def _declare_as_ontology(self, version_info=None):
"""
Declare the distribution level IRI as an ontology, and also make triple
distribution level IRI - version_iri -> version level IRI
TEC: I am not convinced dipper reformatting external data as RDF triples
makes an OWL ontology (nor that it should be considered a goal).
Proper ontologies are built by ontologists. Dipper reformats data
and annotates/decorates it with a minimal set of carefully arranged
terms drawn from from multiple proper ontologies.
Which allows the whole (dipper's RDF triples and parent ontologies)
to function as a single ontology we can reason over when combined
in a store such as SciGraph.
Including more than the minimal ontological terms in dipper's RDF
output constitutes a liability as it allows greater divergence
between dipper artifacts and the proper ontologies.
:param version_info: a string describing version info for the ontology
:return:
"""
model = Model(self.graph)
model.addOntologyDeclaration(self.summary_level_curie)
model.addOWLVersionIRI(self.summary_level_curie,
self.version_level_curie)
if version_info is not None:
model.addOWLVersionInfo(self.distribution_level_turtle_curie,
version_info)
def declareAsOntology(self, graph):
"""
The file we output needs to be declared as an ontology,
including it's version information.
TEC: I am not convinced dipper reformating external data as RDF triples
makes an OWL ontology (nor that it should be considered a goal).
Proper ontologies are built by ontologists. Dipper reformats data
and anotates/decorates it with a minimal set of carefully arranged
terms drawn from from multiple proper ontologies.
Which allows the whole (dipper's RDF triples and parent ontologies)
to function as a single ontology we can reason over when combined
in a store such as SciGraph.
Including more than the minimal ontological terms in dipper's RDF
output constitutes a liability as it allows greater divergence
between dipper artifacts and the proper ontologies.
Further information will be augmented in the dataset object.
:param version:
:return:
"""
# <http://data.monarchinitiative.org/ttl/biogrid.ttl> a owl:Ontology ;
# owl:versionInfo
# <https://archive.monarchinitiative.org/YYYYMM/ttl/biogrid.ttl>
model = Model(graph)
# is self.outfile suffix set yet???
ontology_file_id = 'MonarchData:' + self.name + ".ttl"
model.addOntologyDeclaration(ontology_file_id)
# add timestamp as version info
t = datetime.now()
t_string = t.strftime("%Y-%m-%d")
ontology_version = t_string
# TEC this means the MonarchArchive IRI needs the release updated
# maybe extract the version info from there
# should not hardcode the suffix as it may change
archive_url = 'MonarchArchive:' + 'ttl/' + self.name + '.ttl'
model.addOWLVersionIRI(ontology_file_id, archive_url)
model.addOWLVersionInfo(ontology_file_id, ontology_version)
# TODO make sure this is synced with the Dataset class
return
def declareAsOntology(self, graph):
"""
The file we output needs to be declared as an ontology,
including it's version information.
TEC: I am not convinced dipper reformating external data as RDF triples
makes an OWL ontology (nor that it should be considered a goal).
Proper ontologies are built by ontologists. Dipper reformats data
and anotates/decorates it with a minimal set of carefully arranged
terms drawn from from multiple proper ontologies.
Which allows the whole (dipper's RDF triples and parent ontologies)
to function as a single ontology we can reason over when combined
in a store such as SciGraph.
Including more than the minimal ontological terms in dipper's RDF
output constitutes a liability as it allows greater divergence
between dipper artifacts and the proper ontologies.
Further information will be augmented in the dataset object.
:param version:
:return:
"""
# <http://data.monarchinitiative.org/ttl/biogrid.ttl> a owl:Ontology ;
# owl:versionInfo
# <https://archive.monarchinitiative.org/YYYYMM/ttl/biogrid.ttl>
model = Model(graph)
ontology_file_id = 'MonarchData:' + self.name + ".ttl"
model.addOntologyDeclaration(ontology_file_id)
# add timestamp as version info
t = datetime.now()
t_string = t.strftime("%Y-%m-%d")
ontology_version = t_string
# TEC this means the MonarchArchive IRI needs the release updated
# maybe extract the version info from there
yrmth = str(datetime.now().year) + str(datetime.now().month)
archive_url = 'MonarchArchive:' + yrmth + '/ttl/' + self.name + '.ttl'
model.addOWLVersionIRI(ontology_file_id, archive_url)
model.addOWLVersionInfo(ontology_file_id, ontology_version)
# TODO make sure this is synced with the Dataset class
return
