# Generated by asn2opm Retrofitting Tool V1.0 # Fri Apr 12 10:15:11 1996 SCHEMA NCBI PROPERTIES: "OPM_cluster" "NCBI_Access Link_set", "OPM_cluster" "NCBI_Biblio Cit_art Cit_art_from Cit_jour Cit_book Cit_pat Cit_let Id_pat Id_pat_id Cit_gen Cit_proc Cit_sub Title Patent_priority Affil Affil_std Meeting Cit_let_type Author Auth_list Auth_list_names Imprint CitRetract Cit_sub_medium Author_level Author_role Imprint_prepub CitRetract_type", "OPM_cluster" "NCBI_FeatDef FeatDef FeatDispGroup FeatMolType FeatDefGroupSet", "OPM_cluster" "NCBI_General Date Date_std Person_id Object_id Dbtag Name_std Int_fuzz Int_fuzz_lim Int_fuzz_range User_object User_field User_field_data", "OPM_cluster" "NCBI_Medline Medline_entry Medline_mesh Medline_qual Medline_rn Medline_si Medline_rn_type Medline_si_type", "OPM_cluster" "NCBI_ObjPrt PrintTemplate TemplateName PrintFormat PrintForm UserFormat PrintFormBlock PrintFormBoolean PrintFormEnum PrintFormText", "OPM_cluster" "NCBI_Pub Pub Pub_set", "OPM_cluster" "NCBI_Sequence Bioseq Seq_annot Pubdesc Pubdesc_reftype Seqdesc Heterogen MolInfo_cluster GIBB_cluster Numbering_cluster Seq_cluster CODE_cluster Annot_cluster", "OPM_cluster" "MolInfo_cluster MolInfo MolInfo_biomol MolInfo_tech MolInfo_completeness", "OPM_cluster" "GIBB_cluster GIBB_mol GIBB_mod GIBB_method", "OPM_cluster" "Numbering_cluster Numbering Num_cont Num_enum Num_ref Num_real Num_ref_type", "OPM_cluster" "Seq_cluster Seq_inst Seq_inst_repr Seq_inst_mol Seq_inst_topology Seq_inst_strand Seq_ext Delta_seq Seq_literal Seq_hist Seq_hist_rec Seq_hist_deleted Seq_data", "OPM_cluster" "CODE_cluster IUPACna IUPACaa NCBI2na NCBI4na NCBI8na NCBIpna NCBI8aa NCBIeaa NCBIpaa NCBIstdaa", "OPM_cluster" "Annot_cluster Annot_id Annotdesc Align_def Align_def_align_type Seq_annot Seq_annot_data Seq_annot_db", "OPM_cluster" "NCBI_seqalign Seq_align Seq_align_segs Seq_align_type Dense_diag Dense_seg Packed_seg Std_seg Score Score_value", "OPM_cluster" "EMBL_General EMBL_dbname EMBL_dbname_code EMBL_xref EMBL_block EMBL_block_class EMBL_block_div", "OPM_cluster" "SP_General SP_block SP_block_class", "OPM_cluster" "PIR_General PIR_block", "OPM_cluster" "GenBank_General GB_block", "OPM_cluster" "PRF_General PRF_block PRF_ExtraSrc", "OPM_cluster" "PDB_General PDB_block PDB_replace", "OPM_cluster" "NCBI_SeqCode Seq_code_type Seq_map_table Seq_code_table Seq_code_table_table Seq_code_set", "OPM_cluster" "NCBI_Seqfeat Feat_id Seq_feat Seq_feat_exp_ev SeqFeatData SeqFeatData_bond SeqFeatData_site SeqFeatData_psec_str SeqFeatXref Cdregion Cdregion_frame Genetic_code Code_break Code_break_aa Imp_feat Gb_qual", "OPM_cluster" "NCBI_Rsite Rsite_ref", "OPM_cluster" "NCBI_RNA RNA_ref RNA_ref_ext RNA_ref_type Trna_ext Trna_ext_aa", "OPM_cluster" "NCBI_Gene Gene_ref", "OPM_cluster" "NCBI_Organism Org_ref OrgName OrgName_name OrgMod OrgMod_subtype BinomialOrgName TaxElement TaxElement_fixed_level", "OPM_cluster" "NCBI_BioSource BioSource BioSource_genome BioSource_origin SubSource SubSource_subtype", "OPM_cluster" "NCBI_Protein Prot_ref Prot_ref_processed", "OPM_cluster" "NCBI_TxInit Txinit Txinit_txsystem Txinit_inittype Tx_evidence Tx_evidence_exp_code Tx_evidence_expression_system", "OPM_cluster" "NCBI_Seqloc Seq_id Patent_seq_id Textseq_id Giimport_id PDB_seq_id PDB_mol_id Seq_loc Seq_interval Seq_point Packed_seqpnt Na_strand Seq_bond", "OPM_cluster" "NCBI_Seqres Seq_graph Seq_graph_graph Real_graph Int_graph Byte_graph", "OPM_cluster" "NCBI_Seqset Bioseq_set Bioseq_set_class Seq_entry", "OPM_cluster" "NCBI_Submit Seq_submit Seq_submit_data Submit_block Submit_block_subtype Contact_info" NAMED PRIMITIVE VALUE CLASS TemplateName: TEXT NAMED PRIMITIVE VALUE CLASS Heterogen: TEXT NAMED PRIMITIVE VALUE CLASS IUPACna: TEXT NAMED PRIMITIVE VALUE CLASS IUPACaa: TEXT NAMED PRIMITIVE VALUE CLASS NCBI2na: TEXT NAMED PRIMITIVE VALUE CLASS NCBI4na: TEXT NAMED PRIMITIVE VALUE CLASS NCBI8na: TEXT NAMED PRIMITIVE VALUE CLASS NCBIpna: TEXT NAMED PRIMITIVE VALUE CLASS NCBI8aa: TEXT NAMED PRIMITIVE VALUE CLASS NCBIeaa: TEXT NAMED PRIMITIVE VALUE CLASS NCBIpaa: TEXT NAMED PRIMITIVE VALUE CLASS NCBIstdaa: TEXT NAMED PRIMITIVE VALUE CLASS PDB_mol_id: TEXT CONTROLLED VALUE CLASS Cit_let_type { ( "manuscript", 1 ), ( "letter", 2 ), ( "thesis", 3 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Cit_sub_medium { ( "paper", 1 ), ( "tape", 2 ), ( "floppy", 3 ), ( "email", 4 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Author_level { ( "primary", 1 ), ( "secondary", 2 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Author_role { ( "compiler", 1 ), ( "editor", 2 ), ( "patent-assignee", 3 ), ( "translator", 4 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Imprint_prepub { ( "submitted", 1, "submitted, not accepted" ), ( "in-press", 2, "accepted, not published" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS CitRetract_type { ( "retracted", 1, "this citation retracted" ), ( "notice", 2, "this citation is a retraction notice" ), ( "in-error", 3, "an erratum was published about this" ), ( "erratum", 4 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS FeatMolType { ( "aa", 1, "proteins" ), ( "na", 2, "nucleic acids" ), ( "both", 3, "both" ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Int_fuzz_lim { ( "unk", 0, "unknown" ), ( "gt", 1, "greater than" ), ( "lt", 2, "less than" ), ( "tr", 3, "space to right of position" ), ( "tl", 4, "space to left of position" ), ( "circle", 5, "artificial break at origin of circle" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Medline_rn_type { ( "nameonly", 0 ), ( "cas", 1, "CAS number" ), ( "ec", 2 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Medline_si_type { ( "ddbj", 1, "DNA Data Bank of Japan" ), ( "carbbank", 2, "Carbohydrate Structure Database" ), ( "embl", 3, "EMBL Data Library" ), ( "hdb", 4, "Hybridoma Data Bank" ), ( "genbank", 5, "GenBank" ), ( "hgml", 6, "Human Gene Map Library" ), ( "mim", 7, "Mendelian Inheritance in Man" ), ( "msd", 8, "Microbial Strains Database" ), ( "pdb", 9, "Protein Data Bank (Brookhaven)" ), ( "pir", 10, "Protein Identification Resource" ), ( "prfseqdb", 11, "Protein Research Foundation (Japan)" ), ( "psd", 12, "Protein Sequence Database (Japan)" ), ( "swissprot", 13 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS MolInfo_biomol { ( "unknown", 0 ), ( "genomic", 1 ), ( "pre-RNA", 2, "precursor RNA of any sort really " ), ( "mRNA", 3 ), ( "rRNA", 4 ), ( "tRNA", 5 ), ( "snRNA", 6 ), ( "scRNA", 7 ), ( "peptide", 8 ), ( "other-genetic", 9, "other genetic material" ), ( "genomic-mRNA", 10, "reported a mix of genomic and cdna sequence" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS MolInfo_tech { ( "unknown", 0 ), ( "standard", 1, "standard sequencing" ), ( "est", 2, "Expressed Sequence Tag" ), ( "sts", 3, "Sequence Tagged Site" ), ( "survey", 4, "one-pass genomic sequence" ), ( "genemap", 5, "from genetic mapping techniques" ), ( "physmap", 6, "from physical mapping techniques" ), ( "derived", 7, "derived from other data, not a primary entity" ), ( "concept-trans", 8, "conceptual translation" ), ( "seq-pept", 9, "peptide was sequenced" ), ( "both", 10, "concept transl. w/ partial pept. seq." ), ( "seq-pept-overlap", 11, "sequenced peptide, ordered by overlap" ), ( "seq-pept-homol", 12, "sequenced peptide, ordered by homology" ), ( "concept-trans-a", 13, "conceptual transl. supplied by author" ), ( "other", 255, "use Source.techexp" ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS MolInfo_completeness { ( "unknown", 0 ), ( "complete", 1, "complete biological entity" ), ( "partial", 2, "partial but no details given" ), ( "no-left", 3, "missing 5' or NH3 end" ), ( "no-right", 4, "missing 3' or COOH end" ), ( "no-ends", 5, "missing both ends" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS GIBB_mol { ( "unknown", 0 ), ( "genomic", 1 ), ( "pre-mRNA", 2, "precursor RNA of any sort really " ), ( "mRNA", 3 ), ( "rRNA", 4 ), ( "tRNA", 5 ), ( "snRNA", 6 ), ( "scRNA", 7 ), ( "peptide", 8 ), ( "other-genetic", 9, "other genetic material" ), ( "genomic-mRNA", 10, "reported a mix of genomic and cdna sequence" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS GIBB_mod { ( "dna", 0 ), ( "rna", 1 ), ( "extrachrom", 2 ), ( "plasmid", 3 ), ( "mitochondrial", 4 ), ( "chloroplast", 5 ), ( "kinetoplast", 6 ), ( "cyanelle", 7 ), ( "synthetic", 8 ), ( "recombinant", 9 ), ( "partial", 10 ), ( "complete", 11 ), ( "mutagen", 12, "subject of mutagenesis ?" ), ( "natmut", 13, "natural mutant ?" ), ( "transposon", 14 ), ( "insertion-seq", 15 ), ( "no-left", 16, "missing left end (5' for na, NH2 for aa)" ), ( "no-right", 17, "missing right end (3' or COOH)" ), ( "macronuclear", 18 ), ( "proviral", 19 ), ( "est", 20, "expressed sequence tag" ), ( "sts", 21, "sequence tagged site" ), ( "survey", 22, "one pass survey sequence" ), ( "chromoplast", 23 ), ( "genemap", 24, "is a genetic map" ), ( "restmap", 25, "is an ordered restriction map" ), ( "physmap", 26, "is a physical map (not ordered restriction map)" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS GIBB_method { ( "concept-trans", 1, "conceptual translation" ), ( "seq-pept", 2, "peptide was sequenced" ), ( "both", 3, "concept transl. w/ partial pept. seq." ), ( "seq-pept-overlap", 4, "sequenced peptide, ordered by overlap" ), ( "seq-pept-homol", 5, "sequenced peptide, ordered by homology" ), ( "concept-trans-a", 6, "conceptual transl. supplied by author" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Num_ref_type { ( "not-set", 0 ), ( "sources", 1, "by segmented or const seq sources" ), ( "aligns", 2 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Pubdesc_reftype { ( "seq", 0, "refers to sequence" ), ( "sites", 1, "refers to unspecified features" ), ( "feats", 2 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_inst_repr { ( "not-set", 0, "empty" ), ( "virtual", 1, "no seq data" ), ( "raw", 2, "continuous sequence" ), ( "seg", 3, "segmented sequence" ), ( "const", 4, "constructed sequence" ), ( "ref", 5, "reference to another sequence" ), ( "consen", 6, "consensus sequence or pattern" ), ( "map", 7, "ordered map of any kind" ), ( "delta", 8, "sequence made by changes (delta) to others" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_inst_mol { ( "not-set", 0, "> cdna = rna" ), ( "dna", 1 ), ( "rna", 2 ), ( "aa", 3 ), ( "na", 4, "just a nucleic acid" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_inst_topology { ( "not-set", 0 ), ( "linear", 1 ), ( "circular", 2 ), ( "tandem", 3, "some part of tandem repeat" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_inst_strand { ( "not-set", 0 ), ( "ss", 1, "single strand" ), ( "ds", 2, "double strand" ), ( "mixed", 3 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Align_def_align_type { ( "ref", 1, "set of alignments to the same sequence" ), ( "alt", 2, "set of alternate alignments of the same seqs" ), ( "blocks", 3, "set of aligned blocks in the same seqs" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_annot_db { ( "genbank", 1 ), ( "embl", 2 ), ( "ddbj", 3 ), ( "pir", 4 ), ( "sp", 5 ), ( "bbone", 6 ), ( "pdb", 7 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_align_type { ( "not-set", 0 ), ( "global", 1 ), ( "diags", 2, "unbroken, but not ordered, diagonals" ), ( "partial", 3, "mapping pieces together" ), ( "disc", 4, "discontinuous alignment" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS EMBL_dbname_code { ( "embl", 0 ), ( "genbank", 1 ), ( "ddbj", 2 ), ( "geninfo", 3 ), ( "medline", 4 ), ( "swissprot", 5 ), ( "pir", 6 ), ( "pdb", 7 ), ( "epd", 8 ), ( "ecd", 9 ), ( "tfd", 10 ), ( "flybase", 11 ), ( "prosite", 12 ), ( "enzyme", 13 ), ( "mim", 14 ), ( "ecoseq", 15 ), ( "hiv", 16 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS EMBL_block_class { ( "not-set", 0 ), ( "standard", 1 ), ( "unannotated", 2 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS EMBL_block_div { ( "fun", 0 ), ( "inv", 1 ), ( "mam", 2 ), ( "org", 3 ), ( "phg", 4 ), ( "pln", 5 ), ( "pri", 6 ), ( "pro", 7 ), ( "rod", 8 ), ( "syn", 9 ), ( "una", 10 ), ( "vrl", 11 ), ( "vrt", 12 ), ( "pat", 13 ), ( "est", 14 ), ( "sts", 15 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS SP_block_class { ( "not-set", 0 ), ( "standard", 1, "conforms to all SWISSPROT checks" ), ( "prelim", 2, "only seq and biblio checked" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_code_type { ( "iupacna", 1, "IUPAC 1 letter nuc acid code" ), ( "iupacaa", 2, "IUPAC 1 letter amino acid code" ), ( "ncbi2na", 3, "2 bit nucleic acid code" ), ( "ncbi4na", 4, "4 bit nucleic acid code" ), ( "ncbi8na", 5, "8 bit extended nucleic acid code" ), ( "ncbipna", 6, "nucleic acid probabilities" ), ( "ncbi8aa", 7, "8 bit extended amino acid codes" ), ( "ncbieaa", 8, "extended ASCII 1 letter aa codes" ), ( "ncbipaa", 9, "amino acid probabilities" ), ( "iupacaa3", 10, "3 letter code only for display" ), ( "ncbistdaa", 11, "consecutive codes for std aas, 0-25" ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Seq_feat_exp_ev { ( "experimental", 1, "any reasonable experimental check" ), ( "not-experimental", 2 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS SeqFeatData_bond { ( "disulfide", 1 ), ( "thiolester", 2 ), ( "xlink", 3 ), ( "thioether", 4 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS SeqFeatData_site { ( "active", 1 ), ( "binding", 2 ), ( "cleavage", 3 ), ( "inhibit", 4 ), ( "modified", 5 ), ( "glycosylation", 6 ), ( "myristoylation", 7 ), ( "mutagenized", 8 ), ( "metal-binding", 9 ), ( "phosphorylation", 10 ), ( "acetylation", 11 ), ( "amidation", 12 ), ( "methylation", 13 ), ( "hydroxylation", 14 ), ( "sulfatation", 15 ), ( "oxidative-deamination", 16 ), ( "pyrrolidone-carboxylic-acid", 17 ), ( "gamma-carboxyglutamic-acid", 18 ), ( "blocked", 19 ), ( "lipid-binding", 20 ), ( "np-binding", 21 ), ( "dna-binding", 22 ), ( "signal-peptide", 23 ), ( "transit-peptide", 24 ), ( "transmembrane-region", 25 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS SeqFeatData_psec_str { ( "helix", 1, "any helix" ), ( "sheet", 2, "beta sheet" ), ( "turn", 3 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Cdregion_frame { ( "not-set", 0, "not set, code uses one" ), ( "one", 1 ), ( "two", 2 ), ( "three", 3 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS RNA_ref_type { ( "unknown", 0 ), ( "premsg", 1 ), ( "mRNA", 2 ), ( "tRNA", 3 ), ( "rRNA", 4 ), ( "snRNA", 5 ), ( "scRNA", 6 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS OrgMod_subtype { ( "strain", 2 ), ( "substrain", 3 ), ( "type", 4 ), ( "subtype", 5 ), ( "variety", 6 ), ( "serotype", 7 ), ( "serogroup", 8 ), ( "serovar", 9 ), ( "cultivar", 10 ), ( "pathovar", 11 ), ( "chemovar", 12 ), ( "biovar", 13 ), ( "biotype", 14 ), ( "group", 15 ), ( "subgroup", 16 ), ( "isolate", 17 ), ( "common", 18 ), ( "acronym", 19 ), ( "dosage", 20, "chromosome dosage of hybrid" ), ( "nat-host", 21, "natural host of this specimen" ), ( "sub-species", 22 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS TaxElement_fixed_level { ( "other", 0, "level must be set in string" ), ( "family", 1 ), ( "order", 2 ), ( "class", 3 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS BioSource_genome { ( "unknown", 0 ), ( "genomic", 1 ), ( "chloroplast", 2 ), ( "chromoplast", 3 ), ( "kinetoplast", 4 ), ( "mitochondrion", 5 ), ( "plastid", 6 ), ( "macronuclear", 7 ), ( "extrachrom", 8 ), ( "plasmid", 9 ), ( "transposon", 10 ), ( "insertion-seq", 11 ), ( "cyanelle", 12 ), ( "proviral", 13 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS BioSource_origin { ( "unknown", 0 ), ( "natural", 1, "normal biological entity" ), ( "natmut", 2, "naturally occuring mutant" ), ( "mut", 3, "artificially mutagenized" ), ( "artificial", 4, "artificially engineered" ), ( "synthetic", 5, "purely synthetic" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS SubSource_subtype { ( "chromosome", 1 ), ( "map", 2 ), ( "clone", 3 ), ( "subclone", 4 ), ( "haplotype", 5 ), ( "genotype", 6 ), ( "sex", 7 ), ( "cell-line", 8 ), ( "cell-type", 9 ), ( "tissue-type", 10 ), ( "clone-lib", 11 ), ( "dev-stage", 12 ), ( "frequency", 13 ), ( "germline", 14 ), ( "rearranged", 15 ), ( "lab-host", 16 ), ( "pop-variant", 17 ), ( "tissue-lib", 18 ), ( "plasmid-name", 19 ), ( "transposon-name", 20 ), ( "insertion-seq-name", 21 ), ( "plastid-name", 22 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Prot_ref_processed { ( "not-set", 0 ), ( "preprotein", 1 ), ( "mature", 2 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Txinit_txsystem { ( "unknown", 0 ), ( "pol1", 1, "eukaryotic Pol I" ), ( "pol2", 2, "eukaryotic Pol II" ), ( "pol3", 3, "eukaryotic Pol III" ), ( "bacterial", 4 ), ( "viral", 5 ), ( "rna", 6, "RNA replicase" ), ( "organelle", 7 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Txinit_inittype { ( "unknown", 0 ), ( "single", 1 ), ( "multiple", 2 ), ( "region", 3 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Tx_evidence_exp_code { ( "unknown", 0 ), ( "rna-seq", 1, "direct RNA sequencing" ), ( "rna-size", 2, "RNA length measurement" ), ( "np-map", 3, "nuclease protection mapping with homologous sequence ladder" ), ( "np-size", 4, "nuclease protected fragment length measurement" ), ( "pe-seq", 5, "dideoxy RNA sequencing " ), ( "cDNA-seq", 6, "full-length cDNA sequencing" ), ( "pe-map", 7, "primer extension mapping with homologous sequence ladder " ), ( "pe-size", 8, "primer extension product length measurement" ), ( "pseudo-seq", 9, "full-length processed pseudogene sequencing" ), ( "rev-pe-map", 10, "see NOTE (1) below" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Tx_evidence_expression_system { ( "unknown", 0 ), ( "physiological", 1 ), ( "in-vitro", 2 ), ( "oocyte", 3 ), ( "transfection", 4 ), ( "transgenic", 5 ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Na_strand { ( "unknown", 0 ), ( "plus", 1 ), ( "minus", 2 ), ( "both", 3, "in forward orientation" ), ( "both-rev", 4, "in reverse orientation" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Bioseq_set_class { ( "not-set", 0 ), ( "nuc-prot", 1, "nuc acid and coded proteins" ), ( "segset", 2, "segmented sequence + parts" ), ( "conset", 3, "constructed sequence + parts" ), ( "parts", 4, "parts for 2 or 3" ), ( "gibb", 5, "geninfo backbone" ), ( "gi", 6, "geninfo" ), ( "genbank", 7, "converted genbank" ), ( "pir", 8, "converted pir" ), ( "pub-set", 9, "all the seqs from a single publication" ), ( "equiv", 10, "a set of equivalent maps or seqs" ), ( "swissprot", 11, "converted SWISSPROT" ), ( "pdb-entry", 12, "a complete PDB entry" ), ( "mut-set", 13, "set of mutations" ), ( "pop-set", 14, "population study" ), ( "phy-set", 15, "phylogenetic study" ), ( "other", 255 ) } CODE_TYPE: INTEGER CONTROLLED VALUE CLASS Submit_block_subtype { ( "new", 1, "new data" ), ( "update", 2, "update by author" ), ( "revision", 3, "3rd party (non-author) update" ), ( "other", 255 ) } CODE_TYPE: INTEGER OBJECT CLASS Link_set ATTRIBUTE num: [1,1] INTEGER DESCRIPTION: "number of links to this doc type" ATTRIBUTE uids: list-of [0,] INTEGER DESCRIPTION: "the links" ATTRIBUTE weights: list-of [0,] INTEGER DESCRIPTION: "the weights" OBJECT CLASS Cit_art DESCRIPTION: "article in journal or book" ATTRIBUTE title: [0,1] Title DESCRIPTION: "title of paper (ANSI requires)" ATTRIBUTE authors: [0,1] Auth_list DESCRIPTION: "authors (ANSI requires)" ATTRIBUTE from: [1,1] Cit_art_from OBJECT CLASS Cit_art_from DESCRIPTION: "journal or book" ATTRIBUTE journal: [0,1] Cit_jour ATTRIBUTE book: [0,1] Cit_book ATTRIBUTE proc: [0,1] Cit_proc OBJECT CLASS Cit_jour DESCRIPTION: "Journal citation" ATTRIBUTE title: [1,1] Title DESCRIPTION: "title of journal" ATTRIBUTE imp: [1,1] Imprint OBJECT CLASS Cit_book DESCRIPTION: "Book citation" ATTRIBUTE title: [1,1] Title DESCRIPTION: "Title of book" ATTRIBUTE coll: [0,1] Title DESCRIPTION: "part of a collection" ATTRIBUTE authors: [1,1] Auth_list DESCRIPTION: "authors" ATTRIBUTE imp: [1,1] Imprint OBJECT CLASS Cit_proc DESCRIPTION: "Meeting proceedings" ATTRIBUTE book: [1,1] Cit_book DESCRIPTION: "citation to meeting" ATTRIBUTE meet: [1,1] Meeting DESCRIPTION: "time and location of meeting" OBJECT CLASS Cit_pat DESCRIPTION: "patent citation" ATTRIBUTE title: [1,1] TEXT ATTRIBUTE authors: [1,1] Auth_list DESCRIPTION: "author/inventor" ATTRIBUTE country: [1,1] TEXT DESCRIPTION: "Patent Document Country" ATTRIBUTE doc_type: [1,1] TEXT DESCRIPTION: "Patent Document Type" ATTRIBUTE number: [1,1] TEXT DESCRIPTION: "Patent Document Number" ATTRIBUTE date_issue: [1,1] Date DESCRIPTION: "Patent Issue/Pub Date" ATTRIBUTE class: list-of [0,] TEXT DESCRIPTION: "Patent Doc Class Code " ATTRIBUTE app_number: [0,1] TEXT DESCRIPTION: "Patent Doc Appl Number" ATTRIBUTE app_date: [0,1] Date DESCRIPTION: "Patent Appl File Date" ATTRIBUTE applicants: [0,1] Auth_list DESCRIPTION: "Applicants" ATTRIBUTE assignees: [0,1] Auth_list DESCRIPTION: "Assignees" ATTRIBUTE priority: list-of [0,] Patent_priority DESCRIPTION: "Priorities" ATTRIBUTE abstract: [0,1] TEXT DESCRIPTION: "abstract of patent" OBJECT CLASS Patent_priority ATTRIBUTE country: [1,1] TEXT DESCRIPTION: "Patent country code" ATTRIBUTE number: [1,1] TEXT DESCRIPTION: "number assigned in that country" ATTRIBUTE date: [1,1] Date DESCRIPTION: "date of application" OBJECT CLASS Id_pat DESCRIPTION: "just to identify a patent" ATTRIBUTE country: [1,1] TEXT DESCRIPTION: "Patent Document Country" ATTRIBUTE id: [1,1] Id_pat_id DESCRIPTION: "Patent Doc Appl Number" ATTRIBUTE doc_type: [0,1] TEXT DESCRIPTION: "Patent Doc Type" OBJECT CLASS Id_pat_id ATTRIBUTE number: [0,1] TEXT DESCRIPTION: "Patent Document Number" ATTRIBUTE app_number: [0,1] TEXT OBJECT CLASS Cit_let DESCRIPTION: "letter, thesis, or manuscript" ATTRIBUTE cit: [1,1] Cit_book DESCRIPTION: "same fields as a book" ATTRIBUTE man_id: [0,1] TEXT DESCRIPTION: "Manuscript identifier" ATTRIBUTE type: [0,1] Cit_let_type DESCRIPTION: "NOTE: this is just to cite a" OBJECT CLASS Cit_sub DESCRIPTION: "citation for a direct submission" ATTRIBUTE authors: [1,1] Auth_list DESCRIPTION: "not necessarily authors of the paper" ATTRIBUTE imp: [0,1] Imprint DESCRIPTION: "this only used to get date.. will go" ATTRIBUTE medium: [0,1] Cit_sub_medium ATTRIBUTE date: [0,1] Date DESCRIPTION: "replaces imp, will become required" ATTRIBUTE descr: [0,1] TEXT DESCRIPTION: "description of changes for public view" OBJECT CLASS Cit_gen DESCRIPTION: "NOT from ANSI, this is a catchall" ATTRIBUTE cit: [0,1] TEXT DESCRIPTION: "anything, not parsable" ATTRIBUTE authors: [0,1] Auth_list ATTRIBUTE muid: [0,1] INTEGER DESCRIPTION: "medline uid" ATTRIBUTE journal: [0,1] Title ATTRIBUTE volume: [0,1] TEXT ATTRIBUTE issue: [0,1] TEXT ATTRIBUTE pages: [0,1] TEXT ATTRIBUTE date: [0,1] Date ATTRIBUTE serial_number: [0,1] INTEGER DESCRIPTION: "for GenBank style references" ATTRIBUTE title: [0,1] TEXT DESCRIPTION: "eg. cit='unpublished',title='title'" OBJECT CLASS Auth_list ATTRIBUTE names: [1,1] Auth_list_names DESCRIPTION: "free for all" ATTRIBUTE affil: [0,1] Affil DESCRIPTION: "author affiliation" OBJECT CLASS Auth_list_names ATTRIBUTE std: list-of [0,] Author DESCRIPTION: "full citations" ATTRIBUTE ml: list-of [0,] TEXT DESCRIPTION: "MEDLINE, semi-structured" ATTRIBUTE str: list-of [0,] TEXT OBJECT CLASS Author ATTRIBUTE name: [1,1] Person_id DESCRIPTION: "Author, Primary or Secondary" ATTRIBUTE level: [0,1] Author_level ATTRIBUTE role: [0,1] Author_role ATTRIBUTE affil: [0,1] Affil ATTRIBUTE is_corr: [0,1] BOOLEAN DESCRIPTION: "TRUE if corressponding author" OBJECT CLASS Affil ATTRIBUTE str: [0,1] TEXT DESCRIPTION: "unparsed string" ATTRIBUTE std: [0,1] Affil_std DESCRIPTION: "Title Group" OBJECT CLASS Affil_std DESCRIPTION: "std representation" ATTRIBUTE affil: [0,1] TEXT DESCRIPTION: "Author Affiliation, Name" ATTRIBUTE div: [0,1] TEXT DESCRIPTION: "Author Affiliation, Division" ATTRIBUTE city: [0,1] TEXT DESCRIPTION: "Author Affiliation, City" ATTRIBUTE sub: [0,1] TEXT DESCRIPTION: "Author Affiliation, County Sub" ATTRIBUTE country: [0,1] TEXT DESCRIPTION: "Author Affiliation, Country" ATTRIBUTE street: [0,1] TEXT DESCRIPTION: "street address, not ANSI" ATTRIBUTE email: [0,1] TEXT ATTRIBUTE fax: [0,1] TEXT ATTRIBUTE phone: [0,1] TEXT ATTRIBUTE postal_code: [0,1] TEXT OBJECT CLASS Title ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "Title, Anal,Coll,Mono AJB" ATTRIBUTE tsub: [0,1] TEXT DESCRIPTION: "Title, Subordinate A B" ATTRIBUTE trans: [0,1] TEXT DESCRIPTION: "Title, Translated AJB" ATTRIBUTE jta: [0,1] TEXT DESCRIPTION: "Title, Abbreviated J" ATTRIBUTE iso_jta: [0,1] TEXT DESCRIPTION: "specifically ISO jta J" ATTRIBUTE ml_jta: [0,1] TEXT DESCRIPTION: "specifically MEDLINE jta J" ATTRIBUTE coden: [0,1] TEXT DESCRIPTION: "a coden J" ATTRIBUTE issn: [0,1] TEXT DESCRIPTION: "ISSN J" ATTRIBUTE abr: [0,1] TEXT DESCRIPTION: "Title, Abbreviated B" ATTRIBUTE isbn: [0,1] TEXT DESCRIPTION: "ISBN B" OBJECT CLASS Imprint DESCRIPTION: "Imprint group" ATTRIBUTE date: [1,1] Date DESCRIPTION: "date of publication" ATTRIBUTE volume: [0,1] TEXT ATTRIBUTE issue: [0,1] TEXT ATTRIBUTE pages: [0,1] TEXT ATTRIBUTE section: [0,1] TEXT ATTRIBUTE pub: [0,1] Affil DESCRIPTION: "publisher, required for book" ATTRIBUTE cprt: [0,1] Date DESCRIPTION: "copyright date, ' ' '" ATTRIBUTE part_sup: [0,1] TEXT DESCRIPTION: "part/sup of volume" ATTRIBUTE language: [1,1] TEXT DESCRIPTION: "put here for simplicity" ATTRIBUTE prepub: [0,1] Imprint_prepub ATTRIBUTE part_supi: [0,1] TEXT DESCRIPTION: "part/sup on issue" ATTRIBUTE retract: [0,1] CitRetract DESCRIPTION: "retraction info" OBJECT CLASS CitRetract ATTRIBUTE type: [1,1] CitRetract_type DESCRIPTION: "this is a published erratum" ATTRIBUTE exp: [0,1] TEXT DESCRIPTION: "citation and/or explanation" OBJECT CLASS Meeting ATTRIBUTE number: [1,1] TEXT ATTRIBUTE date: [1,1] Date ATTRIBUTE place: [0,1] Affil OBJECT CLASS FeatDef ATTRIBUTE typelabel: [1,1] TEXT DESCRIPTION: "short label for type eg 'CDS'" ATTRIBUTE menulabel: [1,1] TEXT DESCRIPTION: "label for a menu eg 'Coding Region'" ATTRIBUTE featdef_key: [1,1] INTEGER DESCRIPTION: "unique for this feature definition" ATTRIBUTE seqfeat_key: [1,1] INTEGER DESCRIPTION: "SeqFeat.data.choice from objfeat.h" ATTRIBUTE entrygroup: [1,1] INTEGER DESCRIPTION: "Group for data entry" ATTRIBUTE displaygroup: [1,1] INTEGER DESCRIPTION: "Group for data display" ATTRIBUTE molgroup: [1,1] FeatMolType DESCRIPTION: "Type of Molecule used for" OBJECT CLASS FeatDispGroup ATTRIBUTE groupkey: [1,1] INTEGER ATTRIBUTE groupname: [1,1] TEXT OBJECT CLASS FeatDefGroupSet ATTRIBUTE groups: list-of [1,] FeatDispGroup ATTRIBUTE defs: list-of [1,] FeatDef OBJECT CLASS Date ATTRIBUTE str: [0,1] TEXT DESCRIPTION: "for those unparsed dates" ATTRIBUTE std: [0,1] Date_std DESCRIPTION: "use this if you can" OBJECT CLASS Date_std DESCRIPTION: "NOTE: this is NOT a unix tm struct" ATTRIBUTE year: [1,1] INTEGER DESCRIPTION: "full year (including 1900)" ATTRIBUTE month: [0,1] INTEGER DESCRIPTION: "month (1-12)" ATTRIBUTE day: [0,1] INTEGER DESCRIPTION: "day of month (1-31)" ATTRIBUTE season: [0,1] TEXT DESCRIPTION: "for 'spring', 'may-june', etc" OBJECT CLASS Dbtag ATTRIBUTE db: [1,1] TEXT DESCRIPTION: "name of database or system" ATTRIBUTE tag: [1,1] Object_id DESCRIPTION: "appropriate tag" OBJECT CLASS Object_id ATTRIBUTE id: [0,1] INTEGER ATTRIBUTE str: [0,1] TEXT DESCRIPTION: "Person-id is to define a std element for people" OBJECT CLASS Person_id ATTRIBUTE dbtag: [0,1] Dbtag DESCRIPTION: "any defined database tag" ATTRIBUTE name: [0,1] Name_std DESCRIPTION: "structured name" ATTRIBUTE ml: [0,1] TEXT DESCRIPTION: "MEDLINE name (semi-structured)" ATTRIBUTE str: [0,1] TEXT DESCRIPTION: "unstructured name" OBJECT CLASS Name_std DESCRIPTION: "Structured names" ATTRIBUTE last: [1,1] TEXT ATTRIBUTE first: [0,1] TEXT ATTRIBUTE middle: [0,1] TEXT ATTRIBUTE full: [0,1] TEXT DESCRIPTION: "full name eg. 'J. John Poop, Esq'" ATTRIBUTE initials: [0,1] TEXT DESCRIPTION: "first + middle initials" ATTRIBUTE suffix: [0,1] TEXT DESCRIPTION: "Jr, Sr, III" ATTRIBUTE title: [0,1] TEXT DESCRIPTION: "Dr., Sister, etc" OBJECT CLASS Int_fuzz ATTRIBUTE p_m: [0,1] INTEGER DESCRIPTION: "plus or minus fixed amount" ATTRIBUTE range: [0,1] Int_fuzz_range ATTRIBUTE pct: [0,1] INTEGER DESCRIPTION: "% plus or minus (x10) 0-1000" ATTRIBUTE lim: [0,1] Int_fuzz_lim DESCRIPTION: "something else" ATTRIBUTE alt: set-of [0,] INTEGER DESCRIPTION: "set of alternatives for the integer" OBJECT CLASS Int_fuzz_range DESCRIPTION: "max to min" ATTRIBUTE max: [1,1] INTEGER ATTRIBUTE min: [1,1] INTEGER OBJECT CLASS User_object ATTRIBUTE class: [0,1] TEXT DESCRIPTION: "endeavor which designed this object" ATTRIBUTE type: [1,1] Object_id DESCRIPTION: "type of object within class" ATTRIBUTE data: list-of [1,] User_field DESCRIPTION: "the object itself" OBJECT CLASS User_field ATTRIBUTE label: [1,1] Object_id DESCRIPTION: "field label" ATTRIBUTE num: [0,1] INTEGER DESCRIPTION: "required for strs, ints, reals, oss" ATTRIBUTE data: [1,1] User_field_data OBJECT CLASS User_field_data DESCRIPTION: "field contents" ATTRIBUTE str: [0,1] TEXT ATTRIBUTE int: [0,1] INTEGER ATTRIBUTE real: [0,1] REAL ATTRIBUTE bool: [0,1] BOOLEAN ATTRIBUTE os: [0,1] TEXT ATTRIBUTE object: [0,1] User_object DESCRIPTION: "for using other definitions" ATTRIBUTE strs: list-of [0,] TEXT ATTRIBUTE ints: list-of [0,] INTEGER ATTRIBUTE reals: list-of [0,] REAL ATTRIBUTE oss: list-of [0,] TEXT ATTRIBUTE fields: list-of [0,] User_field ATTRIBUTE objects: list-of [0,] User_object OBJECT CLASS Medline_entry ATTRIBUTE uid: [1,1] INTEGER DESCRIPTION: "MEDLINE UID" ATTRIBUTE em: [1,1] Date DESCRIPTION: "Entry Month" ATTRIBUTE cit: [1,1] Cit_art DESCRIPTION: "article citation" ATTRIBUTE abstract: [0,1] TEXT ATTRIBUTE mesh: set-of [0,] Medline_mesh ATTRIBUTE substance: set-of [0,] Medline_rn ATTRIBUTE xref: set-of [0,] Medline_si ATTRIBUTE idnum: set-of [0,] TEXT DESCRIPTION: "ID Number (grants, contracts)" ATTRIBUTE gene: set-of [0,] TEXT OBJECT CLASS Medline_mesh ATTRIBUTE mp: [1,1] BOOLEAN DESCRIPTION: "TRUE if main point (*)" ATTRIBUTE term: [1,1] TEXT DESCRIPTION: "the MeSH term" ATTRIBUTE qual: set-of [0,] Medline_qual DESCRIPTION: "qualifiers" OBJECT CLASS Medline_qual ATTRIBUTE mp: [1,1] BOOLEAN DESCRIPTION: "TRUE if main point" ATTRIBUTE subh: [1,1] TEXT DESCRIPTION: "the subheading" OBJECT CLASS Medline_rn DESCRIPTION: "medline substance records" ATTRIBUTE type: [1,1] Medline_rn_type DESCRIPTION: "EC number" ATTRIBUTE cit: [0,1] TEXT DESCRIPTION: "CAS or EC number if present" ATTRIBUTE name: [1,1] TEXT DESCRIPTION: "name (always present)" OBJECT CLASS Medline_si DESCRIPTION: "medline cross reference records" ATTRIBUTE type: [1,1] Medline_si_type DESCRIPTION: "SwissProt" ATTRIBUTE cit: [0,1] TEXT DESCRIPTION: "the citation/accession number" OBJECT CLASS PrintTemplate ATTRIBUTE name: [1,1] TemplateName DESCRIPTION: "name for this template" ATTRIBUTE labelfrom: [0,1] TEXT DESCRIPTION: "ASN.1 path to get label from" ATTRIBUTE format: [1,1] PrintFormat OBJECT CLASS PrintFormat ATTRIBUTE asn1: [1,1] TEXT DESCRIPTION: "ASN.1 partial path for this" ATTRIBUTE label: [0,1] TEXT DESCRIPTION: "printable label" ATTRIBUTE prefix: [0,1] TEXT ATTRIBUTE suffix: [0,1] TEXT ATTRIBUTE form: [1,1] PrintForm OBJECT CLASS PrintForm DESCRIPTION: "Forms for various ASN.1 components" ATTRIBUTE block: [0,1] PrintFormBlock ATTRIBUTE boolean: [0,1] PrintFormBoolean ATTRIBUTE enum: [0,1] PrintFormEnum ATTRIBUTE text: [0,1] PrintFormText ATTRIBUTE use_template: [0,1] TemplateName ATTRIBUTE user: [0,1] UserFormat ATTRIBUTE null: [0,1] VARCHAR(4) DESCRIPTION: "rarely used" OBJECT CLASS UserFormat ATTRIBUTE printfunc: [1,1] TEXT ATTRIBUTE defaultfunc: [0,1] TEXT OBJECT CLASS PrintFormBlock DESCRIPTION: "for SEQUENCE, SET" ATTRIBUTE separator: [0,1] TEXT ATTRIBUTE components: list-of [1,] PrintFormat OBJECT CLASS PrintFormBoolean ATTRIBUTE true: [0,1] TEXT ATTRIBUTE false: [0,1] TEXT OBJECT CLASS PrintFormEnum ATTRIBUTE values: list-of [0,] TEXT OBJECT CLASS PrintFormText ATTRIBUTE textfunc: [0,1] TEXT OBJECT CLASS Pub ATTRIBUTE gen: [0,1] Cit_gen DESCRIPTION: "general or generic unparsed" ATTRIBUTE sub: [0,1] Cit_sub DESCRIPTION: "submission" ATTRIBUTE medline: [0,1] Medline_entry ATTRIBUTE muid: [0,1] INTEGER DESCRIPTION: "medline uid" ATTRIBUTE article: [0,1] Cit_art ATTRIBUTE journal: [0,1] Cit_jour ATTRIBUTE book: [0,1] Cit_book ATTRIBUTE proc: [0,1] Cit_proc DESCRIPTION: "proceedings of a meeting" ATTRIBUTE patent: [0,1] Cit_pat ATTRIBUTE pat_id: [0,1] Id_pat DESCRIPTION: "identify a patent" ATTRIBUTE man: [0,1] Cit_let DESCRIPTION: "manuscript, thesis, or letter" ATTRIBUTE equiv: set-of [0,] Pub DESCRIPTION: "to cite a variety of ways" OBJECT CLASS Pub_set ATTRIBUTE pub: set-of [0,] Pub ATTRIBUTE medline: set-of [0,] Medline_entry ATTRIBUTE article: set-of [0,] Cit_art ATTRIBUTE journal: set-of [0,] Cit_jour ATTRIBUTE book: set-of [0,] Cit_book ATTRIBUTE proc: set-of [0,] Cit_proc DESCRIPTION: "proceedings of a meeting" ATTRIBUTE patent: set-of [0,] Cit_pat OBJECT CLASS Bioseq ATTRIBUTE id: set-of [1,] Seq_id DESCRIPTION: "equivalent identifiers" ATTRIBUTE descr: set-of [0,] Seqdesc DESCRIPTION: "descriptors" ATTRIBUTE inst: [1,1] Seq_inst DESCRIPTION: "the sequence data" ATTRIBUTE annot: set-of [0,] Seq_annot DESCRIPTION: "*** Descriptors *****************************" OBJECT CLASS Seqdesc ATTRIBUTE mol_type: [0,1] GIBB_mol DESCRIPTION: "type of molecule" ATTRIBUTE modif: set-of [0,] GIBB_mod DESCRIPTION: "modifiers" ATTRIBUTE method: [0,1] GIBB_method DESCRIPTION: "sequencing method" ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "a name for this sequence" ATTRIBUTE title: [0,1] TEXT DESCRIPTION: "a title for this sequence" ATTRIBUTE org: [0,1] Org_ref DESCRIPTION: "if all from one organism" ATTRIBUTE comment: [0,1] TEXT DESCRIPTION: "a more extensive comment" ATTRIBUTE num: [0,1] Numbering DESCRIPTION: "a numbering system" ATTRIBUTE maploc: [0,1] Dbtag DESCRIPTION: "map location of this sequence" ATTRIBUTE pir: [0,1] PIR_block DESCRIPTION: "PIR specific info" ATTRIBUTE genbank: [0,1] GB_block DESCRIPTION: "GenBank specific info" ATTRIBUTE pub: [0,1] Pubdesc DESCRIPTION: "a reference to the publication" ATTRIBUTE region: [0,1] TEXT DESCRIPTION: "overall region (globin locus)" ATTRIBUTE user: [0,1] User_object DESCRIPTION: "user defined object" ATTRIBUTE sp: [0,1] SP_block DESCRIPTION: "SWISSPROT specific info" ATTRIBUTE dbxref: [0,1] Dbtag DESCRIPTION: "xref to other databases" ATTRIBUTE embl: [0,1] EMBL_block DESCRIPTION: "EMBL specific information" ATTRIBUTE create_date: [0,1] Date DESCRIPTION: "date entry first created/released" ATTRIBUTE update_date: [0,1] Date DESCRIPTION: "date of last update" ATTRIBUTE prf: [0,1] PRF_block DESCRIPTION: "PRF specific information" ATTRIBUTE pdb: [0,1] PDB_block DESCRIPTION: "PDB specific information" ATTRIBUTE het: [0,1] Heterogen DESCRIPTION: "cofactor, etc associated but not bound" ATTRIBUTE source: [0,1] BioSource DESCRIPTION: "source of materials, includes Org-ref" ATTRIBUTE molinfo: [0,1] MolInfo DESCRIPTION: "info on the molecule and techniques" OBJECT CLASS MolInfo ATTRIBUTE biomol: [1,1] MolInfo_biomol ATTRIBUTE tech: [1,1] MolInfo_tech ATTRIBUTE techexp: [0,1] TEXT DESCRIPTION: "explanation if tech not enough" ATTRIBUTE completeness: [1,1] MolInfo_completeness OBJECT CLASS Numbering DESCRIPTION: "any display numbering system" ATTRIBUTE cont: [0,1] Num_cont DESCRIPTION: "continuous numbering" ATTRIBUTE enum: [0,1] Num_enum DESCRIPTION: "enumerated names for residues" ATTRIBUTE ref: [0,1] Num_ref DESCRIPTION: "by reference to another sequence" ATTRIBUTE real: [0,1] Num_real DESCRIPTION: "supports mapping to a float system" OBJECT CLASS Num_cont DESCRIPTION: "continuous display numbering system" ATTRIBUTE refnum: [1,1] INTEGER DESCRIPTION: "number assigned to first residue" ATTRIBUTE has_zero: [1,1] BOOLEAN DESCRIPTION: "0 used?" ATTRIBUTE ascending: [1,1] BOOLEAN DESCRIPTION: "ascending numbers?" OBJECT CLASS Num_enum DESCRIPTION: "any tags to residues" ATTRIBUTE num: [1,1] INTEGER DESCRIPTION: "number of tags to follow" ATTRIBUTE names: list-of [1,] TEXT DESCRIPTION: "the tags" OBJECT CLASS Num_ref DESCRIPTION: "by reference to other sequences" ATTRIBUTE type: [1,1] Num_ref_type DESCRIPTION: "by alignments given below" ATTRIBUTE aligns: [0,1] Seq_align OBJECT CLASS Num_real DESCRIPTION: "mapping to floating point system" ATTRIBUTE a: [1,1] REAL DESCRIPTION: "from an integer system used by Bioseq" ATTRIBUTE b: [1,1] REAL DESCRIPTION: "position = (a * int_position) + b" ATTRIBUTE units: [0,1] TEXT OBJECT CLASS Pubdesc DESCRIPTION: "how sequence presented in pub" ATTRIBUTE pub: set-of [1,] Pub DESCRIPTION: "the citation(s)" ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "name used in paper" ATTRIBUTE fig: [0,1] TEXT DESCRIPTION: "figure in paper" ATTRIBUTE num: [0,1] Numbering DESCRIPTION: "numbering from paper" ATTRIBUTE numexc: [0,1] BOOLEAN DESCRIPTION: "numbering problem with paper" ATTRIBUTE poly_a: [0,1] BOOLEAN DESCRIPTION: "poly A tail indicated in figure?" ATTRIBUTE maploc: [0,1] TEXT DESCRIPTION: "map location reported in paper" ATTRIBUTE seq_raw: [0,1] TEXT DESCRIPTION: "original sequence from paper" ATTRIBUTE align_group: [0,1] INTEGER DESCRIPTION: "this seq aligned with others in paper" ATTRIBUTE comment: [0,1] TEXT DESCRIPTION: "any comment on this pub in context" ATTRIBUTE reftype: [1,1] Pubdesc_reftype DESCRIPTION: "refers to specified features" OBJECT CLASS Seq_inst DESCRIPTION: "the sequence data itself" ATTRIBUTE repr: [1,1] Seq_inst_repr ATTRIBUTE mol: [1,1] Seq_inst_mol ATTRIBUTE length: [0,1] INTEGER DESCRIPTION: "length of sequence in residues" ATTRIBUTE fuzz: [0,1] Int_fuzz DESCRIPTION: "length uncertainty" ATTRIBUTE topology: [1,1] Seq_inst_topology ATTRIBUTE strand: [0,1] Seq_inst_strand DESCRIPTION: "default ds for DNA, ss for RNA, pept" ATTRIBUTE seq_data: [0,1] Seq_data DESCRIPTION: "the sequence" ATTRIBUTE ext: [0,1] Seq_ext DESCRIPTION: "extensions for special types" ATTRIBUTE hist: [0,1] Seq_hist DESCRIPTION: "sequence history" OBJECT CLASS Seq_ext ATTRIBUTE seg: list-of [0,] Seq_loc DESCRIPTION: "segmented sequences" ATTRIBUTE ref: [0,1] Seq_loc DESCRIPTION: "hot link to another sequence (a view)" ATTRIBUTE map: list-of [0,] Seq_feat DESCRIPTION: "ordered map of markers" ATTRIBUTE delta: list-of [0,] Delta_seq OBJECT CLASS Delta_seq ATTRIBUTE loc: [0,1] Seq_loc DESCRIPTION: "point to a sequence" ATTRIBUTE literal: [0,1] Seq_literal DESCRIPTION: "a piece of sequence" OBJECT CLASS Seq_literal ATTRIBUTE length: [1,1] INTEGER DESCRIPTION: "must give a length in residues" ATTRIBUTE fuzz: [0,1] Int_fuzz DESCRIPTION: "could be unsure" ATTRIBUTE seq_data: [0,1] Seq_data DESCRIPTION: "may have the data" OBJECT CLASS Seq_hist ATTRIBUTE assembly: set-of [0,] Seq_align DESCRIPTION: "how was this assembled?" ATTRIBUTE replaces: [0,1] Seq_hist_rec DESCRIPTION: "seq makes these seqs obsolete" ATTRIBUTE replaced_by: [0,1] Seq_hist_rec DESCRIPTION: "these seqs make this one obsolete" ATTRIBUTE deleted: [0,1] Seq_hist_deleted OBJECT CLASS Seq_hist_deleted ATTRIBUTE bool: [0,1] BOOLEAN ATTRIBUTE date: [0,1] Date OBJECT CLASS Seq_hist_rec ATTRIBUTE date: [0,1] Date ATTRIBUTE ids: set-of [1,] Seq_id DESCRIPTION: "*** Various internal sequence representations ************" OBJECT CLASS Seq_data DESCRIPTION: "sequence representations" ATTRIBUTE iupacna: [0,1] IUPACna DESCRIPTION: "IUPAC 1 letter nuc acid code" ATTRIBUTE iupacaa: [0,1] IUPACaa DESCRIPTION: "IUPAC 1 letter amino acid code" ATTRIBUTE ncbi2na: [0,1] NCBI2na DESCRIPTION: "2 bit nucleic acid code" ATTRIBUTE ncbi4na: [0,1] NCBI4na DESCRIPTION: "4 bit nucleic acid code" ATTRIBUTE ncbi8na: [0,1] NCBI8na DESCRIPTION: "8 bit extended nucleic acid code" ATTRIBUTE ncbipna: [0,1] NCBIpna DESCRIPTION: "nucleic acid probabilities" ATTRIBUTE ncbi8aa: [0,1] NCBI8aa DESCRIPTION: "8 bit extended amino acid codes" ATTRIBUTE ncbieaa: [0,1] NCBIeaa DESCRIPTION: "extended ASCII 1 letter aa codes" ATTRIBUTE ncbipaa: [0,1] NCBIpaa DESCRIPTION: "amino acid probabilities" ATTRIBUTE ncbistdaa: [0,1] NCBIstdaa DESCRIPTION: "consecutive codes for std aas" OBJECT CLASS Annot_id ATTRIBUTE local: [0,1] Object_id ATTRIBUTE ncbi: [0,1] INTEGER ATTRIBUTE general: [0,1] Dbtag OBJECT CLASS Annotdesc ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "a short name for this collection" ATTRIBUTE title: [0,1] TEXT DESCRIPTION: "a title for this collection" ATTRIBUTE comment: [0,1] TEXT DESCRIPTION: "a more extensive comment" ATTRIBUTE pub: [0,1] Pubdesc DESCRIPTION: "a reference to the publication" ATTRIBUTE user: [0,1] User_object DESCRIPTION: "user defined object" ATTRIBUTE create_date: [0,1] Date DESCRIPTION: "date entry first created/released" ATTRIBUTE update_date: [0,1] Date DESCRIPTION: "date of last update" ATTRIBUTE src: [0,1] Seq_id DESCRIPTION: "source sequence from which annot came" ATTRIBUTE align: [0,1] Align_def DESCRIPTION: "definition of the SeqAligns" OBJECT CLASS Align_def ATTRIBUTE align_type: [1,1] Align_def_align_type ATTRIBUTE ids: set-of [0,] Seq_id DESCRIPTION: "used for the one ref seqid for now" OBJECT CLASS Seq_annot ATTRIBUTE id: set-of [0,] Annot_id ATTRIBUTE db: [0,1] Seq_annot_db ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "source if 'other' above" ATTRIBUTE desc: set-of [0,] Annotdesc DESCRIPTION: "used only for stand alone Seq-annots" ATTRIBUTE data: [1,1] Seq_annot_data DESCRIPTION: "used for communication between tools" OBJECT CLASS Seq_annot_data ATTRIBUTE ftable: set-of [0,] Seq_feat ATTRIBUTE align: set-of [0,] Seq_align ATTRIBUTE graph: set-of [0,] Seq_graph ATTRIBUTE ids: set-of [0,] Seq_id DESCRIPTION: "used for communication between tools" ATTRIBUTE locs: set-of [0,] Seq_loc OBJECT CLASS Seq_align ATTRIBUTE type: [1,1] Seq_align_type ATTRIBUTE dim: [0,1] INTEGER DESCRIPTION: "dimensionality" ATTRIBUTE score: set-of [0,] Score DESCRIPTION: "for whole alignment" ATTRIBUTE segs: [1,1] Seq_align_segs ATTRIBUTE bounds: set-of [0,] Seq_loc DESCRIPTION: "regions of sequence over which align" OBJECT CLASS Seq_align_segs DESCRIPTION: "alignment data" ATTRIBUTE dendiag: list-of [0,] Dense_diag ATTRIBUTE denseg: [0,1] Dense_seg ATTRIBUTE std: list-of [0,] Std_seg ATTRIBUTE packed: [0,1] Packed_seg ATTRIBUTE disc: set-of [0,] Seq_align OBJECT CLASS Dense_diag DESCRIPTION: "for (multiway) diagonals" ATTRIBUTE dim: [1,1] INTEGER DESCRIPTION: "dimensionality" ATTRIBUTE ids: list-of [1,] Seq_id DESCRIPTION: "sequences in order" ATTRIBUTE starts: list-of [1,] INTEGER DESCRIPTION: "start OFFSETS in ids order" ATTRIBUTE len: [1,1] INTEGER DESCRIPTION: "len of aligned segments" ATTRIBUTE strands: list-of [0,] Na_strand ATTRIBUTE scores: set-of [0,] Score DESCRIPTION: "Dense-seg: the densist packing for sequence alignments only." OBJECT CLASS Dense_seg DESCRIPTION: "for (multiway) global or partial alignments" ATTRIBUTE dim: [1,1] INTEGER DESCRIPTION: "dimensionality" ATTRIBUTE numseg: [1,1] INTEGER DESCRIPTION: "number of segments here" ATTRIBUTE ids: list-of [1,] Seq_id DESCRIPTION: "sequences in order" ATTRIBUTE starts: list-of [1,] INTEGER DESCRIPTION: "start OFFSETS in ids order within segs" ATTRIBUTE lens: list-of [1,] INTEGER DESCRIPTION: "lengths in ids order within segs" ATTRIBUTE strands: list-of [0,] Na_strand ATTRIBUTE scores: list-of [0,] Score DESCRIPTION: "score for each seg" OBJECT CLASS Packed_seg DESCRIPTION: "for (multiway) global or partial alignments" ATTRIBUTE dim: [1,1] INTEGER DESCRIPTION: "dimensionality" ATTRIBUTE numseg: [1,1] INTEGER DESCRIPTION: "number of segments here" ATTRIBUTE ids: list-of [1,] Seq_id DESCRIPTION: "sequences in order" ATTRIBUTE starts: list-of [1,] INTEGER DESCRIPTION: "start OFFSETS in ids order for whole alignment" ATTRIBUTE present: [1,1] TEXT DESCRIPTION: "Boolean if each sequence present or absent in" ATTRIBUTE lens: list-of [1,] INTEGER DESCRIPTION: "length of each segment" ATTRIBUTE strands: list-of [0,] Na_strand ATTRIBUTE scores: list-of [0,] Score DESCRIPTION: "score for each segment" OBJECT CLASS Std_seg ATTRIBUTE dim: [1,1] INTEGER DESCRIPTION: "dimensionality" ATTRIBUTE ids: list-of [0,] Seq_id ATTRIBUTE loc: list-of [1,] Seq_loc ATTRIBUTE scores: set-of [0,] Score DESCRIPTION: "use of Score is discouraged for external ASN.1 specifications" OBJECT CLASS Score ATTRIBUTE id: [0,1] Object_id ATTRIBUTE value: [1,1] Score_value DESCRIPTION: "use of Score-set is encouraged for external ASN.1 specifications" OBJECT CLASS Score_value ATTRIBUTE real: [0,1] REAL ATTRIBUTE int: [0,1] INTEGER OBJECT CLASS EMBL_dbname ATTRIBUTE code: [0,1] EMBL_dbname_code ATTRIBUTE name: [0,1] TEXT OBJECT CLASS EMBL_xref ATTRIBUTE dbname: [1,1] EMBL_dbname ATTRIBUTE id: list-of [1,] Object_id OBJECT CLASS EMBL_block ATTRIBUTE class: [1,1] EMBL_block_class ATTRIBUTE div: [0,1] EMBL_block_div ATTRIBUTE creation_date: [1,1] Date ATTRIBUTE update_date: [1,1] Date ATTRIBUTE extra_acc: list-of [0,] TEXT ATTRIBUTE keywords: list-of [0,] TEXT ATTRIBUTE xref: list-of [0,] EMBL_xref OBJECT CLASS SP_block DESCRIPTION: "SWISSPROT specific descriptions" ATTRIBUTE class: [1,1] SP_block_class ATTRIBUTE extra_acc: set-of [0,] TEXT DESCRIPTION: "old SWISSPROT ids" ATTRIBUTE imeth: [1,1] BOOLEAN DESCRIPTION: "seq known to start with Met" ATTRIBUTE plasnm: set-of [0,] TEXT DESCRIPTION: "plasmid names carrying gene" ATTRIBUTE seqref: set-of [0,] Seq_id DESCRIPTION: "xref to other sequences" ATTRIBUTE dbref: set-of [0,] Dbtag DESCRIPTION: "xref to non-sequence dbases" ATTRIBUTE keywords: set-of [0,] TEXT DESCRIPTION: "keywords" ATTRIBUTE created: [0,1] Date DESCRIPTION: "creation date" ATTRIBUTE sequpd: [0,1] Date DESCRIPTION: "sequence update" ATTRIBUTE annotupd: [0,1] Date DESCRIPTION: "annotation update" OBJECT CLASS PIR_block DESCRIPTION: "PIR specific descriptions" ATTRIBUTE had_punct: [0,1] BOOLEAN DESCRIPTION: "had punctuation in sequence ?" ATTRIBUTE host: [0,1] TEXT ATTRIBUTE source: [0,1] TEXT DESCRIPTION: "source line" ATTRIBUTE summary: [0,1] TEXT ATTRIBUTE genetic: [0,1] TEXT ATTRIBUTE includes: [0,1] TEXT ATTRIBUTE placement: [0,1] TEXT ATTRIBUTE superfamily: [0,1] TEXT ATTRIBUTE keywords: list-of [0,] TEXT ATTRIBUTE cross_reference: [0,1] TEXT ATTRIBUTE date: [0,1] TEXT ATTRIBUTE seq_raw: [0,1] TEXT DESCRIPTION: "seq with punctuation" ATTRIBUTE seqref: set-of [0,] Seq_id DESCRIPTION: "xref to other sequences" OBJECT CLASS GB_block DESCRIPTION: "GenBank specific descriptions" ATTRIBUTE extra_accessions: list-of [0,] TEXT ATTRIBUTE source: [0,1] TEXT DESCRIPTION: "source line" ATTRIBUTE keywords: list-of [0,] TEXT ATTRIBUTE origin: [0,1] TEXT ATTRIBUTE date: [0,1] TEXT DESCRIPTION: "OBSOLETE old form Entry Date" ATTRIBUTE entry_date: [0,1] Date DESCRIPTION: "replaces date" ATTRIBUTE div: [0,1] TEXT DESCRIPTION: "GenBank division" ATTRIBUTE taxonomy: [0,1] TEXT DESCRIPTION: "continuation line of organism" OBJECT CLASS PRF_block ATTRIBUTE extra_src: [0,1] PRF_ExtraSrc ATTRIBUTE keywords: list-of [0,] TEXT OBJECT CLASS PRF_ExtraSrc ATTRIBUTE host: [0,1] TEXT ATTRIBUTE part: [0,1] TEXT ATTRIBUTE state: [0,1] TEXT ATTRIBUTE strain: [0,1] TEXT ATTRIBUTE taxon: [0,1] TEXT OBJECT CLASS PDB_block DESCRIPTION: "PDB specific descriptions" ATTRIBUTE deposition: [1,1] Date DESCRIPTION: "deposition date month,year" ATTRIBUTE class: [1,1] TEXT ATTRIBUTE compound: list-of [1,] TEXT ATTRIBUTE source: list-of [1,] TEXT ATTRIBUTE exp_method: [0,1] TEXT DESCRIPTION: "present if NOT X-ray diffraction" ATTRIBUTE replace: [0,1] PDB_replace DESCRIPTION: "replacement history" OBJECT CLASS PDB_replace ATTRIBUTE date: [1,1] Date ATTRIBUTE ids: list-of [1,] TEXT DESCRIPTION: "entry ids replace by this one" OBJECT CLASS Seq_map_table DESCRIPTION: "for tables of sequence mappings " ATTRIBUTE from: [1,1] Seq_code_type DESCRIPTION: "code to map from" ATTRIBUTE to: [1,1] Seq_code_type DESCRIPTION: "code to map to" ATTRIBUTE num: [1,1] INTEGER DESCRIPTION: "number of rows in table" ATTRIBUTE start_at: [1,1] INTEGER DESCRIPTION: "index offset of first element" ATTRIBUTE table: list-of [1,] INTEGER DESCRIPTION: "table of values, in from-to order" OBJECT CLASS Seq_code_table DESCRIPTION: "for names of coded values" ATTRIBUTE code: [1,1] Seq_code_type DESCRIPTION: "name of code" ATTRIBUTE num: [1,1] INTEGER DESCRIPTION: "number of rows in table" ATTRIBUTE one_letter: [1,1] BOOLEAN DESCRIPTION: "symbol is ALWAYS 1 letter?" ATTRIBUTE start_at: [1,1] INTEGER DESCRIPTION: "index offset of first element" ATTRIBUTE table: list-of [1,] Seq_code_table_table DESCRIPTION: "an explanatory name or string" ATTRIBUTE comps: list-of [0,] INTEGER DESCRIPTION: "pointers to complement nuc acid" OBJECT CLASS Seq_code_table_table ATTRIBUTE symbol: [1,1] TEXT DESCRIPTION: "the printed symbol or letter" ATTRIBUTE name: [1,1] TEXT OBJECT CLASS Seq_code_set DESCRIPTION: "for distribution" ATTRIBUTE codes: set-of [0,] Seq_code_table ATTRIBUTE maps: set-of [0,] Seq_map_table OBJECT CLASS Feat_id ATTRIBUTE gibb: [0,1] INTEGER DESCRIPTION: "geninfo backbone" ATTRIBUTE giim: [0,1] Giimport_id DESCRIPTION: "geninfo import" ATTRIBUTE local: [0,1] Object_id DESCRIPTION: "for local software use" ATTRIBUTE general: [0,1] Dbtag DESCRIPTION: "for use by various databases" OBJECT CLASS Seq_feat ATTRIBUTE id: [0,1] Feat_id ATTRIBUTE data: [1,1] SeqFeatData DESCRIPTION: "the specific data" ATTRIBUTE partial: [0,1] BOOLEAN DESCRIPTION: "incomplete in some way?" ATTRIBUTE except: [0,1] BOOLEAN DESCRIPTION: "something funny about this?" ATTRIBUTE comment: [0,1] TEXT ATTRIBUTE product: [0,1] Seq_loc DESCRIPTION: "product of process" ATTRIBUTE location: [1,1] Seq_loc DESCRIPTION: "feature made from" ATTRIBUTE qual: list-of [0,] Gb_qual DESCRIPTION: "qualifiers" ATTRIBUTE title: [0,1] TEXT DESCRIPTION: "for user defined label" ATTRIBUTE ext: [0,1] User_object DESCRIPTION: "user defined structure extension" ATTRIBUTE cit: [0,1] Pub_set DESCRIPTION: "citations for this feature" ATTRIBUTE exp_ev: [0,1] Seq_feat_exp_ev DESCRIPTION: "similarity, pattern, etc" ATTRIBUTE xref: set-of [0,] SeqFeatXref DESCRIPTION: "cite other relevant features" ATTRIBUTE dbxref: set-of [0,] Dbtag DESCRIPTION: "support for xref to other databases" OBJECT CLASS SeqFeatData ATTRIBUTE gene: [0,1] Gene_ref ATTRIBUTE org: [0,1] Org_ref ATTRIBUTE cdregion: [0,1] Cdregion ATTRIBUTE prot: [0,1] Prot_ref ATTRIBUTE rna: [0,1] RNA_ref ATTRIBUTE pub: [0,1] Pubdesc DESCRIPTION: "publication applies to this seq " ATTRIBUTE seq: [0,1] Seq_loc DESCRIPTION: "to annotate origin from another seq" ATTRIBUTE imp: [0,1] Imp_feat ATTRIBUTE region: [0,1] TEXT DESCRIPTION: "named region (globin locus)" ATTRIBUTE comment: [0,1] VARCHAR(4) DESCRIPTION: "just a comment" ATTRIBUTE bond: [0,1] SeqFeatData_bond ATTRIBUTE site: [0,1] SeqFeatData_site ATTRIBUTE rsite: [0,1] Rsite_ref DESCRIPTION: "restriction site (for maps really)" ATTRIBUTE user: [0,1] User_object DESCRIPTION: "user defined structure" ATTRIBUTE txinit: [0,1] Txinit DESCRIPTION: "transcription initiation" ATTRIBUTE num: [0,1] Numbering DESCRIPTION: "a numbering system" ATTRIBUTE psec_str: [0,1] SeqFeatData_psec_str DESCRIPTION: "beta or gamma turn" ATTRIBUTE non_std_residue: [0,1] TEXT DESCRIPTION: "non-standard residue here in seq" ATTRIBUTE het: [0,1] Heterogen DESCRIPTION: "cofactor, prosthetic grp, etc, bound to seq" ATTRIBUTE biosrc: [0,1] BioSource OBJECT CLASS SeqFeatXref DESCRIPTION: "both optional because can have one or both" ATTRIBUTE id: [0,1] Feat_id DESCRIPTION: "the feature copied" ATTRIBUTE data: [0,1] SeqFeatData DESCRIPTION: "the specific data" OBJECT CLASS Cdregion ATTRIBUTE orf: [0,1] BOOLEAN DESCRIPTION: "just an ORF ?" ATTRIBUTE frame: [1,1] Cdregion_frame DESCRIPTION: "reading frame" ATTRIBUTE conflict: [0,1] BOOLEAN DESCRIPTION: "conflict" ATTRIBUTE gaps: [0,1] INTEGER DESCRIPTION: "number of gaps on conflict/except" ATTRIBUTE mismatch: [0,1] INTEGER DESCRIPTION: "number of mismatches on above" ATTRIBUTE code: [0,1] Genetic_code DESCRIPTION: "genetic code used" ATTRIBUTE code_break: list-of [0,] Code_break DESCRIPTION: "individual exceptions" ATTRIBUTE stops: [0,1] INTEGER DESCRIPTION: "number of stop codons on above" OBJECT CLASS Genetic_code ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "name of a code" ATTRIBUTE id: [0,1] INTEGER DESCRIPTION: "id in dbase" ATTRIBUTE ncbieaa: [0,1] TEXT DESCRIPTION: "indexed to IUPAC extended" ATTRIBUTE ncbi8aa: [0,1] TEXT DESCRIPTION: "indexed to NCBI8aa" ATTRIBUTE ncbistdaa: [0,1] TEXT DESCRIPTION: "indexed to NCBIstdaa" ATTRIBUTE sncbieaa: [0,1] TEXT DESCRIPTION: "start, indexed to IUPAC extended" ATTRIBUTE sncbi8aa: [0,1] TEXT DESCRIPTION: "start, indexed to NCBI8aa" ATTRIBUTE sncbistdaa: [0,1] TEXT DESCRIPTION: "start, indexed to NCBIstdaa" OBJECT CLASS Code_break DESCRIPTION: "specific codon exceptions" ATTRIBUTE loc: [1,1] Seq_loc DESCRIPTION: "location of exception" ATTRIBUTE aa: [1,1] Code_break_aa DESCRIPTION: "NCBIstdaa code" OBJECT CLASS Code_break_aa DESCRIPTION: "the amino acid" ATTRIBUTE ncbieaa: [0,1] INTEGER DESCRIPTION: "ASCII value of NCBIeaa code" ATTRIBUTE ncbi8aa: [0,1] INTEGER DESCRIPTION: "NCBI8aa code" ATTRIBUTE ncbistdaa: [0,1] INTEGER OBJECT CLASS Imp_feat ATTRIBUTE key: [1,1] TEXT ATTRIBUTE loc: [0,1] TEXT DESCRIPTION: "original location string" ATTRIBUTE descr: [0,1] TEXT DESCRIPTION: "text description" OBJECT CLASS Gb_qual ATTRIBUTE qual: [1,1] TEXT ATTRIBUTE val: [1,1] TEXT OBJECT CLASS Rsite_ref ATTRIBUTE str: [0,1] TEXT DESCRIPTION: "may be unparsable" ATTRIBUTE db: [0,1] Dbtag DESCRIPTION: "pointer to a restriction site database" OBJECT CLASS RNA_ref ATTRIBUTE type: [1,1] RNA_ref_type ATTRIBUTE pseudo: [0,1] BOOLEAN ATTRIBUTE ext: [0,1] RNA_ref_ext DESCRIPTION: "for tRNAs" OBJECT CLASS RNA_ref_ext ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "for naming 'other' type" ATTRIBUTE tRNA: [0,1] Trna_ext OBJECT CLASS Trna_ext DESCRIPTION: "tRNA feature extensions" ATTRIBUTE aa: [0,1] Trna_ext_aa ATTRIBUTE codon: set-of [0,] INTEGER DESCRIPTION: "codon(s) as in Genetic-code" ATTRIBUTE anticodon: [0,1] Seq_loc DESCRIPTION: "location of anticodon" OBJECT CLASS Trna_ext_aa DESCRIPTION: "aa this carries" ATTRIBUTE iupacaa: [0,1] INTEGER ATTRIBUTE ncbieaa: [0,1] INTEGER ATTRIBUTE ncbi8aa: [0,1] INTEGER ATTRIBUTE ncbistdaa: [0,1] INTEGER OBJECT CLASS Gene_ref ATTRIBUTE locus: [0,1] TEXT DESCRIPTION: "Official gene symbol" ATTRIBUTE allele: [0,1] TEXT DESCRIPTION: "Official allele designation" ATTRIBUTE desc: [0,1] TEXT DESCRIPTION: "descriptive name" ATTRIBUTE maploc: [0,1] TEXT DESCRIPTION: "descriptive map location" ATTRIBUTE pseudo: [1,1] BOOLEAN DESCRIPTION: "pseudogene" ATTRIBUTE db: set-of [0,] Dbtag DESCRIPTION: "ids in other dbases" ATTRIBUTE syn: set-of [0,] TEXT DESCRIPTION: "synonyms for locus" OBJECT CLASS Org_ref ATTRIBUTE taxname: [0,1] TEXT DESCRIPTION: "preferred formal name" ATTRIBUTE common: [0,1] TEXT DESCRIPTION: "common name" ATTRIBUTE mod: set-of [0,] TEXT DESCRIPTION: "unstructured modifiers" ATTRIBUTE db: set-of [0,] Dbtag DESCRIPTION: "ids in taxonomic or culture dbases" ATTRIBUTE syn: set-of [0,] TEXT DESCRIPTION: "synonyms for taxname or common" ATTRIBUTE orgname: [0,1] OrgName OBJECT CLASS OrgName ATTRIBUTE name: [0,1] OrgName_name DESCRIPTION: "when genus not known" ATTRIBUTE attrib: [0,1] TEXT DESCRIPTION: "attribution of name" ATTRIBUTE mod: list-of [0,] OrgMod ATTRIBUTE lineage: [0,1] TEXT DESCRIPTION: "lineage with semicolon separators" ATTRIBUTE gcode: [0,1] INTEGER DESCRIPTION: "genetic code (see CdRegion)" ATTRIBUTE mgcode: [0,1] INTEGER DESCRIPTION: "mitochondrial genetic code" OBJECT CLASS OrgName_name ATTRIBUTE binomial: [0,1] BinomialOrgName DESCRIPTION: "genus/species type name" ATTRIBUTE virus: [0,1] TEXT DESCRIPTION: "virus names are different" ATTRIBUTE hybrid: list-of [0,] OrgName DESCRIPTION: "hybrid between organisms" ATTRIBUTE namedhybrid: [0,1] BinomialOrgName DESCRIPTION: "some hybrids have genus x species name" ATTRIBUTE partial: list-of [0,] TaxElement OBJECT CLASS OrgMod ATTRIBUTE subtype: [1,1] OrgMod_subtype ATTRIBUTE subname: [1,1] TEXT ATTRIBUTE attrib: [0,1] TEXT DESCRIPTION: "attribution/source of name" OBJECT CLASS BinomialOrgName ATTRIBUTE genus: [1,1] TEXT DESCRIPTION: "required" ATTRIBUTE species: [0,1] TEXT DESCRIPTION: "species required if subspecies used" ATTRIBUTE subspecies: [0,1] TEXT OBJECT CLASS TaxElement ATTRIBUTE fixed_level: [1,1] TaxElement_fixed_level ATTRIBUTE level: [0,1] TEXT ATTRIBUTE name: [1,1] TEXT OBJECT CLASS BioSource ATTRIBUTE genome: [1,1] BioSource_genome ATTRIBUTE origin: [1,1] BioSource_origin ATTRIBUTE org: [1,1] Org_ref ATTRIBUTE subtype: list-of [0,] SubSource OBJECT CLASS SubSource ATTRIBUTE subtype: [1,1] SubSource_subtype ATTRIBUTE name: [1,1] TEXT ATTRIBUTE attrib: [0,1] TEXT DESCRIPTION: "attribution/source of this name" OBJECT CLASS Prot_ref ATTRIBUTE name: set-of [0,] TEXT DESCRIPTION: "protein name" ATTRIBUTE desc: [0,1] TEXT DESCRIPTION: "description (instead of name)" ATTRIBUTE ec: set-of [0,] TEXT DESCRIPTION: "E.C. number(s)" ATTRIBUTE activity: set-of [0,] TEXT DESCRIPTION: "activities" ATTRIBUTE db: set-of [0,] Dbtag DESCRIPTION: "ids in other dbases" ATTRIBUTE processed: [1,1] Prot_ref_processed OBJECT CLASS Txinit ATTRIBUTE name: [1,1] TEXT DESCRIPTION: "descriptive name of initiation site" ATTRIBUTE syn: list-of [0,] TEXT DESCRIPTION: "synonyms" ATTRIBUTE gene: list-of [0,] Gene_ref DESCRIPTION: "gene(s) transcribed" ATTRIBUTE protein: list-of [0,] Prot_ref DESCRIPTION: "protein(s) produced" ATTRIBUTE rna: list-of [0,] TEXT DESCRIPTION: "rna(s) produced" ATTRIBUTE expression: [0,1] TEXT DESCRIPTION: "tissue/time of expression" ATTRIBUTE txsystem: [1,1] Txinit_txsystem ATTRIBUTE txdescr: [0,1] TEXT DESCRIPTION: "modifiers on txsystem" ATTRIBUTE txorg: [0,1] Org_ref DESCRIPTION: "organism supplying transcription apparatus" ATTRIBUTE mapping_precise: [1,1] BOOLEAN DESCRIPTION: "mapping precise or approx" ATTRIBUTE location_accurate: [1,1] BOOLEAN DESCRIPTION: "does Seq-loc reflect mapping" ATTRIBUTE inittype: [0,1] Txinit_inittype ATTRIBUTE evidence: set-of [0,] Tx_evidence OBJECT CLASS Tx_evidence ATTRIBUTE exp_code: [1,1] Tx_evidence_exp_code ATTRIBUTE expression_system: [1,1] Tx_evidence_expression_system ATTRIBUTE low_prec_data: [1,1] BOOLEAN ATTRIBUTE from_homolog: [1,1] BOOLEAN DESCRIPTION: "experiment actually done on" OBJECT CLASS Seq_id ATTRIBUTE local: [0,1] Object_id DESCRIPTION: "local use" ATTRIBUTE gibbsq: [0,1] INTEGER DESCRIPTION: "Geninfo backbone seqid" ATTRIBUTE gibbmt: [0,1] INTEGER DESCRIPTION: "Geninfo backbone moltype" ATTRIBUTE giim: [0,1] Giimport_id DESCRIPTION: "Geninfo import id" ATTRIBUTE genbank: [0,1] Textseq_id ATTRIBUTE embl: [0,1] Textseq_id ATTRIBUTE pir: [0,1] Textseq_id ATTRIBUTE swissprot: [0,1] Textseq_id ATTRIBUTE patent: [0,1] Patent_seq_id ATTRIBUTE other: [0,1] Textseq_id DESCRIPTION: "catch all" ATTRIBUTE general: [0,1] Dbtag DESCRIPTION: "for other databases" ATTRIBUTE gi: [0,1] INTEGER DESCRIPTION: "GenInfo Integrated Database" ATTRIBUTE ddbj: [0,1] Textseq_id DESCRIPTION: "DDBJ" ATTRIBUTE prf: [0,1] Textseq_id DESCRIPTION: "PRF SEQDB" ATTRIBUTE pdb: [0,1] PDB_seq_id DESCRIPTION: "PDB sequence" OBJECT CLASS Patent_seq_id ATTRIBUTE seqid: [1,1] INTEGER DESCRIPTION: "number of sequence in patent" ATTRIBUTE cit: [1,1] Id_pat DESCRIPTION: "patent citation" OBJECT CLASS Textseq_id ATTRIBUTE name: [0,1] TEXT ATTRIBUTE accession: [0,1] TEXT ATTRIBUTE release: [0,1] TEXT ATTRIBUTE version: [0,1] INTEGER OBJECT CLASS Giimport_id ATTRIBUTE id: [1,1] INTEGER DESCRIPTION: "the id to use here" ATTRIBUTE db: [0,1] TEXT DESCRIPTION: "dbase used in" ATTRIBUTE release: [0,1] TEXT DESCRIPTION: "the release" OBJECT CLASS PDB_seq_id ATTRIBUTE mol: [1,1] PDB_mol_id DESCRIPTION: "the molecule name" ATTRIBUTE chain: [1,1] INTEGER DESCRIPTION: "a single ASCII character, chain id" ATTRIBUTE rel: [0,1] Date DESCRIPTION: "release date, month and year" OBJECT CLASS Seq_loc ATTRIBUTE null: [0,1] VARCHAR(4) DESCRIPTION: "not placed" ATTRIBUTE empty: [0,1] Seq_id DESCRIPTION: "to NULL one Seq-id in a collection" ATTRIBUTE whole: [0,1] Seq_id DESCRIPTION: "whole sequence" ATTRIBUTE int: [0,1] Seq_interval DESCRIPTION: "from to" ATTRIBUTE packed_int: list-of [0,] Seq_interval ATTRIBUTE pnt: [0,1] Seq_point ATTRIBUTE packed_pnt: [0,1] Packed_seqpnt ATTRIBUTE mix: list-of [0,] Seq_loc ATTRIBUTE equiv: set-of [0,] Seq_loc DESCRIPTION: "equivalent sets of locations" ATTRIBUTE bond: [0,1] Seq_bond ATTRIBUTE feat: [0,1] Feat_id DESCRIPTION: "indirect, through a Seq-feat" OBJECT CLASS Seq_interval ATTRIBUTE from: [1,1] INTEGER ATTRIBUTE to: [1,1] INTEGER ATTRIBUTE strand: [0,1] Na_strand ATTRIBUTE id: [1,1] Seq_id DESCRIPTION: "WARNING: this used to be optional" ATTRIBUTE fuzz_from: [0,1] Int_fuzz ATTRIBUTE fuzz_to: [0,1] Int_fuzz OBJECT CLASS Seq_point ATTRIBUTE point: [1,1] INTEGER ATTRIBUTE strand: [0,1] Na_strand ATTRIBUTE id: [1,1] Seq_id DESCRIPTION: "WARNING: this used to be optional" ATTRIBUTE fuzz: [0,1] Int_fuzz OBJECT CLASS Packed_seqpnt ATTRIBUTE strand: [0,1] Na_strand ATTRIBUTE id: [1,1] Seq_id ATTRIBUTE fuzz: [0,1] Int_fuzz ATTRIBUTE points: list-of [1,] INTEGER OBJECT CLASS Seq_bond DESCRIPTION: "bond between residues" ATTRIBUTE a: [1,1] Seq_point DESCRIPTION: "connection to a least one residue" ATTRIBUTE b: [0,1] Seq_point DESCRIPTION: "other end may not be available" OBJECT CLASS Seq_graph ATTRIBUTE title: [0,1] TEXT ATTRIBUTE comment: [0,1] TEXT ATTRIBUTE loc: [1,1] Seq_loc DESCRIPTION: "region this applies to" ATTRIBUTE title_x: [0,1] TEXT DESCRIPTION: "title for x-axis" ATTRIBUTE title_y: [0,1] TEXT ATTRIBUTE comp: [0,1] INTEGER DESCRIPTION: "compression (residues/value)" ATTRIBUTE a: [0,1] REAL DESCRIPTION: "for scaling values" ATTRIBUTE b: [0,1] REAL DESCRIPTION: "display = (a x value) + b" ATTRIBUTE numval: [1,1] INTEGER DESCRIPTION: "number of values in graph" ATTRIBUTE graph: [1,1] Seq_graph_graph OBJECT CLASS Seq_graph_graph ATTRIBUTE real: [0,1] Real_graph ATTRIBUTE int: [0,1] Int_graph ATTRIBUTE byte: [0,1] Byte_graph OBJECT CLASS Real_graph ATTRIBUTE max: [1,1] REAL DESCRIPTION: "top of graph" ATTRIBUTE min: [1,1] REAL DESCRIPTION: "bottom of graph" ATTRIBUTE axis: [1,1] REAL DESCRIPTION: "value to draw axis on" ATTRIBUTE values: list-of [1,] REAL OBJECT CLASS Int_graph ATTRIBUTE max: [1,1] INTEGER ATTRIBUTE min: [1,1] INTEGER ATTRIBUTE axis: [1,1] INTEGER ATTRIBUTE values: list-of [1,] INTEGER OBJECT CLASS Byte_graph DESCRIPTION: "integer from 0-255" ATTRIBUTE max: [1,1] INTEGER ATTRIBUTE min: [1,1] INTEGER ATTRIBUTE axis: [1,1] INTEGER ATTRIBUTE values: [1,1] TEXT OBJECT CLASS Bioseq_set DESCRIPTION: "just a collection" ATTRIBUTE id: [0,1] Object_id ATTRIBUTE coll: [0,1] Dbtag DESCRIPTION: "to identify a collection" ATTRIBUTE level: [0,1] INTEGER DESCRIPTION: "nesting level" ATTRIBUTE class: [1,1] Bioseq_set_class ATTRIBUTE release: [0,1] TEXT ATTRIBUTE date: [0,1] Date ATTRIBUTE descr: set-of [0,] Seqdesc ATTRIBUTE seq_set: list-of [1,] Seq_entry ATTRIBUTE annot: set-of [0,] Seq_annot OBJECT CLASS Seq_entry ATTRIBUTE seq: [0,1] Bioseq ATTRIBUTE set: [0,1] Bioseq_set OBJECT CLASS Seq_submit ATTRIBUTE sub: [1,1] Submit_block ATTRIBUTE data: [1,1] Seq_submit_data DESCRIPTION: "deletions of entries" OBJECT CLASS Seq_submit_data ATTRIBUTE entrys: set-of [0,] Seq_entry DESCRIPTION: "sequence(s)" ATTRIBUTE annots: set-of [0,] Seq_annot DESCRIPTION: "annotation(s)" ATTRIBUTE delete: set-of [0,] Seq_id OBJECT CLASS Submit_block ATTRIBUTE contact: [1,1] Contact_info DESCRIPTION: "who to contact" ATTRIBUTE cit: [1,1] Cit_sub DESCRIPTION: "citation for this submission" ATTRIBUTE hup: [1,1] BOOLEAN DESCRIPTION: "hold until publish" ATTRIBUTE reldate: [0,1] Date DESCRIPTION: "release by date" ATTRIBUTE subtype: [0,1] Submit_block_subtype ATTRIBUTE tool: [0,1] TEXT DESCRIPTION: "tool used to make submission" ATTRIBUTE user_tag: [0,1] TEXT DESCRIPTION: "user supplied id for this submission" ATTRIBUTE comment: [0,1] TEXT DESCRIPTION: "user comments/advice to database" OBJECT CLASS Contact_info DESCRIPTION: "who to contact to discuss the submission" ATTRIBUTE name: [0,1] TEXT DESCRIPTION: "OBSOLETE: will be removed" ATTRIBUTE address: list-of [0,] TEXT ATTRIBUTE phone: [0,1] TEXT ATTRIBUTE fax: [0,1] TEXT ATTRIBUTE email: [0,1] TEXT ATTRIBUTE telex: [0,1] TEXT ATTRIBUTE owner_id: [0,1] Object_id DESCRIPTION: "for owner accounts" ATTRIBUTE password: [0,1] TEXT ATTRIBUTE last_name: [0,1] TEXT DESCRIPTION: "structured to replace name above" ATTRIBUTE first_name: [0,1] TEXT ATTRIBUTE middle_initial: [0,1] TEXT ATTRIBUTE contact: [0,1] Author DESCRIPTION: "WARNING: this will replace the above"