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qualifier_types

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  • qualifier_types 4.12 KiB
    # Feature qualifiers for EMBL/GenBank feature tables
    # 
    # From: http://www.ebi.ac.uk/~faruque/art/keyqual.txt
    #
    # valid qualifier types are:
    #         (::)		(text:text,text:text)
    #         EC		"n.n.n.n"
    #         feature		dbname::accno:location
    #         item		single text item
    #         list		one of the listed values
    #         modbase         one of the stored modbase values
    #         none		no value
    #         number		nn
    #         (other)		(text)
    #         location	a valid location range (or feature label)
    #         real		n.n within specified range
    #         ref     	[nn]
    #         text		any text, no quotes added, spaces allowed if quoted
    #         "text"		quoted text, double any contained quotes
    #         "opt"		optional quoted text, double any contained quotes
    #         "list"		quoted text, list of accepted values
    # 
    # if not specified, the default is text (so anything is accepted)
    # 
    # Name           required   Type    Value(s) ..
    allele           no         "text"
    anticodon        yes        (::)    pos aa
    bound_moiety     no         "text"
    cell_line        no         "text"
    cell_type        no         "text"
    chromosome       no         "opt"
    citation         no         ref
    clone            no         "text"
    clone_lib        no         "text"
    codon            no         (::)    seq aa
    codon_start      yes        number  1 3
    cons_splice      yes        (::)    5'site 3'site
    country          no         "text"
    cultivar         no         "text"
    db_xref          no         "text"
    dev_stage        no         "text"
    direction        yes        list    LEFT RIGHT BOTH
    ecotype          no         "text"
    EC_number        no         "text"
    environmental_sample   no   none
    estimated_length no         "text"
    evidence         yes        list    EXPERIMENTAL NOT_EXPERIMENTAL
    exception        no         "text"
    focus            no         none
    frequency        yes        real    0.0  1.0
    function         yes        "text"
    gene             no         "text"
    germline         yes        none
    haplotype        no         "text"
    insertion_seq    no         "text"
    isolation_source no         "text"
    isolate          no         "text"
    kinetoplast      no         "opt"
    label            yes        item
    lab_host         no         "text"
    locus_tag        no         "text"
    macronuclear     no         none
    map              no         "text"
    mod_base         no         modbase
    mol_type         no         "text"
    note             no         "text"
    number           yes        number  1 99999999
    operon           no         "text"
    organell         no         "text"
    organism         yes        "text"
    partial          yes        none
    PCR_conditions   no         "text"
    phenotype        no         "text"
    plasmid          no         "text"
    pop_variant      no         "text"
    product          no         "text"
    protein_id       no         "text"
    proviral         yes        none
    pseudo           yes        none
    rearranged       yes        none
    replace          no         "text"
    rpt_family       no         "text"
    rpt_type         no         list    TANDEM INVERTED FLANKING TERMINAL DIRECT \
                                        DISPERSED OTHER
    rpt_unit         no         "text"
    segment          no         "text"
    sequenced_mol    no         "list"  "cDNA" "cDNA to genomic RNA" \
                                        "cDNA to mRNA" "cDNA to other RNA" \
                                        "cDNA to rRNA" "DNA" "mRNA" \
                                        "RNA" "rRNA" "scRNA" "snRNA" "tRNA"
    serotype         no         "text"
    serovar          no         "text"
    sex              no         "text"
    specific_host    no         "text"
    specimen_voucher no         "text"
    standard_name    no         "text"
    strain           no         "text"
    sub_clone        no         "text"
    sub_species      no         "text"
    sub_strain       no         "text"
    tissue_lib       no         "text"  
    tissue_type      no         "text"
    transgenic       no         "text"
    translation      no         "text"
    transl_except    no         (::)    pos aa
    transl_table     no         number  1 11
    transposon       no         "text"
    usedin           no         feature
    variety          no         "text"
    virion           no         none