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genex-cvs-commit
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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>
\ 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: 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>
\ 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: 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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--- 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 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 t...
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