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revision 1.44, Sat Oct 21 06:43:10 2006 UTC revision 1.45, Fri Nov 3 00:44:01 2006 UTC
# Line 7  Line 7 
7              <Fields>              <Fields>
8                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
9                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
                     <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>  
10                  </Field>                  </Field>
11                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
12                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
                     <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>  
13                  </Field>                  </Field>
14                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string">
15                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
16                      genome is taken. It is possible to have in the database more than one genome for a                      genome is taken. It is possible to have in the database more than one genome for a
17                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
                     <DataGen>StringGen('PKVKVK999')</DataGen>  
18                  </Field>                  </Field>
19                  <Field name="access-code" type="key-string">                  <Field name="access-code" type="key-string">
20                      <Notes>The access code determines which users can look at the data relating to this genome.                      <Notes>The access code determines which users can look at the data relating to this genome.
21                      Each user is associated with a set of access codes. In order to view a genome, one of                      Each user is associated with a set of access codes. In order to view a genome, one of
22                      the user's access codes must match this value.</Notes>                      the user's access codes must match this value.</Notes>
                     <DataGen>RandParam('low','medium','high')</DataGen>  
23                  </Field>                  </Field>
24                  <Field name="complete" type="boolean">                  <Field name="complete" type="boolean">
25                      <Notes>TRUE if the genome is complete, else FALSE</Notes>                      <Notes>TRUE if the genome is complete, else FALSE</Notes>
# Line 33  Line 29 
29                      separated by semi-colons (and optional white space), starting with the domain and ending with                      separated by semi-colons (and optional white space), starting with the domain and ending with
30                      the disambiguated genus and species (which is the organism's scientific name plus an                      the disambiguated genus and species (which is the organism's scientific name plus an
31                      identifying string).</Notes>                      identifying string).</Notes>
                     <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),  
                                                   ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>  
32                  </Field>                  </Field>
33                  <Field name="primary-group" type="name-string">                  <Field name="primary-group" type="name-string">
34                      <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group                      <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
# Line 48  Line 42 
42                  </Field>                  </Field>
43              </Fields>              </Fields>
44              <Indexes>              <Indexes>
45                  <Index Unique="false">                  <Index>
46                      <Notes>This index allows the applications to find all genomes associated with                      <Notes>This index allows the applications to find all genomes associated with
47                      a specific access code, so that a complete list of the genomes users can view                      a specific access code, so that a complete list of the genomes users can view
48                      may be generated.</Notes>                      may be generated.</Notes>
# Line 59  Line 53 
53                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
54                      </IndexFields>                      </IndexFields>
55                  </Index>                  </Index>
56                  <Index Unique="false">                  <Index>
57                      <Notes>This index allows the applications to find all genomes associated with                      <Notes>This index allows the applications to find all genomes associated with
58                      a specific primary (NMPDR) group.</Notes>                      a specific primary (NMPDR) group.</Notes>
59                      <IndexFields>                      <IndexFields>
# Line 69  Line 63 
63                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
64                      </IndexFields>                      </IndexFields>
65                  </Index>                  </Index>
66                  <Index Unique="false">                  <Index>
67                      <Notes>This index allows the applications to find all genomes for a particular                      <Notes>This index allows the applications to find all genomes for a particular
68                      species.</Notes>                      species.</Notes>
69                      <IndexFields>                      <IndexFields>
# Line 86  Line 80 
80              <Fields>              <Fields>
81                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
82                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
                     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>  
83                  </Field>                  </Field>
84                  <Field name="description" type="text">                  <Field name="description" type="text">
85                      <Notes>Description the source. The description can be a street address or a citation.</Notes>                      <Notes>Description the source. The description can be a street address or a citation.</Notes>
                     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>  
86                  </Field>                  </Field>
87              </Fields>              </Fields>
88          </Entity>          </Entity>
# Line 113  Line 105 
105                  <Field name="sequence" type="text">                  <Field name="sequence" type="text">
106                      <Notes>String consisting of the residues. Each residue is described by a single                      <Notes>String consisting of the residues. Each residue is described by a single
107                      character in the string.</Notes>                      character in the string.</Notes>
                     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>  
108                  </Field>                  </Field>
109                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
110                      <Notes>String describing the quality data for each base pair. Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
# Line 122  Line 113 
113                      10^-30. A higher quality number a better chance of a correct match. It is possible                      10^-30. A higher quality number a better chance of a correct match. It is possible
114                      that the quality data is not known for a sequence. If that is the case, the quality                      that the quality data is not known for a sequence. If that is the case, the quality
115                      vector will contain the [b]unknown[/b].</Notes>                      vector will contain the [b]unknown[/b].</Notes>
                     <DataGen>unknown</DataGen>  
116                  </Field>                  </Field>
117              </Fields>              </Fields>
118          </Entity>          </Entity>
# Line 134  Line 124 
124              <Fields>              <Fields>
125                  <Field name="feature-type" type="string">                  <Field name="feature-type" type="string">
126                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature.</Notes>
                     <DataGen>RandParam('peg','rna')</DataGen>  
127                  </Field>                  </Field>
128                  <Field name="alias" type="medium-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
129                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
                     <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
130                  </Field>                  </Field>
131                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
132                      <Notes>[i](optional)[/i] A translation of this feature's residues into character                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
133                      codes, formed by concatenating the pieces of the feature together. For a                      codes, formed by concatenating the pieces of the feature together. For a
134                      protein encoding group, this is the protein characters. For other types                      protein encoding group, this is the protein characters. For other types
135                      it is the DNA characters.</Notes>                      it is the DNA characters.</Notes>
                     <DataGen testCount="0"></DataGen>  
136                  </Field>                  </Field>
137                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
138                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
139                      the feature's initial residues.</Notes>                      the feature's initial residues.</Notes>
                     <DataGen testCount="0"></DataGen>  
140                  </Field>                  </Field>
141                  <Field name="assignment" type="text">                  <Field name="assignment" type="text">
142                      <Notes>Default functional assignment for this feature.</Notes>                      <Notes>Default functional assignment for this feature.</Notes>
143                  </Field>                  </Field>
144                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
145                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
                     <DataGen>1</DataGen>  
146                  </Field>                  </Field>
147                  <Field name="keywords" type="text" searchable="1">                  <Field name="keywords" type="text" searchable="1">
148                      <Notes>This is a list of search keywords for the feature. It includes the                      <Notes>This is a list of search keywords for the feature. It includes the
# Line 167  Line 152 
152                      <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The                      <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The
153                      links are to other websites that have useful about the gene that the feature represents, and                      links are to other websites that have useful about the gene that the feature represents, and
154                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
                     <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .  
                     "&amp;Number=" . IntGen(1,99)</DataGen>  
155                  </Field>                  </Field>
156                  <Field name="conservation" type="float" relation="FeatureConservation">                  <Field name="conservation" type="float" relation="FeatureConservation">
157                      <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is                      <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
# Line 176  Line 159 
159                      than 1 is a reflect of the degree to which gap characters interfere in the alignment                      than 1 is a reflect of the degree to which gap characters interfere in the alignment
160                      between the feature and its close relatives.</Notes>                      between the feature and its close relatives.</Notes>
161                  </Field>                  </Field>
162                    <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
163                        <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
164                        cases, this will be a word describing whether the essentiality is confirmed (essential)
165                        or potential (potential-essential), hyperlinked to the document from which the
166                        essentiality was curated. If a feature is not essential, this field will have no
167                        values; otherwise, it may have multiple values.</Notes>
168                    </Field>
169                    <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
170                        <Notes>A value indicating the virulence of the feature, coded as HTML. In most
171                        cases, this will be a phrase or SA number hyperlinked to the document from which
172                        the virulence information was curated. If the feature is not virulent, this field
173                        will have no values; otherwise, it may have multiple values.</Notes>
174                    </Field>
175                    <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
176                        <Notes>A value indicating whether or not the feature can be found in the
177                        Immune Epitope Database. If the feature has not been matched to that database,
178                        this field will have no values. Otherwise, it will have an epitope name and/or
179                        sequence, hyperlinked to the database.</Notes>
180                    </Field>
181              </Fields>              </Fields>
182              <Indexes>              <Indexes>
183                  <Index>                  <Index>
# Line 197  Line 199 
199              <Fields>              <Fields>
200                  <Field name="EC" type="string" relation="RoleEC">                  <Field name="EC" type="string" relation="RoleEC">
201                      <Notes>EC code for this role.</Notes>                      <Notes>EC code for this role.</Notes>
                     <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>  
202                  </Field>                  </Field>
203                  <Field name="abbr" type="name-string">                  <Field name="abbr" type="name-string">
204                      <Notes>Abbreviated name for the role, generally non-unique, but useful                      <Notes>Abbreviated name for the role, generally non-unique, but useful
# Line 337  Line 338 
338                      <Notes>Access code possessed by this                      <Notes>Access code possessed by this
339                      user. A user can have many access codes; a genome is accessible to the user if its                      user. A user can have many access codes; a genome is accessible to the user if its
340                      access code matches any one of the user's access codes.</Notes>                      access code matches any one of the user's access codes.</Notes>
                     <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>  
341                  </Field>                  </Field>
342              </Fields>              </Fields>
343          </Entity>          </Entity>
# Line 547  Line 547 
547                  </Field>                  </Field>
548              </Fields>              </Fields>
549          </Relationship>          </Relationship>
550          <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="1M">          <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="MM">
551              <Notes>This relationship describes the analysis of a free PDB as produced from a              <Notes>This relationship describes the analysis of a free PDB as produced from a
552              particular topic.</Notes>              particular topic.</Notes>
553              <Fields>              <Fields>
# Line 568  Line 568 
568                  </Field>                  </Field>
569              </Fields>              </Fields>
570          </Relationship>          </Relationship>
571          <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="1M">          <Relationship name="IncludesBound" from="DrugTopic" to="PDB" arity="MM">
572              <Note>This relationship connects a free PDB to its bound counterparts.</Note>              <Note>This relationship connects a drug topic to its bound PDBs. (A separate
573                relationship is used to connect the free PDBs.)</Note>
574            </Relationship>
575            <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="MM">
576                <Note>This relationship connects free PDBs to their bound counterparts.</Note>
577          </Relationship>          </Relationship>
578          <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">          <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">
579              <Notes>This relationship connects a feature to a protein database (PDB) that              <Notes>This relationship connects a feature to a protein database (PDB) that
# Line 862  Line 866 
866                      [b]-[/b] if it is backward.</Notes>                      [b]-[/b] if it is backward.</Notes>
867                  </Field>                  </Field>
868              </Fields>              </Fields>
869              <FromIndex Unique="false">              <FromIndex>
870                  <Notes>This index allows the application to find all the segments of a feature in                  <Notes>This index allows the application to find all the segments of a feature in
871                  the proper order.</Notes>                  the proper order.</Notes>
872                  <IndexFields>                  <IndexFields>

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