prototype Sequence_collection

Sequence_collection.ace

////////////////////////////////////////////////////////////////////
// Sequence_collection class
//      describes an assembly
//      holds information describing the sequences in this collection
////////////////////////////////////////////////////////////////////

?Sequence_collection      Title ?Text
   Origin     Name Text // name that the author gave it
              Other_name ?Text //If we like this over the DB_info option?
              Species UNIQUE ?Species
              Strain UNIQUE ?Strain
	      Laboratory ?Laboratory
              Evidence #Evidence
              DB_info Database ?Database ?Database_field ?Accession_number
   History    Releases ?Text //a list of releases this assembly is used in
              First_WS_release Int // first release this assembly was used // poss redundant
              Latest_WS_release Int // latest release where it was used // poss redundant
	      Supercedes    UNIQUE ?Sequence_collection XREF Superceded_by
	      Superceded_by UNIQUE ?Sequence_collection XREF Supercedes
   Remark ?Text #Evidence
   Confidential_remark ?Text
   Status UNIQUE Live #Evidence
                 Dead #Evidence
                 Suppressed #Evidence
   Sequences Chromosome_prefix UNIQUE Text // copied from Species.pm
             Chromosome_names Text
	     Chromosome ?Sequence
	     Mitochondrion_name UNIQUE Text
	     Mitochondrion ?Sequence
	     Pep_prefix UNIQUE Text
	     Pepdir_prefix UNIQUE Text
	     CDS_regex UNIQUE Text
	     Seq_name_regex UNIQUE Text
	     CDS_regex_noend UNIQUE Text
	     Wormpep_prefix UNIQUE Text
	     Assembly_type UNIQUE chromosome
				  contig
	     Seq_db UNIQUE Text
	     Wormpep_files Text
	     Upload_db_name Text


//////////////////////////////////////////////////////////////////////
// Added Full_name, Short_name, G_species to ?Species
//////////////////////////////////////////////////////////////////////

?Species Common_name ?Text // e.g. "root knot nematode"
         Other_name  ?Text // e.g. PB2861
         NCBITaxonomyID UNIQUE Int
	 Full_name UNIQUE Text    // e.g. 'Caenorhabditis elegans'
	 Short_name UNIQUE Text   // e.g. 'C. elegans'
	 G_species UNIQUE Text    // e.g. 'c_elegans'
	 Phylogeny Kingdom UNIQUE Text
                   Phylum UNIQUE Text
                   Subphylum UNIQUE Text
                   Class UNIQUE Text
                   Order UNIQUE Text
                   Family UNIQUE Text
                   Genus UNIQUE Text