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| 1 : | parrello | 1.1 | <Database> |
| 2 : | <Title>Sample ERDB Database</Title> | ||
| 3 : | <Notes>This XML file defines a small genetic database that demonstrates the features of | ||
| 4 : | the ERDB database engine.</Notes> | ||
| 5 : | <Entities> | ||
| 6 : | <Entity name="Genome" keyType="string"> | ||
| 7 : | <DisplayInfo theme="nmpdr" col="1" row="1" /> | ||
| 8 : | <Notes>A Genome contains the sequence data for a particular individual organism.</Notes> | ||
| 9 : | <Fields> | ||
| 10 : | <Field name="scientific-name" type="string"> | ||
| 11 : | <Notes>Scientific name of this genome, usually consisting of the genus, | ||
| 12 : | species, and unique characterization.</Notes> | ||
| 13 : | </Field> | ||
| 14 : | <Field name="version" type="string"> | ||
| 15 : | <Notes>Version string for this genome, generally consisting of the genome ID followed | ||
| 16 : | by a period and a string of digits.</Notes> | ||
| 17 : | </Field> | ||
| 18 : | <Field name="pegs" type="int"> | ||
| 19 : | <Notes>Number of [[protein encoding genes]] for this organism</Notes> | ||
| 20 : | </Field> | ||
| 21 : | <Field name="rnas" type="int"> | ||
| 22 : | <Notes>Number of RNA features found for this organism.</Notes> | ||
| 23 : | </Field> | ||
| 24 : | <Field name="oxygen" type="string"> | ||
| 25 : | <Notes>Indication of this organism's behavior relating to environmental oxygen.</Notes> | ||
| 26 : | </Field> | ||
| 27 : | <Field name="pathogenic" type="semi-boolean"> | ||
| 28 : | <Notes>Y/N/? flag indicating whether or not this organism is pathogenic.</Notes> | ||
| 29 : | </Field> | ||
| 30 : | </Fields> | ||
| 31 : | <Indexes> | ||
| 32 : | <Index> | ||
| 33 : | <Notes>This index allows the applications to search for genome by scientific | ||
| 34 : | name.</Notes> | ||
| 35 : | <IndexFields> | ||
| 36 : | <IndexField name="scientific-name" order="ascending" /> | ||
| 37 : | </IndexFields> | ||
| 38 : | </Index> | ||
| 39 : | </Indexes> | ||
| 40 : | </Entity> | ||
| 41 : | <Entity name="Contig" keyType="string"> | ||
| 42 : | <DisplayInfo theme="nmpdr" col="3" row="1" /> | ||
| 43 : | <Notes>A contig is a contiguous run of base pairs. The contig's ID consists of the | ||
| 44 : | genome ID followed by a name that identifies which contig this is for the parent | ||
| 45 : | genome.</Notes> | ||
| 46 : | <Fields> | ||
| 47 : | <Field name="sequence" type="dna"> | ||
| 48 : | <Notes>String consisting of the base pairs.</Notes> | ||
| 49 : | </Field> | ||
| 50 : | </Fields> | ||
| 51 : | </Entity> | ||
| 52 : | <Entity name="Feature" keyType="string"> | ||
| 53 : | <DisplayInfo theme="seed" col="2" row="3" /> | ||
| 54 : | <Notes>A feature (sometimes also called a "gene") is a part of a genome that | ||
| 55 : | is of special interest. Features may be spread across multiple contigs of a | ||
| 56 : | genome, but never across more than one genome. Features can be assigned to | ||
| 57 : | roles via spreadsheet cells, and are the targets of annotation. Each feature | ||
| 58 : | in the database has a unique FIG ID.</Notes> | ||
| 59 : | <Fields> | ||
| 60 : | <Field name="feature-type" type="string"> | ||
| 61 : | <Notes>Code indicating the type of this feature. Among the codes currently | ||
| 62 : | supported are "peg" for a protein encoding gene, "bs" for a | ||
| 63 : | binding site, "opr" for an operon, and so forth.</Notes> | ||
| 64 : | </Field> | ||
| 65 : | <Field name="translation" type="text" relation="FeatureTranslation"> | ||
| 66 : | <Notes>(optional) A translation of this feature's residues into | ||
| 67 : | protein character codes, formed by concatenating the pieces | ||
| 68 : | of the feature together. Only protein encoding genes have | ||
| 69 : | translations.</Notes> | ||
| 70 : | </Field> | ||
| 71 : | <Field name="assignment" type="text"> | ||
| 72 : | <Notes>Default functional assignment for this feature.</Notes> | ||
| 73 : | </Field> | ||
| 74 : | <Field name="assignment-maker" type="string"> | ||
| 75 : | <Notes>Name of the user who made the functional assignment</Notes> | ||
| 76 : | </Field> | ||
| 77 : | <Field name="assignment-quality" type="char"> | ||
| 78 : | <Notes>Quality of the functional assignment, usually a space, but may be | ||
| 79 : | W (indicating weak) or X (indicating experimental)</Notes> | ||
| 80 : | </Field> | ||
| 81 : | </Fields> | ||
| 82 : | </Entity> | ||
| 83 : | </Entities> | ||
| 84 : | <Relationships> | ||
| 85 : | <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M"> | ||
| 86 : | <DisplayInfo theme="seed" caption="Has" /> | ||
| 87 : | <Notes>This relationship connects a genome to all of its features. This | ||
| 88 : | relationship is redundant in a sense, because the genome ID is part | ||
| 89 : | of the feature ID; however, it makes the creation of certain queries more | ||
| 90 : | convenient because you can drag in filtering information for a feature's | ||
| 91 : | genome.</Notes> | ||
| 92 : | <Fields> | ||
| 93 : | <Field name="type" type="string"> | ||
| 94 : | <Notes>Feature type (eg. peg, rna)</Notes> | ||
| 95 : | </Field> | ||
| 96 : | </Fields> | ||
| 97 : | <FromIndex> | ||
| 98 : | <Notes>This index enables the application to view the features of a | ||
| 99 : | Genome sorted by type.</Notes> | ||
| 100 : | <IndexFields> | ||
| 101 : | <IndexField name="type" order="ascending" /> | ||
| 102 : | </IndexFields> | ||
| 103 : | </FromIndex> | ||
| 104 : | </Relationship> | ||
| 105 : | <Relationship name="HasContig" from="Genome" to="Contig" arity="1M"> | ||
| 106 : | <DisplayInfo caption="Consists Of" theme="nmpdr" /> | ||
| 107 : | <Notes>This relationship connects a genome to the contigs that contain the actual genetic | ||
| 108 : | information.</Notes> | ||
| 109 : | </Relationship> | ||
| 110 : | <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM"> | ||
| 111 : | <DisplayInfo caption="Is\nLocation\nOf" theme="seed" /> | ||
| 112 : | <Notes>This relationship connects a feature to the contig segments that work together | ||
| 113 : | to effect it. The segments are numbered sequentially starting from 1. The database is | ||
| 114 : | required to place an upper limit on the length of each segment. If a segment is longer | ||
| 115 : | than the maximum, it can be broken into smaller bits. The upper limit enables applications | ||
| 116 : | to locate all features that contain a specific residue. For example, if the upper limit | ||
| 117 : | is 100 and we are looking for a feature that contains residue 234 of contig *ABC*, we | ||
| 118 : | can look for features with a begin point between 135 and 333. The results can then be | ||
| 119 : | filtered by direction and length of the segment.</Notes> | ||
| 120 : | <Fields> | ||
| 121 : | <Field name="locN" type="int"> | ||
| 122 : | <Notes>Sequence number of this segment.</Notes> | ||
| 123 : | </Field> | ||
| 124 : | <Field name="beg" type="int"> | ||
| 125 : | <Notes>Index (1-based) of the first residue in the contig that | ||
| 126 : | belongs to the segment.</Notes> | ||
| 127 : | </Field> | ||
| 128 : | <Field name="len" type="int"> | ||
| 129 : | <Notes>Number of residues in the segment. A length of 0 identifies | ||
| 130 : | a specific point between residues. This is the point before the residue if the direction | ||
| 131 : | is forward and the point after the residue if the direction is backward.</Notes> | ||
| 132 : | </Field> | ||
| 133 : | <Field name="dir" type="char"> | ||
| 134 : | <Notes>Direction of the segment: + if it is forward and | ||
| 135 : | - if it is backward.</Notes> | ||
| 136 : | </Field> | ||
| 137 : | </Fields> | ||
| 138 : | <FromIndex> | ||
| 139 : | <Notes>This index allows the application to find all the segments of a feature in | ||
| 140 : | the proper order.</Notes> | ||
| 141 : | <IndexFields> | ||
| 142 : | <IndexField name="locN" order="ascending" /> | ||
| 143 : | </IndexFields> | ||
| 144 : | </FromIndex> | ||
| 145 : | <ToIndex> | ||
| 146 : | <Notes>This index is the one used by applications to find all the feature | ||
| 147 : | segments that contain a specific residue.</Notes> | ||
| 148 : | <IndexFields> | ||
| 149 : | <IndexField name="beg" order="ascending" /> | ||
| 150 : | </IndexFields> | ||
| 151 : | </ToIndex> | ||
| 152 : | </Relationship> | ||
| 153 : | </Relationships> | ||
| 154 : | </Database> |
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