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| 1 : | parrello | 1.1 | <?xml version="1.0" encoding="utf-8" ?> |
| 2 : | <Database> | ||
| 3 : | <Title>Sprout Genome and Subsystem Database</Title> | ||
| 4 : | <Entities> | ||
| 5 : | <Entity name="Genome" keyType="name-string"> | ||
| 6 : | <Notes>A [i]genome[/i] contains the sequence data for a particular individual organism.</Notes> | ||
| 7 : | <Fields> | ||
| 8 : | <Field name="genus" type="name-string"> | ||
| 9 : | <Notes>Genus of the relevant organism.</Notes> | ||
| 10 : | <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen> | ||
| 11 : | </Field> | ||
| 12 : | <Field name="species" type="name-string"> | ||
| 13 : | parrello | 1.8 | <Notes>Species of the relevant organism.</Notes> |
| 14 : | parrello | 1.1 | <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen> |
| 15 : | parrello | 1.8 | </Field> |
| 16 : | parrello | 1.1 | <Field name="unique-characterization" type="medium-string"> |
| 17 : | parrello | 1.8 | <Notes>The unique characterization identifies the particular organism instance from which the |
| 18 : | genome is taken. It is possible to have in the database more than one genome for a | ||
| 19 : | parrello | 1.1 | particular species, and every individual organism has variations in its DNA.</Notes> |
| 20 : | parrello | 1.8 | <DataGen>StringGen('PKVKVK999')</DataGen> |
| 21 : | parrello | 1.1 | </Field> |
| 22 : | <Field name="access-code" type="key-string"> | ||
| 23 : | parrello | 1.8 | <Notes>The access code determines which users can look at the data relating to this genome. |
| 24 : | Each user is associated with a set of access codes. In order to view a genome, one of | ||
| 25 : | the user's access codes must match this value.</Notes> | ||
| 26 : | <DataGen>RandParam('low','medium','high')</DataGen> | ||
| 27 : | </Field> | ||
| 28 : | parrello | 1.15 | <Field name="complete" type="boolean"> |
| 29 : | <Notes>TRUE if the genome is complete, else FALSE</Notes> | ||
| 30 : | </Field> | ||
| 31 : | parrello | 1.8 | <Field name="taxonomy" type="text"> |
| 32 : | <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements | ||
| 33 : | separated by semi-colons (and optional white space), starting with the domain and ending with | ||
| 34 : | the disambiguated genus and species (which is the organism's scientific name plus an | ||
| 35 : | identifying string).</Notes> | ||
| 36 : | <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'), | ||
| 37 : | ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen> | ||
| 38 : | </Field> | ||
| 39 : | <Field name="group-name" type="name-string" relation="GenomeGroups"> | ||
| 40 : | <Notes>The group identifies a special grouping of organisms that would be displayed on a particular | ||
| 41 : | page or of particular interest to a research group or web site. A single genome can belong to multiple | ||
| 42 : | such groups or none at all.</Notes> | ||
| 43 : | </Field> | ||
| 44 : | parrello | 1.1 | </Fields> |
| 45 : | <Indexes> | ||
| 46 : | <Index> | ||
| 47 : | <Notes>This index allows the applications to find all genomes associated with | ||
| 48 : | a specific access code, so that a complete list of the genomes users can view | ||
| 49 : | may be generated.</Notes> | ||
| 50 : | <IndexFields> | ||
| 51 : | <IndexField name="access-code" order="ascending" /> | ||
| 52 : | <IndexField name="genus" order="ascending" /> | ||
| 53 : | <IndexField name="species" order="ascending" /> | ||
| 54 : | <IndexField name="unique-characterization" order="ascending" /> | ||
| 55 : | </IndexFields> | ||
| 56 : | </Index> | ||
| 57 : | <Index Unique="false"> | ||
| 58 : | <Notes>This index allows the applications to find all genomes for a particular | ||
| 59 : | species.</Notes> | ||
| 60 : | <IndexFields> | ||
| 61 : | <IndexField name="genus" order="ascending" /> | ||
| 62 : | <IndexField name="species" order="ascending" /> | ||
| 63 : | <IndexField name="unique-characterization" order="ascending" /> | ||
| 64 : | </IndexFields> | ||
| 65 : | </Index> | ||
| 66 : | </Indexes> | ||
| 67 : | </Entity> | ||
| 68 : | <Entity name="Source" keyType="medium-string"> | ||
| 69 : | <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization | ||
| 70 : | or a paper citation.</Notes> | ||
| 71 : | <Fields> | ||
| 72 : | <Field name="URL" type="string" relation="SourceURL"> | ||
| 73 : | parrello | 1.8 | <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes> |
| 74 : | <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen> | ||
| 75 : | </Field> | ||
| 76 : | parrello | 1.1 | <Field name="description" type="text"> |
| 77 : | parrello | 1.8 | <Notes>Description the source. The description can be a street address or a citation.</Notes> |
| 78 : | <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen> | ||
| 79 : | </Field> | ||
| 80 : | parrello | 1.1 | </Fields> |
| 81 : | </Entity> | ||
| 82 : | <Entity name="Contig" keyType="name-string"> | ||
| 83 : | <Notes>A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the | ||
| 84 : | genome ID followed by a name that identifies which contig this is for the parent genome. As | ||
| 85 : | is the case with all keys in this database, the individual components are separated by a | ||
| 86 : | period. | ||
| 87 : | [p]A contig can contain over a million residues. For performance reasons, therefore, | ||
| 88 : | the contig is split into multiple pieces called [i]sequences[/i]. The sequences | ||
| 89 : | contain the characters that represent the residues as well as data on the quality of | ||
| 90 : | the residue identification.</Notes> | ||
| 91 : | </Entity> | ||
| 92 : | <Entity name="Sequence" keyType="name-string"> | ||
| 93 : | <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into | ||
| 94 : | sequences so that we don't have to have the entire contig in memory when we are | ||
| 95 : | manipulating it. The key of the sequence is the contig ID followed by the index of | ||
| 96 : | the begin point.</Notes> | ||
| 97 : | <Fields> | ||
| 98 : | <Field name="sequence" type="text"> | ||
| 99 : | parrello | 1.8 | <Notes>String consisting of the residues. Each residue is described by a single |
| 100 : | character in the string.</Notes> | ||
| 101 : | <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen> | ||
| 102 : | </Field> | ||
| 103 : | parrello | 1.1 | <Field name="quality-vector" type="text"> |
| 104 : | parrello | 1.9 | <Notes>String describing the quality data for each base pair. Individual values will |
| 105 : | parrello | 1.8 | be separated by periods. The value represents negative exponent of the probability |
| 106 : | of error. Thus, for example, a quality of 30 indicates the probability of error is | ||
| 107 : | 10^-30. A higher quality number a better chance of a correct match. It is possible | ||
| 108 : | parrello | 1.9 | that the quality data is not known for a sequence. If that is the case, the quality |
| 109 : | parrello | 1.8 | vector will contain the [b]unknown[/b].</Notes> |
| 110 : | <DataGen>unknown</DataGen> | ||
| 111 : | </Field> | ||
| 112 : | parrello | 1.1 | </Fields> |
| 113 : | </Entity> | ||
| 114 : | <Entity name="Feature" keyType="name-string"> | ||
| 115 : | <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features | ||
| 116 : | may be spread across multiple contigs of a genome, but never across more than | ||
| 117 : | one genome. Features can be assigned to roles via spreadsheet cells, | ||
| 118 : | and are the targets of annotation.</Notes> | ||
| 119 : | <Fields> | ||
| 120 : | <Field name="feature-type" type="string"> | ||
| 121 : | parrello | 1.8 | <Notes>Code indicating the type of this feature.</Notes> |
| 122 : | <DataGen>RandParam('peg','rna')</DataGen> | ||
| 123 : | </Field> | ||
| 124 : | parrello | 1.14 | <Field name="alias" type="medium-string" relation="FeatureAlias"> |
| 125 : | parrello | 1.9 | <Notes>Alternative name for this feature. A feature can have many aliases.</Notes> |
| 126 : | parrello | 1.8 | <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen> |
| 127 : | </Field> | ||
| 128 : | parrello | 1.1 | <Field name="translation" type="text" relation="FeatureTranslation"> |
| 129 : | parrello | 1.8 | <Notes>[i](optional)[/i] A translation of this feature's residues into character |
| 130 : | codes, formed by concatenating the pieces of the feature together. For a | ||
| 131 : | protein encoding group, this is the protein characters. For other types | ||
| 132 : | it is the DNA characters.</Notes> | ||
| 133 : | <DataGen testCount="0"></DataGen> | ||
| 134 : | </Field> | ||
| 135 : | parrello | 1.1 | <Field name="upstream-sequence" type="text" relation="FeatureUpstream"> |
| 136 : | parrello | 1.8 | <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of |
| 137 : | the feature's initial residues.</Notes> | ||
| 138 : | <DataGen testCount="0"></DataGen> | ||
| 139 : | </Field> | ||
| 140 : | parrello | 1.1 | <Field name="active" type="boolean"> |
| 141 : | parrello | 1.11 | <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes> |
| 142 : | parrello | 1.8 | <DataGen>1</DataGen> |
| 143 : | </Field> | ||
| 144 : | <Field name="link" type="text" relation="FeatureLink"> | ||
| 145 : | <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The | ||
| 146 : | links are to other websites that have useful about the gene that the feature represents, and | ||
| 147 : | are coded as raw HTML, using [b]<a href="[i]link[/i]">[i]text[/i]</a>[/b] notation.</Notes> | ||
| 148 : | <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} . | ||
| 149 : | "&Number=" . IntGen(1,99)</DataGen> | ||
| 150 : | </Field> | ||
| 151 : | parrello | 1.1 | </Fields> |
| 152 : | parrello | 1.8 | <Indexes> |
| 153 : | <Index> | ||
| 154 : | <Notes>This index allows the user to find the feature corresponding to | ||
| 155 : | the specified alias name.</Notes> | ||
| 156 : | <IndexFields> | ||
| 157 : | <IndexField name="alias" order="ascending" /> | ||
| 158 : | </IndexFields> | ||
| 159 : | </Index> | ||
| 160 : | </Indexes> | ||
| 161 : | parrello | 1.1 | </Entity> |
| 162 : | <Entity name="Role" keyType="string"> | ||
| 163 : | <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature. | ||
| 164 : | One of the main goals of the database is to record the roles of the various features.</Notes> | ||
| 165 : | parrello | 1.8 | <Fields> |
| 166 : | <Field name="name" type="string" relation="RoleName"> | ||
| 167 : | <Notes>Expanded name of the role. This value is generally only available for roles | ||
| 168 : | that are encoded as EC numbers.</Notes> | ||
| 169 : | <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen> | ||
| 170 : | </Field> | ||
| 171 : | parrello | 1.15 | <Field name="abbr" type="name-string"> |
| 172 : | <Notes>Abbreviated name for the role, generally non-unique, but useful | ||
| 173 : | in column headings for HTML tables.</Notes> | ||
| 174 : | </Field> | ||
| 175 : | parrello | 1.8 | </Fields> |
| 176 : | parrello | 1.1 | </Entity> |
| 177 : | <Entity name="Annotation" keyType="name-string"> | ||
| 178 : | <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations | ||
| 179 : | parrello | 1.8 | are currently the only objects that may be inserted directly into the database. All other |
| 180 : | information is loaded from data exported by the SEED. | ||
| 181 : | [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation | ||
| 182 : | is the target feature ID followed by a timestamp.</Notes> | ||
| 183 : | <Fields> | ||
| 184 : | <Field name="time" type="date"> | ||
| 185 : | <Notes>Date and time of the annotation.</Notes> | ||
| 186 : | </Field> | ||
| 187 : | <Field name="annotation" type="text"> | ||
| 188 : | <Notes>Text of the annotation.</Notes> | ||
| 189 : | </Field> | ||
| 190 : | parrello | 1.1 | </Fields> |
| 191 : | </Entity> | ||
| 192 : | parrello | 1.15 | <Entity name="Reaction" keyType="key-string"> |
| 193 : | <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID | ||
| 194 : | is generally a small number preceded by a letter.</Notes> | ||
| 195 : | <Fields> | ||
| 196 : | <Field name="url" type="string" relation="ReactionURL"> | ||
| 197 : | <Notes>HTML string containing a link to a web location that describes the | ||
| 198 : | reaction. This field is optional.</Notes> | ||
| 199 : | </Field> | ||
| 200 : | <Field name="rev" type="boolean"> | ||
| 201 : | <Notes>TRUE if this reaction is reversible, else FALSE</Notes> | ||
| 202 : | </Field> | ||
| 203 : | </Fields> | ||
| 204 : | </Entity> | ||
| 205 : | <Entity name="Compound" keyType="name-string"> | ||
| 206 : | <Notes>A [i]compound[/i] is a chemical that participates in a reaction. | ||
| 207 : | All compounds have a unique ID and may also have one or more names.</Notes> | ||
| 208 : | <Fields> | ||
| 209 : | <Field name="name-priority" type="int" relation="CompoundName"> | ||
| 210 : | <Notes>Priority of a compound name. The name with the loweset | ||
| 211 : | priority is the main name of this compound.</Notes> | ||
| 212 : | </Field> | ||
| 213 : | <Field name="name" type="name-string" relation="CompoundName"> | ||
| 214 : | <Notes>Descriptive name for the compound. A compound may | ||
| 215 : | have several names.</Notes> | ||
| 216 : | </Field> | ||
| 217 : | <Field name="cas-id" type="name-string" relation="CompoundCAS"> | ||
| 218 : | <Notes>Chemical Abstract Service ID for this compound (optional).</Notes> | ||
| 219 : | </Field> | ||
| 220 : | </Fields> | ||
| 221 : | <Indexes> | ||
| 222 : | <Index> | ||
| 223 : | <Notes>This index allows the user to find the compound corresponding to | ||
| 224 : | the specified name.</Notes> | ||
| 225 : | <IndexFields> | ||
| 226 : | <IndexField name="name" order="ascending" /> | ||
| 227 : | </IndexFields> | ||
| 228 : | </Index> | ||
| 229 : | <Index> | ||
| 230 : | <Notes>This index allows the user to access the compound names in | ||
| 231 : | priority order.</Notes> | ||
| 232 : | <IndexFields> | ||
| 233 : | <IndexField name="id" order="ascending" /> | ||
| 234 : | <IndexField name="name-priority" order="ascending" /> | ||
| 235 : | </IndexFields> | ||
| 236 : | </Index> | ||
| 237 : | </Indexes> | ||
| 238 : | </Entity> | ||
| 239 : | parrello | 1.5 | <Entity name="Subsystem" keyType="string"> |
| 240 : | parrello | 1.1 | <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems |
| 241 : | is an important tool for recognizing parallel genetic features in different organisms.</Notes> | ||
| 242 : | parrello | 1.15 | <Fields> |
| 243 : | <Field name="curator" type="string"> | ||
| 244 : | <Notes>Name of the person currently in charge of the subsystem.</Notes> | ||
| 245 : | </Field> | ||
| 246 : | <Field name="notes" type="text"> | ||
| 247 : | <Notes>Descriptive notes about the subsystem.</Notes> | ||
| 248 : | </Field> | ||
| 249 : | </Fields> | ||
| 250 : | </Entity> | ||
| 251 : | <Entity name="RoleSubset" keyType="string"> | ||
| 252 : | <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The | ||
| 253 : | subset names are generally very short, non-unique strings. The ID of the parent | ||
| 254 : | subsystem is prefixed to the subset ID in order to make it unique.</Notes> | ||
| 255 : | </Entity> | ||
| 256 : | <Entity name="GenomeSubset" keyType="string"> | ||
| 257 : | <Notes>A [i]genome subset[/i] is a named collection of genomes that participate | ||
| 258 : | in a particular subsystem. The subset names are generally very short, non-unique | ||
| 259 : | strings. The ID of the parent subsystem is prefixed to the subset ID in order | ||
| 260 : | to make it unique.</Notes> | ||
| 261 : | parrello | 1.1 | </Entity> |
| 262 : | parrello | 1.13 | <Entity name="SSCell" keyType="medium-string"> |
| 263 : | parrello | 1.1 | <Notes>Part of the process of locating and assigning features is creating a spreadsheet of |
| 264 : | genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one | ||
| 265 : | of the positions on the spreadsheet.</Notes> | ||
| 266 : | </Entity> | ||
| 267 : | <Entity name="SproutUser" keyType="name-string"> | ||
| 268 : | <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The | ||
| 269 : | user object is keyed on the user's login name.</Notes> | ||
| 270 : | <Fields> | ||
| 271 : | parrello | 1.8 | <Field name="description" type="string"> |
| 272 : | <Notes>Full name or description of this user.</Notes> | ||
| 273 : | </Field> | ||
| 274 : | parrello | 1.1 | <Field name="access-code" type="key-string" relation="UserAccess"> |
| 275 : | parrello | 1.8 | <Notes>Access code possessed by this |
| 276 : | parrello | 1.1 | user. A user can have many access codes; a genome is accessible to the user if its |
| 277 : | access code matches any one of the user's access codes.</Notes> | ||
| 278 : | parrello | 1.8 | <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen> |
| 279 : | </Field> | ||
| 280 : | parrello | 1.1 | </Fields> |
| 281 : | </Entity> | ||
| 282 : | parrello | 1.8 | <Entity name="Property" keyType="int"> |
| 283 : | <Notes>A [i]property[/i] is a type of assertion that could be made about the properties of | ||
| 284 : | a particular feature. Each property instance is a key/value pair and can be associated | ||
| 285 : | with many different features. Conversely, a feature can be associated with many key/value | ||
| 286 : | pairs, even some that notionally contradict each other. For example, there can be evidence | ||
| 287 : | that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes> | ||
| 288 : | <Fields> | ||
| 289 : | <Field name="property-name" type="name-string"> | ||
| 290 : | <Notes>Name of this property.</Notes> | ||
| 291 : | </Field> | ||
| 292 : | <Field name="property-value" type="string"> | ||
| 293 : | <Notes>Value associated with this property. For each property | ||
| 294 : | name, there must by a property record for all of its possible | ||
| 295 : | values.</Notes> | ||
| 296 : | </Field> | ||
| 297 : | </Fields> | ||
| 298 : | <Indexes> | ||
| 299 : | <Index> | ||
| 300 : | <Notes>This index enables the application to find all values for a specified property | ||
| 301 : | name, or any given name/value pair.</Notes> | ||
| 302 : | <IndexFields> | ||
| 303 : | <IndexField name="property-name" order="ascending" /> | ||
| 304 : | <IndexField name="property-value" order="ascending" /> | ||
| 305 : | </IndexFields> | ||
| 306 : | </Index> | ||
| 307 : | </Indexes> | ||
| 308 : | </Entity> | ||
| 309 : | <Entity name="Diagram" keyType="name-string"> | ||
| 310 : | <Notes>A functional diagram describes the chemical reactions, often comprising a single | ||
| 311 : | subsystem. A diagram is identified by a short name and contains a longer descriptive name. | ||
| 312 : | The actual diagram shows which functional roles guide the reactions along with the inputs | ||
| 313 : | and outputs; the database, however, only indicate which roles belong to a particular | ||
| 314 : | map.</Notes> | ||
| 315 : | <Fields> | ||
| 316 : | <Field name="name" type="text"> | ||
| 317 : | <Notes>Descriptive name of this diagram.</Notes> | ||
| 318 : | </Field> | ||
| 319 : | </Fields> | ||
| 320 : | </Entity> | ||
| 321 : | <Entity name="ExternalAliasOrg" keyType="name-string"> | ||
| 322 : | <Notes>An external alias is a feature name for a functional assignment that is not a | ||
| 323 : | FIG ID. Functional assignments for external aliases are kept in a separate section of | ||
| 324 : | the database. This table contains a description of the relevant organism for an | ||
| 325 : | external alias functional assignment.</Notes> | ||
| 326 : | <Fields> | ||
| 327 : | <Field name="org" type="text"> | ||
| 328 : | <Notes>Descriptive name of the target organism for this external alias.</Notes> | ||
| 329 : | </Field> | ||
| 330 : | </Fields> | ||
| 331 : | </Entity> | ||
| 332 : | <Entity name="ExternalAliasFunc" keyType="name-string"> | ||
| 333 : | <Notes>An external alias is a feature name for a functional assignment that is not a | ||
| 334 : | FIG ID. Functional assignments for external aliases are kept in a separate section of | ||
| 335 : | the database. This table contains the functional role for the external alias functional | ||
| 336 : | assignment.</Notes> | ||
| 337 : | <Fields> | ||
| 338 : | <Field name="func" type="text"> | ||
| 339 : | <Notes>Functional role for this external alias.</Notes> | ||
| 340 : | </Field> | ||
| 341 : | </Fields> | ||
| 342 : | </Entity> | ||
| 343 : | parrello | 1.6 | <Entity name="Coupling" keyType="medium-string"> |
| 344 : | <Notes>A coupling is a relationship between two features. The features are | ||
| 345 : | physically close on the contig, and there is evidence that they generally | ||
| 346 : | belong together. The key of this entity is formed by combining the coupled | ||
| 347 : | parrello | 1.8 | feature IDs with a space.</Notes> |
| 348 : | parrello | 1.6 | <Fields> |
| 349 : | <Field name="score" type="int"> | ||
| 350 : | <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH | ||
| 351 : | indicates that two genes near each other on one genome are very similar to | ||
| 352 : | genes near each other on another genome. The score only counts PCHs for which | ||
| 353 : | the genomes are very different. (In other words, we have a pairing that persists | ||
| 354 : | between different organisms.) A higher score implies a stronger meaning to the | ||
| 355 : | clustering.</Notes> | ||
| 356 : | </Field> | ||
| 357 : | </Fields> | ||
| 358 : | </Entity> | ||
| 359 : | <Entity name="PCH" keyType="string"> | ||
| 360 : | <Notes>A PCH (physically close homolog) connects a clustering (which is a | ||
| 361 : | pair of physically close features on a contig) to a second pair of physically | ||
| 362 : | close features that are similar to the first. Essentially, the PCH is a | ||
| 363 : | relationship between two clusterings in which the first clustering's features | ||
| 364 : | are similar to the second clustering's features. The simplest model for | ||
| 365 : | this would be to simply relate clusterings to each other; however, not all | ||
| 366 : | physically close pairs qualify as clusterings, so we relate a clustering to | ||
| 367 : | a pair of features. The key is the clustering key followed by the IDs | ||
| 368 : | of the features in the second pair.</Notes> | ||
| 369 : | <Fields> | ||
| 370 : | <Field name="used" type="boolean"> | ||
| 371 : | <Notes>TRUE if this PCH is used in scoring the attached clustering, | ||
| 372 : | else FALSE. If a clustering has a PCH for a particular genome and many | ||
| 373 : | similar genomes are present, then a PCH will probably exist for the | ||
| 374 : | similar genomes as well. When this happens, only one of the PCHs will | ||
| 375 : | be scored: the others are considered duplicates of the same evidence.</Notes> | ||
| 376 : | </Field> | ||
| 377 : | </Fields> | ||
| 378 : | </Entity> | ||
| 379 : | parrello | 1.1 | </Entities> |
| 380 : | <Relationships> | ||
| 381 : | parrello | 1.6 | <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM"> |
| 382 : | <Notes>This relationship connects a feature to all the functional couplings | ||
| 383 : | in which it participates. A functional coupling is a recognition of the fact | ||
| 384 : | that the features are close to each other on a chromosome, and similar | ||
| 385 : | features in other genomes also tend to be close.</Notes> | ||
| 386 : | <Fields> | ||
| 387 : | <Field name="pos" type="int"> | ||
| 388 : | <Notes>Ordinal position of the feature in the coupling. Currently, | ||
| 389 : | this is either "1" or "2".</Notes> | ||
| 390 : | </Field> | ||
| 391 : | </Fields> | ||
| 392 : | <ToIndex> | ||
| 393 : | <Notes>This index enables the application to view the features of | ||
| 394 : | a coupling in the proper order. The order influences the way the | ||
| 395 : | PCHs are examined.</Notes> | ||
| 396 : | <IndexFields> | ||
| 397 : | <IndexField name="pos" order="ascending" /> | ||
| 398 : | </IndexFields> | ||
| 399 : | </ToIndex> | ||
| 400 : | </Relationship> | ||
| 401 : | <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M"> | ||
| 402 : | <Notes>This relationship connects a functional coupling to the physically | ||
| 403 : | close homologs (PCHs) which affirm that the coupling is meaningful.</Notes> | ||
| 404 : | </Relationship> | ||
| 405 : | <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM"> | ||
| 406 : | <Notes>This relationship connects a PCH to the features that represent its | ||
| 407 : | evidence. Each PCH is connected to a parent coupling that relates two features | ||
| 408 : | on a specific genome. The PCH's evidence that the parent coupling is functional | ||
| 409 : | is the existence of two physically close features on a different genome that | ||
| 410 : | correspond to the features in the coupling. Those features are found on the | ||
| 411 : | far side of this relationship.</Notes> | ||
| 412 : | <Fields> | ||
| 413 : | <Field name="pos" type="int"> | ||
| 414 : | <Notes>Ordinal position of the feature in the coupling that corresponds | ||
| 415 : | to our target feature. There is a one-to-one correspondence between the | ||
| 416 : | features connected to the PCH by this relationship and the features | ||
| 417 : | connected to the PCH's parent coupling. The ordinal position is used | ||
| 418 : | to decode that relationship. Currently, this field is either "1" or | ||
| 419 : | "2".</Notes> | ||
| 420 : | </Field> | ||
| 421 : | </Fields> | ||
| 422 : | <FromIndex> | ||
| 423 : | <Notes>This index enables the application to view the features of | ||
| 424 : | a PCH in the proper order.</Notes> | ||
| 425 : | <IndexFields> | ||
| 426 : | <IndexField name="pos" order="ascending" /> | ||
| 427 : | </IndexFields> | ||
| 428 : | </FromIndex> | ||
| 429 : | </Relationship> | ||
| 430 : | parrello | 1.1 | <Relationship name="HasContig" from="Genome" to="Contig" arity="1M"> |
| 431 : | <Notes>This relationship connects a genome to the contigs that contain the actual genetic | ||
| 432 : | information.</Notes> | ||
| 433 : | </Relationship> | ||
| 434 : | <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM"> | ||
| 435 : | <Notes>This relationship connects a genome to the sources that mapped it. A genome can | ||
| 436 : | come from a single source or from a cooperation among multiple sources.</Notes> | ||
| 437 : | </Relationship> | ||
| 438 : | <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M"> | ||
| 439 : | <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the | ||
| 440 : | contig into sequences, we get a performance boost from only needing to keep small portions | ||
| 441 : | of a contig in memory at any one time. This relationship connects the contig to its | ||
| 442 : | constituent sequences.</Notes> | ||
| 443 : | <Fields> | ||
| 444 : | <Field name="len" type="int"> | ||
| 445 : | parrello | 1.15 | <Notes>Length of the sequence.</Notes> |
| 446 : | </Field> | ||
| 447 : | parrello | 1.1 | <Field name="start-position" type="int"> |
| 448 : | parrello | 1.15 | <Notes>Index (1-based) of the point in the contig where this |
| 449 : | sequence starts.</Notes> | ||
| 450 : | </Field> | ||
| 451 : | parrello | 1.1 | </Fields> |
| 452 : | <FromIndex> | ||
| 453 : | <Notes>This index enables the application to find all of the sequences in | ||
| 454 : | parrello | 1.8 | a contig in order, and makes it easier to find a particular residue section.</Notes> |
| 455 : | parrello | 1.1 | <IndexFields> |
| 456 : | <IndexField name="start-position" order="ascending" /> | ||
| 457 : | <IndexField name="len" order="ascending" /> | ||
| 458 : | </IndexFields> | ||
| 459 : | </FromIndex> | ||
| 460 : | </Relationship> | ||
| 461 : | <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M"> | ||
| 462 : | <Notes>This relationship connects a feature to its annotations.</Notes> | ||
| 463 : | </Relationship> | ||
| 464 : | <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M"> | ||
| 465 : | <Notes>This relationship connects an annotation to the user who made it.</Notes> | ||
| 466 : | </Relationship> | ||
| 467 : | <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM"> | ||
| 468 : | <Notes>This relationship connects subsystems to the genomes that use | ||
| 469 : | it. If the subsystem has been curated for the genome, then the subsystem's roles will also be | ||
| 470 : | connected to the genome features through the [b]SSCell[/b] object.</Notes> | ||
| 471 : | parrello | 1.15 | <Fields> |
| 472 : | <Field name="variant-code" type="key-string"> | ||
| 473 : | <Notes>Numeric code indicating the subsystem variant to which this | ||
| 474 : | genome belongs. Each subsystem can have multiple variants. A variant | ||
| 475 : | code of [b]-1[/b] indicates that the genome's roles apply to all | ||
| 476 : | variants. A variant code of [b]0[/b] indicates that the genome's | ||
| 477 : | participation is considered iffy.</Notes> | ||
| 478 : | </Field> | ||
| 479 : | </Fields> | ||
| 480 : | <ToIndex> | ||
| 481 : | <Notes>This index enables the application to find all of the genomes using | ||
| 482 : | a subsystem in order by variant code, which is how we wish to display them | ||
| 483 : | in the spreadsheets.</Notes> | ||
| 484 : | <IndexFields> | ||
| 485 : | <IndexField name="variant-code" order="ascending" /> | ||
| 486 : | </IndexFields> | ||
| 487 : | </ToIndex> | ||
| 488 : | parrello | 1.1 | </Relationship> |
| 489 : | <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM"> | ||
| 490 : | <Notes>This relationship connects roles to the subsystems that implement them. </Notes> | ||
| 491 : | parrello | 1.15 | <Fields> |
| 492 : | <Field name="column-number" type="int"> | ||
| 493 : | <Notes>Column number for this role in the specified subsystem's | ||
| 494 : | spreadsheet.</Notes> | ||
| 495 : | </Field> | ||
| 496 : | </Fields> | ||
| 497 : | <ToIndex> | ||
| 498 : | <Notes>This index enables the application to see the subsystem roles | ||
| 499 : | in column order. The ordering of the roles is usually significant, | ||
| 500 : | so it is important to preserve it.</Notes> | ||
| 501 : | <IndexFields> | ||
| 502 : | <IndexField name="column-number" order="ascending" /> | ||
| 503 : | </IndexFields> | ||
| 504 : | </ToIndex> | ||
| 505 : | parrello | 1.1 | </Relationship> |
| 506 : | <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M"> | ||
| 507 : | <Notes>This relationship connects a subsystem's spreadsheet cell to the | ||
| 508 : | genome for the spreadsheet column.</Notes> | ||
| 509 : | </Relationship> | ||
| 510 : | <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M"> | ||
| 511 : | <Notes>This relationship connects a subsystem's spreadsheet cell to the | ||
| 512 : | role for the spreadsheet row.</Notes> | ||
| 513 : | </Relationship> | ||
| 514 : | <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM"> | ||
| 515 : | <Notes>This relationship connects a subsystem's spreadsheet cell to the | ||
| 516 : | features assigned to it.</Notes> | ||
| 517 : | parrello | 1.15 | <Fields> |
| 518 : | <Field name="cluster-number" type="int"> | ||
| 519 : | <Notes>ID of this feature's cluster. Clusters represent families of | ||
| 520 : | related proteins participating in a subsystem.</Notes> | ||
| 521 : | </Field> | ||
| 522 : | </Fields> | ||
| 523 : | </Relationship> | ||
| 524 : | <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM"> | ||
| 525 : | <Notes>This relationship connects a reaction to the compounds that participate | ||
| 526 : | in it.</Notes> | ||
| 527 : | <Fields> | ||
| 528 : | <Field name="product" type="boolean"> | ||
| 529 : | <Notes>TRUE if the compound is a product of the reaction, FALSE if | ||
| 530 : | it is a substrate. When a reaction is written on paper in | ||
| 531 : | chemical notation, the substrates are left of the arrow and the | ||
| 532 : | products are to the right. Sorting on this field will cause | ||
| 533 : | the substrates to appear first, followed by the products. If the | ||
| 534 : | reaction is reversible, then the notion of substrates and products | ||
| 535 : | is not at intuitive; however, a value here of FALSE still puts the | ||
| 536 : | compound left of the arrow and a value of TRUE still puts it to the | ||
| 537 : | right.</Notes> | ||
| 538 : | </Field> | ||
| 539 : | parrello | 1.16 | <Field name="stoichometry" type="key-string"> |
| 540 : | parrello | 1.15 | <Notes>Number of molecules of the compound that participate in a |
| 541 : | single instance of the reaction. For example, if a reaction | ||
| 542 : | produces two water molecules, the stoichometry of water for the | ||
| 543 : | reaction would be two. When a reaction is written on paper in | ||
| 544 : | chemical notation, the stoichometry is the number next to the | ||
| 545 : | chemical formula of the compound.</Notes> | ||
| 546 : | </Field> | ||
| 547 : | <Field name="main" type="boolean"> | ||
| 548 : | <Notes>TRUE if this compound is one of the main participants in | ||
| 549 : | the reaction, else FALSE. It is permissible for none of the | ||
| 550 : | compounds in the reaction to be considered main, in which | ||
| 551 : | case this value would be FALSE for all of the relevant | ||
| 552 : | compounds.</Notes> | ||
| 553 : | </Field> | ||
| 554 : | <Field name="loc" type="key-string"> | ||
| 555 : | <Notes>An optional character string that indicates the relative | ||
| 556 : | position of this compound in the reaction's chemical formula. The | ||
| 557 : | location affects the way the compounds present as we cross the | ||
| 558 : | relationship from the reaction side. The product/substrate flag | ||
| 559 : | comes first, then the value of this field, then the main flag. | ||
| 560 : | The default value is an empty string; however, the empty string | ||
| 561 : | sorts first, so if this field is used, it should probably be | ||
| 562 : | used for every compound in the reaction.</Notes> | ||
| 563 : | </Field> | ||
| 564 : | </Fields> | ||
| 565 : | <ToIndex> | ||
| 566 : | <Notes>This index presents the compounds in the reaction in the | ||
| 567 : | order they should be displayed when writing it in chemical notation. | ||
| 568 : | All the substrates appear before all the products, and within that | ||
| 569 : | ordering, the main compounds appear first.</Notes> | ||
| 570 : | <IndexField name="product" order="ascending" /> | ||
| 571 : | <IndexField name="loc" order="ascending" /> | ||
| 572 : | <IndexField name="main" order="descending" /> | ||
| 573 : | </ToIndex> | ||
| 574 : | parrello | 1.1 | </Relationship> |
| 575 : | <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM"> | ||
| 576 : | <Notes>This relationship connects a feature to the contig segments that work together | ||
| 577 : | to effect it. The segments are numbered sequentially starting from 1. The database is | ||
| 578 : | required to place an upper limit on the length of each segment. If a segment is longer | ||
| 579 : | than the maximum, it can be broken into smaller bits. | ||
| 580 : | [p]The upper limit enables applications to locate all features that contain a specific | ||
| 581 : | residue. For example, if the upper limit is 100 and we are looking for a feature that | ||
| 582 : | contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point | ||
| 583 : | between 135 and 333. The results can then be filtered by direction and length of the | ||
| 584 : | segment.</Notes> | ||
| 585 : | <Fields> | ||
| 586 : | <Field name="locN" type="int"> | ||
| 587 : | parrello | 1.8 | <Notes>Sequence number of this segment.</Notes> |
| 588 : | </Field> | ||
| 589 : | parrello | 1.1 | <Field name="beg" type="int"> |
| 590 : | parrello | 1.8 | <Notes>Index (1-based) of the first residue in the contig that |
| 591 : | belongs to the segment.</Notes> | ||
| 592 : | </Field> | ||
| 593 : | parrello | 1.1 | <Field name="len" type="int"> |
| 594 : | parrello | 1.8 | <Notes>Number of residues in the segment. A length of 0 identifies |
| 595 : | a specific point between residues. This is the point before the residue if the direction | ||
| 596 : | is forward and the point after the residue if the direction is backward.</Notes> | ||
| 597 : | </Field> | ||
| 598 : | parrello | 1.1 | <Field name="dir" type="char"> |
| 599 : | parrello | 1.8 | <Notes>Direction of the segment: [b]+[/b] if it is forward and |
| 600 : | [b]-[/b] if it is backward.</Notes> | ||
| 601 : | </Field> | ||
| 602 : | parrello | 1.1 | </Fields> |
| 603 : | <FromIndex Unique="false"> | ||
| 604 : | <Notes>This index allows the application to find all the segments of a feature in | ||
| 605 : | parrello | 1.8 | the proper order.</Notes> |
| 606 : | parrello | 1.1 | <IndexFields> |
| 607 : | <IndexField name="locN" order="ascending" /> | ||
| 608 : | </IndexFields> | ||
| 609 : | </FromIndex> | ||
| 610 : | <ToIndex> | ||
| 611 : | <Notes>This index is the one used by applications to find all the feature | ||
| 612 : | segments that contain a specific residue.</Notes> | ||
| 613 : | <IndexFields> | ||
| 614 : | <IndexField name="beg" order="ascending" /> | ||
| 615 : | </IndexFields> | ||
| 616 : | </ToIndex> | ||
| 617 : | </Relationship> | ||
| 618 : | <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM"> | ||
| 619 : | <Notes>This relationship is one of two that relate features to each other. It | ||
| 620 : | connects features that are very similar but on separate genomes. A | ||
| 621 : | bidirectional best hit relationship exists between two features [b]A[/b] | ||
| 622 : | and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome | ||
| 623 : | and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes> | ||
| 624 : | <Fields> | ||
| 625 : | <Field name="genome" type="name-string"> | ||
| 626 : | parrello | 1.8 | <Notes>ID of the genome containing the target (to) feature.</Notes> |
| 627 : | </Field> | ||
| 628 : | <Field name="sc" type="float"> | ||
| 629 : | <Notes>score for this relationship</Notes> | ||
| 630 : | </Field> | ||
| 631 : | parrello | 1.1 | </Fields> |
| 632 : | <FromIndex> | ||
| 633 : | <Notes>This index allows the application to find a feature's best hit for | ||
| 634 : | parrello | 1.8 | a specific target genome.</Notes> |
| 635 : | parrello | 1.1 | <IndexFields> |
| 636 : | <IndexField name="genome" order="ascending" /> | ||
| 637 : | </IndexFields> | ||
| 638 : | </FromIndex> | ||
| 639 : | </Relationship> | ||
| 640 : | parrello | 1.8 | <Relationship name="HasProperty" from="Feature" to="Property" arity="MM"> |
| 641 : | <Notes>This relationship connects a feature to its known property values. | ||
| 642 : | The relationship contains text data that indicates the paper or organization | ||
| 643 : | that discovered evidence that the feature possesses the property. So, for | ||
| 644 : | example, if two papers presented evidence that a feature is essential, | ||
| 645 : | there would be an instance of this relationship for both.</Notes> | ||
| 646 : | <Fields> | ||
| 647 : | <Field name="evidence" type="text"> | ||
| 648 : | <Notes>URL or citation of the paper or | ||
| 649 : | institution that reported evidence of the relevant feature possessing | ||
| 650 : | the specified property value.</Notes> | ||
| 651 : | </Field> | ||
| 652 : | </Fields> | ||
| 653 : | </Relationship> | ||
| 654 : | <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM"> | ||
| 655 : | <Notes>This relationship connects a role to the diagrams on which it | ||
| 656 : | appears. A role frequently identifies an enzyme, and can appear in many | ||
| 657 : | diagrams. A diagram generally contains many different roles.</Notes> | ||
| 658 : | </Relationship> | ||
| 659 : | <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M"> | ||
| 660 : | <Notes>This relationship connects a subsystem to the spreadsheet cells | ||
| 661 : | used to analyze and display it. The cells themselves can be thought of | ||
| 662 : | as a grid with Roles on one axis and Genomes on the other. The | ||
| 663 : | various features of the subsystem are then assigned to the cells.</Notes> | ||
| 664 : | </Relationship> | ||
| 665 : | <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM"> | ||
| 666 : | <Notes>This relationship identifies the users trusted by each | ||
| 667 : | particular user. When viewing functional assignments, the | ||
| 668 : | assignment displayed is the most recent one by a user trusted | ||
| 669 : | by the current user. The current user implicitly trusts himself. | ||
| 670 : | If no trusted users are specified in the database, the user | ||
| 671 : | also implicitly trusts the user [b]FIG[/b].</Notes> | ||
| 672 : | </Relationship> | ||
| 673 : | parrello | 1.15 | <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM"> |
| 674 : | <Notes>This relationship connects a role subset to the roles that it covers. | ||
| 675 : | A subset is, essentially, a named group of roles belonging to a specific | ||
| 676 : | subsystem, and this relationship effects that. Note that will a role | ||
| 677 : | may belong to many subsystems, a subset belongs to only one subsystem, | ||
| 678 : | and all roles in the subset must have that subsystem in common.</Notes> | ||
| 679 : | </Relationship> | ||
| 680 : | <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM"> | ||
| 681 : | <Notes>This relationship connects a subset to the genomes that it covers. | ||
| 682 : | A subset is, essentially, a named group of genomes participating in a specific | ||
| 683 : | subsystem, and this relationship effects that. Note that while a genome | ||
| 684 : | may belong to many subsystems, a subset belongs to only one subsystem, | ||
| 685 : | and all genomes in the subset must have that subsystem in common.</Notes> | ||
| 686 : | </Relationship> | ||
| 687 : | <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M"> | ||
| 688 : | <Notes>This relationship connects a subsystem to its constituent | ||
| 689 : | role subsets. Note that some roles in a subsystem may not belong to a | ||
| 690 : | subset, so the relationship between roles and subsystems cannot be | ||
| 691 : | derived from the relationships going through the subset.</Notes> | ||
| 692 : | </Relationship> | ||
| 693 : | <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M"> | ||
| 694 : | <Notes>This relationship connects a subsystem to its constituent | ||
| 695 : | genome subsets. Note that some genomes in a subsystem may not belong to a | ||
| 696 : | subset, so the relationship between genomes and subsystems cannot be | ||
| 697 : | derived from the relationships going through the subset.</Notes> | ||
| 698 : | </Relationship> | ||
| 699 : | <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM"> | ||
| 700 : | <Notes>This relationship connects a role to the reactions it catalyzes. | ||
| 701 : | The purpose of a role is to create proteins that trigger certain | ||
| 702 : | chemical reactions. A single reaction can be triggered by many roles, | ||
| 703 : | and a role can trigger many reactions.</Notes> | ||
| 704 : | </Relationship> | ||
| 705 : | parrello | 1.1 | </Relationships> |
| 706 : | </Database> |
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