Andrew P. Gibson Jeroen F.J. Laros 2012-10-08T00:00:00 Zuotian Tatum 2014-01-31T00:00:00 0.6 a transcript annotation may have forward orientation on the reference sequence of a chromosome. an annotation is annotated at a location on a reference sequence. how an annotation can be places and orientated on a reference sequence. rsa:AnnotationLocation A location is considered as an instance separate from the annotation. A single annotation can be associated with multiple locations and a single location can be associated with multiple annotations. Similar to annotation constraint in OA. Not a BFO:spacial_region. The location of an annotated sequence feature on a reference sequence. annotation location rsa:FeatureAnnotation Place holder. feature annotation rsa:GenomeAssembly An information entity encapsulating a set of RSA:ReferenceSequences that are often used together to represent the total sequence content of an organism. Its version number (in some cases, the timestamp) is crucial for data integration. RSA:ReferenceSequence is RO:proper_part_of RSA:ReferenceAssembly. reference assembly rsa:Junction rsa:Orientation example: gene DMD has reverse orientation on the reference sequence representing chromosome X. model the stranded-ness in double strand sequences and how annotations can be interpreted on single strand sequences. orientation rsa:Point rsa:ReferenceSequence Both transcript sequences and chromosome sequences can be used as reference sequences, so instances of RSA:ReferenceSequence can be ro:proper_part_of another instance. This part of relationship is important for data integration scenarios, and this part of relationship works only if RSA:SequenceAnnotation is defined by the sequence content, as the sequence content of a transcript can be part of the sequence content of a chromosome, but not by the physical bearer of the sequence (a file). It can represent sequential information captured by a biological molecule, but may represent a (possibly empty) set of molecules. Syntactic sequences that has a role as reference of an annotation. Instances of this class are sequence representations such as a FASTA file. reference sequence rsa:Region rsa:SequenceAnnotation a narrower concept than SO:sequence_feature. Only represent the abstract sequences that represent molecular sequences. sequence annotation rsa:VariationAnnotation Place holder. variation annotation forward reverse 0.6 Andrew P. Gibson Jeroen F.J. Laros 2012-10-08T00:00:00 Zuotian Tatum 2014-01-31T00:00:00 0.6