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revision 1.30, Sun Jul 9 21:16:47 2006 UTC revision 1.47, Mon Jan 22 20:24:53 2007 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>
32                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                  </Field>
33                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                  <Field name="primary-group" type="name-string">
34                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
35                        (either based on the organism name or the default value "Supporting"), whereas there can be
36                        multiple named groups or even none.</Notes>
37                  </Field>                  </Field>
38                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="group-name" type="name-string" relation="GenomeGroups">
39                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
# Line 54  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
58                        a specific primary (NMPDR) group.</Notes>
59                        <IndexFields>
60                            <IndexField name="primary-group" order="ascending" />
61                            <IndexField name="genus" order="ascending" />
62                            <IndexField name="species" order="ascending" />
63                            <IndexField name="unique-characterization" order="ascending" />
64                        </IndexFields>
65                    </Index>
66                    <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 71  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 98  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 107  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 119  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>
140                      <DataGen testCount="0"></DataGen>                  </Field>
141                    <Field name="assignment" type="text">
142                        <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>
146                      <DataGen>1</DataGen>                  </Field>
147                    <Field name="keywords" type="text" searchable="1">
148                        <Notes>This is a list of search keywords for the feature. It includes the
149                        functional assignment, subsystem roles, and special properties.</Notes>
150                  </Field>                  </Field>
151                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
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>
155                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                  </Field>
156                      "&amp;Number=" . IntGen(1,99)</DataGen>                  <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
158                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
159                        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>
161                    </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>                  </Field>
181              </Fields>              </Fields>
182              <Indexes>              <Indexes>
# Line 169  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 277  Line 306 
306                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
307                  </Field>                  </Field>
308                  <Field name="classification" type="string" relation="SubsystemClass">                  <Field name="classification" type="string" relation="SubsystemClass">
309                      <Notes>General classification data about the subsystem.</Notes>                      <Notes>Classification string, colon-delimited. This string organizes the
310                        subsystems into a hierarchy.</Notes>
311                  </Field>                  </Field>
312              </Fields>              </Fields>
313          </Entity>          </Entity>
# Line 308  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 408  Line 437 
437                  </Field>                  </Field>
438              </Fields>              </Fields>
439          </Entity>          </Entity>
440            <Entity name="Family" keyType="id-string">
441                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
442                families provide a mechanism for verifying the accuracy of functional assignments
443                and are also used in determining phylogenetic trees.</Notes>
444                <Fields>
445                    <Field name="function" type="text">
446                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
447                    </Field>
448                    <Field name="size" type="int">
449                        <Notes>The number of proteins in this family. This may be larger than the
450                        number of PEGs included in the family, since the family may also contain external
451                        IDs.</Notes>
452                    </Field>
453                </Fields>
454            </Entity>
455      </Entities>      </Entities>
456      <Relationships>      <Relationships>
457            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
458                <Notes>This relationship connects a protein family to all of its PEGs and connects
459                each PEG to all of its protein families.</Notes>
460            </Relationship>
461          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
462              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
463              in which it participates. A functional coupling is a recognition of the fact              in which it participates. A functional coupling is a recognition of the fact
# Line 445  Line 493 
493                      <Notes>Feature type (eg. peg, rna)</Notes>                      <Notes>Feature type (eg. peg, rna)</Notes>
494                  </Field>                  </Field>
495              </Fields>              </Fields>
496              <ToIndex>              <FromIndex>
497                  <Notes>This index enables the application to view the features of a                  <Notes>This index enables the application to view the features of a
498                  Genome sorted by type.</Notes>                  Genome sorted by type.</Notes>
499                  <IndexFields>                  <IndexFields>
500                      <IndexField name="type" order="ascending" />                      <IndexField name="type" order="ascending" />
501                  </IndexFields>                  </IndexFields>
502              </ToIndex>              </FromIndex>
503          </Relationship>          </Relationship>
504          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
505              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
# Line 663  Line 711 
711                      [b]-[/b] if it is backward.</Notes>                      [b]-[/b] if it is backward.</Notes>
712                  </Field>                  </Field>
713              </Fields>              </Fields>
714              <FromIndex Unique="false">              <FromIndex>
715                  <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
716                  the proper order.</Notes>                  the proper order.</Notes>
717                  <IndexFields>                  <IndexFields>
# Line 678  Line 726 
726                  </IndexFields>                  </IndexFields>
727              </ToIndex>              </ToIndex>
728          </Relationship>          </Relationship>
         <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">  
             <Notes>This relationship is one of two that relate features to each other. It  
             connects features that are very similar but on separate genomes. A  
             bidirectional best hit relationship exists between two features [b]A[/b]  
             and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome  
             and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes>  
             <Fields>  
                 <Field name="genome" type="name-string">  
                     <Notes>ID of the genome containing the target (to) feature.</Notes>  
                 </Field>  
                 <Field name="sc" type="float">  
                     <Notes>score for this relationship</Notes>  
                 </Field>  
             </Fields>  
             <FromIndex>  
                 <Notes>This index allows the application to find a feature's best hit for  
                 a specific target genome.</Notes>  
                 <IndexFields>  
                     <IndexField name="genome" order="ascending" />  
                 </IndexFields>  
             </FromIndex>  
         </Relationship>  
729          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
730              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
731              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 765  Line 791 
791              chemical reactions. A single reaction can be triggered by many roles,              chemical reactions. A single reaction can be triggered by many roles,
792              and a role can trigger many reactions.</Notes>              and a role can trigger many reactions.</Notes>
793          </Relationship>          </Relationship>
794            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
795                <Notes>This relationship connects a feature to the subsystems in which it
796                participates. This is technically redundant information, but it is used
797                so often that it deserves its own table.</Notes>
798                <Fields>
799                    <Field name="genome" type="name-string">
800                        <Notes>ID of the genome containing the feature</Notes>
801                    </Field>
802                    <Field name="type" type="key-string">
803                        <Notes>Feature type (eg. peg, rna)</Notes>
804                    </Field>
805                </Fields>
806                <ToIndex>
807                    <Notes>This index enables the application to view the features of a
808                    subsystem sorted by genome and feature type.</Notes>
809                    <IndexFields>
810                        <IndexField name="genome" order="ascending" />
811                        <IndexField name="type" order="ascending" />
812                    </IndexFields>
813                </ToIndex>
814            </Relationship>
815      </Relationships>      </Relationships>
816  </Database>  </Database>

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