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Revision 1.3 - (view) (download) (as text)
| 1 : | bartels | 1.1 | <?xml version="1.0" encoding="UTF-8"?> |
| 2 : | |||
| 3 : | bartels | 1.3 | <project_space label="GBergeyDB" superspace="GenDB"> |
| 4 : | bartels | 1.1 | |
| 5 : | <object label="Domain"> | ||
| 6 : | <scalar label="name" type="CHAR(250)" /> | ||
| 7 : | </object> | ||
| 8 : | |||
| 9 : | <object label="Phyla"> | ||
| 10 : | <scalar label="name" type="CHAR(250)" /> | ||
| 11 : | <object label="Domain" type="Domain" /> | ||
| 12 : | </object> | ||
| 13 : | bartels | 1.2 | |
| 14 : | bartels | 1.1 | <object label="Class"> |
| 15 : | <scalar label="name" type="CHAR(250)" /> | ||
| 16 : | <object label="Phyla" type="Phyla" /> | ||
| 17 : | </object> | ||
| 18 : | |||
| 19 : | bartels | 1.2 | <object label="GOrder"> |
| 20 : | bartels | 1.1 | <scalar label="name" type="CHAR(250)" /> |
| 21 : | <object label="Class" type="Class" /> | ||
| 22 : | </object> | ||
| 23 : | |||
| 24 : | <object label="Family"> | ||
| 25 : | <scalar label="name" type="CHAR(250)" /> | ||
| 26 : | bartels | 1.2 | <object label="GOrder" type="GOrder" /> |
| 27 : | bartels | 1.1 | </object> |
| 28 : | |||
| 29 : | <object label="Genus"> | ||
| 30 : | <scalar label="name" type="CHAR(250)" /> | ||
| 31 : | <object label="Family" type="Family" /> | ||
| 32 : | bartels | 1.2 | <scalar label="form" type="INT"/> |
| 33 : | </object> | ||
| 34 : | |||
| 35 : | <object label="Species"> | ||
| 36 : | <scalar label="name" type="CHAR(250)" /> | ||
| 37 : | <object label="Genus" type="Genus" /> | ||
| 38 : | bartels | 1.1 | </object> |
| 39 : | |||
| 40 : | <object label="Genome"> | ||
| 41 : | <scalar label="name" type="CHAR(250)" /> | ||
| 42 : | <object label="Genus" type="Genus" /> | ||
| 43 : | bartels | 1.2 | <object label="Species" type="Species" /> |
| 44 : | bartels | 1.1 | <scalar label="strain" type="CHAR(125)" /> |
| 45 : | <scalar label="gramStain" type="CHAR(125)" /> | ||
| 46 : | <scalar label="taxid" type="CHAR(16)" /> | ||
| 47 : | <scalar label="ncNumber" type="CHAR(125)" /> | ||
| 48 : | <scalar label="ncbiNumber" type="INT" /> | ||
| 49 : | <scalar label="CMRAlias" type="CHAR(125)" /> | ||
| 50 : | <scalar label="CMRID" type="INT" /> | ||
| 51 : | <scalar label="carbon" type="CHAR(250)" /> | ||
| 52 : | <scalar label="chromosomeType" type="CHAR(250)" /> | ||
| 53 : | bartels | 1.3 | <!-- |
| 54 : | bartels | 1.1 | <object label="Contact" type="Contact" /> |
| 55 : | bartels | 1.2 | <array> |
| 56 : | <object label="FundingOrganisation" type="Institution" /> | ||
| 57 : | </array> | ||
| 58 : | <array> | ||
| 59 : | <object label="GenomeDatabase" type="GenomeDatabase" /> | ||
| 60 : | </array> | ||
| 61 : | <array> | ||
| 62 : | <object label="Institution" type="Institution" /> | ||
| 63 : | </array> | ||
| 64 : | bartels | 1.3 | --> |
| 65 : | bartels | 1.1 | <scalar label="desease" type="INT" /> |
| 66 : | bartels | 1.2 | <scalar label="energy" type="CHAR(250)" /> |
| 67 : | bartels | 1.1 | <scalar label="oxygen" type="CHAR(250)" /> |
| 68 : | <scalar label="obligate" type="CHAR(125)" /> | ||
| 69 : | <scalar label="doubleTimeMins" type="INT" /> | ||
| 70 : | <scalar label="pH" type="FLOAT" /> | ||
| 71 : | <scalar label="temperature" type="INT" /> | ||
| 72 : | <scalar label="habitat" type="CHAR(250)" /> | ||
| 73 : | <scalar label="extremophile" type="CHAR(250)" /> | ||
| 74 : | <scalar label="shape" type="CHAR(125)" /> | ||
| 75 : | <scalar label="width" type="FLOAT" /> | ||
| 76 : | bartels | 1.3 | <!-- <scalar label="genomeSize" type="INT" /> --> |
| 77 : | <!-- <scalar label="noORFs" type="INT" /> --> | ||
| 78 : | bartels | 1.1 | <scalar label="motile" type="CHAR(125)" /> |
| 79 : | <scalar label="numberChromosomes" type="INT" /> | ||
| 80 : | <scalar label="totalReplicons" type="INT" /> | ||
| 81 : | bartels | 1.2 | <scalar label="hxh" type="INT" /> |
| 82 : | bartels | 1.1 | <scalar label="sequencingStatus" type="CHAR(250)" /> |
| 83 : | <scalar label="orderOfPublication" type="INT" /> | ||
| 84 : | bartels | 1.3 | <!-- <object label="Publication" type="Publication" /> --> |
| 85 : | bartels | 1.2 | <array> |
| 86 : | <scalar label="addFeatures" type="CHAR(250)" /> | ||
| 87 : | </array> | ||
| 88 : | bartels | 1.3 | <!-- 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 : | bartels | 1.1 | </object> |
| 93 : | |||
| 94 : | bartels | 1.3 | |
| 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> | ||
| 127 : | |||
| 128 : | |||
| 129 : | bartels | 1.1 | <object label="Publication"> |
| 130 : | <scalar label="pubmed" type="INT" /> | ||
| 131 : | <scalar label="url" type="CHAR(250)" /> | ||
| 132 : | <scalar label="year" type="INT" /> | ||
| 133 : | <scalar label="journal" type="CHAR(250)" /> | ||
| 134 : | <scalar label="number" type="INT" /> | ||
| 135 : | <scalar label="pages" type="CHAR(250)" /> | ||
| 136 : | </object> | ||
| 137 : | |||
| 138 : | bartels | 1.2 | <object label="Institution"> |
| 139 : | bartels | 1.1 | <scalar label="name" type="CHAR(250)" /> |
| 140 : | <scalar label="url" type="CHAR(250)" /> | ||
| 141 : | </object> | ||
| 142 : | |||
| 143 : | <object label="GenomeDatabase"> | ||
| 144 : | <scalar label="name" type="CHAR(250)" /> | ||
| 145 : | <scalar label="url" type="CHAR(250)" /> | ||
| 146 : | </object> | ||
| 147 : | |||
| 148 : | <object label="Contact"> | ||
| 149 : | <scalar label="name" type="CHAR(250)" /> | ||
| 150 : | <scalar label="url" type="CHAR(250)" /> | ||
| 151 : | <scalar label="email" type="CHAR(250)" /> | ||
| 152 : | </object> | ||
| 153 : | |||
| 154 : | <object label="GenomeFeatures"> | ||
| 155 : | <scalar label="name" type="CHAR(250)" /> | ||
| 156 : | <scalar label="value" type="CHAR(250)" /> | ||
| 157 : | </object> | ||
| 158 : | |||
| 159 : | bartels | 1.3 | <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 : | bartels | 1.1 | </project_space> |
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