fix URLs, a number of these no longer work

bioperl · Sep 25, 2018 · acd2ec2 · acd2ec2
1 parent c98b3b5
commit acd2ec2
Showing 1 changed file with 14 additions and 16 deletions.
diff --git a/lib/Bio/Ontology/DocumentRegistry.pm b/lib/Bio/Ontology/DocumentRegistry.pm
@@ -1,7 +1,7 @@
 #
 # BioPerl module for Bio::Ontology::DocumentRegistry
 #
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
 #
 # Cared for by Allen Day <allenday@ucla.edu>
 #
@@ -46,15 +46,15 @@ the Bioperl mailing list.  Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
-=head2 Support 
+=head2 Support
 
 Please direct usage questions or support issues to the mailing list:
 
 I<bioperl-l@bioperl.org>
 
-rather than to the module maintainer directly. Many experienced and 
-reponsive experts will be able look at the problem and quickly 
-address it. Please include a thorough description of the problem 
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
 with code and data examples if at all possible.
 
 =head2 Reporting Bugs
@@ -88,31 +88,29 @@ my $instance;
 
 BEGIN {
 $instance = {
+    # No longer maintained, only OBO and OWL supported
    'Sequence Ontology' => {
 	    ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.ontology?rev=HEAD",
         definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
         format => 'soflat',
                                     },
    'Sequence Ontology OBO' => {
-	    ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD",
-        definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
+	    ontology => "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo",
+        # definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
         format => 'obo',
                                     },
-   
+
    #### TODO Server http://umn.dl.sourceforge.net/ does not respond, are there
-   #### alternative sources? 
+   #### alternative sources?
    'Sequence Ontology Feature Annotation' => {
         ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology',
         definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition',
         format => 'soflat',
                                     },
+    # TODO: No longer available as separate files
     'Gene Ontology' => {
-         ontology => [
-							 'http://www.geneontology.org/ontology/function.ontology',
-							 'http://www.geneontology.org/ontology/process.ontology',
-							 'http://www.geneontology.org/ontology/component.ontology'
-							],
-			definitions => 'http://www.geneontology.org/ontology/GO.defs',
+         ontology => 'http://purl.obolibrary.org/obo/go/go-basic.obo',
+			#definitions => 'http://www.geneontology.org/ontology/GO.defs',
          format => 'soflat',
 							  },
             };
@@ -153,7 +151,7 @@ sub get_instance {
            (1) URI for the ontology file
            (2) URI for the ontology definitions file
            (3) format of the files (dagedit, obo, etc)
- Args    : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component 
+ Args    : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
            (Gene Ontology)'
 
 =cut