line 115  Line 184 
184    <scalar label="value" type="CHAR(250)" />    <scalar label="value" type="CHAR(250)" />
185  </object>  </object>
186    
187    <object label="SOP">
188      <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
189      <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
190      <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
191      <scalar label="note" type="TEXT"/>
192      <index>
193          <attribute label="name"/>
194          <attribute label="date"/>
195      </index>
196    </object>
197    
198    <object label="SequenceLog">
199      <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
200      <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
201      <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
202      <scalar label="date" type="int"/> <!-- Date of the event -->
203      <object label="organism" type="GenomesDB::Organism"/>
204    </object>
205    
206    <object label="File">
207      <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
208      <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
209      <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
210      <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
211      <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
212      <scalar label="uid" type="text" /> <!-- User id of the file -->
213      <index>
214        <attribute label="name" />
215        <attribute label="path" />
216        <attribute label="creation_time"/>
217      </index>
218    </object>
219    
220  </project_space>  </project_space>

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