diff --git a/misc-scripts/ontology/README b/misc-scripts/ontology/README index e44ca3bdcc7ca49c6bf253c5349dfc82253174ef..93e68c4f8f24f2d70f30c71189833966d8552ab6 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