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1 : parrello 1.1 <?xml version="1.0" encoding="UTF-8"?>
2 :     <Database>
3 :     <Title>Similarity Block Database</Title>
4 :     <Entities>
5 :     <Entity name="Genome" keyType="name-string">
6 :     <Notes>A [i]genome[/i] contains the sequence data for a particular
7 :     individual organism.</Notes>
8 :     <Fields>
9 :     <Field name="description" type="string">
10 :     <Notes>Brief description of this genome.</Notes>
11 :     </Field>
12 :     </Fields>
13 :     </Entity>
14 :     <Entity name="Contig" keyType="name-string">
15 :     <Notes>A [i]contig[/i] is a contiguous run of nucleotides. The contig's
16 :     ID consists of the genome ID followed by a name that identifies
17 :     which contig this is for the parent genome. The individual components
18 :     are separated by a colon.</Notes>
19 :     <Fields>
20 :     <Field name="len" type="int">
21 :     <Notes>Number of nucleotides in this contig.</Notes>
22 :     </Field>
23 :     </Fields>
24 :     </Entity>
25 :     <Entity name="GroupBlock" keyType="name-string">
26 :     <Notes>A [i]group block[/i] is a set of similar genome regions. All the
27 :     regions are the same length, although they may go in different
28 :     directions. The ID of the group will be a single letter and a set
29 :     of digits. The initial letter is [b]K[/b] for a group generated by
30 :     similarities and [b]S[/b] for a singleton group describing a
31 :     region with no similarities. The result is that every position
32 :     in a contig belongs to at least one group, though some will
33 :     belong to several.</Notes>
34 :     <Fields>
35 :     <Field name="len" type="int">
36 :     <Notes>Number of nucleotides in the regions belonging to
37 :     this group.</Notes>
38 :     </Field>
39 :     <Field name="pattern" type="text">
40 :     <Notes>A representation of the nucleotides in the group,
41 :     with question marks substituted for positions that are
42 :     not identical for all group members.</Notes>
43 :     </Field>
44 :     <Field name="variance" type="float">
45 :     <Notes>The proportion of nucleotides that vary between
46 :     regions in this group. For example, a value of 0 means all
47 :     regions are identical at every position. A value of
48 :     0.5 means all regions are identical at exactly half of
49 :     the positions. For a DNA sequence of length 100, a value
50 :     of 0.03 means all regions are identical at every position
51 :     but 3. The variance does not indicate the degree
52 :     of dissimilarity, just how much of each region needs to be
53 :     examined for SNPs.</Notes>
54 :     </Field>
55 :     </Fields>
56 :     </Entity>
57 :     </Entities>
58 :     <Relationships>
59 :     <Relationship name="ContainsRegionIn" from="GroupBlock" to="Contig" arity="MM">
60 :     <Notes>This relationship connects contigs to the group blocks represented on
61 :     them. Each instance in this relationship represents a region on a
62 :     contig.</Notes>
63 :     <Fields>
64 :     <Field name="position" type="int">
65 :     <Notes>Index (1-based) of the region's leftmost nucleotide
66 :     in the contig.</Notes>
67 :     </Field>
68 :     <Field name="direction" type="char">
69 :     <Notes>[b]+[/b] for a forward region, [b]-[/b] for a reverse
70 :     region.</Notes>
71 :     </Field>
72 :     <Field name="content" type="text">
73 :     <Notes>Nucleotide sequence of variance in this region
74 :     (upper case). For a forward region, this is the exact
75 :     content of each position of variance in the region.
76 :     For a reverse region, it is the complement in
77 :     reverse order.</Notes>
78 :     </Field>
79 :     <Field name="len" type="int">
80 :     <Notes>Length of this region. The length is redundant, but
81 :     we place it here anyway so that we can use it to sort
82 :     the regions.</Notes>
83 :     </Field>
84 :     </Fields>
85 :     <FromIndex>
86 :     <Notes>This index enables the application to find all of the
87 :     regions in a contig in the order they are present in the
88 :     contig.</Notes>
89 :     <IndexFields>
90 :     <IndexField name="position" order="ascending" />
91 :     <IndexField name="len" order="descending" />
92 :     </IndexFields>
93 :     </FromIndex>
94 :     </Relationship>
95 :     <Relationship name="HasInstanceOf" from="Genome" to="GroupBlock" arity="MM">
96 :     <Notes>This relationship connects a genome to the groups represented
97 :     in its contigs. It provides a fast was to get an ordered list of
98 :     groups for a genome. The group lists for genomes can then be
99 :     merged to determine the common groups of a set of genomes.</Notes>
100 :     </Relationship>
101 :     <Relationship name="ConsistsOf" from="Genome" to="Contig" arity="1M">
102 :     <Notes>This relationship connects a genome to its contigs.</Notes>
103 :     </Relationship>
104 :     </Relationships>
105 :     </Database>

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