Commit 317a2125 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Update documentation slightly.

parent 6c9580d1
......@@ -4,17 +4,18 @@
MOTIVATION
--------------------------------------------------------------------
Starting with release 55 of Ensembl we provide an
ensembl_ontology_NN database. It replaces the older ensembl_go_NN
database which used to be loaded straight from the public table
dumps provided by the Gene Ontology group (and hence weren't really
an Ensembl database to start with). The older ensembl_go_NN
database also had an external Perl API associated with it which
often made working with GO terms in Ensembl slightly awkward, or at
least more cumbersome than what it needed to be.
Starting with release 55 of Ensembl we provide an ontology database
called ensembl_ontology_NN (where 'NN' is the number of the
release). It replaces the older ensembl_go_NN database which used
to be loaded straight from the public table dumps provided by the
Gene Ontology group (and hence weren't really an Ensembl database to
start with). The older ensembl_go_NN database also had an external
Perl API associated with it which often made working with GO terms
in Ensembl slightly awkward, or at least more cumbersome than what
it needed to be.
The new database, and its associated native Ensembl Core API, is an
attempt to make it simple to work with ontology terms in Ensembl.
attempt to make it easy to work with ontology terms in Ensembl.
The database also contains Sequence Ontology (SO) terms even though
these are not yet cross-referenced or otherwise used by Ensembl.
......@@ -40,7 +41,8 @@
- subset
The 'subset' table contains information about each of the subsets
of the loaded ontologies.
of the loaded ontologies. GO subsets includes, for example,
GOSlim GOA ('goslim_goa').
- term
The 'term' table contains the ontology term accession, name,
......@@ -191,7 +193,7 @@
$term->ancestors()
ADDITIONS TO THE EXISTING API
ADDITIONS TO THE EXISTING ENSEMBL CORE API
--------------------------------------------------------------------
To enable to use ontology terms in querying for Ensembl objects,
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment