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Commit d7d38fbf authored by Monika Komorowska's avatar Monika Komorowska
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Changes for automated HTML generation.

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......@@ -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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