source: trunk/bio/tutorial/malariamine/webapp/resources/default-template-queries.xml @ 23462

Revision 23462, 16.8 KB checked in by julie, 16 months ago (diff)

remove templates with goannotation.evidence codes, the model has been changed
Line 
1<?xml version="1.0"?>
2<userprofile>
3  <items/>
4  <bags/>
5  <queries>
6  </queries>
7<template-queries>
8<template name="GO_name_Gene" title="GO term name/id --&gt; Genes in one specific organism." longDescription="Search for genes in a specified organism that is associated with a particular GO annotation." comment="">
9  <query name="GO_name_Gene" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.goAnnotation.ontologyTerm.identifier Gene.goAnnotation.ontologyTerm.name" sortOrder="Gene.symbol asc" constraintLogic="A and B">
10    <pathDescription pathString="Gene.goAnnotation" description="GO annotation">
11    </pathDescription>
12    <node path="Gene" type="Gene">
13    </node>
14    <node path="Gene.organism" type="Organism">
15    </node>
16    <node path="Gene.organism.name" type="String">
17      <constraint op="=" value="Plasmodium falciparum 3D7" description="Search for genes in:" identifier="" editable="true" code="B">
18      </constraint>
19    </node>
20    <node path="Gene.goAnnotation" type="GOAnnotation">
21    </node>
22    <node path="Gene.goAnnotation.ontologyTerm" type="OntologyTerm">
23    </node>
24    <node path="Gene.goAnnotation.ontologyTerm.name" type="String">
25      <constraint op="CONTAINS" value="DNA binding" description="GO Term" identifier="" editable="true" code="A" extraValue="">
26      </constraint>
27    </node>
28  </query>
29</template>
30<template name="GOname_GOidentifier" title="GO term name --&gt; GO term identifier." longDescription="Find the GO identifier for a specific term." comment="">
31  <query name="GOname_GOidentifier" model="genomic" view="GOTerm.name GOTerm.identifier GOTerm.description" sortOrder="GOTerm.name asc">
32    <node path="GOTerm" type="GOTerm">
33    </node>
34    <node path="GOTerm.name" type="String">
35      <constraint op="LIKE" value="*blastoderm*" description="" identifier="" editable="true" code="A">
36      </constraint>
37    </node>
38  </query>
39</template>
40<template name="GOtermidentifier_name" title="GO term identifier --&gt; GO term name." longDescription="Give the GO term name for a particular GO term identifier. (Data Source: GO)" comment="">
41  <query name="GOtermidentifier_name" model="genomic" view="GOTerm.identifier GOTerm.name GOTerm.description" sortOrder="GOTerm.identifier asc">
42    <node path="GOTerm" type="GOTerm">
43    </node>
44    <node path="GOTerm.identifier" type="String">
45      <constraint op="=" value="GO:0007350" description="" identifier="" editable="true" code="A">
46      </constraint>
47    </node>
48  </query>
49</template>
50<template name="Gene_GO" title="Gene --&gt; GO terms." longDescription="Search for GO annotations for a particular gene." comment="06.06.07 updated to work from gene class - Philip">
51  <query name="Gene_GO" model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.goAnnotation.qualifier Gene.goAnnotation:ontologyTerm.identifier Gene.goAnnotation:ontologyTerm.name Gene.goAnnotation:ontologyTerm.namespace" sortOrder="Gene.primaryIdentifier asc">
52    <pathDescription pathString="Gene.goAnnotation" description="GO annotation">
53    </pathDescription>
54    <node path="Gene" type="Gene">
55      <constraint op="LOOKUP" value="PFL2660w" description="Show GO annotations for gene:" identifier="Gene.class" editable="true" code="A">
56      </constraint>
57    </node>
58    <node path="Gene.goAnnotation" type="GOAnnotation">
59    </node>
60  </query>
61</template>
62<template name="Gene_Identifiers" title="Gene --&gt; All identifiers." longDescription="Show all identifiers for a gene, given an identifier." comment="07:02:07:Updated to work from gene identifier - Rachel.">
63  <query name="Gene_Identifiers" model="genomic" view="Gene.secondaryIdentifier Gene.primaryIdentifier Gene.symbol Gene.name" sortOrder="Gene.secondaryIdentifier asc">
64    <node path="Gene" type="Gene">
65    </node>
66    <node path="Gene.secondaryIdentifier" type="String">
67      <constraint op="=" value="PFL2660w" description="Gene.secondaryIdentifier" identifier="Gene.secondaryIdentifier" editable="true" code="A">
68      </constraint>
69    </node>
70  </query>
71</template>
72<template name="Gene_Protein" title="Gene --&gt; Proteins." longDescription="Show the proteins for a particular gene." comment="06.06.07 updated to work from gene class - Philip">
73  <query name="Gene_Protein" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.proteins.primaryIdentifier Gene.proteins.primaryAccession" sortOrder="Gene.primaryIdentifier asc">
74    <pathDescription pathString="Gene.proteins" description="Protein">
75    </pathDescription>
76    <node path="Gene" type="Gene">
77      <constraint op="LOOKUP" value="PFL2660w" description="" identifier="" editable="true" code="A">
78      </constraint>
79    </node>
80    <node path="Gene.proteins" type="Protein">
81    </node>
82  </query>
83</template>
84<template name="Gene_To_Protein_Type_Converter" title="Gene to protein type converter" longDescription="" comment="">
85  <query name="Gene_To_Protein_Type_Converter" model="genomic" view="Gene.id Gene.proteins.id" sortOrder="Gene.id asc">
86    <node path="Gene" type="Gene">
87    </node>
88    <node path="Gene.id" type="Integer">
89      <constraint op="=" value="0" description="Gene.id" identifier="Gene.id" editable="true" code="A">
90      </constraint>
91    </node>
92  </query>
93</template>
94<template name="Gene_allGOTerms" title="Gene --&gt; GO terms and parents of those terms." longDescription="Given a gene show the associated GO terms, and the all parents to the top of the directed graph." comment="">
95  <query name="Gene_allGOTerms" model="genomic" view="Gene.secondaryIdentifier Gene.symbol Gene.goAnnotation.ontologyTerm.relations.childTerm.identifier Gene.goAnnotation.ontologyTerm.relations.childTerm.name Gene.goAnnotation.ontologyTerm.relations.relationship Gene.goAnnotation.ontologyTerm.relations.parentTerm.identifier Gene.goAnnotation.ontologyTerm.relations.parentTerm.name" sortOrder="Gene.secondaryIdentifier asc">
96    <pathDescription pathString="Gene.goAnnotation" description="GO annotation">
97    </pathDescription>
98    <node path="Gene" type="Gene">
99      <constraint op="LOOKUP" value="PFL2660w" description="Show GO annotations for gene:" identifier="Gene.class" editable="true" code="A" extraValue="">
100      </constraint>
101    </node>
102    <node path="Gene.goAnnotation" type="GOAnnotation">
103    </node>
104    <node path="Gene.goAnnotation.ontologyTerm" type="OntologyTerm">
105    </node>
106    <node path="Gene.goAnnotation.ontologyTerm.relations" type="OntologyRelation">
107    </node>
108    <node path="Gene.goAnnotation.ontologyTerm.relations.childTerm" type="OntologyTerm">
109    </node>
110    <node path="Gene.goAnnotation.ontologyTerm.relations.parentTerm" type="OntologyTerm">
111    </node>
112  </query>
113</template>
114<template name="Gene_particularGoannotation" title="Gene + GO term name --&gt; Gene with the GO term name." longDescription="Show if the following gene has the following GO term." comment="">
115  <query name="Gene_particularGoannotation" model="genomic" view="Gene.secondaryIdentifier Gene.symbol Gene:goAnnotation.ontologyTerm.identifier Gene:goAnnotation.ontologyTerm.name" sortOrder="Gene.secondaryIdentifier asc" constraintLogic="A and B">
116    <node path="Gene" type="Gene">
117      <constraint op="LOOKUP" value="CG9015" description="For the gene(s):" identifier="" editable="true" code="A">
118      </constraint>
119    </node>
120    <node path="Gene:goAnnotation" type="GOAnnotation">
121    </node>
122    <node path="Gene:goAnnotation.ontologyTerm" type="OntologyTerm">
123    </node>
124    <node path="Gene:goAnnotation.ontologyTerm.name" type="String">
125      <constraint op="=" value="*transcription factor*" description="GO Term" identifier="" editable="true" code="B" extraValue="">
126      </constraint>
127    </node>
128  </query>
129</template>
130<template name="Organism_Protein" title="Organism --&gt; All proteins." longDescription="Show all the proteins from a particular organism." comment="">
131  <query name="Organism_Protein" model="genomic" view="Protein.primaryIdentifier Protein.primaryAccession" sortOrder="Protein.primaryIdentifier asc">
132    <node path="Protein" type="Protein">
133    </node>
134    <node path="Protein.organism" type="Organism">
135    </node>
136    <node path="Protein.organism.name" type="String">
137      <constraint op="=" value="Plasmodium falciparum 3D7" description="Show all the proteins from the organism:" identifier="Organism.name" editable="true" code="A">
138      </constraint>
139    </node>
140  </query>
141</template>
142<template name="Protein_GOterms" title="Protein --&gt; GO terms." longDescription="Show all GO terms that have been associated with the gene that codes for the following protein." comment="06.06.07 updated to work from protein class - Philip">
143  <query name="Protein_GOterms" model="genomic" view="Protein.primaryAccession Protein.genes.secondaryIdentifier Protein.genes.symbol Protein.genes.goAnnotation:ontologyTerm.namespace Protein.genes.goAnnotation:ontologyTerm.identifier Protein.genes.goAnnotation:ontologyTerm.name" sortOrder="Protein.primaryAccession asc">
144    <pathDescription pathString="Protein.genes" description="Gene">
145    </pathDescription>
146    <node path="Protein" type="Protein">
147      <constraint op="LOOKUP" value="B3FEM5" description="" identifier="Protein.class" editable="true" code="A">
148      </constraint>
149    </node>
150    <node path="Protein.genes" type="Gene">
151    </node>
152    <node path="Protein.genes.goAnnotation" type="GOAnnotation">
153    </node>
154  </query>
155</template>
156<template name="Protein_GOtermsSpecificOntology" title="Protein --&gt; GO terms from a specific GO ontology." longDescription="Show the GO annotations for a protein or proteins from a specifc GO ontology (cellular_component, molecular_function, biological_process)." comment="">
157  <query name="Protein_GOtermsSpecificOntology" model="genomic" view="Protein.primaryAccession Protein.primaryIdentifier Protein.genes.primaryIdentifier Protein.genes.secondaryIdentifier Protein.genes.symbol Protein.genes.goAnnotation.ontologyTerm.namespace Protein.genes.goAnnotation.ontologyTerm.identifier Protein.genes.goAnnotation.ontologyTerm.name" sortOrder="Protein.primaryAccession asc" constraintLogic="A and B">
158    <pathDescription pathString="Protein.genes" description="Gene">
159    </pathDescription>
160    <node path="Protein" type="Protein">
161      <constraint op="LOOKUP" value="B3FEM5" description="Show GO annotaion for the following protein(s):" identifier="" editable="true" code="A" extraValue="D. melanogaster">
162      </constraint>
163    </node>
164    <node path="Protein.genes" type="Gene">
165    </node>
166    <node path="Protein.genes.goAnnotation" type="GOAnnotation">
167    </node>
168    <node path="Protein.genes.goAnnotation.ontologyTerm" type="OntologyTerm">
169    </node>
170    <node path="Protein.genes.goAnnotation.ontologyTerm.namespace" type="String">
171      <constraint op="=" value="cellular_component" description="from the ontology:" identifier="" editable="true" code="B" extraValue="">
172      </constraint>
173    </node>
174  </query>
175</template>
176<template name="Protein_To_Gene_Type_Converter" title="Protein to gene type converter" longDescription="" comment="">
177  <query name="Protein_To_Gene_Type_Converter" model="genomic" view="Protein.id Protein.genes.id" sortOrder="Protein.id asc">
178    <node path="Protein" type="Protein">
179    </node>
180    <node path="Protein.id" type="Integer">
181      <constraint op="=" value="0" description="Protein.id" identifier="Protein.id" editable="true" code="A">
182      </constraint>
183    </node>
184  </query>
185</template>
186</template-queries>
187<tags>
188  <tag name="im:aspect:Genomics" objectIdentifier="Gene_Protein" type="template">
189  </tag>
190  <tag name="im:aspect:Genomics" objectIdentifier="GO_name_Gene" type="template">
191  </tag>
192  <tag name="im:aspect:Genomics" objectIdentifier="Organism_GoTerm_Gene" type="template">
193  </tag>
194  <tag name="im:aspect:Genomics" objectIdentifier="Gene_particularGoannotation" type="template">
195  </tag>
196  <tag name="im:aspect:Genomics" objectIdentifier="Gene_allGOTerms" type="template">
197  </tag>
198  <tag name="im:aspect:Genomics" objectIdentifier="Gene_GO" type="template">
199  </tag>
200  <tag name="im:aspect:Genomics" objectIdentifier="SequenceFeature.overlappingFeatures" type="collection">
201  </tag>
202  <tag name="im:aspect:Genomics" objectIdentifier="Chromosome.genes" type="collection">
203  </tag>
204  <tag name="im:aspect:Genomics" objectIdentifier="SequenceFeature.chromosome" type="reference">
205  </tag>
206  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.Transcript" type="class">
207  </tag>
208  <tag name="im:aspect:Genomics" objectIdentifier="Gene.transcripts" type="collection">
209  </tag>
210  <tag name="im:aspect:Genomics" objectIdentifier="Gene.UTRs" type="collection">
211  </tag>
212  <tag name="im:aspect:Genomics" objectIdentifier="SequenceFeature.chromosomeLocation" type="reference">
213  </tag>
214  <tag name="im:aspect:Genomics" objectIdentifier="Chromosome.transcripts" type="collection">
215  </tag>
216  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.GOTerm" type="class">
217  </tag>
218  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.Gene" type="class">
219  </tag>
220  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.NcRNA" type="class">
221  </tag>
222  <tag name="im:aspect:Genomics" objectIdentifier="SequenceFeature.sequence" type="reference">
223  </tag>
224  <tag name="im:aspect:Genomics" objectIdentifier="CDS.MRNA" type="reference">
225  </tag>
226  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.UTR" type="class">
227  </tag>
228  <tag name="im:aspect:Genomics" objectIdentifier="Transcript.gene" type="reference">
229  </tag>
230  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.ChromosomeBand" type="class">
231  </tag>
232  <tag name="im:aspect:Genomics" objectIdentifier="Protein.genes" type="collection">
233  </tag>
234  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.Chromosome" type="class">
235  </tag>
236  <tag name="im:aspect:Genomics" objectIdentifier="MRNA.UTRs" type="collection">
237  </tag>
238  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.SnoRNA" type="class">
239  </tag>
240  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.MRNA" type="class">
241  </tag>
242  <tag name="im:aspect:Genomics" objectIdentifier="Transcript.introns" type="collection">
243  </tag>
244  <tag name="im:aspect:Genomics" objectIdentifier="Chromosome.features" type="collection">
245  </tag>
246  <tag name="im:aspect:Genomics" objectIdentifier="org.intermine.model.bio.TFBindingSite" type="class">
247  </tag>
248  <tag name="im:aspect:Proteins" objectIdentifier="Gene_Protein" type="template">
249  </tag>
250  <tag name="im:aspect:Proteins" objectIdentifier="Protein_GOtermsSpecificOntology" type="template">
251  </tag>
252  <tag name="im:aspect:Proteins" objectIdentifier="org.intermine.model.bio.Protein" type="class">
253  </tag>
254  <tag name="im:aspect:Proteins" objectIdentifier="Gene.proteins" type="collection">
255  </tag>
256  <tag name="im:aspect:Proteins" objectIdentifier="Protein.sequence" type="reference">
257  </tag>
258  <tag name="im:aspect:Proteins" objectIdentifier="org.intermine.model.bio.ProteinDomain" type="class">
259  </tag>
260  <tag name="im:aspect:Proteins" objectIdentifier="CDS.polypeptides" type="collection">
261  </tag>
262  <tag name="im:aspect:Proteins" objectIdentifier="org.intermine.model.bio.ProteinInteraction" type="class">
263  </tag>
264  <tag name="im:aspect:Proteins" objectIdentifier="CDS.protein" type="reference">
265  </tag>
266  <tag name="im:aspect:Proteins" objectIdentifier="ProteinInteraction.protein" type="reference">
267  </tag>
268  <tag name="im:aspect:Proteins" objectIdentifier="Protein.proteinDomains" type="collection">
269  </tag>
270  <tag name="im:aspect:Proteins" objectIdentifier="Protein.features" type="collection">
271  </tag>
272  <tag name="im:aspect:Proteins" objectIdentifier="Protein.keywords" type="collection">
273  </tag>
274  <tag name="im:converter" objectIdentifier="Protein_To_Gene_Type_Converter" type="template">
275  </tag>
276  <tag name="im:converter" objectIdentifier="Gene_To_Protein_Type_Converter" type="template">
277  </tag>
278  <tag name="im:preferredBagType" objectIdentifier="org.intermine.model.bio.Gene" type="class">
279  </tag>
280  <tag name="im:preferredBagType" objectIdentifier="org.intermine.model.bio.Protein" type="class">
281  </tag>
282  <tag name="im:summary" objectIdentifier="Protein.comments" type="collection">
283  </tag>
284  <tag name="im:summary" objectIdentifier="RegulatoryRegion.gene" type="reference">
285  </tag>
286  <tag name="im:summary" objectIdentifier="BioEntity.synonyms" type="collection">
287  </tag>
288  <tag name="im:summary" objectIdentifier="Gene.proteins" type="collection">
289  </tag>
290  <tag name="im:summary" objectIdentifier="MicroarrayOligo.transcript" type="reference">
291  </tag>
292  <tag name="im:summary" objectIdentifier="BioEntity.organism" type="reference">
293  </tag>
294  <tag name="im:summary" objectIdentifier="Protein.genes" type="collection">
295  </tag>
296  <tag name="im:summary" objectIdentifier="BindingSite.factor" type="reference">
297  </tag>
298  <tag name="im:summary" objectIdentifier="Gene.publications" type="collection">
299  </tag>
300  <tag name="im:summary" objectIdentifier="Protein.publications" type="collection">
301  </tag>
302</tags>
303</userprofile>
Note: See TracBrowser for help on using the repository browser.