From 694f7b645b5a69232be9b5773c3d9f3f6a57cce0 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 15 May 2015 13:35:33 +0100
Subject: [PATCH] better SO description and updated tests
---
.../EnsEMBL/Utils/SequenceOntologyMapper.pm | 54 +++++++++----------
modules/t/sequenceOntologyMapper.t | 2 +-
.../ontology/ontology/term.txt | 1 +
3 files changed, 29 insertions(+), 28 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/SequenceOntologyMapper.pm b/modules/Bio/EnsEMBL/Utils/SequenceOntologyMapper.pm
index 39c96c0667..76d1086452 100644
--- a/modules/Bio/EnsEMBL/Utils/SequenceOntologyMapper.pm
+++ b/modules/Bio/EnsEMBL/Utils/SequenceOntologyMapper.pm
@@ -88,47 +88,47 @@ my %transcript_so_mapping =
'transcribed_unprocessed_pseudogene'=> 'SO:0000516', # pseudogenic_transcript
'processed_pseudogene' => 'SO:0000043', # processed_pseudogene
'unprocessed_pseudogene' => 'SO:0000336', # pseudogene
- 'unitary_pseudogene' => 'SO:0000336',
+ 'unitary_pseudogene' => 'SO:0000336', # pseudogene
'pseudogene' => 'SO:0000336', # pseudogene
- 'transcribed_processed_pseudogene' => 'SO:0000043',
+ 'transcribed_processed_pseudogene' => 'SO:0000043', # processed_pseudogene
'retrotransposed' => 'SO:0000569', #retrotransposed
- 'ncrna_host' => 'SO:0000483',
- 'polymorphic_pseudogene' => 'SO:0000336',
- 'lincRNA' => 'SO:0001463',
- 'ncrna_host' => 'SO:0000483',
- '3prime_overlapping_ncrna' => 'SO:0000483',
- 'TR_V_gene' => 'SO:0000466',
- 'TR_V_pseudogene' => 'SO:0000336',
+ 'ncrna_host' => 'SO:0000483', # nc_primary_transcript
+ 'polymorphic_pseudogene' => 'SO:0000336', # pseudogene
+ 'lincRNA' => 'SO:0001463', # lincRNA
+ 'ncrna_host' => 'SO:0000483', # nc_primary_transcript
+ '3prime_overlapping_ncrna' => 'SO:0000483', # nc_primary_transcript
+ 'TR_V_gene' => 'SO:0000466', # V_gene_segment
+ 'TR_V_pseudogene' => 'SO:0000336', # pseudogene
'TR_J_gene' => 'SO:0000470',
'IG_C_gene' => 'SO:0000478',
- 'IG_C_pseudogene' => 'SO:0000336',
- 'TR_C_gene' => 'SO:0000478',
- 'IG_J_pseudogene' => 'SO:0000336',
+ 'IG_C_pseudogene' => 'SO:0000336', # pseudogene
+ 'TR_C_gene' => 'SO:0000478', # C_gene_segment
+ 'IG_J_pseudogene' => 'SO:0000336', # pseudogene
'miRNA' => 'SO:0000276', #miRNA
- 'miRNA_pseudogene' => 'SO:0000336',
+ 'miRNA_pseudogene' => 'SO:0000336', # pseudogene
'disrupted_domain' => 'SO:0000681', # aberrant_processed_transcript
'rRNA' => 'SO:0000252', #rRNA
- 'rRNA_pseudogene' => 'SO:0000777',
- 'scRNA_pseudogene' => 'SO:0000336',
+ 'rRNA_pseudogene' => 'SO:0000777', # pseudogenic_rRNA
+ 'scRNA_pseudogene' => 'SO:0000336', # pseudogene
'snoRNA' => 'SO:0000275', # snoRNA
- 'snoRNA_pseudogene' => 'SO:0000336',
+ 'snoRNA_pseudogene' => 'SO:0000336', # pseudogene
'snRNA' => 'SO:0000274', # snRNA
- 'snRNA_pseudogene' => 'SO:0000336',
+ 'snRNA_pseudogene' => 'SO:0000336', # pseudogene
);
my %utr_so_mapping =
(
- 'UTR' => 'SO:0000203',
- 'five_prime_utr' => 'SO:0000204',
- 'three_prime_utr' => 'SO:0000205'
+ 'UTR' => 'SO:0000203', # UTR
+ 'five_prime_utr' => 'SO:0000204', # five_prime_UTR
+ 'three_prime_utr' => 'SO:0000205' # three_prime_UTR
);
my %region_so_mapping =
(
- 'chromosome' => 'SO:0000340',
- 'supercontig' => 'SO:0000148',
- 'scaffold' => 'SO:0000148',
- 'contig' => 'SO:0000149'
+ 'chromosome' => 'SO:0000340', # chromosome
+ 'supercontig' => 'SO:0000148', # supercontig
+ 'scaffold' => 'SO:0000148', # supercontig
+ 'contig' => 'SO:0000149' # contig
);
my %feature_so_mapping =
@@ -137,9 +137,9 @@ my %feature_so_mapping =
'Bio::EnsEMBL::Gene' => 'SO:0000704', # gene
'Bio::EnsEMBL::Transcript' => 'SO:0000673', # transcript
'Bio::EnsEMBL::Exon' => 'SO:0000147', # exon
- 'Bio::EnsEMBL::UTR' => 'SO:0000203',
- 'Bio::EnsEMBL::ExonTranscript' => 'SO:0000147',
- 'Bio::EnsEMBL::CDS' => 'SO:0000316',
+ 'Bio::EnsEMBL::UTR' => 'SO:0000203', # UTR
+ 'Bio::EnsEMBL::ExonTranscript' => 'SO:0000147', # Exon
+ 'Bio::EnsEMBL::CDS' => 'SO:0000316', # CDS
'Bio::EnsEMBL::Slice' => 'SO:0000001', # region
'Bio::EnsEMBL::SimpleFeature' => 'SO:0001411', # biological_region
'Bio::EnsEMBL::MiscFeature' => 'SO:0001411', # biological_region
diff --git a/modules/t/sequenceOntologyMapper.t b/modules/t/sequenceOntologyMapper.t
index 1aec5bfba5..b6c37236d2 100644
--- a/modules/t/sequenceOntologyMapper.t
+++ b/modules/t/sequenceOntologyMapper.t
@@ -77,7 +77,7 @@ my $mappings =
# exons
{ obj => Bio::EnsEMBL::Exon->new, accession => 'SO:0000147', name => 'exon' },
# slices
- { obj => $db->get_SliceAdaptor->fetch_by_region('chromosome', '20', 30_270_000, 31_200_000), accession => 'SO:0000001', name => 'region' },
+ { obj => $db->get_SliceAdaptor->fetch_by_region('chromosome', '20', 30_270_000, 31_200_000), accession => 'SO:0000340', name => 'chromosome' },
# simple features
{ obj => Bio::EnsEMBL::SimpleFeature->new(), accession => 'SO:0001411', name => 'biological_region' },
# misc features
diff --git a/modules/t/test-genome-DBs/ontology/ontology/term.txt b/modules/t/test-genome-DBs/ontology/ontology/term.txt
index a1135770ff..c572b72cc4 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/term.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/term.txt
@@ -161,3 +161,4 @@
40788 5 NULL SO:0001217 protein_coding_gene """"" []" 0 0
40842 5 NULL SO:0001272 tRNA_gene """"" []" 0 0
41072 5 NULL SO:0001503 processed_transcript """A transcript for which no open reading frame has been identified and for which no other function has been determined."" [MGI:hdeen]" 0 0
+41494 5 SOFA SO:0000340 chromosome "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] 0 0
--
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