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[Genex-cvs-commit] genex-www/genex-2 AM_Spots.html,1.2,1.3 BlastHits.html,1.2,1.3 ExperimentSet.html,1.2,1.3 ExternalDatabase.html,1.2,1.3 Feature.html,1.2,1.3 HotSpots.html,1.2,1.3 PhysicalBioAssay.html,1.1,1.2 QuantitationLink.html,1.1,1.2 QuantitationType.html,1.1,1.2 SF_ExternalDBLink.html,1.2,1.3
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From: <jas...@us...> - 2002-10-17 16:57:46
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Update of /cvsroot/genex/genex-www/genex-2
In directory usw-pr-cvs1:/tmp/cvs-serv8950
Modified Files:
AM_Spots.html BlastHits.html ExperimentSet.html
ExternalDatabase.html Feature.html HotSpots.html
PhysicalBioAssay.html QuantitationLink.html
QuantitationType.html SF_ExternalDBLink.html
Log Message:
new
Index: AM_Spots.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/AM_Spots.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** AM_Spots.html 29 Aug 2002 13:58:07 -0000 1.2
--- AM_Spots.html 17 Oct 2002 16:57:43 -0000 1.3
***************
*** 3,5 ****
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: AM_Spots Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The AM_Spots table provides the expression level for each spot on an PhysicalBioAssay. It is directly linked to the SequenceFeature whose expression level has been measured. Additionally, it may be linked directly to an AL_Spot row through the SpotLink table in order to deal with spots that are not represented by a SequenceFeature (e.g. control spots) or with SequenceFeatures that are replicated on a given ArrayDesign.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td>Array Layout Spot</td><td>int4</td><td>true</td><td>maps 1-to-1 with the layout</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td>Array Measurement</td><td>int4</td><td>true</td><td>the PhysicalBioAssay to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>spot_value</td><td>Spot Value</td><td>float</td><td>true</td><td>the actual expression level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td><a href="Feature.html">Feature</a></td><td>feature_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td><a href="PhysicalBioAssay.html">PhysicalBioAssay</a></td><td>pba_pk</td><td>LOOKUP_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk pba_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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--- 3,5 ----
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: AM_Spots Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The AM_Spots table provides the expression level for each spot on an PhysicalBioAssay. It is directly linked to the Reporter whose expression level has been measured. Additionally, it may be linked directly to an AL_Spot row through the SpotLink table in order to deal with spots that are not represented by a Reporter (e.g. control spots) or with Reporters that are replicated on a given ArrayDesign.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td>Array Layout Spot</td><td>int4</td><td>true</td><td>maps 1-to-1 with the layout</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td>Array Measurement</td><td>int4</td><td>true</td><td>the PhysicalBioAssay to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>spot_value</td><td>Spot Value</td><td>float</td><td>true</td><td>the actual expression level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td><a href="Feature.html">Feature</a></td><td>feature_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td><a href="PhysicalBioAssay.html">PhysicalBioAssay</a></td><td>pba_pk</td><td>LOOKUP_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk pba_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: BlastHits.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/BlastHits.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** BlastHits.html 29 Aug 2002 13:58:07 -0000 1.2
--- BlastHits.html 17 Oct 2002 16:57:43 -0000 1.3
***************
*** 3,5 ****
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: BlastHits Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The BlastHits table allows any number of blast results to be associated with a given SequenceFeature.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>expect_value</td><td>Expectation Value</td><td>float</td><td>true</td><td>??will probably have to be based on log(E), since these values can be very tiny...</td></tr><tr bgcolor="#D8E4F7"><td>match_accession</td><td>Match Accession</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>Sequence Feature</td><td>int4</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td><a href="SequenceFeature.html">SequenceFeature</a></td><td>sf_pk</td><td>MANY_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>match_accession sf_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>blasthits_sf_fk</td></tr></table><br></body></html>
\ No newline at end of file
--- 3,5 ----
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: BlastHits Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The BlastHits table allows any number of blast results to be associated with a given Reporter.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>expect_value</td><td>Expectation Value</td><td>float</td><td>true</td><td>??will probably have to be based on log(E), since these values can be very tiny...</td></tr><tr bgcolor="#D8E4F7"><td>match_accession</td><td>Match Accession</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>Sequence Feature</td><td>int4</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td><a href="Reporter.html">Reporter</a></td><td>rep_pk</td><td>MANY_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>match_accession rep_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>blasthits_rep_fk</td></tr></table><br></body></html>
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Index: ExperimentSet.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/ExperimentSet.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ExperimentSet.html 29 Aug 2002 13:58:07 -0000 1.2
--- ExperimentSet.html 17 Oct 2002 16:57:43 -0000 1.3
***************
*** 3,5 ****
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ExperimentSet Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExperimentSet table groups a set of PhysicalBioAssay rows into a coherent collection representing a conceptually related set of treatments (e.g. time series or quantity series) of the same genetic elements. In its standard use, all PhysicalBioAssays belonging to a single ExperimentSet will derive from the same ArrayDesign and will have been assayed by the same group. However, there may be cases in which virtual ExperimentSets may be created to link PhysicalBioAssays that illustrate some interesting relationship, even though they do not meet these criteria.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>analysis_description</td><td>Analysis Description</td><td>text</td><td>false</td><td> high level description of how experiment was analyzed</td></tr><tr bgcolor="#D8E4F7"><td>archive_bundle_ref</td><td>Archive Bundle Reference</td><td>varchar(128)</td><td>false</td><td> path to image files etc. the linking of particular files in the bundle with specific PhysicalBioAssays is going to be done through some convention, as yet to be determined...</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>biology_description</td><td>Biology Description</td><td>text</td><td>false</td><td> gives the intended purpose of the experiment</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td>Primary Citation</td><td>int4</td><td>false</td><td> publication in which experiment was described</td></tr><tr bgcolor="#D8E4F7"><td>es_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>local_accession</td><td>Local Accession Number</td><td>varchar(128)</td><td>false</td><td> id of experiment in submitter's database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Experiment Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the experiment info it is important to destinquish between this and the rw_groupname because if data is imported from another DB then the owner of the data will not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>quantity_series_type</td><td>Quantity Series Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab, only appropriate for quantity series</td></tr><tr bgcolor="#D8E4F7"><td>release_date</td><td>Release Date</td><td>datetime</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr><tr bgcolor="#D8E4F7"><td>submission_date</td><td>Submission Date</td><td>datetime</td><td>true</td><td> indicates when XML was uploaded to NCGR</td></tr><tr bgcolor="#D8E4F7"><td>treatment_type</td><td>Treatment Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td><a href="Citation.html">Citation</a></td><td>cit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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--- 3,5 ----
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ExperimentSet Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExperimentSet table groups a set of PhysicalBioAssay rows into a coherent collection representing a conceptually related set of treatments (e.g. time series or quantity series) of the same genetic elements. In its standard use, all PhysicalBioAssays belonging to a single ExperimentSet will derive from the same ArrayDesign and will have been assayed by the same group. However, there may be cases in which virtual ExperimentSets may be created to link PhysicalBioAssays that illustrate some interesting relationship, even though they do not meet these criteria.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>analysis_description</td><td>Analysis Description</td><td>text</td><td>false</td><td> high level description of how experiment was analyzed</td></tr><tr bgcolor="#D8E4F7"><td>archive_bundle_ref</td><td>Archive Bundle Reference</td><td>varchar(128)</td><td>false</td><td> path to image files etc. the linking of particular files in the bundle with specific PhysicalBioAssays is going to be done through some convention, as yet to be determined...</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>biology_description</td><td>Biology Description</td><td>text</td><td>false</td><td> gives the intended purpose of the experiment</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td>Primary Citation</td><td>int4</td><td>false</td><td> publication in which experiment was described</td></tr><tr bgcolor="#D8E4F7"><td>creation_date</td><td>Creation Date</td><td>datetime</td><td>true</td><td> indicates when the experiment was created</td></tr><tr bgcolor="#D8E4F7"><td>es_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>local_accession</td><td>Local Accession Number</td><td>varchar(128)</td><td>false</td><td> id of experiment in submitter's database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Experiment Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the experiment info it is important to destinquish between this and the rw_groupname because if data is imported from another DB then the owner of the data will not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>quantity_series_type</td><td>Quantity Series Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab, only appropriate for quantity series</td></tr><tr bgcolor="#D8E4F7"><td>release_date</td><td>Release Date</td><td>datetime</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr><tr bgcolor="#D8E4F7"><td>treatment_type</td><td>Treatment Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td><a href="Citation.html">Citation</a></td><td>cit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: ExternalDatabase.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/ExternalDatabase.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ExternalDatabase.html 29 Aug 2002 13:58:07 -0000 1.2
--- ExternalDatabase.html 17 Oct 2002 16:57:43 -0000 1.3
***************
*** 3,5 ****
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ExternalDatabase Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExternalDatabase table gives information that may be used to access databases outside of GeneX for information about SequenceFeatures. The information stored here is used to create hyperlinks in HTML output of various routines.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>main_url</td><td>Main DB URL</td><td>varchar(128)</td><td>true</td><td> the primary url for the database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Database Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>parameterized_url</td><td>Parameterized URL</td><td>varchar(128)</td><td>false</td><td> if present this url contains the pattern %%ID%%, which can be replaced by the DB accession number in order to retrieve a dynamic WWW page for the sequence feature</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ExternalDatabase Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExternalDatabase table gives information that may be used to access databases outside of GeneX for information about Reporters. The information stored here is used to create hyperlinks in HTML output of various routines.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>main_url</td><td>Main DB URL</td><td>varchar(128)</td><td>true</td><td> the primary url for the database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Database Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>parameterized_url</td><td>Parameterized URL</td><td>varchar(128)</td><td>false</td><td> if present this url contains the pattern %%ID%%, which can be replaced by the DB accession number in order to retrieve a dynamic WWW page for the sequence feature</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: Feature.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/Feature.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Feature.html 29 Aug 2002 13:58:07 -0000 1.2
--- Feature.html 17 Oct 2002 16:57:43 -0000 1.3
***************
*** 3,5 ****
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: Feature Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Feature table gives detail information concerning each individual element (spot) of a given ArrayDesign. In particular, it indicates the location of the spot on the Array and characterizes the genetic material that will be bound to an instance of the ArrayDesign at the given location.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td>Array Layout</td><td>int4</td><td>true</td><td>the ArrayDesign to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>feature_concentration</td><td>Feature Concentration</td><td>float</td><td>false</td><td>used to indicate the concentration of the probe on the array (may differ from the default value in the referenced ArrayDesign, but will be measured in the same units)</td></tr><tr bgcolor="#D8E4F7"><td>feature_description</td><td>Feature Description</td><td>varchar(128)</td><td>false</td><td>a meaningful description of the genetic material that will be placed on an instance at this position; in some cases, e.g. foreign DNA used as a control, the sf_fk will be left null, and this field will provide the only description of what material has been used, and hence the significance of expression levels observed at these positions in an instance of the ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_identifier</td><td>Feature Identifier</td><td>varchar(128)</td><td>false</td><td>the GOD file identifier for the position on the ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_type</td><td>Feature Type</td><td>varchar(128)</td><td>true</td><td>distinguishes various kinds of control spot from those linked to SequenceFeatures iff type = seqfeat then sf_fk must be supplied</td></tr><tr bgcolor="#D8E4F7"><td>grid_image_location</td><td>Grid Image Location</td><td>varchar(128)</td><td>false</td><td>these fields specify the position of the spot with respect to the entire Array; their purpose is to allow our software to generate a virtual image that can be compared to the actual image for an PhysicalBioAssay instance. The x and y are specified relative to the origin of distinct blocks of spots; the location of the block is given by the grid_image_location. They may be left null for data without images. the current specification seems problematic, in that unless we know how to translate a grid location into an x-y coordinate for the block, we don't know how to lay out the blocks. Further, it would seem to make more sense to translate at insert time into a simple x-y spec for each spot, since this makes the virtual image easier to calculate, and the latter will be done many times, while the insert will only occur once... JES: Mon Oct 9 15:59:26 MST 2000 Changed to type varchar to support 'Field1', 'A15', etc</td></tr><tr bgcolor="#D8E4F7"><td>pin_identifier</td><td>Pin</td><td>varchar(128)</td><td>false</td><td>Indicates which pin of the spotter is used to print this spot.</td></tr><tr bgcolor="#D8E4F7"><td>print_sequence</td><td>Print Sequence</td><td>int4</td><td>false</td><td>Indicates the order of printing of spots on a single visit of a pin to a source well. Used in replicate resolution coupled with sf_fk and source_visit, and tracking systematic variation in spot data. A value of 0 represents a virtual spot that represents the result of resolving replicates across print_sequence.</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>Sequence Feature</td><td>int4</td><td>false</td><td>indicates what genetic element will be placed on an instance at this location; may be null, in the case of controls which are not characterized to the level of detail required by SequenceFeature</td></tr><tr bgcolor="#D8E4F7"><td>source_visit</td><td>Source Visit</td><td>int4</td><td>false</td><td>Distinguishes the visits to a source well that is represented by the sf_fk relationship to the sequence feature. If used, assumes that a sequence feature entry represents a unique source well. Used coupled with print_sequence and sf_fk to resolve replicates. A value of 0 represents a virtual spot that represents the value resulting from resolving replicates across source visits.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_end</td><td>Sub-sequence End</td><td>int4</td><td>false</td><td>these fields indicate the subsequence of the SequenceFeature actually used on the Array. When these are left null, the entire SequenceFeature is implied. These may be useful when a PCR product or oligonucleotide is used on the array.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_start</td><td>Sub-sequence Start</td><td>int4</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>x_image_location</td><td>X Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>y_image_location</td><td>Y Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td><a href="ArrayDesign.html">ArrayDesign</a></td><td>ad_pk</td><td>LOOKUP_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td><a href="SequenceFeature.html">SequenceFeature</a></td><td>sf_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_identifier ad_fk</td></tr><tr bgcolor="#D8E4F7"><td>x_image_location y_image_location grid_image_location ad_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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--- 3,5 ----
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: Feature Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Feature table gives detail information concerning each individual element (spot) of a given ArrayDesign. In particular, it indicates the location of the spot on the Array and characterizes the genetic material that will be bound to an instance of the ArrayDesign at the given location.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td>Array Layout</td><td>int4</td><td>true</td><td>the ArrayDesign to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>feature_concentration</td><td>Feature Concentration</td><td>float</td><td>false</td><td>used to indicate the concentration of the probe on the array (may differ from the default value in the referenced ArrayDesign, but will be measured in the same units)</td></tr><tr bgcolor="#D8E4F7"><td>feature_description</td><td>Feature Description</td><td>varchar(128)</td><td>false</td><td>a meaningful description of the genetic material that will be placed on an instance at this position; in some cases, e.g. foreign DNA used as a control, the rep_fk will be left null, and this field will provide the only description of what material has been used, and hence the significance of expression levels observed at these positions in an instance of the ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_identifier</td><td>Feature Identifier</td><td>varchar(128)</td><td>false</td><td>the GOD file identifier for the position on the ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_type</td><td>Feature Type</td><td>varchar(128)</td><td>true</td><td>distinguishes various kinds of control spot from those linked to Reporters iff type = seqfeat then rep_fk must be supplied</td></tr><tr bgcolor="#D8E4F7"><td>grid_col_image_location</td><td>Grid Column Number</td><td>varchar(128)</td><td>false</td><td>This field supports designs that track the grids in a row,column format</td></tr><tr bgcolor="#D8E4F7"><td>grid_image_location</td><td>Grid Image Location</td><td>varchar(128)</td><td>false</td><td>these fields specify the position of the spot with respect to the entire Array; their purpose is to allow our software to generate a virtual image that can be compared to the actual image for an PhysicalBioAssay instance. The x and y are specified relative to the origin of distinct blocks of spots; the location of the block is given by the grid_image_location. They may be left null for data without images. the current specification seems problematic, in that unless we know how to translate a grid location into an x-y coordinate for the block, we don't know how to lay out the blocks. Further, it would seem to make more sense to translate at insert time into a simple x-y spec for each spot, since this makes the virtual image easier to calculate, and the latter will be done many times, while the insert will only occur once... JES: Mon Oct 9 15:59:26 MST 2000 Changed to type varchar to support 'Field1', 'A15', etc</td></tr><tr bgcolor="#D8E4F7"><td>grid_row_image_location</td><td>Grid Row Number</td><td>varchar(128)</td><td>false</td><td>This field supports designs that track the grids in a row,column format</td></tr><tr bgcolor="#D8E4F7"><td>pin_identifier</td><td>Pin</td><td>varchar(128)</td><td>false</td><td>Indicates which pin of the spotter is used to print this spot.</td></tr><tr bgcolor="#D8E4F7"><td>print_sequence</td><td>Print Sequence</td><td>int4</td><td>false</td><td>Indicates the order of printing of spots on a single visit of a pin to a source well. Used in replicate resolution coupled with rep_fk and source_visit, and tracking systematic variation in spot data. A value of 0 represents a virtual spot that represents the result of resolving replicates across print_sequence.</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>Sequence Feature</td><td>int4</td><td>false</td><td>indicates what genetic element will be placed on an instance at this location; may be null, in the case of controls which are not characterized to the level of detail required by Reporter</td></tr><tr bgcolor="#D8E4F7"><td>source_visit</td><td>Source Visit</td><td>int4</td><td>false</td><td>Distinguishes the visits to a source well that is represented by the rep_fk relationship to the sequence feature. If used, assumes that a sequence feature entry represents a unique source well. Used coupled with print_sequence and rep_fk to resolve replicates. A value of 0 represents a virtual spot that represents the value resulting from resolving replicates across source visits.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_end</td><td>Sub-sequence End</td><td>int4</td><td>false</td><td>these fields indicate the subsequence of the Reporter actually used on the Array. When these are left null, the entire Reporter is implied. These may be useful when a PCR product or oligonucleotide is used on the array.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_start</td><td>Sub-sequence Start</td><td>int4</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>x_image_location</td><td>X Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>y_image_location</td><td>Y Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td><a href="ArrayDesign.html">ArrayDesign</a></td><td>ad_pk</td><td>LOOKUP_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td><a href="Reporter.html">Reporter</a></td><td>rep_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_identifier ad_fk</td></tr><tr bgcolor="#D8E4F7"><td>x_image_location y_image_location grid_row_image_location grid_col_image_location grid_image_location ad_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: HotSpots.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/HotSpots.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** HotSpots.html 29 Aug 2002 13:58:07 -0000 1.2
--- HotSpots.html 17 Oct 2002 16:57:43 -0000 1.3
***************
*** 3,5 ****
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: HotSpots Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>LINKING</th><th> The HotSpots table indicates a subset of SequenceFeatures whose expression levels changed above a given threshold during the course of an experiment. It can be used to quickly access experiments in which genes of interest seemed to be important. It applies to the processed ratio values derived by comparing levels of expression under treatments to those under control conditions. ??It remains to be seen if this wouldn't better be done as a view. Not doing ??so introduces consistency problems if PhysicalBioAssays are added to ??experiments or values are changed.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>es_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>sf_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>threshold_type</td><td>threshold_type</td><td>varchar(128)</td><td>false</td><td> controlled vocab, specifies the threshold used to select the interesting genes, may further specify if the sense is up-regulation down-regulation or an absolute change above the threshold level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>LINKING_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td><a href="SequenceFeature.html">SequenceFeature</a></td><td>sf_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>sf_fk es_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>hotspots_es_fk</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>hotspots_sf_fk</td></tr></table><br></body></html>
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</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: HotSpots Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>LINKING</th><th> The HotSpots table indicates a subset of Reporters whose expression levels changed above a given threshold during the course of an experiment. It can be used to quickly access experiments in which genes of interest seemed to be important. It applies to the processed ratio values derived by comparing levels of expression under treatments to those under control conditions. ??It remains to be seen if this wouldn't better be done as a view. Not doing ??so introduces consistency problems if PhysicalBioAssays are added to ??experiments or values are changed.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>es_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>rep_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>threshold_type</td><td>threshold_type</td><td>varchar(128)</td><td>false</td><td> controlled vocab, specifies the threshold used to select the interesting genes, may further specify if the sense is up-regulation down-regulation or an absolute change above the threshold level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>LINKING_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td><a href="Reporter.html">Reporter</a></td><td>rep_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>rep_fk es_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>hotspots_es_fk</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>hotspots_rep_fk</td></tr></table><br></body></html>
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Index: PhysicalBioAssay.html
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RCS file: /cvsroot/genex/genex-www/genex-2/PhysicalBioAssay.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
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--- PhysicalBioAssay.html 17 Oct 2002 16:57:43 -0000 1.2
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</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: PhysicalBioAssay Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The PhysicalBioAssay table is used in two related, but distinct fashions: to represent the primary data for gene expression experiments and to represent processed data such as averaged values across replicates or ratio values for treatment vs. controls. In representing the primary data, it describes an instance of an ArrayDesign that has been used to assay gene expression levels in a preparation of the mRNA from a sample that has been subjected to a specific treatment in the context of an experiment. It contains detailed information as to the treatment and protocols used on this ArrayDesign instance. The actual expression levels for each spot are stored in the PhysicalBioAssaySpots table. In general, the PhysicalBioAssay table has the same relationship to the PhysicalBioAssaySpots table as the ArrayDesign table has to the ArrayDesignSpots table. However, there several cases in which the relationship breaks down to some extent. First, there may be PhysicalBioAssays for which no ArrayDesign is given. Second, for spots that represent controls on a given ArrayDesign, we may choose not to store expression levels for the control spots. Finally, in cases of ArrayDesigns with replicate spots (i.e. the same SequenceFeature is used in different locations on the ArrayDesign), replicates will be broken out into separate PhysicalBioAssay rows. For example, an ArrayDesign with 1000 distinct SequenceFeatures, each of which has been replicated 2 times on the ArrayDesign will have 3000 corresponding ArrayDesignSpot rows, while a given instance of the ArrayDesign will be represented by three distinct PhysicalBioAssay rows, each of which has 1000 corresponding PhysicalBioAssaySpots rows. A related example is when mutiple channels are used to detect the signal of the expression level for each spot. In this case, an ArrayDesign that has 1000 distinct SequenceFeatures may be represented by two or more PhysicalBioAssay rows, each with 1000 PhysicalBioAssaySpot rows representing the expression level reported by one channel. PhysicalBioAssays that represent primary data will be grouped into sets around the ReplicateDef table. This set of primary data may then be used to define derived PhysicalBioAssays representing the averaged values across members of the replicate set. Further, these ReplicateDefs can be used to describe TreatmentDefs which define the levels of the treatment and associated control ReplicateDefs. The TreatmentDef may reference a third type of PhysicalBioAssay that is derived from the ratio between the averaged values for the treatment replicates and the averaged values of the control replicates.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td>Array</td><td>int4</td><td>true</td><td>The chip or array used with this assay</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td> a more verbose description of the purpose of this PhysicalBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Primary Experiment Set</td><td>int4</td><td>true</td><td> the primary experiment in which the PhysicalBioAssay was taken (the ExperimentSet in which it was submitted)</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Array Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the array info it is important to destinquish between this and the rw_groupname because if data is imported from another DB then the owner of the data will not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td><a href="Array.html">Array</a></td><td>array_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>MANY_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: PhysicalBioAssay Table
! </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The PhysicalBioAssay table is used in two related, but distinct fashions: to represent the primary data for gene expression experiments and to represent processed data such as averaged values across replicates or ratio values for treatment vs. controls. In representing the primary data, it describes an instance of an ArrayDesign that has been used to assay gene expression levels in a preparation of the mRNA from a sample that has been subjected to a specific treatment in the context of an experiment. It contains detailed information as to the treatment and protocols used on this ArrayDesign instance. The actual expression levels for each spot are stored in the PhysicalBioAssaySpots table. In general, the PhysicalBioAssay table has the same relationship to the PhysicalBioAssaySpots table as the ArrayDesign table has to the ArrayDesignSpots table. However, there several cases in which the relationship breaks down to some extent. First, there may be PhysicalBioAssays for which no ArrayDesign is given. Second, for spots that represent controls on a given ArrayDesign, we may choose not to store expression levels for the control spots. Finally, in cases of ArrayDesigns with replicate spots (i.e. the same Reporter is used in different locations on the ArrayDesign), replicates will be broken out into separate PhysicalBioAssay rows. For example, an ArrayDesign with 1000 distinct Reporters, each of which has been replicated 2 times on the ArrayDesign will have 3000 corresponding ArrayDesignSpot rows, while a given instance of the ArrayDesign will be represented by three distinct PhysicalBioAssay rows, each of which has 1000 corresponding PhysicalBioAssaySpots rows. A related example is when mutiple channels are used to detect the signal of the expression level for each spot. In this case, an ArrayDesign that has 1000 distinct Reporters may be represented by two or more PhysicalBioAssay rows, each with 1000 PhysicalBioAssaySpot rows representing the expression level reported by one channel. PhysicalBioAssays that represent primary data will be grouped into sets around the ReplicateDef table. This set of primary data may then be used to define derived PhysicalBioAssays representing the averaged values across members of the replicate set. Further, these ReplicateDefs can be used to describe TreatmentDefs which define the levels of the treatment and associated control ReplicateDefs. The TreatmentDef may reference a third type of PhysicalBioAssay that is derived from the ratio between the averaged values for the treatment replicates and the averaged values of the control replicates.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td>Array</td><td>int4</td><td>true</td><td>The chip or array used with this assay</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td> a more verbose description of the purpose of this PhysicalBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Primary Experiment Set</td><td>int4</td><td>true</td><td> the primary experiment in which the PhysicalBioAssay was taken (the ExperimentSet in which it was submitted)</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Array Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the array info it is important to destinquish between this and the rw_groupname because if data is imported from another DB then the owner of the data will not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td><a href="Array.html">Array</a></td><td>array_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>MANY_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BF...
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