WS230 Models.wrm

From WormBaseWiki
Jump to navigationJump to search

Back

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