From c69d3f076f54c701ddf03ab6e06ad0e31b68cbaf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 1 Jun 2009 10:56:50 +0000
Subject: [PATCH] Change names of methods in OntologyTermAdaptor.
Mention new fetch_all_by_GOTerm_accession() method.
---
misc-scripts/ontology/README | 29 ++++++++++++++++++-----------
1 file changed, 18 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/ontology/README b/misc-scripts/ontology/README
index e44ca3bdcc..93e68c4f8f 100644
--- a/misc-scripts/ontology/README
+++ b/misc-scripts/ontology/README
@@ -135,23 +135,23 @@
$adaptor->fetch_by_dbID_list(\@dbIDs)
2.b by their (immediate) parent term
- $adaptor->fetch_by_parent_term($term)
+ $adaptor->fetch_all_by_parent_term($term)
2.c by their (immediate) child term
- $adaptor->fetch_by_child_term($term)
+ $adaptor->fetch_all_by_child_term($term)
2.d by an ancestor term
- $adaptor->fetch_all_by_parent_term($term)
+ $adaptor->fetch_all_by_ancestor_term($term)
2.e by a descendant term
- $adaptor->fetch_all_by_child_term($term)
+ $adaptor->fetch_all_by_descendant_term($term)
3. Fetching a structure that encodes the ancestor relationships of
a term.
$adaptor->_fetch_ancestor_chart($term)
- Given an ontology term, which is a Bio::EnsEMBL::OntologyTerm
- object, some operations from the second set of operations above are
+ Given an ontology term, which is a Bio::EnsEMBL::OntologyTerm
+ object, some operations from the second set of operations above are
also available on the object itself (2.b--2.e):
4. Fetching a set of terms from the database
@@ -173,11 +173,18 @@
--------------------------------------------------------------------
To enable to use ontology terms in querying for Ensembl objects,
- a method called fetch_all_by_GOTerm() was added to GeneAdaptor,
- TranscriptAdaptor, and to TranslationAdaptor. Given a GO term
- object, this method uses the DBEntryAdaptor to fetch objects
- that are cross-referenced with the GO term or with any of its
- descendants.
+ two methods were added to GeneAdaptor, TranscriptAdaptor, and to
+ TranslationAdaptor:
+
+ - fetch_all_by_GOTerm()
+
+ - fetch_all_by_GOTerm_accession()
+
+ Given a GO term object, the fetch_all_by_GOTerm() method uses
+ the DBEntryAdaptor to fetch objects that are cross-referenced
+ with the GO term or with any of its descendants. The
+ fetch_all_by_GOTerm_accession() method works similarly, but
+ instead of a GO term object it takes a GO term accession.
COMPLETE EXAMPLE PROGRAMS
--
GitLab