From d7d38fbf94171b43137cf25654b32f8abea2d442 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Tue, 8 Mar 2011 15:30:40 +0000
Subject: [PATCH] Changes for automated HTML generation.
---
sql/table.sql | 132 +++-----------------------------------------------
1 file changed, 7 insertions(+), 125 deletions(-)
diff --git a/sql/table.sql b/sql/table.sql
index da1d604282..f65f23e6d3 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -7,124 +7,6 @@
# - same name is given in foreign key relations
-/**
-Insert this HTML in the 'Introduction' section:
-
-
-<p>
-This document gives a high-level description of the tables that
-make up the EnsEMBL core schema. Tables are grouped into logical
-groups, and the purpose of each table is explained. It is intended to
-allow people to familiarise themselves with the schema when
-encountering it for the first time, or when they need to use some
-tables that they've not used before. Note that while some of the more
-important columns in some of the tables are discussed, this document
-makes no attempt to enumerate all of the names, types and contents of
-every single table. Some concepts which are referred to in the table
-descriptions are given at the end of this document; these are linked
-to from the table description where appropriate.
-</p>
-
-<p>
-Different tables are populated throughout the gene build process:
-</p>
-
-<table border="1" cellpadding="10">
-<tr>
-<th>Step</th>
-<th>Process</th>
-</tr>
-<tr>
-<td>0</td>
-
-<td>Create empty schema, populate meta table</td>
-</tr>
-<tr>
-<td>1</td>
-<td>Load DNA - populates dna, clone, contig, chromosome, assembly tables</td>
-</tr>
-<tr>
-<td>2</td>
-<td>Analyze DNA (raw computes) - populates genomic feature/analysis tables</td>
-</tr>
-<tr>
-<td>3</td>
-
-<td>Build genes - populates exon, transcript,etc. gene-related tables</td>
-</tr>
-<tr>
-<td>4a</td>
-<td>Analyze genes - populate protein_feature, xref tables, interpro</td>
-</tr>
-<tr>
-<td>4b</td>
-<td>ID mapping</td>
-</tr>
-</table>
-
-<p>
-This document refers to version <strong>61</strong> of the EnsEMBL
-core schema.
-</p>
-
-
-*/
-
-
-/**
-Append this HTMl to the generated page before the </body> </html> tags:
-
-<hr />
-<h2>Concepts</h2>
-
-<dl>
-<dt><strong><a name="co-ordinates">co-ordinates</a></strong></dt>
-<dd>
-<p>There are several different co-ordinate systems used in the EnsEMBL database and API. For every co-ordinate system, the fundamental
-unit is one base. The differences between co-ordinate systems lie in where a particular numbered base lies, and the start
-position it is relative to. CONTIG co-ordinates, also called 'raw contig' co-ordinates or 'clone fragments' are relative to
-the first base of the first contig of a clone. Note that the numbering is from 1, i.e. the very first base of the first contig
-of a clone is numbered 1, not 0. In CHROMOSOMAL co-ordinates, the co-ordinates are relative to the first base of the chromosome.
-Again, numbering is from 1. The seq_region table can store sequence regions in any of the co-ordinate systems defined in the
-coord_system table.
-</p>
-</dd>
-<dt><strong><a name="supercontigs">supercontigs</a></strong></dt>
-<dd>
-<p>A supercontig is made up of a group of adjacent or overlapping contigs.</p>
-</dd>
-<dt><strong><a name="sticky_rank">sticky_rank</a></strong></dt>
-<dd>
-<p>The sticky_rank differentiates between fragments of the same exon; i.e for exons that span multiple contigs, all the fragments
-would have the same ID, but different sticky_rank values
-
-</p>
-</dd>
-<dt><strong><a name="stable_id">stable_id</a></strong></dt>
-<dd>
-<p>Gene predictions have changed over the various releases of the EnsEMBL databases. To allow the user to track particular gene
-predictions over changing co-ordinates, each gene-related prediction is given a 'stable identifier'. If a prediction looks
-similar between two releases, we try to give it the same name, even though it may have changed position and/or had some sequence
-changes.
-</p>
-</dd>
-<dt><strong><a name="cigar_line">cigar_line</a></strong></dt>
-<dd>
-<p>This allows the compact storage of gapped alignments by storing the maximum extent of the matches and then a text string which
-encodes the placement of gaps inside the alignment. Colloquially inside EnsEMBL this is called a and its adoption has shrunk
-the number of rows in the feature table around 4-fold.
-</p>
-</dd>
-</dl>
-<hr />
-
-
-*/
-
-
-
-
-
/**
@header Fundamental Tables
@desc A PDF document of the schema is available <a href="fundamental_tables_core.pdf">here</a>.
@@ -1171,7 +1053,7 @@ CREATE TABLE ditag_feature (
@column perc_ident Alignment percentage identity.
@column cigar_line Used to encode gapped alignments.
@column external_db_id Foreign key references to the @link external_db table.
-@column hcoverage
+@column hcoverage Hit coverage.
@column external_data External data.
@column pair_dna_align_feature_id The id of the dna feature aligned.
@@ -2118,7 +2000,7 @@ This includes which IDs where deleted, created and related to each other. Each e
@column new_version Stable id version.
@column mapping_session_id Foreign key references to the @link mapping_session table.
@column type ENUM('gene', 'transcript', 'translation') NOT NULL,
-@column score Mapping score.
+@column score Combined mapping score.
@see mapping_session
@@ -2236,8 +2118,8 @@ CREATE TABLE dependent_xref(
@column db_name Database name.
@column db_release Database release.
@column status Status, e.g. 'KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO'.
-@column dbprimary_acc_linkable
-@column priority Priority.
+@column dbprimary_acc_linkable Indicates if primary accessions can be linked to from the EnsEMBL web site.
+@column priority Determines the order in which the sources are displayed on the EnsEMBL web site.
@column db_display_name Database display name.
@column type Type, e.g. 'ARRAY', 'ALT_TRANS', 'ALT_GENE', 'MISC', 'LIT', 'PRIMARY_DB_SYNONYM', 'ENSEMBL'.
@column secondary_db_name Secondary database name.
@@ -2399,7 +2281,7 @@ Some ENSPs are associated with multiple closely related Swissprot entries which
For this reason a single Ensembl - external db object relationship in the object_xref table can be associated with multiple evidence tags in the ontology_xref table.
@column object_xref_id Composite key. Foreign key references to the @link object_xref table.
-@column source_xref_id Composite key.
+@column source_xref_id Composite key. Foreign key references to the @link xref table.
@column linkage_type Composite key. <a href="http://www.geneontology.org/GO.evidence.shtml">Evidence tags</a>
@see object_xref
@@ -2461,8 +2343,8 @@ CREATE TABLE seq_region_synonym (
@column target_score Target mapping query score.
@column ensembl_id Foreign key references to the @link seq_region, @link transcript, @link gene, @translation tables depending on ensembl_object_type.
@column ensembl_object_type Ensembl object type: 'RawContig', 'Transcript', 'Gene','Translation'.
-@column parent
-
+@column parent Foreign key references to the @link dependent_xref table, in case the unmapped object is dependent on a primary external reference which wasn't mapped to an ensembl one.
+
*/
--
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