OBO-Edit 2.2
18:07:2013 16:25
sbol
1.2
jackie
definition
amino acid modification
biosapiens
database of genomic structural variation
RNA modification
SBOL Visual represented terms
SO feature annotation
amino acid 1 letter code
amino acid 3 letter code
biosapiens protein feature ontology
dbsnp variant terms
DBVAR
ensembl variant terms
subset_property
synonym_type_property
database_cross_reference
has_exact_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
in_subset
jackie
2013-07-17T01:58:14Z
sbol
has_property
has_property
jackie
2013-07-17T23:02:30Z
sbol
is_represented_by
is_represented_by
Pictogram that serves as representation of a DNAComponent, indicating the function of the DNAComponent in the enclosing design.
jackie
2013-04-11T15:19:00Z
sbol
SBOL:0000000
SBOL Visual Symbol
SBOL:0000000
Symbol to represent a regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
jackie
2013-04-11T15:19:30Z
SO:0000167
sbol
SBOL:0000001
promoter symbol
SBOL:0000001
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.
jackie
2013-04-11T15:25:29Z
sbol
SBOL:0000002
assembly scar symbol
SBOL:0000002
Symbol to represent a regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
jackie
2013-04-11T18:23:06Z
SO:0000057
sbol
SBOL:0000003
operator symbol
SBOL:0000003
Symbol to represent a contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
jackie
2013-04-11T18:23:06Z
SO:0000316
sbol
SBOL:0000004
cds symbol
SBOL:0000004
Symbol to represent a region in mRNA where ribosome assembles.
jackie
2013-04-11T18:23:06Z
SO:0000139
sbol
SBOL:0000005
ribosome entry site symbol
SBOL:0000005
Symbol to represent the sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
jackie
2013-04-11T18:23:06Z
SO:0000141
sbol
SBOL:0000006
terminator symbol
SBOL:0000006
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.
jackie
2013-04-11T18:23:06Z
SO:0000627
sbol
SBOL:0000007
insulator symbol
SBOL:0000007
Symbol to represent a region of DNA sequence that codes for a ribonuclease cleavage site on the RNA transcript.
jackie
2013-04-11T18:23:06Z
sbol
SBOL:0000008
ribonuclease site symbol
SBOL:0000008
Symbol to represent a RNA secondary structure that affects the stability of an RNA molecule.
jackie
2013-04-11T18:23:06Z
SO:0001957
sbol
SBOL:0000009
rna stability element symbol
SBOL:0000009
Symbol to represent a polypeptide_region that codes for a protease cleavage site.
jackie
2013-04-11T18:23:06Z
SO:0001956
sbol
SBOL:0000010
protease site symbol
SBOL:0000010
Symbol to represent a polypeptide region that proves structure in a protein that affects the stability of the protein.
jackie
2013-04-11T18:23:06Z
SO:0001955
sbol
SBOL:0000011
protein stability element symbol
SBOL:0000011
Symbol to represent the origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
jackie
2013-04-11T18:23:06Z
SO:0000296
sbol
SBOL:0000012
origin of replication symbol
SBOL:0000012
Symbol to represent the origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
SO:0000296
Symbol to represent a non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.
jackie
2013-04-11T18:23:06Z
SO:0005850
sbol
SBOL:0000013
primer binding site symbol
SBOL:0000013
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.
jackie
2013-04-11T18:23:06Z
SO:0001687
sbol
SBOL:0000014
restriction enzyme recognition site symbol
SBOL:0000014
Symbol to represent a restriction enzyme recognition site that, when cleaved, results in no overhangs.
jackie
2013-04-11T18:23:06Z
SO:0001691
sbol
SBOL:0000015
blunt restriction site symbol
SBOL:0000015
Symbol to represent a restriction enzyme recognition site that, when cleaved, results in 5-prime overhangs.
jackie
2013-04-11T18:23:06Z
sbol
SBOL:0000016
5' sticky restriction site symbol
SBOL:0000016
Symbol to represent a restriction enzyme recognition site that, when cleaved, results in 3-prime overhangs.
jackie
2013-04-11T18:23:06Z
sbol
SBOL:0000017
3' sticky restriction site symbol
SBOL:0000017
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.
jackie
2013-04-11T18:23:06Z
SO:0001932
sbol
SBOL:0000018
5' overhang symbol
SBOL:0000018
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.
jackie
2013-04-11T18:23:06Z
SO:0001933
sbol
SBOL:0000019
3' overhang symbol
SBOL:0000019
Symbol to represent a region of DNA sequence where developer information is encoded.
jackie
2013-04-11T18:23:06Z
sbol
SBOL:0000020
signature symbol
SBOL:0000020
Symbol to represent a region of a DNA sequence not covered by other SBOL Visual symbols.
jackie
2013-04-11T18:23:06Z
sbol
SBOL:0000021
user defined symbol
SBOL:0000021
jackie
2013-07-17T01:44:12Z
sbol
SBOL:0000022
SBOL:Core Term
true
SBOL:0000022
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.
jackie
2013-07-17T01:27:13Z
sbol
SBOL:0000023
DNAComponent
SBOL:0000023
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.
jackie
2013-07-17T01:45:49Z
sbol
SBOL:0000024
Collection
SBOL:0000024
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.
jackie
2013-07-17T01:46:01Z
sbol
SBOL:0000025
DNASequence
SBOL:0000025
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.
jackie
2013-07-17T01:48:15Z
sbol
SBOL:0000026
SequenceAnnotation
SBOL:0000026
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).
jackie
2013-07-17T01:53:34Z
sbol
SBOL:0000027
type
SBOL:0000027
A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
http://en.wikipedia.org/wiki/Operator_(biology)#Operator
operator segment
sequence
SO:0000057
operator
SO:0000057
A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
SO:ma
http://en.wikipedia.org/wiki/Operator_(biology)#Operator
wiki
Region in mRNA where ribosome assembles.
ribosome entry site
sequence
SO:0000139
ribosome_entry_site
SO:0000139
Region in mRNA where ribosome assembles.
SO:ke
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
http://en.wikipedia.org/wiki/Terminator_(genetics)
terminator sequence
sequence
SO:0000141
terminator
SO:0000141
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://en.wikipedia.org/wiki/Terminator_(genetics)
wiki
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
promoter sequence
sequence
SO:0000167
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.
promoter
SO:0000167
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
SO:regcreative
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
http://en.wikipedia.org/wiki/Origin_of_replication
ori
origin of replication
sequence
SO:0000296
origin_of_replication
SO:0000296
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://en.wikipedia.org/wiki/Origin_of_replication
wiki
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
coding sequence
sequence
SO:0000316
CDS
SO:0000316
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
SO:ma
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
Shine Dalgarno sequence
Shine-Dalgarno sequence
five prime ribosome binding site
sequence
RBS
SO:0000552
Not found in Eukaryotic sequence.
Shine_Dalgarno_sequence
SO:0000552
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
SO:jh
http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
wiki
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
http://en.wikipedia.org/wiki/Insulator_(genetics)
insulator element
sequence
SO:0000627
insulator
SO:0000627
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
SO:regcreative
http://en.wikipedia.org/wiki/Insulator_(genetics)
wiki
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
kareneilbeck
2010-06-07T03:12:20Z
http://en.wikipedia.org/wiki/Kozak_consensus_sequence
kozak consensus
kozak consensus sequence
kozak sequence
sequence
SO:0001647
kozak_sequence
SO:0001647
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
SO:ke
http://en.wikipedia.org/wiki/Kozak_consensus_sequence
wikipedia
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.
kareneilbeck
2010-10-29T12:29:57Z
restriction endonuclease recognition site
restriction enzyme recognition site
sequence
SO:0001687
restriction_enzyme_recognition_site
SO:0001687
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.
SO:ke
kareneilbeck
2010-10-29T12:39:53Z
blunt end restriction enzyme cleavage site
sequence
SO:0001691
blunt_end_restriction_enzyme_cleavage_site
SO:0001691
kareneilbeck
2010-10-29T12:40:50Z
sequence
sticky end restriction enzyme cleavage site
SO:0001692
sticky_end_restriction_enzyme_cleavage_site
SO:0001692
A terminal region of DNA sequence where the end of the region is not blunt ended.
kareneilbeck
2010-10-29T12:48:35Z
single strand overhang
sequence
sticky end
SO:0001695
restriction_enzyme_single_strand_overhang
SO:0001695
A terminal region of DNA sequence where the end of the region is not blunt ended.
SO:ke
OBO-Edit 2.2
18:07:2013 16:25
sbol
1.2
jackie
jackie
2013-07-17T01:56:48Z
sbol
is_property_of
is_property_of
Reference image symbolizes represented entity.
jackie
2013-07-17T01:26:09Z
sbol
represents
represents