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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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