format-version: 1.2
date: 24:05:2005 17:23
saved-by: cjm
auto-generated-by: DAG-Edit 1.419 rev 3
default-namespace: feature_property
remark: cvs version: $Revision: 1.1 $
remark: converted by Chris Mungall; source: http://www.ncbi.nlm.nih.gov/collab/FT

[Typedef]
id: GENBANK_SOFP:allele
name: allele
is_a: SOFP:feature_property
domain: SO:000110
def: "name of the allele for the given gene " []
range: xsd:string
comment: all gene-related features (exon, CDS etc) for a given  gene should share the same /allele qualifier value;  the /allele qualifier value must, by definition, be  different from the /gene qualifier value; when used with  the variation feature key, the allele qualifier value  should be that of the variant.

[Typedef]
id: GENBANK_SOFP:anticodon
name: genbank:anticodon
is_a: SOFP:feature_property
domain: SO:000110
def: "location of the anticodon of tRNA and the amino acid for which it codes" []
range: xsd:string
range_def: "(pos:<base_range>,aa:<amino_acid>) where base_range is the position of the anticodon and amino_acid is the abbreviation for the amino acid encoded" []
comments: Note the difference between GENBANK_SOFP:anticodon and SOFP:anticodon; the former includes the base range

[Typedef]
id: GENBANK_SOFP:bound_moiety
name: bound_moiety
is_a: SOFP:feature_property
domain: SO:000110
def: "name of the molecule/complex that may bind to the  given feature " []
range: xsd:string
comment: Multiple /bound_moiety qualifiers are legal on 'promoter'  and 'enhancer' features. A single /bound_moiety qualifier  is legal on the 'misc_binding', 'oriT' and 'protein_bind' features.

[Typedef]
id: GENBANK_SOFP:cell_line
name: cell_line
is_a: SOFP:feature_property
domain: SO:000110
def: "cell line from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:cell_type
name: cell_type
is_a: SOFP:feature_property
domain: SO:000110
def: "cell type from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:chromosome
name: chromosome
is_a: SOFP:feature_property
domain: SO:000110
def: "chromosome (e.g. Chromosome number) from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:citation
name: citation
is_a: SOFP:feature_property
domain: SO:000110
def: "reference to a citation listed in the entry reference field" []
range: xsd:integer
range_def: "[integer-number] where integer-number is the number of the reference as enumerated in the reference field" []
comment: used to indicate the citation providing the claim of and/or evidence for a feature; brackets are used for conformity.

[Typedef]
id: GENBANK_SOFP:clone
name: clone
is_a: SOFP:feature_property
domain: SO:000110
def: "clone from which the sequence was obtained" []
range: xsd:string
comment: not more than one clone should be specified for a given source  feature; to indicate that the sequence was obtained from multiple clones, multiple source features should be given.

[Typedef]
id: GENBANK_SOFP:clone_lib
name: clone_lib
is_a: SOFP:feature_property
domain: SO:000110
def: "clone library from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:codon
name: codon
is_a: SOFP:feature_property
domain: SO:000110
def: "specifies a codon which is different from any found in the reference genetic code" []
range: xsd:string
range_def: "(seq:'codon-sequence',aa:<amino_acid>) where 'codon-sequence' contains the bases of the codon  and <amino_acid> is the abbreviation for the translated amino  acid, the abbreviation for a modified unusual amino_acids from  section 7.5, or the word OTHER" []
comment: used to specify unusual genetic codes, organellar codes, etc, that are different from the 'normal' code for the organism; the codon specified by 'seq' codes for the amino acid or stop codon specified by 'aa'; the codon that is specified is used throughout the CDS; amino acids that are not on the controlled vocabulary list  can be annotated by using 'aa:OTHER' as the amino acid  designation, and by giving the name of the residue in a /note  qualifier; only nucleotides a, g, c or t can be used in  'codon-sequence'; multiple /codon qualifiers should be used to describe ambiguous nucleotides.

[Typedef]
id: GENBANK_SOFP:codon_start
name: codon_start
is_a: SOFP:feature_property
domain: SO:000110
def: "indicates the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature." []
range: xsd:integer
range_def: "1 or 2 or 3" []

[Typedef]
id: GENBANK_SOFP:compare
name: compare
is_a: SOFP:feature_property
domain: SO:000110
def: "Reference details of an existing public INSD entry  to which a comparison is made" []
range: xsd:string
comment: This qualifier may be used on the following features: misc_difference, conflict, unsure, old_sequence  and variation. The features 'old_sequence' and 'conflict' must have either a /citation or a /compare qualifier.  Multiple /compare qualifiers with different contents are  allowed within a single feature.  This qualifier is not intended for large-scale annotation  of variations, such as SNPs.

[Typedef]
id: GENBANK_SOFP:cons_splice
name: cons_splice
is_a: SOFP:feature_property
domain: SO:000110
def: "differentiates between intron splice sites that conform to the 5'-GT ... AG-3' splice site consensus" []
range: xsd:string
range_def: "(5'site:<value>, 3'site:<value>), where <value>  can be 'YES', 'NO' or 'ABSENT'" [] /cons_splice=(5'site:ABSENT, 3'site:NO)
comment: since the vast majority of splice sites conform to the  consensus, this qualifier should be used only when one  does not and the sequence has been checked; 'ABSENT'  can be used when one of the termini is not part of the  sequence and information on splice site is not  available.

[Typedef]
id: GENBANK_SOFP:country
name: country
is_a: SOFP:feature_property
domain: SO:000110
def: "Geographical origin of sequenced sample, intended for epidemiological or population studies." []
range: xsd:string
range_def: "'<country_value>[:<region>][, <locality>]' where  country_value is any value from the controlled vocabulary at  URL:http://www.ncbi.nlm.nih.gov/projects/collab/country.html " [] /country='France:Cote d'Azur, Antibes' /country='Atlantic Ocean:Charlie Gibbs Fracture Zone'
comment: Intended to provide a reference to the site where the source organism was isolated or sampled. Regions and localities should be indicated where possible. Note that the physical geography  of the isolation or sampling site should be represented in /isolation_source. 

[Typedef]
id: GENBANK_SOFP:cultivar
name: cultivar
is_a: SOFP:feature_property
domain: SO:000110
def: "cultivar (cultivated variety) of plant from which sequence was  obtained. " []
range: xsd:string /cultivar='Tenuifolius' /cultivar='Candy Cane' /cultivar='IR36'
comment: 'cultivar' is applied solely to products of artificial  selection; use the variety qualifier for natural, named  plant and fungal varieties; 

[Typedef]
id: GENBANK_SOFP:db_xref
name: db_xref
is_a: SOFP:feature_property
domain: SO:000110
def: "database cross-reference: pointer to related information in  another database." []
range: xsd:string
range_def: "'<database>:<identifier>' where database is the name of the database containing related information, and  identifier is the internal identifier of the related information according to the naming conventions of the cross-referenced  database." []
comment: the complete list of allowed database types is kept on  NCBI's public WWW server, at URL:  http://www.ncbi.nlm.nih.gov/projects/collab/

[Typedef]
id: GENBANK_SOFP:dev_stage
name: dev_stage
is_a: SOFP:feature_property
domain: SO:000110
def: "if the sequence was obtained from an organism in a specific  developmental stage, it is specified with this qualifier" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:direction
name: direction
is_a: SOFP:feature_property
domain: SO:000110
def: "direction of DNA replication" []
range: xsd:string
range_def: "left, right, or both where left indicates toward the 5' end of the entry sequence (as presented) and right indicates toward the 3' end" []

[Typedef]
id: GENBANK_SOFP:EC_number
name: EC_number
is_a: SOFP:feature_property
domain: SO:000110
def: "Enzyme Commission number for enzyme product of sequence" []
range: xsd:string
comment: valid values for EC numbers are defined in the list prepared by the IUPAC-IUB Commission on Biochemical Enzyme Nomenclature  (published in Enzyme Nomenclature 1984 New York: Academic  Press (1984) or a more recent revision thereof).

[Typedef]
id: GENBANK_SOFP:ecotype
name: ecotype
is_a: SOFP:feature_property
domain: SO:000110
def: "a population within a given species displaying genetically  based, phenotypic traits that reflect adaptation to a local  habitat." []
comment: an example of such a population is one that has adapted hairier than normal leaves as a response to an especially sunny habitat. 'Ecotype' is often applied to standard genetic stocks of Arabidopsis thaliana, but it can be applied to any sessile  organism.

[Typedef]
id: GENBANK_SOFP:environmental_sample
name: environmental_sample
is_a: SOFP:feature_property
domain: SO:000110
def: "identifies sequences derived by direct molecular isolation (PCR, DGGE, or other anonymous methods) from  an environmental sample with no reliable identification  of the source organism" []
range: xsd:boolean
comment: used only with the source feature key; source feature  keys containing the /environmental_sample qualifier  should also contain the /isolation_source qualifier.

[Typedef]
id: GENBANK_SOFP:estimated_length
name: estimated_length
is_a: SOFP:feature_property
domain: SO:000110
def: "estimated length of the gap in the sequence" []
range: xsd:string
range_def: "unknown or <integer>" [] /estimated_length=342

[Typedef]
id: GENBANK_SOFP:evidence
name: evidence
is_a: SOFP:feature_property
domain: SO:000110
def: "value indicating the nature of supporting evidence, distinguishing between experimentally determined and theoretically derived data" []
range: xsd:string
range_def: "experimental, not_experimental" []
comment: experimental indicates that the feature identification or assignment is supported by direct experimental evidence; not_experimental indicates that the data for the feature are derived (eg promotor as identified by consensus match). 

[Typedef]
id: GENBANK_SOFP:exception
name: exception
is_a: SOFP:feature_property
domain: SO:000110
def: "indicates that the amino acid or RNA sequence will not translate or agree with the DNA sequence according  to standard biological rules." []
range: xsd:string /exception='reasons given in citation'
comment: only to be used to describe biological mechanisms such  as RNA editing; where the exception cannot easily be described  a published citation must be referred to; protein translation of /exception CDS will be different from the according conceptual  translation;  - must not be used where transl_except would be adequate, e.g. in case of stop codon completion use: /transl_except=(pos:6883,aa:TERM) /note='TAA stop codon is completed by addition of 3' A  residues to mRNA'. - must not be used for ribosomal slippage, instead use join  operator, e.g.: CDS join(486..1784,1787..4810) /note='ribosomal slip on tttt sequence at 1784..1787'

[Typedef]
id: GENBANK_SOFP:focus
name: focus
is_a: SOFP:feature_property
domain: SO:000110
def: "defines the source feature of primary biological interest for  records that have multiple source features originating from  different organisms " []
range: xsd:boolean
comment: the /focus qualifier identifies the organism which is  displayed in the organism line and determines the  DDBJ/EMBL/GenBank taxonomic division the entry will appear in; if no translation table is specified, the organism with /focus  will define the translation table; within an entry with several  source features, only one will exist with /focus on it; multi-source entries with a /transgenic source feature  do not require a /focus qualifier.

[Typedef]
id: GENBANK_SOFP:frequency
name: frequency
is_a: SOFP:feature_property
domain: SO:000110
def: "frequency of the occurrence of a feature" []
range: xsd:string
range_def: "text representing the fraction of population carrying the variation expressed as a decimal fraction" []

[Typedef]
id: GENBANK_SOFP:function
name: function
is_a: SOFP:feature_property
domain: SO:000110
def: "function attributed to a sequence" []
range: xsd:string
comment: /function is used when the gene name and/or product name do not  convey the function attributable to a sequence.

[Typedef]
id: GENBANK_SOFP:gene
name: gene
is_a: SOFP:feature_property
domain: SO:000110
def: "symbol of the gene corresponding to a sequence region" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:germline
name: germline
is_a: SOFP:feature_property
domain: SO:000110
def: "if the sequence shown is DNA and a member of the immunoglobulin  family, this qualifier is used to denote that the sequence is from unrearranged DNA. " []
range: xsd:boolean
comment: /germline cannot be used in the same entry/record as /rearranged

[Typedef]
id: GENBANK_SOFP:haplotype
name: haplotype
is_a: SOFP:feature_property
domain: SO:000110
def: "haplotype of organism from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:insertion_seq
name: insertion_seq
is_a: SOFP:feature_property
domain: SO:000110
def: "insertion sequence element from which the sequence  was obtained" []
range: xsd:string
comment: /insertion_seq is legal on repeat_region feature key;   

[Typedef]
id: GENBANK_SOFP:isolate
name: isolate
is_a: SOFP:feature_property
domain: SO:000110
def: "individual isolate from which the sequence was obtained" []
range: xsd:string /isolate='DGGE band PSBAC-13'

[Typedef]
id: GENBANK_SOFP:isolation_source
name: isolation_source
is_a: SOFP:feature_property
domain: SO:000110
def: "describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived" []
range: xsd:string Pelleted ration-fed steer #67' /isolation_source='permanent Antarctic sea ice' /isolation_source='denitrifying activated sludge from carbon_limited continuous reactor' 
comment: used only with the source feature key; source feature keys containing an /environmental_sample qualifier should also contain an /isolation_source qualifier; the /country qualifier should be used to  describe the country and major geographical sub-region.

[Typedef]
id: GENBANK_SOFP:label
name: label
is_a: SOFP:feature_property
domain: SO:000110
def: "a label used to permanently tag a feature" []
range: xsd:string
range_def: "feature_label " []
comment: feature labels follow the naming conventions for all feature table objects (see Sections 3.1 and 3.4)

[Typedef]
id: GENBANK_SOFP:lab_host
name: lab_host
is_a: SOFP:feature_property
domain: SO:000110
def: "laboratory host used to propagate the organism from which the  sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:locus_tag
name: locus_tag
is_a: SOFP:feature_property
domain: SO:000110
def: "feature tag assigned for tracking purposes " [] but not '<1-5 letters><5-9 digit integer>[.<integer>]' /locus_tag='YPO0002'
comment: /locus_tag can be used with any feature where /gene is valid;  identical /locus_tag values may be used within an entry/record,  but only if the identical /locus_tag values are associated  with the same gene; in all other circumstances the /locus_tag  value must be unique within that entry/record. Multiple  /locus_tag values are not allowed within one feature for  entries created after 15-OCT-2004.  If a /locus_tag needs to be re-assigned the /old_locus_tag  qualifier should be used to store the old value. Existing  records where multiple /locus_tag qualifiers are present  will be retrofitted by January 2005.  The /locus_tag value should not be in a format which resembles  INSD accession numbers, accession.version, or /proteid_id  identifiers.

[Typedef]
id: GENBANK_SOFP:map
name: map
is_a: SOFP:feature_property
domain: SO:000110
def: "genomic map position of feature" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:macronuclear
name: macronuclear
is_a: SOFP:feature_property
domain: SO:000110
def: "if the sequence shown is DNA and from an organism which  undergoes chromosomal differentiation between macronuclear and micronuclear stages, this qualifier is used to denote that the  sequence is from macronuclear DNA. " []
range: xsd:boolean

[Typedef]
id: GENBANK_SOFP:mod_base
name: mod_base
is_a: SOFP:feature_property
domain: SO:000110
def: "abbreviation for a modified nucleotide base" []
range: xsd:string
comment: modified nucleotides not found in the restricted vocabulary list can be annotated by entering '/mod_base=OTHER' with '/note='name of modified base''

[Typedef]
id: GENBANK_SOFP:mol_type
name: mol_type
is_a: SOFP:feature_property
domain: SO:000110
def: "in vivo molecule type of sequence " []
range: xsd:string
range_def: "'genomic DNA', 'genomic RNA', 'mRNA', 'tRNA', 'rRNA', 'snoRNA', 'snRNA', 'scRNA', 'pre-RNA', 'other RNA', 'other DNA', 'unassigned DNA', 'unassigned RNA'" []
comment: these text values describe the in vivo molecule that has been sequenced and not the sequencing technique that has been used (e.g. mRNA is a valid value, cDNA is not); the value 'genomic DNA' does not imply that the molecule is nuclear (e.g. organelle and plasmid DNA should be described  using 'genomic DNA'); ribosomal RNA genes should be described using 'genomic DNA'; 'rRNA' should only be used if the ribosomal RNA molecule itself has been sequenced; /mol_type is mandatory on every source feature key; all /mol_type values within one entry/record must be the same; values 'other RNA' and 'other DNA' should be applied to  synthetic molecules, values 'unassigned DNA', 'unassigned  RNA' should be applied were in vivo molecule is unknown;

[Typedef]
id: GENBANK_SOFP:note
name: note
is_a: SOFP:feature_property
domain: SO:000110
def: "any comment or additional information" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:number
name: number
is_a: SOFP:feature_property
domain: SO:000110
def: "a number to indicate the order of genetic elements (e.g., exons or introns) in the 5' to 3' direction" []
range: xsd:string
range_def: "unquoted text (single token) " [] /number=6B
comment: text limited to integers, letters or combination of integers  and/or letters represented as an unquoted single token  (e.g. 5a, XIIb); any additional terms should be included in  /standard_name. Example: /number=2A /standard_name='long'

[Typedef]
id: GENBANK_SOFP:old_locus_tag
name: old_locus_tag
is_a: SOFP:feature_property
domain: SO:000110
def: "feature tag assigned for tracking purposes " [] /locus_tag='YPO0002'
comment: /old_locus_tag can be used with any feature where /gene is  valid and where a /locus_tag qualifier is present.  Identical /old_locus_tag values may be used within an  entry/record, but only if the identical /old_locus_tag values  are associated with the same gene; in all other circumstances  the /old_locus_tag value must be unique within that entry/record.  Multiple/old_locus_tag qualifiers with distinct values are  allowed within a single feature; /old_locus_tag and /locus_tag  values must not be identical within a single feature.

[Typedef]
id: GENBANK_SOFP:operon 
name: operon 
is_a: SOFP:feature_property
domain: SO:000110
def: "name of the operon the feature belongs to" []
range: xsd:string
comment: currently valid only on Prokaryota-specific features

[Typedef]
id: GENBANK_SOFP:organelle
name: organelle
is_a: SOFP:feature_property
domain: SO:000110
def: "type of membrane-bound intracellular structure from which the  sequence was obtained" []
range: xsd:string
range_def: "mitochondrion, nucleomorph, plastid, mitochondrion:kinetoplast, plastid:chloroplast, plastid:apicoplast, plastid:chromoplast, plastid:cyanelle, plastid:leucoplast, plastid:proplastid," [] /organelle='nucleomorph' /organelle='plastid' /organelle='mitochondrion:kinetoplast' /organelle='plastid:chloroplast' /organelle='plastid:apicoplast' /organelle='plastid:chromoplast' /organelle='plastid:cyanelle' /organelle='plastid:leucoplast' /organelle='plastid:proplastid'

[Typedef]
id: GENBANK_SOFP:organism
name: organism
is_a: SOFP:feature_property
domain: SO:000110
def: "scientific name of the organism that provided the  sequenced genetic material. " []
range: xsd:string
comment: the organism name which appears on the OS or ORGANISM line  will match the value of the /organism qualifier of the  source key in the simplest case of a one-source sequence. NOTE: in chado, this is redundant with the organism table

[Typedef]
id: GENBANK_SOFP:partial
name: partial
is_a: SOFP:feature_property
domain: SO:000110
def: "differentiates between complete regions and partial ones" []
range: xsd:boolean
comment: not to be used for new entries from 15-DEC-2001; use '<' and '>' signs in the location descriptors to indicate that the sequence is partial. 

[Typedef]
id: GENBANK_SOFP:PCR_conditions
name: PCR_conditions
is_a: SOFP:feature_property
domain: SO:000110
def: "description of reaction conditions and components for PCR " []
range: xsd:string
range_def: "'text' " []
comment: used with primer_bind key

[Typedef]
id: GENBANK_SOFP:phenotype
name: phenotype
is_a: SOFP:feature_property
domain: SO:000110
def: "phenotype conferred by the feature" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:pop_variant
name: pop_variant
is_a: SOFP:feature_property
domain: SO:000110
def: "population variant from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:plasmid
name: plasmid
is_a: SOFP:feature_property
domain: SO:000110
def: "name of plasmid from which sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:product
name: product
is_a: SOFP:feature_property
domain: SO:000110
def: "name of a product encoded by a sequence" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:protein_id
name: protein_id
is_a: SOFP:feature_property
domain: SO:000110
def: "protein identifier, issued by International collaborators. this qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point." []
range: xsd:string
comment: when the protein sequence encoded by the CDS changes, only  the version number of the /protein_id value is incremented;  the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. 

[Typedef]
id: GENBANK_SOFP:proviral
name: proviral
is_a: SOFP:feature_property
domain: SO:000110
def: "if the sequence shown is viral and integrated into another organism's genome, this qualifier is used to denote that " []
range: xsd:boolean
comment: /proviral cannot be used in the same entry/record as /virion

[Typedef]
id: GENBANK_SOFP:pseudo
name: pseudo
is_a: SOFP:feature_property
domain: SO:000110
def: "indicates that this feature is a non-functional version of the element named by the feature key" []
range: xsd:boolean

[Typedef]
id: GENBANK_SOFP:rearranged
name: rearranged
is_a: SOFP:feature_property
domain: SO:000110
def: "if the sequence shown is DNA and a member of the immunoglobulin  family, this qualifier is used to denote that the sequence is from rearranged DNA. " []
range: xsd:boolean
comment: /rearranged cannot be used in the same entry/record as /germline

[Typedef]
id: GENBANK_SOFP:replace
name: replace
is_a: SOFP:feature_property
domain: SO:000110
def: "indicates that the sequence identified a feature's intervals is replaced by the sequence shown in 'text'; if no sequence is  contained within the qualifier, this indicates a deletion." []
range: xsd:string /replace='' 

[Typedef]
id: GENBANK_SOFP:rpt_family
name: rpt_family
is_a: SOFP:feature_property
domain: SO:000110
def: "type of repeated sequence; 'Alu' or 'Kpn', for example" []
range: xsd:string
comment: preferred usage is to qualify the repeat_region instead of any of the constituent repeat_units

[Typedef]
id: GENBANK_SOFP:rpt_type
name: rpt_type
is_a: SOFP:feature_property
domain: SO:000110
def: "organization of repeated sequence" []
range: xsd:string
range_def: "tandem, inverted, flanking, terminal, direct, dispersed, and other" []
comment: preferred usage is to qualify the repeat_region instead of any of the constituent repeat_units. definitions of these values will be added in a future release of this document. see Singer, M. Int Rev Cytol 76, 67-112 (1982); Cell 26, 293-95 (1981); Hardman, N. Biochem J 234, 1-11 (1986).

[Typedef]
id: GENBANK_SOFP:rpt_unit
name: rpt_unit
is_a: SOFP:feature_property
domain: SO:000110
def: "identity of repeat unit" []
range: xsd:string
range_def: "'text' or <base_range>" [] /rpt_unit=202..245
comment: used to indicate the literal sequence, or the base range of the sequence that constitutes a repeat_region or a single repeat_unit; the repeat family name should not be entered in /rpt_unit='text'; /rpt_family should be used instead.

[Typedef]
id: GENBANK_SOFP:segment
name: segment
is_a: SOFP:feature_property
domain: SO:000110
def: "name of viral or phage segment sequenced" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:serotype
name: serotype
is_a: SOFP:feature_property
domain: SO:000110
def: "serological variety of a species characterized by its antigenic properties" []
range: xsd:string
comment: used only with the source feature key; the Bacteriological Code recommends the use of the term 'serovar' instead of 'serotype' for the  prokaryotes; see the International Code of Nomenclature of Bacteria (1990 Revision) Appendix 10.B 'Infraspecific Terms'.

[Typedef]
id: GENBANK_SOFP:serovar
name: serovar
is_a: SOFP:feature_property
domain: SO:000110
def: "serological variety of a species (usually a prokaryote) characterized by its antigenic properties" []
range: xsd:string
comment: used only with the source feature key; the Bacteriological Code recommends the use of the term 'serovar' instead of 'serotype' for prokaryotes; see the International Code of Nomenclature of Bacteria (1990 Revision) Appendix 10.B 'Infraspecific Terms'.

[Typedef]
id: GENBANK_SOFP:sex
name: sex
is_a: SOFP:feature_property
domain: SO:000110
def: "sex of the organism from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:specific_host
name: specific_host
is_a: SOFP:feature_property
domain: SO:000110
def: "natural host from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:specimen_voucher
name: specimen_voucher
is_a: SOFP:feature_property
domain: SO:000110
def: "an identifier of the individual or collection of the source organism and the place where it is currently stored, usually an institution." []
range: xsd:string Herbarium)'

[Typedef]
id: GENBANK_SOFP:standard_name
name: standard_name
is_a: SOFP:feature_property
domain: SO:000110
def: "accepted standard name for this feature" []
range: xsd:string
comment: use /standard_name to give full gene name, but use /gene to give gene symbol (in the above example /gene='Dt').

[Typedef]
id: GENBANK_SOFP:strain
name: strain
is_a: SOFP:feature_property
domain: SO:000110
def: "strain from which sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:sub_clone
name: sub_clone
is_a: SOFP:feature_property
domain: SO:000110
def: "sub-clone from which sequence was obtained" []
range: xsd:string
comment: the comments on /clone apply to /sub_clone

[Typedef]
id: GENBANK_SOFP:sub_species
name: sub_species
is_a: SOFP:feature_property
domain: SO:000110
def: "name of sub-species of organism from which sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:sub_strain
name: sub_strain
is_a: SOFP:feature_property
domain: SO:000110
def: "sub_strain from which sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:tissue_lib
name: tissue_lib
is_a: SOFP:feature_property
domain: SO:000110
def: "tissue library from which sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:tissue_type
name: tissue_type
is_a: SOFP:feature_property
domain: SO:000110
def: "tissue type from which the sequence was obtained" []
range: xsd:string

[Typedef]
id: GENBANK_SOFP:transgenic
name: transgenic
is_a: SOFP:feature_property
domain: SO:000110
def: "identifies the source feature of the organism which was the recipient of transgenic DNA" []
range: xsd:boolean
comment: transgenic sequences must at least have two source  feature keys; the source feature key describing the  organism of the recipient DNA must span the whole  sequence; the /transgenic qualifier identifies the  organism which is displayed in the organism line and  determines that the entry will appear in the  DDBJ/EMBL/GenBank Synthetic Construct division; multi-source entries including a /transgenic source  feature should not have a /focus qualifier.  

[Typedef]
id: GENBANK_SOFP:translation
name: translation
is_a: SOFP:feature_property
domain: SO:000110
def: "automatically generated one-letter abbreviated amino acid sequence derived from either the universal genetic code or the table as specified in /transl_table and as determined by exceptions in the /transl_except and /codon qualifiers" []
range: xsd:string
range_def: "IUPAC one-letter amino acid abbreviation, 'X' is to be used for AA exceptions." []
comment: to be used with CDS feature only; this is a mandatory qualifier  to the CDS feature key except for /pseudo CDSs; see /transl_table for definition and location of genetic code Tables. 

[Typedef]
id: GENBANK_SOFP:transl_except
name: transl_except
is_a: SOFP:feature_property
domain: SO:000110
def: "translational exception: single codon the translation of which does not conform to genetic code defined by Organism and /codon=" []
range: xsd:string
range_def: "(pos:location,aa:<amino_acid>) where amino_acid is the amino acid coded by the codon at the base_range position" [] /transl_except=(pos:1017,aa:TERM) /transl_except=(pos:2000..2001,aa:TERM) /transl_except=(pos:X22222:15..17,aa:Ala)
comment: if the amino acid is not on the restricted vocabulary list use e.g., '/transl_except=(pos:213..215,aa:OTHER)' with '/note='name of unusual amino acid''; for modified amino-acid selenocysteine use three letter code 'Sec' (one letter code 'U' in amino-acid sequence) /transl_except=(pos:1002..1004,aa:Sec); for partial termination codons where TAA stop codon is completed by the addition of 3' A residues to the mRNA either a single base_position or a base_range is used, e.g. if partial stop codon is a single base: /transl_except=(pos:1017,aa:TERM) if partial stop codon consists of two bases: /transl_except=(pos:2000..2001,aa:TERM) with '/note='stop codon completed by the addition of 3' A residues  to the mRNA'.

[Typedef]
id: GENBANK_SOFP:transl_table
name: transl_table
is_a: SOFP:feature_property
domain: SO:000110
def: "definition of genetic code table used if other than universal genetic code table. Tables used are described in appendix V, section 7.5.5." []
range: xsd:integer
range_def: "<integer; 1=universal table 1;2=non-universal table 2;..." []
comment: genetic code exceptions outside range of specified tables are reported in /codon or /transl_except qualifiers.

[Typedef]
id: GENBANK_SOFP:transposon
name: transposon
is_a: SOFP:feature_property
domain: SO:000110
def: "transposable element from which the sequence was  obtained" []
range: xsd:string
comment: /transposon is legal on repeat_region feature key; 

[Typedef]
id: GENBANK_SOFP:usedin
name: usedin
is_a: SOFP:feature_property
domain: SO:000110
def: "indicates that the feature is used in a compound feature in another entry" []
range: xsd:string
range_def: "Accession-number:feature-name or  Database_name::Acc_number:feature_label" []
comment: database_name is an abbreviation for the name of the database in which the entry for the accession number can be found.

[Typedef]
id: GENBANK_SOFP:variety
name: variety
is_a: SOFP:feature_property
domain: SO:000110
def: "variety (= varietas, a formal Linnaean rank) of organism  from which sequence was derived." []
range: xsd:string
comment: use the cultivar qualifier for cultivated plant  varieties, i.e., products of artificial selection; varieties other than plant and fungal variatas should be annotated via /note, e.g. /note='breed:Cukorova'

[Typedef]
id: GENBANK_SOFP:virion
name: virion
is_a: SOFP:feature_property
domain: SO:000110
def: "viral genomic sequence as it is encapsidated (distinguished  from its proviral form integrated in a host cell's chromosome) " []
range: xsd:boolean
comment: /virion cannot be used in the same entry/record as /proviral
