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revision 1.1, Wed May 4 03:24:43 2005 UTC revision 1.2, Thu Jun 9 19:06:55 2005 UTC
# Line 11  Line 11 
11                                  </Field>                                  </Field>
12                          </Fields>                          </Fields>
13                  </Entity>                  </Entity>
14          <Entity name="Contig" keyType="name-string">          <Entity name="Contig" keyType="key-string">
15              <Notes>A [i]contig[/i] is a contiguous run of nucleotides. The contig's              <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                          ID consists of the genome ID followed by a name that identifies
17                          which contig this is for the parent genome. The individual components                          which contig this is for the parent genome. The individual components
18                          are separated by a colon.</Notes>                          are separated by a colon.</Notes>
                         <Fields>  
                                 <Field name="len" type="int">  
                                         <Notes>Number of nucleotides in this contig.</Notes>  
                                 </Field>  
                         </Fields>  
19          </Entity>          </Entity>
20          <Entity name="GroupBlock" keyType="name-string">          <Entity name="GroupBlock" keyType="int">
21              <Notes>A [i]group block[/i] is a set of similar genome regions. All the              <Notes>A [i]group block[/i] is a set of similar genome regions.
22                          regions are the same length, although they may go in different                          A group block can represent a gene or an inter-genic region.
23                          directions. The ID of the group will be a single letter and a set                          The result is that every position in a contig belongs to exactly
24                          of digits. The initial letter is [b]K[/b] for a group generated by                          one block, though some will belong to several.</Notes>
                         similarities and [b]S[/b] for a singleton group describing a  
                         region with no similarities. The result is that every position  
                         in a contig belongs to at least one group, though some will  
                         belong to several.</Notes>  
25              <Fields>              <Fields>
26                  <Field name="len" type="int">                  <Field name="len" type="int">
27                                          <Notes>Number of nucleotides in the regions belonging to                                          <Notes>Number of nucleotides in the regions belonging to
28                                          this group.</Notes>                                          this block. This may include insertion markers ([b]-[/b]).</Notes>
29                                  </Field>                                  </Field>
30                                  <Field name="pattern" type="text">                                  <Field name="pattern" type="text">
31                                          <Notes>A representation of the nucleotides in the group,                                          <Notes>A representation of the nucleotides in the group,
# Line 46  Line 37 
37                                          regions in this group. For example, a value of 0 means all                                          regions in this group. For example, a value of 0 means all
38                                          regions are identical at every position. A value of                                          regions are identical at every position. A value of
39                                          0.5 means all regions are identical at exactly half of                                          0.5 means all regions are identical at exactly half of
40                                          the positions. For a DNA sequence of length 100, a value                                          the positions. For a block length of 100, a value
41                                          of 0.03 means all regions are identical at every position                                          of 0.03 means all regions are identical at every position
42                                          but 3. The variance does not indicate the degree                                          but 3. The variance does not indicate the degree
43                                          of dissimilarity, just how much of each region needs to be                                          of dissimilarity, just how much of each region needs to be
44                                          examined for SNPs.</Notes>                                          examined for SNPs.</Notes>
45                                  </Field>                                  </Field>
46                                    <Field name="snip-count" type="int">
47                                            <Notes>The number of positions at which the nucleotides
48                                            vary between regions in this group. The variance value
49                                            is this number divided by the block length.</Notes>
50                                    </Field>
51                                    <Field name="description" type="string">
52                                            <Notes>Descriptive name of this block. This will be
53                                            the gene name for gene blocks, and a generated
54                                            string for inter-genic blocks.</Notes>
55                                    </Field>
56              </Fields>              </Fields>
57          </Entity>          </Entity>
58      </Entities>                  <Entity name="Region" keyType="name-string">
59      <Relationships>                          <Notes>A [i]region[/i] describes a location in a contig, and
60          <Relationship name="ContainsRegionIn" from="GroupBlock" to="Contig" arity="MM">                          essentially bridges the gap between blocks and contigs. Each
61              <Notes>This relationship connects contigs to the group blocks represented on                          instance of this object corresponds to a single segment on
62                          them. Each instance in this relationship represents a region on a                          a contig. The key is the region's sprout-style location
63                          contig.</Notes>                          string.</Notes>
64              <Fields>              <Fields>
65                                    <Field name="contigID" type="key-string">
66                                            <Notes>Name of the contig containing this region.</Notes>
67                                    </Field>
68                  <Field name="position" type="int">                  <Field name="position" type="int">
69                                          <Notes>Index (1-based) of the region's leftmost nucleotide                                          <Notes>Index (1-based) of the region's leftmost nucleotide
70                                          in the contig.</Notes>                                          in the contig.</Notes>
# Line 77  Line 81 
81                                          reverse order.</Notes>                                          reverse order.</Notes>
82                                  </Field>                                  </Field>
83                                  <Field name="len" type="int">                                  <Field name="len" type="int">
84                                          <Notes>Length of this region. The length is redundant, but                                          <Notes>Length of this region. This may be slightly smaller
85                                          we place it here anyway so that we can use it to sort                                          than the block length.</Notes>
86                                          the regions.</Notes>                                  </Field>
87                                    <Field name="peg" type="name-string">
88                                            <Notes>PEG identifier for this block if it is a gene block,
89                                            or aa string generated from the nearby PEGs if it is an
90                                            inter-genic block</Notes>
91                                    </Field>
92                </Fields>
93                    </Entity>
94        </Entities>
95        <Relationships>
96            <Relationship name="ContainsRegion" from="Contig" to="Region" arity="1M">
97                <Notes>This relationship connects contigs to the regions on
98                            them.</Notes>
99                            <Fields>
100                    <Field name="position" type="int">
101                                            <Notes>Index (1-based) of the region's leftmost nucleotide
102                                            in the contig.</Notes>
103                                    </Field>
104                                    <Field name="len" type="int">
105                                            <Notes>Length of this region. This may be slightly smaller
106                                            than the block length.</Notes>
107                                  </Field>                                  </Field>
108              </Fields>              </Fields>
109              <FromIndex>              <ToIndex>
110                  <Notes>This index enables the application to find all of the                  <Notes>This index enables the application to find all of the
111                                  regions in a contig in the order they are present in the                                  regions in a contig in the order they are present in the
112                                  contig.</Notes>                                  contig.</Notes>
# Line 90  Line 114 
114                      <IndexField name="position" order="ascending" />                      <IndexField name="position" order="ascending" />
115                      <IndexField name="len" order="descending" />                      <IndexField name="len" order="descending" />
116                  </IndexFields>                  </IndexFields>
117              </FromIndex>              </ToIndex>
118            </Relationship>
119                    <Relationship name="IncludesRegion" from="GroupBlock" to="Region" arity="1M">
120                            <Notes>This relationship connects a block to the regions it covers. Note
121                            that since the ID of the region is its Sprout-style location string,
122                            often it is not necessary to cross to the [b]Region[/b] table when
123                            accessing this relationship.</Notes>
124          </Relationship>          </Relationship>
125          <Relationship name="HasInstanceOf" from="Genome" to="GroupBlock" arity="MM">          <Relationship name="HasInstanceOf" from="Genome" to="GroupBlock" arity="MM">
126              <Notes>This relationship connects a genome to the groups represented              <Notes>This relationship connects a genome to the groups represented

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