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revision 1.1, Wed May 4 03:24:43 2005 UTC revision 1.4, Wed Feb 1 03:18:07 2006 UTC
# Line 9  Line 9 
9                                  <Field name="description" type="string">                                  <Field name="description" type="string">
10                                          <Notes>Brief description of this genome.</Notes>                                          <Notes>Brief description of this genome.</Notes>
11                                  </Field>                                  </Field>
12                    <Field name="group-name" type="name-string">
13                        <Notes>Name of this genome's close-strain group.</Notes>
14                    </Field>
15    
16                          </Fields>                          </Fields>
17                <Indexes>
18                    <Index>
19                        <Notes>This index sorts the genomes by group so that
20                        close strains are placed next to each other.</Notes>
21                        <IndexFields>
22                            <IndexField name="group-name" order="ascending" />
23                            <IndexField name="id" order="ascending" />
24                        </IndexFields>
25                    </Index>
26                </Indexes>
27                  </Entity>                  </Entity>
28          <Entity name="Contig" keyType="name-string">          <Entity name="Contig" keyType="key-string">
29              <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
30                          ID consists of the genome ID followed by a name that identifies                          ID consists of the genome ID followed by a name that identifies
31                          which contig this is for the parent genome. The individual components                          which contig this is for the parent genome. The individual components
32                          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>  
33          </Entity>          </Entity>
34          <Entity name="GroupBlock" keyType="name-string">          <Entity name="GroupBlock" keyType="name-string">
35              <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.
36                          regions are the same length, although they may go in different              A group block can represent a gene or an inter-genic region.
37                          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
38                          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>  
39              <Fields>              <Fields>
40                  <Field name="len" type="int">                  <Field name="len" type="int">
41                                          <Notes>Number of nucleotides in the regions belonging to                                          <Notes>Number of nucleotides in the regions belonging to
42                                          this group.</Notes>                      this block. This may include insertion markers ([b]-[/b]).</Notes>
43                                  </Field>                                  </Field>
44                                  <Field name="pattern" type="text">                                  <Field name="pattern" type="text">
45                                          <Notes>A representation of the nucleotides in the group,                                          <Notes>A representation of the nucleotides in the group,
# Line 46  Line 51 
51                                          regions in this group. For example, a value of 0 means all                                          regions in this group. For example, a value of 0 means all
52                                          regions are identical at every position. A value of                                          regions are identical at every position. A value of
53                                          0.5 means all regions are identical at exactly half of                                          0.5 means all regions are identical at exactly half of
54                                          the positions. For a DNA sequence of length 100, a value                      the positions. For a block length of 100, a value
55                                          of 0.03 means all regions are identical at every position                                          of 0.03 means all regions are identical at every position
56                                          but 3. The variance does not indicate the degree                                          but 3. The variance does not indicate the degree
57                                          of dissimilarity, just how much of each region needs to be                                          of dissimilarity, just how much of each region needs to be
58                                          examined for SNPs.</Notes>                                          examined for SNPs.</Notes>
59                                  </Field>                                  </Field>
60                    <Field name="snip-count" type="int">
61                        <Notes>The number of positions at which the nucleotides
62                        vary between regions in this group. The variance value
63                        is this number divided by the block length.</Notes>
64                    </Field>
65                    <Field name="description" type="string">
66                        <Notes>Descriptive name of this block. This will be
67                        the gene name for gene blocks, and a generated
68                        string for inter-genic blocks.</Notes>
69                    </Field>
70              </Fields>              </Fields>
71          </Entity>          </Entity>
72      </Entities>          <Entity name="Region" keyType="name-string">
73      <Relationships>              <Notes>A [i]region[/i] describes a location in a contig, and
74          <Relationship name="ContainsRegionIn" from="GroupBlock" to="Contig" arity="MM">              essentially bridges the gap between blocks and contigs. Each
75              <Notes>This relationship connects contigs to the group blocks represented on              instance of this object corresponds to a single segment on
76                          them. Each instance in this relationship represents a region on a              a contig. The key is the region's sprout-style location
77                          contig.</Notes>              string.</Notes>
78              <Fields>              <Fields>
79                    <Field name="contigID" type="key-string">
80                        <Notes>Name of the contig containing this region.</Notes>
81                    </Field>
82                  <Field name="position" type="int">                  <Field name="position" type="int">
83                                          <Notes>Index (1-based) of the region's leftmost nucleotide                                          <Notes>Index (1-based) of the region's leftmost nucleotide
84                                          in the contig.</Notes>                                          in the contig.</Notes>
# Line 77  Line 95 
95                                          reverse order.</Notes>                                          reverse order.</Notes>
96                                  </Field>                                  </Field>
97                                  <Field name="len" type="int">                                  <Field name="len" type="int">
98                                          <Notes>Length of this region. The length is redundant, but                      <Notes>Length of this region. This may be slightly smaller
99                                          we place it here anyway so that we can use it to sort                      than the block length.</Notes>
100                                          the regions.</Notes>                  </Field>
101                    <Field name="end" type="int">
102                        <Notes>Index (1-based) of the region's rightmost nucleotide
103                        in the contig.</Notes>
104                    </Field>
105                    <Field name="peg" type="name-string">
106                        <Notes>PEG identifier for this block if it is a gene block,
107                        or a string generated from the nearby PEGs if it is an
108                        inter-genic block</Notes>
109                                  </Field>                                  </Field>
110              </Fields>              </Fields>
111              <FromIndex>              <Indexes>
112                    <Index>
113                        <Notes>This index enables the application to find regions
114                        that overlap a specific section of the contig.  The index
115                        can be used to find the first region whose end point is at
116                        or follows the start of the section in question. Because
117                        every nucleotide is in at most one region, this guarantees
118                        that if any region overlaps the section, the region found
119                        by the index will.</Notes>
120                        <IndexFields>
121                            <IndexField name="end" order="ascending" />
122                        </IndexFields>
123                    </Index>
124                </Indexes>
125            </Entity>
126        </Entities>
127        <Relationships>
128            <Relationship name="ContainsRegion" from="Contig" to="Region" arity="1M">
129                <Notes>This relationship connects contigs to the regions on
130                them.</Notes>
131                <Fields>
132                    <Field name="position" type="int">
133                        <Notes>Index (1-based) of the region's leftmost nucleotide
134                        in the contig.</Notes>
135                    </Field>
136                    <Field name="len" type="int">
137                        <Notes>Length of this region. This may be slightly smaller
138                        than the block length.</Notes>
139                    </Field>
140                </Fields>
141                <ToIndex>
142                  <Notes>This index enables the application to find all of the                  <Notes>This index enables the application to find all of the
143                                  regions in a contig in the order they are present in the                                  regions in a contig in the order they are present in the
144                                  contig.</Notes>                                  contig.</Notes>
# Line 90  Line 146 
146                      <IndexField name="position" order="ascending" />                      <IndexField name="position" order="ascending" />
147                      <IndexField name="len" order="descending" />                      <IndexField name="len" order="descending" />
148                  </IndexFields>                  </IndexFields>
149              </FromIndex>              </ToIndex>
150            </Relationship>
151            <Relationship name="IncludesRegion" from="GroupBlock" to="Region" arity="1M">
152                <Notes>This relationship connects a block to the regions it covers. Note
153                that since the ID of the region is its Sprout-style location string,
154                often it is not necessary to cross to the [b]Region[/b] table when
155                accessing this relationship.</Notes>
156          </Relationship>          </Relationship>
157          <Relationship name="HasInstanceOf" from="Genome" to="GroupBlock" arity="MM">          <Relationship name="HasInstanceOf" from="Genome" to="GroupBlock" arity="MM">
158              <Notes>This relationship connects a genome to the groups represented              <Notes>This relationship connects a genome to the groups represented

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