GitLab

Go status set to XREF now instead of KNWONXREF so that if a gene has a GO reference it does not automatically get set to be a known gene. Added new external source Fantom

alternative splicing tables added, dependent_xref table added, go_xref types that were missed somehow have now been added

support will be available once a schema patch has been committed and
databases have been patched...

databases in Registry.

not really a general purpose method but quite specific to what the web
team will want to do later.

Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae stable ID incrementation and verification.

Entry added for Tgut_symbols. These are the gene symbols assigned to Taeniopygia guttata (zebra finch) genes by Dave Burt.

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.

  Description   : Given a child ontology term, returns a hash
                  structure containing its ancestor terms, up to and
                  including any root term.  In GO, relations of the
                  type 'is_a' and 'part_of' are included, but not
                  'regulates' etc.

  Example       : my %chart =
                    %{ $ot_adaptor->fetch_ancestor_chart($term) };

  Return type   : A reference to a hash structure like this:

    {
      'GO:XXXXXXX' => {
        'term' =>           # ref to Bio::EnsEMBL::OntologyTerm object
        'is_a'    => [...], # listref of Bio::EnsEMBL::OntologyTerm
        'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
      },
      'GO:YYYYYYY' => {
        # Similarly for all ancestors,
        # and including the query term itself.
      }
    }