format-version: 1.2 date: 18:07:2013 16:25 saved-by: jackie auto-generated-by: OBO-Edit 2.2 subsetdef: biosapiens "biosapiens protein feature ontology" subsetdef: DBVAR "database of genomic structural variation" subsetdef: SBOLV "SBOL Visual represented terms" subsetdef: SOFA "SO feature annotation" synonymtypedef: aa1 "amino acid 1 letter code" synonymtypedef: aa3 "amino acid 3 letter code" synonymtypedef: AAMOD "amino acid modification" synonymtypedef: BS "biosapiens" synonymtypedef: dbsnp "dbsnp variant terms" synonymtypedef: dbvar "DBVAR" synonymtypedef: ebi_variants "ensembl variant terms" synonymtypedef: RNAMOD "RNA modification" EXACT default-namespace: sbol [Term] id: SBOL:0000000 name: SBOL Visual Symbol def: "Pictogram that serves as representation of a DNAComponent, indicating the function of the DNAComponent in the enclosing design." [] relationship: represents SBOL:0000023 ! DNAComponent created_by: jackie creation_date: 2013-04-11T15:19:00Z [Term] id: SBOL:0000001 name: promoter symbol def: "Symbol to represent a regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [] xref: SO:0000167 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000167 ! promoter created_by: jackie creation_date: 2013-04-11T15:19:30Z [Term] id: SBOL:0000002 name: assembly scar symbol def: "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." [] is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T15:25:29Z [Term] id: SBOL:0000003 name: operator symbol def: "Symbol to represent a regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [] xref: SO:0000057 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000057 ! operator created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000004 name: cds symbol def: "Symbol to represent a contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [] xref: SO:0000316 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000316 ! CDS created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000005 name: ribosome entry site symbol def: "Symbol to represent a region in mRNA where ribosome assembles." [] xref: SO:0000139 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000139 ! ribosome_entry_site created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000006 name: terminator symbol def: "Symbol to represent the sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [] xref: SO:0000141 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000141 ! terminator created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000007 name: insulator symbol def: "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." [] xref: SO:0000627 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000627 ! insulator created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000008 name: ribonuclease site symbol def: "Symbol to represent a region of DNA sequence that codes for a ribonuclease cleavage site on the RNA transcript." [] is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0000296 ! origin_of_replication created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000009 name: rna stability element symbol def: "Symbol to represent a RNA secondary structure that affects the stability of an RNA molecule." [] xref: SO:0001957 is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000010 name: protease site symbol def: "Symbol to represent a polypeptide_region that codes for a protease cleavage site." [] xref: SO:0001956 is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000011 name: protein stability element symbol def: "Symbol to represent a polypeptide region that proves structure in a protein that affects the stability of the protein." [] xref: SO:0001955 is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000012 name: origin of replication symbol def: "Symbol to represent the origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [SO:0000296] xref: SO:0000296 is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000013 name: primer binding site symbol def: "Symbol to represent a non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [] xref: SO:0005850 is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000014 name: restriction enzyme recognition site symbol def: "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." [] xref: SO:0001687 is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000015 name: blunt restriction site symbol def: "Symbol to represent a restriction enzyme recognition site that, when cleaved, results in no overhangs." [] xref: SO:0001691 is_a: SBOL:0000014 ! restriction enzyme recognition site symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000016 name: 5' sticky restriction site symbol def: "Symbol to represent a restriction enzyme recognition site that, when cleaved, results in 5-prime overhangs." [] is_a: SBOL:0000014 ! restriction enzyme recognition site symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000017 name: 3' sticky restriction site symbol def: "Symbol to represent a restriction enzyme recognition site that, when cleaved, results in 3-prime overhangs." [] is_a: SBOL:0000014 ! restriction enzyme recognition site symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000018 name: 5' overhang symbol def: "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." [] xref: SO:0001932 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0001695 ! restriction_enzyme_single_strand_overhang created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000019 name: 3' overhang symbol def: "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." [] xref: SO:0001933 is_a: SBOL:0000000 ! SBOL Visual Symbol relationship: represents SO:0001695 ! restriction_enzyme_single_strand_overhang created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000020 name: signature symbol def: "Symbol to represent a region of DNA sequence where developer information is encoded." [] is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000021 name: user defined symbol def: "Symbol to represent a region of a DNA sequence not covered by other SBOL Visual symbols." [] is_a: SBOL:0000000 ! SBOL Visual Symbol created_by: jackie creation_date: 2013-04-11T18:23:06Z [Term] id: SBOL:0000022 name: SBOL:Core Term is_obsolete: true created_by: jackie creation_date: 2013-07-17T01:44:12Z [Term] id: SBOL:0000023 name: DNAComponent def: "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 [Term] id: SBOL:0000024 name: Collection def: "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 \ngrouping specified by the user." [] created_by: jackie creation_date: 2013-07-17T01:45:49Z [Term] id: SBOL:0000025 name: DNASequence def: "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 [Term] id: SBOL:0000026 name: SequenceAnnotation def: "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 [Term] id: SBOL:0000027 name: type def: "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)." [] relationship: is_property_of SBOL:0000023 ! DNAComponent created_by: jackie creation_date: 2013-07-17T01:53:34Z [Term] id: SO:0000057 name: operator namespace: sequence def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] subset: SBOLV subset: SOFA synonym: "operator segment" EXACT [] xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki" is_a: SBOL:0000027 ! type [Term] id: SO:0000139 name: ribosome_entry_site namespace: sequence def: "Region in mRNA where ribosome assembles." [SO:ke] subset: SBOLV subset: SOFA synonym: "ribosome entry site" EXACT [] is_a: SBOL:0000027 ! type [Term] id: SO:0000141 name: terminator namespace: sequence def: "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] subset: SBOLV subset: SOFA synonym: "terminator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" is_a: SBOL:0000027 ! type [Term] id: SO:0000167 name: promoter namespace: sequence def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] 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. subset: SBOLV subset: SOFA synonym: "promoter sequence" EXACT [] is_a: SBOL:0000027 ! type [Term] id: SO:0000296 name: origin_of_replication namespace: sequence def: "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] subset: SBOLV subset: SOFA synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SBOL:0000027 ! type [Term] id: SO:0000316 name: CDS namespace: sequence def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] subset: SBOLV subset: SOFA synonym: "coding sequence" EXACT [] is_a: SBOL:0000027 ! type [Term] id: SO:0000552 name: Shine_Dalgarno_sequence namespace: sequence def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh] comment: Not found in Eukaryotic sequence. subset: SBOLV synonym: "five prime ribosome binding site" EXACT [] synonym: "RBS" RELATED [] synonym: "Shine Dalgarno sequence" EXACT [] synonym: "Shine-Dalgarno sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000627 name: insulator namespace: sequence def: "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] subset: SBOLV subset: SOFA synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SBOL:0000027 ! type [Term] id: SO:0001647 name: kozak_sequence namespace: sequence def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] subset: SBOLV subset: SOFA synonym: "kozak consensus" EXACT [] synonym: "kozak consensus sequence" EXACT [] synonym: "kozak sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia" is_a: SO:0000139 ! ribosome_entry_site created_by: kareneilbeck creation_date: 2010-06-07T03:12:20Z [Term] id: SO:0001687 name: restriction_enzyme_recognition_site namespace: sequence def: "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] subset: SBOLV synonym: "restriction endonuclease recognition site" EXACT [] synonym: "restriction enzyme recognition site" EXACT [] is_a: SBOL:0000027 ! type created_by: kareneilbeck creation_date: 2010-10-29T12:29:57Z [Term] id: SO:0001691 name: blunt_end_restriction_enzyme_cleavage_site namespace: sequence subset: SBOLV synonym: "blunt end restriction enzyme cleavage site" EXACT [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:39:53Z [Term] id: SO:0001692 name: sticky_end_restriction_enzyme_cleavage_site namespace: sequence subset: SBOLV synonym: "sticky end restriction enzyme cleavage site" RELATED [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:40:50Z [Term] id: SO:0001695 name: restriction_enzyme_single_strand_overhang namespace: sequence def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] subset: SBOLV synonym: "single strand overhang" EXACT [] synonym: "sticky end" RELATED [] is_a: SBOL:0000027 ! type created_by: kareneilbeck creation_date: 2010-10-29T12:48:35Z [Typedef] id: has_property name: has_property created_by: jackie creation_date: 2013-07-17T01:58:14Z [Typedef] id: is_property_of name: is_property_of created_by: jackie creation_date: 2013-07-17T01:56:48Z [Typedef] id: is_represented_by name: is_represented_by is_transitive: true inverse_of: represents ! represents created_by: jackie creation_date: 2013-07-17T23:02:30Z [Typedef] id: represents name: represents def: "Reference image symbolizes represented entity." [] is_transitive: true created_by: jackie creation_date: 2013-07-17T01:26:09Z