TEMP
type: Ontology
auto-generated-by: OBO-Edit 2.2
date: 18:07:2013 16:25
default-namespace: sbol
has_obo_format_version: 1.2
saved-by: jackie

definition
type: AnnotationProperty

amino acid modification
type: AnnotationProperty
sub property of: synonym_type_property

biosapiens
type: AnnotationProperty
sub property of: synonym_type_property

DBVAR
type: AnnotationProperty
comment: database of genomic structural variation
sub property of: subset_property

RNA modification
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

SBOLV
type: AnnotationProperty
comment: SBOL Visual represented terms
sub property of: subset_property

SOFA
type: AnnotationProperty
comment: SO feature annotation
sub property of: subset_property

amino acid 1 letter code
type: AnnotationProperty
sub property of: synonym_type_property

amino acid 3 letter code
type: AnnotationProperty
sub property of: synonym_type_property

biosapiens
type: AnnotationProperty
comment: biosapiens protein feature ontology
sub property of: subset_property

dbsnp variant terms
type: AnnotationProperty
sub property of: synonym_type_property

DBVAR
type: AnnotationProperty
sub property of: synonym_type_property

ensembl variant terms
type: AnnotationProperty
sub property of: synonym_type_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

in_subset
type: AnnotationProperty

has_property
type: ObjectProperty
created by: jackie
creation date: 2013-07-17T01:58:14Z
has_obo_namespace: sbol
id: has_property

is_property_of
type: ObjectProperty
created by: jackie
creation date: 2013-07-17T01:56:48Z
has_obo_namespace: sbol
id: is_property_of

is_represented_by
type: ObjectProperty
inverse of: represents
type: TransitiveProperty
created by: jackie
creation date: 2013-07-17T23:02:30Z
has_obo_namespace: sbol
id: is_represented_by

represents
type: ObjectProperty
type: TransitiveProperty
definition: Reference image symbolizes represented entity.
created by: jackie
creation date: 2013-07-17T01:26:09Z
has_obo_namespace: sbol
id: represents

SBOL Visual Symbol
type: Class
subclass of: Restriction
  on property: represents
  some values from: DNAComponent
definition: Pictogram that serves as representation of a DNAComponent, indicating the function of the DNAComponent in the enclosing design.
created by: jackie
creation date: 2013-04-11T15:19:00Z
has_obo_namespace: sbol
id: SBOL:0000000

promoter symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: promoter
definition: Symbol to represent a regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
created by: jackie
creation date: 2013-04-11T15:19:30Z
database_cross_reference: SO:0000167
has_obo_namespace: sbol
id: SBOL:0000001

assembly scar symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends.
created by: jackie
creation date: 2013-04-11T15:25:29Z
has_obo_namespace: sbol
id: SBOL:0000002

operator symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: operator
definition: Symbol to represent a regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0000057
has_obo_namespace: sbol
id: SBOL:0000003

cds symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: CDS
definition: Symbol to represent a contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0000316
has_obo_namespace: sbol
id: SBOL:0000004

ribosome entry site symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: ribosome_entry_site
definition: Symbol to represent a region in mRNA where ribosome assembles.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0000139
has_obo_namespace: sbol
id: SBOL:0000005

terminator symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: terminator
definition: Symbol to represent the sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0000141
has_obo_namespace: sbol
id: SBOL:0000006

insulator symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: insulator
definition: Symbol to represent a transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0000627
has_obo_namespace: sbol
id: SBOL:0000007

ribonuclease site symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: origin_of_replication
definition: Symbol to represent a region of DNA sequence that codes for a ribonuclease cleavage site on the RNA transcript.
created by: jackie
creation date: 2013-04-11T18:23:06Z
has_obo_namespace: sbol
id: SBOL:0000008

rna stability element symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a RNA secondary structure that affects the stability of an RNA molecule.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001957
has_obo_namespace: sbol
id: SBOL:0000009

protease site symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a polypeptide_region that codes for a protease cleavage site.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001956
has_obo_namespace: sbol
id: SBOL:0000010

protein stability element symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a polypeptide region that proves structure in a protein that affects the stability of the protein.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001955
has_obo_namespace: sbol
id: SBOL:0000011

origin of replication symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent the origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0000296
has_obo_namespace: sbol
id: SBOL:0000012

Axiom
annotated source: origin of replication symbol
annotated property: definition
annotated target: Symbol to represent the origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
database_cross_reference: SO:0000296

primer binding site symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0005850
has_obo_namespace: sbol
id: SBOL:0000013

restriction enzyme recognition site symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001687
has_obo_namespace: sbol
id: SBOL:0000014

blunt restriction site symbol
type: Class
subclass of: restriction enzyme recognition site symbol
definition: Symbol to represent a restriction enzyme recognition site that, when cleaved, results in no overhangs.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001691
has_obo_namespace: sbol
id: SBOL:0000015

5' sticky restriction site symbol
type: Class
subclass of: restriction enzyme recognition site symbol
definition: Symbol to represent a restriction enzyme recognition site that, when cleaved, results in 5-prime overhangs.
created by: jackie
creation date: 2013-04-11T18:23:06Z
has_obo_namespace: sbol
id: SBOL:0000016

3' sticky restriction site symbol
type: Class
subclass of: restriction enzyme recognition site symbol
definition: Symbol to represent a restriction enzyme recognition site that, when cleaved, results in 3-prime overhangs.
created by: jackie
creation date: 2013-04-11T18:23:06Z
has_obo_namespace: sbol
id: SBOL:0000017

5' overhang symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: restriction_enzyme_single_strand_overhang
definition: Symbol to represent a terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001932
has_obo_namespace: sbol
id: SBOL:0000018

3' overhang symbol
type: Class
subclass of: SBOL Visual Symbol
subclass of: Restriction
  on property: represents
  some values from: restriction_enzyme_single_strand_overhang
definition: Symbol to represent a terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.
created by: jackie
creation date: 2013-04-11T18:23:06Z
database_cross_reference: SO:0001933
has_obo_namespace: sbol
id: SBOL:0000019

signature symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a region of DNA sequence where developer information is encoded.
created by: jackie
creation date: 2013-04-11T18:23:06Z
has_obo_namespace: sbol
id: SBOL:0000020

user defined symbol
type: Class
subclass of: SBOL Visual Symbol
definition: Symbol to represent a region of a DNA sequence not covered by other SBOL Visual symbols.
created by: jackie
creation date: 2013-04-11T18:23:06Z
has_obo_namespace: sbol
id: SBOL:0000021

SBOL:Core Term
type: Class
created by: jackie
creation date: 2013-07-17T01:44:12Z
has_obo_namespace: sbol
id: SBOL:0000022
deprecated: true

DNAComponent
type: Class
definition: A DNA component represents a segment of DNA that serves to abstract the DNA sequence as an individual object, which can then be manipulated, combined, and reused in engineering new biological systems.
created by: jackie
creation date: 2013-07-17T01:27:13Z
has_obo_namespace: sbol
id: SBOL:0000023

Collection
type: Class
definition: Collection A collection is an organizational container, a group of DnaComponents. For example, a set of restriction enzyme recognition sites, such as the components commonly used for BBF RFC 10 BioBricks could be grouped. A Collection might contain DNA components used in a specific project, lab, or custom grouping specified by the user.
created by: jackie
creation date: 2013-07-17T01:45:49Z
has_obo_namespace: sbol
id: SBOL:0000024

DNASequence
type: Class
definition: DNA Sequence The DNA sequence is a contiguous sequence of nucleotides. The sequence is a fundamental information object for synthetic biology and is needed to reuse components, replicate synthetic biology work, and to assemble new synthetic biological systems. Therefore, both experimental work and theoretical sequence composition research depend heavily on the exact base pair sequence specification associated with DnaComponents.
created by: jackie
creation date: 2013-07-17T01:46:01Z
has_obo_namespace: sbol
id: SBOL:0000025

SequenceAnnotation
type: Class
definition: Sequence Annotation The sequence annotation is the position and strand orientation of a notable sub-sequence found within the DnaComponent being described. Annotations provide the link which describes the DNA sequence of a component in terms of other components, subComponents. When a DNA component is abstract, SequenceAnnotations specify relative positions between subComponents.
created by: jackie
creation date: 2013-07-17T01:48:15Z
has_obo_namespace: sbol
id: SBOL:0000026

type
type: Class
subclass of: Restriction
  on property: is_property_of
  some values from: DNAComponent
definition: Zero or more values of type URI (IETF RFC 2396) referencing the Sequence Ontology (see Appendix for commonly used terms). These provide a defined terminology of types of DnaComponents. This vocabulary may be extended, (use "Request a Term" http://sequenceontology.org).
created by: jackie
creation date: 2013-07-17T01:53:34Z
has_obo_namespace: sbol
id: SBOL:0000027

operator
type: Class
subclass of: type
definition: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
database_cross_reference: http://en.wikipedia.org/wiki/Operator_(biology)#Operator
has_exact_synonym: operator segment
has_obo_namespace: sequence
id: SO:0000057
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: operator
annotated property: definition
annotated target: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: operator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Operator_(biology)#Operator

ribosome_entry_site
type: Class
subclass of: type
definition: Region in mRNA where ribosome assembles.
has_exact_synonym: ribosome entry site
has_obo_namespace: sequence
id: SO:0000139
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: ribosome_entry_site
annotated property: definition
annotated target: Region in mRNA where ribosome assembles.
database_cross_reference: SO:ke

terminator
type: Class
subclass of: type
definition: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
database_cross_reference: http://en.wikipedia.org/wiki/Terminator_(genetics)
has_exact_synonym: terminator sequence
has_obo_namespace: sequence
id: SO:0000141
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: terminator
annotated property: definition
annotated target: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
database_cross_reference: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

wiki
type: Axiom
annotated source: terminator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Terminator_(genetics)

promoter
type: Class
subclass of: type
definition: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
has_exact_synonym: promoter sequence
has_obo_namespace: sequence
id: SO:0000167
in_subset: SBOLV
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.

Axiom
annotated source: promoter
annotated property: definition
annotated target: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
database_cross_reference: SO:regcreative

origin_of_replication
type: Class
subclass of: type
definition: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
database_cross_reference: http://en.wikipedia.org/wiki/Origin_of_replication
has_exact_synonym: ori
has_exact_synonym: origin of replication
has_obo_namespace: sequence
id: SO:0000296
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: origin_of_replication
annotated property: definition
annotated target: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
database_cross_reference: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

wiki
type: Axiom
annotated source: origin_of_replication
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Origin_of_replication

CDS
type: Class
subclass of: type
definition: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
has_exact_synonym: coding sequence
has_obo_namespace: sequence
id: SO:0000316
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: CDS
annotated property: definition
annotated target: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
database_cross_reference: SO:ma

Shine_Dalgarno_sequence
type: Class
subclass of: ribosome_entry_site
definition: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
database_cross_reference: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
has_exact_synonym: Shine Dalgarno sequence
has_exact_synonym: Shine-Dalgarno sequence
has_exact_synonym: five prime ribosome binding site
has_obo_namespace: sequence
has_related_synonym: RBS
id: SO:0000552
in_subset: SBOLV
comment: Not found in Eukaryotic sequence.

Axiom
annotated source: Shine_Dalgarno_sequence
annotated property: definition
annotated target: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
database_cross_reference: SO:jh

wiki
type: Axiom
annotated source: Shine_Dalgarno_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence

insulator
type: Class
subclass of: type
definition: A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
database_cross_reference: http://en.wikipedia.org/wiki/Insulator_(genetics)
has_exact_synonym: insulator element
has_obo_namespace: sequence
id: SO:0000627
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: insulator
annotated property: definition
annotated target: A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
database_cross_reference: SO:regcreative

wiki
type: Axiom
annotated source: insulator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Insulator_(genetics)

kozak_sequence
type: Class
subclass of: ribosome_entry_site
definition: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
created by: kareneilbeck
creation date: 2010-06-07T03:12:20Z
database_cross_reference: http://en.wikipedia.org/wiki/Kozak_consensus_sequence
has_exact_synonym: kozak consensus
has_exact_synonym: kozak consensus sequence
has_exact_synonym: kozak sequence
has_obo_namespace: sequence
id: SO:0001647
in_subset: SBOLV
in_subset: SOFA

Axiom
annotated source: kozak_sequence
annotated property: definition
annotated target: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
database_cross_reference: SO:ke

wikipedia
type: Axiom
annotated source: kozak_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Kozak_consensus_sequence

restriction_enzyme_recognition_site
type: Class
subclass of: type
definition: The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
created by: kareneilbeck
creation date: 2010-10-29T12:29:57Z
has_exact_synonym: restriction endonuclease recognition site
has_exact_synonym: restriction enzyme recognition site
has_obo_namespace: sequence
id: SO:0001687
in_subset: SBOLV

Axiom
annotated source: restriction_enzyme_recognition_site
annotated property: definition
annotated target: The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
database_cross_reference: SO:ke

blunt_end_restriction_enzyme_cleavage_site
type: Class
subclass of: restriction_enzyme_recognition_site
created by: kareneilbeck
creation date: 2010-10-29T12:39:53Z
has_exact_synonym: blunt end restriction enzyme cleavage site
has_obo_namespace: sequence
id: SO:0001691
in_subset: SBOLV

sticky_end_restriction_enzyme_cleavage_site
type: Class
subclass of: restriction_enzyme_recognition_site
created by: kareneilbeck
creation date: 2010-10-29T12:40:50Z
has_obo_namespace: sequence
has_related_synonym: sticky end restriction enzyme cleavage site
id: SO:0001692
in_subset: SBOLV

restriction_enzyme_single_strand_overhang
type: Class
subclass of: type
definition: A terminal region of DNA sequence where the end of the region is not blunt ended.
created by: kareneilbeck
creation date: 2010-10-29T12:48:35Z
has_exact_synonym: single strand overhang
has_obo_namespace: sequence
has_related_synonym: sticky end
id: SO:0001695
in_subset: SBOLV

Axiom
annotated source: restriction_enzyme_single_strand_overhang
annotated property: definition
annotated target: A terminal region of DNA sequence where the end of the region is not blunt ended.
database_cross_reference: SO:ke