WS230 Models.wrm

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Models Tagged for WS230

This cycle we see introduction of models to supplement the new gff3 dumping functionality being added to the acedb code.

Model Changes

Old

?SO_term Term ?Text

New

?SO_term SO_name ?Text
         SO_definition ?Text
         SO_synonym ?Text
         SO_version ?Text

New

  Sequence_alteration

Old

  Sequence_variant
  Synonym ?Text
  Definition ?Text



New

                Derived_from ?SO_term XREF Derives
                Member_of ?SO_term XREF Member

Old

                Derived_from ?SO_term XREF Derived

New

               Derives ?SO_term XREF Derived_from
               Member ?SO_term XREF Member_of

Old

               Derived ?SO_term XREF Derived_from
         Attributes_of Feature ?Feature XREF SO_term



Ace2SO class: gives a mapping from Acedb objects to their SO terms.

SO_subpart_tags - Tag pointing to subpart of this object, e.g. "Source_exon".

SO_parent_obj_tag - Tag pointing to semantic parent of this object, e.g. "Gene"

SO_children - this object has child objects which refer to it.

?Ace2SO Description UNIQUE Text
        SO_subparts Exons UNIQUE ?SO_Term
                    Introns UNIQUE ?SO_term
                    Coding_region UNIQUE ?SO_term
        No_span
        SO_parent_obj_tag UNIQUE Text
        SO_children


---

         Version SOFA_ontology   UNIQUE Float  // Analogous to GO, the SO version number is only to be attached
                 SOFA_definition UNIQUE Float  // to three parent SOFA terms under Located_sequence_feature



New

          Oligo ?Oligo XREF In_sequence Int UNIQUE Int ?Method 

Old

          Oligo ?Oligo XREF In_sequence Int UNIQUE Int  // for OSP and human mapping mostly

New

            Match_string UNIQUE RefFwd_HitFwd UNIQUE Text
                                RefFwd_HitRev UNIQUE Text
                                RefRev_HitFwd UNIQUE Text
                                RefRev_HitRev UNIQUE Text
            Align_id Text
            Target_species UNIQUE ?Species
            EMBL_dump UNIQUE EMBL_dump_YES
                             EMBL_dump_NO
                      // overrides for embl dump based on method
            EMBL_qualifier Text// additional to those in the method, includes '/'

Old

          Target_species UNIQUE ?Species
          EMBL_dump UNIQUE EMBL_dump_YES
                           EMBL_dump_NO
                      // overrides for embl dump based on method
          EMBL_qualifier Text
                      // additional to those in the method, includes '/'

New

                  SO_term ?SO_term

Old

                  SO_term ?SO_term XREF Feature



Addition

              GFF_SO UNIQUE ?SO_term UNIQUE ?Ace2SO