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revision 1.5, Mon Mar 7 02:05:34 2005 UTC revision 1.6, Thu Jun 9 19:06:55 2005 UTC
# Line 256  Line 256 
256                                          </Field>                                          </Field>
257                                  </Fields>                                  </Fields>
258                  </Entity>                  </Entity>
259            <Entity name="Coupling" keyType="medium-string">
260                <Notes>A coupling is a relationship between two features. The features are
261                physically close on the contig, and there is evidence that they generally
262                belong together. The key of this entity is formed by combining the coupled
263                            feature IDs with a space.</Notes>
264                <Fields>
265                    <Field name="score" type="int">
266                        <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH
267                        indicates that two genes near each other on one genome are very similar to
268                        genes near each other on another genome. The score only counts PCHs for which
269                        the genomes are very different. (In other words, we have a pairing that persists
270                        between different organisms.) A higher score implies a stronger meaning to the
271                        clustering.</Notes>
272                    </Field>
273                </Fields>
274            </Entity>
275            <Entity name="PCH" keyType="string">
276                <Notes>A PCH (physically close homolog) connects a clustering (which is a
277                pair of physically close features on a contig) to a second pair of physically
278                close features that are similar to the first. Essentially, the PCH is a
279                relationship between two clusterings in which the first clustering's features
280                are similar to the second clustering's features. The simplest model for
281                this would be to simply relate clusterings to each other; however, not all
282                physically close pairs qualify as clusterings, so we relate a clustering to
283                a pair of features. The key is the clustering key followed by the IDs
284                of the features in the second pair.</Notes>
285                <Fields>
286                    <Field name="used" type="boolean">
287                        <Notes>TRUE if this PCH is used in scoring the attached clustering,
288                        else FALSE. If a clustering has a PCH for a particular genome and many
289                        similar genomes are present, then a PCH will probably exist for the
290                        similar genomes as well. When this happens, only one of the PCHs will
291                        be scored: the others are considered duplicates of the same evidence.</Notes>
292                    </Field>
293                </Fields>
294            </Entity>
295      </Entities>      </Entities>
296      <Relationships>      <Relationships>
297            <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
298                <Notes>This relationship connects a feature to all the functional couplings
299                in which it participates. A functional coupling is a recognition of the fact
300                that the features are close to each other on a chromosome, and similar
301                features in other genomes also tend to be close.</Notes>
302                <Fields>
303                    <Field name="pos" type="int">
304                        <Notes>Ordinal position of the feature in the coupling. Currently,
305                        this is either "1" or "2".</Notes>
306                    </Field>
307                </Fields>
308                <ToIndex>
309                    <Notes>This index enables the application to view the features of
310                    a coupling in the proper order. The order influences the way the
311                    PCHs are examined.</Notes>
312                    <IndexFields>
313                        <IndexField name="pos" order="ascending" />
314                    </IndexFields>
315                </ToIndex>
316            </Relationship>
317            <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
318                <Notes>This relationship connects a functional coupling to the physically
319                close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
320            </Relationship>
321            <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">
322                <Notes>This relationship connects a PCH to the features that represent its
323                evidence. Each PCH is connected to a parent coupling that relates two features
324                on a specific genome. The PCH's evidence that the parent coupling is functional
325                is the existence of two physically close features on a different genome that
326                correspond to the features in the coupling. Those features are found on the
327                far side of this relationship.</Notes>
328                <Fields>
329                    <Field name="pos" type="int">
330                        <Notes>Ordinal position of the feature in the coupling that corresponds
331                        to our target feature. There is a one-to-one correspondence between the
332                        features connected to the PCH by this relationship and the features
333                        connected to the PCH's parent coupling. The ordinal position is used
334                        to decode that relationship. Currently, this field is either "1" or
335                        "2".</Notes>
336                    </Field>
337                    <Field name="percentMatch" type="float">
338                        <Notes>Percent similarity between our target feature and the
339                        corresponding feature of the coupling.</Notes>
340                    </Field>
341                    <Field name="paralogs" type="int">
342                        <Notes>Number of features on the same genome that are analogous
343                        to our target feature. A higher paralog count indicates less
344                        valuable evidence.</Notes>
345                    </Field>
346                </Fields>
347                <FromIndex>
348                    <Notes>This index enables the application to view the features of
349                    a PCH in the proper order.</Notes>
350                    <IndexFields>
351                        <IndexField name="pos" order="ascending" />
352                    </IndexFields>
353                </FromIndex>
354            </Relationship>
355          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
356              <Notes>This relationship connects a genome to the contigs that contain the actual genetic              <Notes>This relationship connects a genome to the contigs that contain the actual genetic
357              information.</Notes>              information.</Notes>
# Line 358  Line 452 
452                  </IndexFields>                  </IndexFields>
453              </ToIndex>              </ToIndex>
454          </Relationship>          </Relationship>
         <Relationship name="IsClusteredOnChromosomeWith" from="Feature" to="Feature" arity="MM">  
             <Notes>This relationship is one of two that relate features to each other. It connects  
             features that are physically close to each other on a single chromosome.</Notes>  
             <Fields>  
                 <Field name="score" type="int">  
                         <Notes>The number of co-occurrences in genomes that are not  
                         extremely closely-related.</Notes>  
                 </Field>  
             </Fields>  
         </Relationship>  
455          <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">          <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">
456              <Notes>This relationship is one of two that relate features to each other. It              <Notes>This relationship is one of two that relate features to each other. It
457              connects features that are very similar but on separate genomes. A              connects features that are very similar but on separate genomes. A

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