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ontology_builder.py
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import sys
from datetime import datetime
from namespace_term import Term
from namespace_registry import NamespaceRegistry as ns
from ApiCommon import log_it, split_string, get_onto_preferred_prefix
from sparql_client import EndpointClient
from tree_functions import Tree
from databases import Database, Databases, get_db_category_IRI
#-------------------------------------------------
class OntologyBuilder:
#-------------------------------------------------
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def __init__(self, describe_ranges_and_domains=True):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
# load info from data_in used later by describe...() functions
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
self.prefixes = list()
for space in ns.namespaces: self.prefixes.append(space.getTtlPrefixDeclaration())
lines = list()
for space in ns.namespaces: lines.append(space.getSparqlPrefixDeclaration())
rqPrefixes = "\n".join(lines)
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
# store queries used to retrieve ranges and domains of properties from sparql endpoint
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
self.client = EndpointClient("http://localhost:8890/sparql")
self.domain_query_template = rqPrefixes + """
select ?prop ?value (count(distinct ?s) as ?count) where {
values ?prop { $prop }
?s ?prop ?o .
?s rdf:type ?value .
} group by ?prop ?value"""
self.range_query_template = rqPrefixes + """
select ?prop ?value (count(*) as ?count) where {
values ?prop { $prop }
?s ?prop ?o .
optional { ?o rdf:type ?cl . }
BIND(
IF (bound(?cl) , ?cl, IF ( isIRI(?o), 'rdfs:Resource', datatype(?o))
) as ?value)
} group by ?prop ?value"""
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
# domain / ranges to remove
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
self.rdfs_domain_to_remove = dict()
self.rdfs_domain_to_remove[ns.cello.accession] = { ns.skos.Concept }
#self.rdfs_domain_to_remove[ns.cello.category] = { ns.skos.Concept, ns.owl.NamedIndividual }
self.rdfs_domain_to_remove[ns.cello.database] = { ns.skos.Concept }
self.rdfs_domain_to_remove[ns.cello.version] = { ns.owl.NamedIndividual, ns.cello.Database }
self.rdfs_domain_to_remove[ns.cello.alternativeName] = { ns.owl.NamedIndividual }
self.rdfs_domain_to_remove[ns.cello.recommendedName] = { ns.owl.NamedIndividual }
self.rdfs_domain_to_remove[ns.cello.name] = { ns.owl.NamedIndividual }
self.rdfs_domain_to_remove[ns.cello.more_specific_than] = { ns.cello.Xref }
self.rdfs_range_to_remove = dict()
self.rdfs_range_to_remove[ns.cello.seeAlsoXref] = { ns.skos.Concept }
self.rdfs_range_to_remove[ns.cello.isIdentifiedByXref] = { ns.skos.Concept }
self.rdfs_range_to_remove[ns.cello.more_specific_than] = { ns.cello.Xref }
self.rdfs_range_to_remove[ns.cello.database] = { ns.owl.NamedIndividual, ns.cello.CelloConceptScheme }
self.rdfs_range_to_remove[ns.cello.hasGenomeModificationMethod] = { ns.owl.NamedIndividual }
self.rdfs_range_to_remove[ns.cello.comesFromIndividualWithSex] = { ns.owl.NamedIndividual }
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
# add description of terms (subClasses, ...) to terms in namespaces
# - - - - - - - - - - - - - - - - - - - - - - - - - - -
self.describe_cell_line_and_subclasses()
self.describe_genetic_characteristics_and_subclasses()
self.describe_genome_editing_method_and_subclasses()
self.describe_sequence_variation_and_subclasses()
self.describe_publication_hierarchy_based_on_fabio_no_redundancy()
self.describe_terminology_database_and_subclasses()
self.describe_organization_related_terms()
self.describe_misc_terms()
if describe_ranges_and_domains: self.describe_ranges_and_domains()
self.describe_annotation_properties()
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def build_class_tree(self, local_only=False):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# NOW build tree with (local) child - parent relationships based on rdfs:subClassOf()
edges = dict()
relevant_namespaces = ns.namespaces
if local_only: relevant_namespaces = [ ns.cello ]
for space in relevant_namespaces:
for term_id in space.terms:
term: Term = space.terms[term_id]
if not term.isA(ns.owl.Class): continue
for parent_iri in term.props.get(ns.rdfs.subClassOf) or set():
if parent_iri.startswith(ns.cello.pfx) or not local_only:
#print("DEBUG tree", term.iri, "has parent", parent_iri)
if term.iri in edges:
log_it(f"WARNING, multiple parents for {term.iri}: parent {edges[term.iri]} replaced with {parent_iri}")
edges[term.iri] = parent_iri
self.tree = Tree(edges)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_annotation_properties(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ns.describe(ns.cello.version, ns.rdfs.subPropertyOf, ns.dcterms.hasVersion)
ns.describe(ns.cello.modified, ns.rdfs.subPropertyOf, ns.dcterms.modified)
ns.describe(ns.cello.created, ns.rdfs.subPropertyOf, ns.dcterms.created)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_organization_related_terms(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# describing our own terms as subClass/Prop of terms defined elsewhere
# instead of simply using these external terms allow to give them a domain / range
# and additional semantic relationships to other terms
ns.describe(ns.cello.isMemberOf, ns.rdfs.subPropertyOf, ns.schema.memberOf)
ns.describe(ns.cello.city, ns.rdfs.subPropertyOf, ns.schema.location)
ns.describe(ns.cello.country, ns.rdfs.subPropertyOf, ns.schema.location)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_genetic_characteristics_and_subclasses(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# For info
# OBI:0001404 - genetic characteristics information
# OBI:0001364 - genetic alteration information = superclass for seq var + gen.int + gen.ko)
# OBI:0001225 - genetic population background information
ns.describe(ns.OBI._0001225, ns.rdfs.subClassOf, ns.OBI._0001404)
ns.describe(ns.OBI._0001364, ns.rdfs.subClassOf, ns.OBI._0001404)
ns.describe(ns.cello.GeneticIntegration, ns.rdfs.subClassOf, ns.OBI._0001364)
ns.describe(ns.cello.SequenceVariationComment, ns.rdfs.subClassOf, ns.OBI._0001364)
ns.describe(ns.cello.GeneKnockout, ns.rdfs.subClassOf, ns.OBI._0001364)
ns.describe(ns.cello.GenomeAncestry, ns.rdfs.subClassOf, ns.OBI._0001225)
ns.describe(ns.cello.HLATyping, ns.rdfs.subClassOf, ns.OBI._0001404)
ns.describe(ns.cello.ShortTandemRepeatProfile, ns.rdfs.subClassOf, ns.OBI._0001404)
ns.describe(ns.cello.MicrosatelliteInstability, ns.rdfs.subClassOf, ns.OBI._0001404)
ns.describe(ns.cello.KaryotypicInfoComment, ns.rdfs.subClassOf, ns.OBI._0001404)
ns.describe(ns.cello.KaryotypicInfoComment, ns.owl.equivalentClass, ns.OBI._0002769)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_genome_editing_method_and_subclasses(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# NOTE: the description of cello:GenomeModificationMethod is done
# in RdfBuilder.get_ttl_for_local_gem_class() because it
# requires a member variable of RdfBuilder
# external classes for genome modification methods
ns.describe(ns.FBcv._0003008, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.NCIt.C17262, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.NCIt.C44386, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0001152, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0001154, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0002626, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0003134, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0003135, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0003137, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
ns.describe(ns.OBI._0600059, ns.rdfs.subClassOf, ns.cello.GenomeModificationMethod)
# local named individuals of external classes for genome modification methods
ns.describe(ns.cello.CrispCas9, ns.rdf.type, ns.FBcv._0003008)
ns.describe(ns.cello.XRay, ns.rdf.type, ns.NCIt.C17262)
ns.describe(ns.cello.GammaRadiation, ns.rdf.type, ns.NCIt.C44386)
ns.describe(ns.cello.Transfection, ns.rdf.type, ns.OBI._0001152)
ns.describe(ns.cello.Mutagenesis, ns.rdf.type, ns.OBI._0001154)
ns.describe(ns.cello.SiRNAKnockdown, ns.rdf.type, ns.OBI._0002626)
ns.describe(ns.cello.TALEN, ns.rdf.type, ns.OBI._0003134)
ns.describe(ns.cello.ZFN, ns.rdf.type, ns.OBI._0003135)
ns.describe(ns.cello.GeneTrap, ns.rdf.type, ns.OBI._0003137)
ns.describe(ns.cello.Transduction, ns.rdf.type, ns.OBI._0600059)
# local named individuals of generic local class genome modification method
ns.describe(ns.cello.GenomeModificationMethodNOS, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.BacHomologousRecombination, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.CreLoxp, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.CrisprCas9N, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.EbvBasedVectorSirnaKnockdown, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.FloxingCreRecombination, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.GeneTargetedKoMouse, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.HelperDependentAdenoviralVector, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.HomologousRecombination, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.KnockoutFirstConditional, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.KoMouse, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.KoPig, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.MirnaKnockdown, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.NullMutation, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.PElement, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.PiggybacTransposition, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.PrimeEditing, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.PromoterlessGeneTargeting, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.RecombinantAdenoAssociatedVirus, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.ShrnaKnockdown, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.SleepingBeautyTransposition, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.SpontaneousMutation, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.TargetedIntegration, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.TransductionTransfection, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.TransfectionTransduction, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.TransgenicFish, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.TransgenicMouse, ns.rdf.type, ns.cello.GenomeModificationMethod)
ns.describe(ns.cello.TransgenicRat, ns.rdf.type, ns.cello.GenomeModificationMethod)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_ranges_and_domains(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
self.build_class_tree()
for term_id in ns.cello.terms:
term: Term = ns.cello.terms[term_id]
if not term.isA(ns.rdf.Property): continue
# gather domain classes
log_it("DEBUG", "querying prop_name", term.iri, "domains")
domain_dic = dict()
domain_query = self.domain_query_template.replace("$prop", term.iri)
response = self.client.run_query(domain_query)
if not response.get("success"):
log_it("ERROR", response.get("error_type"))
log_it(response.get("error_msg"))
sys.exit(2)
rows = response.get("results").get("bindings")
for row in rows:
value = self.client.apply_prefixes(row.get("value").get("value"))
count = int(row.get("count").get("value"))
domain_dic[value]=count
# simplify domain
domain_set1 = set(domain_dic.keys())
if len(domain_set1)>3:
domain_set = self.tree.get_close_parent_set(domain_set1)
else:
domain_set = set(domain_set1)
for domain_to_remove in self.rdfs_domain_to_remove.get(term.iri) or {}:
domain_set = domain_set - { domain_to_remove }
# DEBUG CODE
# if domain_set1 != domain_set:
# print("domain simplified for", term_id)
# print("simplified :", domain_set)
# print("original :", domain_set1)
# gather range datatypes / classes
log_it("DEBUG", "querying prop_name", term.iri, "ranges")
range_dic = dict()
range_query = self.range_query_template.replace("$prop", term.iri)
response = self.client.run_query(range_query)
if not response.get("success"):
log_it("ERROR", response.get("error_type"))
log_it(response.get("error_msg"))
sys.exit(2)
rows = response.get("results").get("bindings")
for row in rows:
value = self.client.apply_prefixes(row.get("value").get("value"))
count = int(row.get("count").get("value"))
range_dic[value]=count
# ttl comment about domain classes found in data
domain_comments = list()
tmp = list()
for k in domain_dic: tmp.append(f"{k}({domain_dic[k]})")
for line in split_string(" ".join(tmp), 90):
domain_comments.append("# domain classes found in data: " + line)
# simplify ranges
range_set = set(range_dic.keys())
if len(range_set)>3:
range_set = self.tree.get_close_parent_set(range_set)
# hack to replace xsd:date with rdfs:Literal to be OWL2 frienly
if ns.xsd.dateDataType in range_set:
range_set = range_set - { ns.xsd.dateDataType }
range_set.add(ns.rdfs.Literal)
for range_to_remove in self.rdfs_range_to_remove.get(term.iri) or {}:
range_set = range_set - { range_to_remove }
# ttl comment about prop range
range_comments = list()
tmp = list()
for k in range_dic: tmp.append(f"{k}({range_dic[k]})")
for line in split_string(" ".join(tmp), 90):
range_comments.append("# range entities found in data: " + line)
# check prop type
prop_types = set() # we should have a single item in this set (otherwise OWL reasoners dislike it)
for r in range_dic:
if r.startswith("xsd:") or r == ns.rdfs.Literal: prop_types.add("owl:DatatypeProperty")
else: prop_types.add("owl:ObjectProperty")
if len(prop_types) != 1:
log_it("ERROR", term.iri, "has not one and only one type", prop_types)
else:
declared_types = term.props.get(ns.rdf.type) # also includes rdf:Property
found_type = prop_types.pop()
if found_type not in declared_types and ns.owl.AnnotationProperty not in declared_types:
log_it("ERROR", term.iri, f"range declaration {declared_types} does not match data {found_type}")
for domain in domain_set: ns.describe(term.iri, ns.rdfs.domain, domain)
for comment in domain_comments: ns.describe(term.iri, "domain_comments", comment)
for range in range_set: ns.describe(term.iri, ns.rdfs.range, range)
for comment in range_comments: ns.describe(term.iri, "range_comments", comment)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_publication_hierarchy_based_on_fabio_no_redundancy(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Publication hierarchy based on fabio Expression
ns.describe( ns.cello.Publication, ns.rdfs.subClassOf, ns.fabio.Expression)
ns.describe( ns.fabio.Book, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.fabio.BookChapter, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.fabio.JournalArticle, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.fabio.PatentDocument, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.fabio.ReportDocument, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.cello.TechnicalDocument, ns.rdfs.subClassOf, ns.fabio.ReportDocument)
ns.describe( ns.cello.MiscellaneousDocument, ns.rdfs.subClassOf, ns.fabio.ReportDocument)
ns.describe( ns.fabio.ConferencePaper, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.fabio.Thesis, ns.rdfs.subClassOf, ns.cello.Publication)
ns.describe( ns.fabio.BachelorsThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
ns.describe( ns.fabio.MastersThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
ns.describe( ns.fabio.DoctoralThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
ns.describe( ns.cello.MedicalDegreeThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
ns.describe( ns.cello.MedicalDegreeMasterThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
ns.describe( ns.cello.PrivaDocentThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
ns.describe( ns.cello.VeterinaryMedicalDegreeThesis, ns.rdfs.subClassOf, ns.fabio.Thesis)
# Relationships with UniProt
ns.describe( ns.cello.Publication, ns.skos.closeMatch, ns.up.Published_Citation)
ns.describe( ns.fabio.BookChapter, ns.skos.closeMatch, ns.up.Book_Citation) # book citation is for book chapter !
ns.describe( ns.fabio.JournalArticle, ns.skos.closeMatch, ns.up.Journal_Citation )
ns.describe( ns.fabio.PatentDocument, ns.skos.closeMatch, ns.up.Patent_Citation)
ns.describe( ns.fabio.Thesis, ns.skos.closeMatch, ns.up.Thesis_Citation)
ns.describe( ns.fabio.BachelorsThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
ns.describe( ns.fabio.MastersThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
ns.describe( ns.fabio.DoctoralThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
ns.describe( ns.cello.MedicalDegreeThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
ns.describe( ns.cello.MedicalDegreeMasterThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
ns.describe( ns.cello.PrivaDocentThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
ns.describe( ns.cello.VeterinaryMedicalDegreeThesis, ns.skos.broadMatch, ns.up.Thesis_Citation)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_misc_terms(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# - - - - - - - -
# misc classes
# - - - - - - - -
# local classes defined as equivalent of external classes for practical reasons
ns.describe(ns.cello.AnatomicalEntity, ns.owl.equivalentClass, ns.CARO.AnatomicalEntity)
ns.describe(ns.cello.CellType, ns.owl.equivalentClass, ns.CL.CellType)
ns.describe(ns.cello.ChemicalEntity, ns.owl.equivalentClass, ns.CHEBI.ChemicalEntity)
ns.describe(ns.cello.Protein, ns.owl.equivalentClass, ns.CHEBI.Protein)
ns.describe(ns.cello.ImmunoglobulinLightChain, ns.owl.equivalentClass, ns.NCIt.C16720_IGL)
ns.describe(ns.cello.ImmunoglobulinHeavyChain, ns.owl.equivalentClass, ns.NCIt.C16717_IGH)
ns.describe(ns.cello.SequenceVariation, ns.owl.equivalentClass, ns.NCIt.SequenceVariation)
ns.describe(ns.cello.GeneMutation, ns.owl.equivalentClass, ns.NCIt.GeneMutation)
ns.describe(ns.cello.GeneFusion, ns.owl.equivalentClass, ns.NCIt.GeneFusion)
ns.describe(ns.cello.GeneAmplification, ns.owl.equivalentClass, ns.NCIt.GeneAmplification)
ns.describe(ns.cello.GeneDeletion, ns.owl.equivalentClass, ns.NCIt.GeneDeletion)
# some local props defined as sub props of external props for practical reasons
ns.describe(ns.cello.publisher, ns.rdfs.subPropertyOf, ns.dcterms.publisher)
ns.describe(ns.cello.creator, ns.rdfs.subPropertyOf, ns.dcterms.creator)
ns.describe(ns.fabio.hasPubMedCentralId, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.pmcId, ns.rdfs.subPropertyOf, ns.fabio.hasPubMedCentralId)
ns.describe(ns.fabio.hasPubMedId, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.pmid, ns.rdfs.subPropertyOf, ns.fabio.hasPubMedId)
ns.describe(ns.cello.publicationYear, ns.rdfs.subPropertyOf, ns.fabio.hasPublicationYear)
ns.describe(ns.prism.hasDOI, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.doi, ns.rdfs.subPropertyOf, ns.prism.hasDOI)
ns.describe(ns.prism.volume, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.volume, ns.rdfs.subPropertyOf, ns.prism.volume)
ns.describe(ns.cello.startingPage, ns.rdfs.subPropertyOf, ns.prism.startingPage)
ns.describe(ns.cello.endingPage, ns.rdfs.subPropertyOf, ns.prism.endingPage)
ns.describe(ns.cello.publicationDate, ns.rdfs.subPropertyOf, ns.prism.publicationDate)
# describe our disease class as a superclass of ncit disorder and ordo clinical entities
ns.describe(ns.NCIt.C2991_Disease, ns.rdfs.subClassOf, ns.cello.Disease)
ns.describe(ns.ORDO.C001_Clinical_Entity, ns.rdfs.subClassOf, ns.cello.Disease)
ns.describe(ns.cello.Breed, ns.owl.equivalentClass, ns.NCIt.C53692_Breed)
ns.describe(ns.cello.Species, ns.rdfs.subClassOf, ns.NCIt.C40098_Taxon)
ns.describe(ns.cello.Population, ns.rdfs.subClassOf, ns.OBI._0000181)
ns.describe(ns.cello.Gene, ns.owl.equivalentClass, ns.NCIt.C16612)
ns.describe(ns.cello.HLAGene, ns.rdfs.subClassOf, ns.cello.Gene)
ns.describe(ns.cello.HLA_Allele, ns.rdfs.subClassOf, ns.GENO._0000512_Allele)
#ns.describe(ns.cello.Locus, ns.owl.equivalentClass, ns.NCIt.C45822) # locus unused
ns.describe(ns.cello.STR_Allele, ns.rdfs.subClassOf, ns.GENO._0000512_Allele)
ns.describe(ns.cello.Marker, ns.owl.equivalentClass, ns.NCIt.C13441_ShortTandemRepeat)
#ns.describe(ns.cello.Marker, ns.rdfs.subClassOf, ns.cello.Locus) # locus unused
ns.describe(ns.cello.Protein, ns.rdfs.subClassOf, ns.cello.ChemicalEntity)
ns.describe(ns.cello.Protein, ns.skos.closeMatch, ns.up.Protein)
ns.describe(ns.cello.ImmunoglobulinLightChain, ns.rdfs.subClassOf, ns.cello.Protein)
ns.describe(ns.cello.ImmunoglobulinHeavyChain, ns.rdfs.subClassOf, ns.cello.Protein)
# - - - - - - - -
# misc properties
# - - - - - - - -
# ns.describe(ns.cello.hasAllele, ns.rdfs.subPropertyOf, ns.GENO._0000413_has_allele) # unused
# ns.describe(ns.cello.isAlleleOf, ns.rdfs.subPropertyOf, ns.GENO._0000408_is_allele_of) # unused
ns.describe(ns.cello.hasTarget, ns.rdfs.subPropertyOf, ns.schema.observationAbout)
ns.describe(ns.cello.hasSource, ns.rdfs.subPropertyOf, ns.dcterms.source)
ns.describe(ns.cello.appearsIn, ns.rdfs.subPropertyOf, ns.dcterms.source)
ns.describe(ns.cello.references, ns.rdfs.subPropertyOf, ns.dcterms.references)
ns.describe(ns.cello.seeAlsoXref, ns.rdfs.subPropertyOf, ns.rdfs.seeAlso)
ns.describe(ns.cello.isIdentifiedByXref, ns.rdfs.subPropertyOf, ns.rdfs.seeAlso)
ns.describe(ns.cello.isIdentifiedByIRI, ns.rdfs.subPropertyOf, ns.rdfs.seeAlso)
ns.describe(ns.cello.title, ns.rdfs.subPropertyOf, ns.dcterms.title)
ns.describe(ns.cello.conferenceTitle, ns.rdfs.subPropertyOf, ns.cello.title)
ns.describe(ns.cello.bookTitle, ns.rdfs.subPropertyOf, ns.cello.title)
ns.describe(ns.cello.documentTitle, ns.rdfs.subPropertyOf, ns.cello.title)
ns.describe(ns.cello.documentSerieTitle, ns.rdfs.subPropertyOf, ns.cello.title)
ns.describe(ns.cello.hasAnnotation, ns.owl.inverseOf, ns.IAO.is_about_0000136)
ns.describe(ns.cello.editor, ns.rdfs.subPropertyOf, ns.dcterms.contributor)
ns.describe(ns.cello.internalId, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.issn13, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.iso4JournalTitleAbbreviation, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.productId, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.markerId, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.alleleIdentifier, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.accession, ns.rdfs.subPropertyOf, ns.dcterms.identifier)
ns.describe(ns.cello.primaryAccession, ns.rdfs.subPropertyOf, ns.cello.accession)
ns.describe(ns.cello.primaryAccession, ns.owl.equivalentProperty, ns.wd.P3289_AC)
ns.describe(ns.cello.secondaryAccession, ns.rdfs.subPropertyOf, ns.cello.accession)
ns.describe(ns.cello.name, ns.rdfs.subPropertyOf, ns.rdfs.label)
ns.describe(ns.skos.prefLabel, ns.rdfs.subPropertyOf, ns.rdfs.label)
ns.describe(ns.skos.altLabel, ns.rdfs.subPropertyOf, ns.rdfs.label)
ns.describe(ns.skos.hiddenLabel, ns.rdfs.subPropertyOf, ns.rdfs.label)
#ns.describe(ns.cello.shortname, ns.rdfs.subPropertyOf, ns.cello.name)
ns.describe(ns.cello.registeredName, ns.rdfs.subPropertyOf, ns.cello.name)
ns.describe(ns.cello.recommendedName, ns.rdfs.subPropertyOf, ns.skos.prefLabel)
ns.describe(ns.cello.alternativeName, ns.rdfs.subPropertyOf, ns.skos.altLabel)
ns.describe(ns.cello.misspellingName, ns.rdfs.subPropertyOf, ns.skos.hiddenLabel)
ns.describe(ns.cello.hgvs, ns.rdfs.subPropertyOf, ns.skos.notation)
ns.describe(ns.cello.includesObservation, ns.rdfs.subPropertyOf, ns.BFO._0000051_has_part)
ns.describe(ns.cello.hasComponent, ns.rdfs.subPropertyOf, ns.BFO._0000051_has_part)
ns.describe(ns.cello.inRegister, ns.rdfs.subPropertyOf, ns.BFO._0000051_has_part)
ns.describe(ns.cello.hasAntibodyHeavyChain, ns.rdfs.subPropertyOf, ns.BFO._0000051_has_part)
ns.describe(ns.cello.hasAntibodyLightChain, ns.rdfs.subPropertyOf, ns.BFO._0000051_has_part)
ns.describe(ns.cello.zygosity, ns.rdfs.subPropertyOf, ns.GENO._0000608_has_zygozity)
ns.describe(ns.cello.inGroup, ns.rdfs.subPropertyOf, ns.schema.category)
ns.describe(ns.cello.inCollection, ns.rdfs.subPropertyOf, ns.schema.category)
ns.describe(ns.cello.hasProvider, ns.rdfs.subPropertyOf, ns.schema.provider)
ns.describe(ns.cello.establishedBy, ns.rdfs.subPropertyOf, ns.dcterms.source)
ns.describe(ns.cello.isDerivedFromCellType, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.isDerivedFromSite, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasGenomeAncestry, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasHLAtyping, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFomIndividualBelongingToBreed, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasSequenceVariationComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasAnecdotalComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasCautionComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasCharacteristicsComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasBiotechnologyComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasDonorInfoComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasDoublingTimeComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasKaryotypicInfoComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasMiscellaneousInfoComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasMisspellingRecord, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasSenescenceComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasVirologyComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasOmicsComment, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFromIndividualBelongingToPopulation, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasGeneKnockout, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasGeneticIntegration, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasRegistationRecord, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasDiscontinuationRecord, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasMoAbIsotype, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasMoAbTarget, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasMicrosatelliteInstability, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasResistance, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasShortTandemRepeatProfile, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.transformedBy, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFromIndividualWithDisease, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFromIndividualWithDisease, ns.owl.equivalentProperty, ns.wd.P5166_DI)
ns.describe(ns.cello.comesFromIndividualBelongingToSpecies, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFromIndividualBelongingToSpecies, ns.owl.equivalentProperty, ns.wd.P9072_OX)
ns.describe(ns.cello.comesFromIndividualWithSex, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFromIndividualWithSex, ns.skos.closeMatch, ns.wd.P21_SX)
# ns.describe(ns.cello.comesFromIndividualAtAge, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation) # no, cos is a datatype prop so far
ns.describe(ns.cello.comesFromSameIndividualAs, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.comesFromSameIndividualAs, ns.owl.equivalentProperty, ns.wd.P3578_OI)
ns.describe(ns.cello.hasParentCellLine, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasParentCellLine, ns.owl.equivalentProperty, ns.wd.P3432_HI)
ns.describe(ns.cello.hasParentCellLine, ns.owl.inverseOf, ns.cello.hasChildCellLine)
ns.describe(ns.cello.hasChildCellLine, ns.rdfs.subPropertyOf, ns.cello.hasAnnotation)
ns.describe(ns.cello.hasChildCellLine, ns.owl.inverseOf, ns.cello.hasParentCellLine)
ns.describe(ns.cello.more_specific_than, ns.rdfs.subPropertyOf, ns.skos.broader)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_terminology_database_and_subclasses(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Describe root cellosaurus terminology class
ns.describe(ns.cello.CelloConceptScheme, ns.rdfs.subClassOf, ns.skos.ConceptScheme)
# Describe parent class of our Database class and equivalence to uniprot Database
ns.describe(ns.cello.Database, ns.rdfs.subClassOf, ns.NCIt.C15426_Database)
ns.describe(ns.cello.Database, ns.owl.equivalentClass, ns.up.Database)
ns.describe(ns.cello.Xref, ns.rdfs.subClassOf, ns.NCIt.C43621_Xref)
# we add programmaticaly the subClassOf relationships between Database and its children
# so that we can take advantage of close_parent_set() method during computation of domain / ranges of related properties
databases = Databases()
for k in databases.categories():
cat = databases.categories()[k]
cat_label = cat["label"]
cat_IRI = get_db_category_IRI(cat_label)
cat_id = cat_IRI.split(":")[1]
ns.cello.registerClass(cat_id)
ns.describe(cat_IRI, ns.rdfs.subClassOf, ns.cello.Database)
ns.describe(cat_IRI, ns.rdfs.label, ns.xsd.string(cat_label))
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_sequence_variation_and_subclasses(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# describe children of SequenceVariation class
ns.describe( ns.cello.GeneMutation, ns.rdfs.subClassOf, ns.cello.SequenceVariation )
ns.describe( ns.cello.GeneFusion, ns.rdfs.subClassOf, ns.cello.SequenceVariation )
ns.describe( ns.cello.GeneAmplification, ns.rdfs.subClassOf, ns.cello.SequenceVariation )
ns.describe( ns.cello.GeneDeletion, ns.rdfs.subClassOf, ns.cello.SequenceVariation )
ns.describe( ns.cello.RepeatExpansion, ns.rdfs.subClassOf, ns.cello.GeneMutation )
#ns.describe( ns.cello.SimpleMutation, ns.rdfs.subClassOf, ns.cello.GeneMutation ) # SimpleMutation is not used
#ns.describe( ns.cello.UnexplicitMutation, ns.rdfs.subClassOf, ns.cello.GeneMutation ) # SimpleMutation is not used
ns.describe( ns.cello.GeneDuplication, ns.rdfs.subClassOf, ns.cello.GeneAmplification )
ns.describe( ns.cello.GeneTriplication, ns.rdfs.subClassOf, ns.cello.GeneAmplification )
ns.describe( ns.cello.GeneQuadruplication, ns.rdfs.subClassOf, ns.cello.GeneAmplification )
ns.describe( ns.cello.GeneExtensiveAmplification, ns.rdfs.subClassOf, ns.cello.GeneAmplification )
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def describe_cell_line_and_subclasses(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# describe cell line class hierarchy
ns.describe(ns.cello.CancerCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.ConditionallyImmortalizedCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.EmbryonicStemCell, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.FactorDependentCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.FiniteCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.HybridCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.Hybridoma, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.InducedPluripotentStemCell, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.SomaticStemCell, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.SpontaneouslyImmortalizedCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.StromalCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.TelomeraseImmortalizedCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
ns.describe(ns.cello.TransformedCellLine, ns.rdfs.subClassOf, ns.cello.CellLine)
# describe equivalent classes in wikidata
ns.describe(ns.cello.CancerCellLine, ns.owl.equivalentClass, ns.wd.Q23058136)
ns.describe(ns.cello.ConditionallyImmortalizedCellLine, ns.owl.equivalentClass, ns.wd.Q27653145)
ns.describe(ns.cello.EmbryonicStemCell, ns.owl.equivalentClass, ns.wd.Q107102664)
ns.describe(ns.cello.FactorDependentCellLine, ns.owl.equivalentClass, ns.wd.Q27627225)
ns.describe(ns.cello.FiniteCellLine, ns.owl.equivalentClass, ns.wd.Q27671617)
ns.describe(ns.cello.HybridCellLine, ns.owl.equivalentClass, ns.wd.Q27555050)
ns.describe(ns.cello.Hybridoma, ns.owl.equivalentClass, ns.wd.Q27554370)
ns.describe(ns.cello.InducedPluripotentStemCell, ns.owl.equivalentClass, ns.wd.Q107103143)
ns.describe(ns.cello.SomaticStemCell, ns.owl.equivalentClass, ns.wd.Q107103129)
ns.describe(ns.cello.SpontaneouslyImmortalizedCellLine, ns.owl.equivalentClass, ns.wd.Q27555319)
ns.describe(ns.cello.StromalCellLine, ns.owl.equivalentClass, ns.wd.Q27671698)
ns.describe(ns.cello.TelomeraseImmortalizedCellLine, ns.owl.equivalentClass, ns.wd.Q27653701)
ns.describe(ns.cello.TransformedCellLine, ns.owl.equivalentClass, ns.wd.Q27555384)
ns.describe(ns.cello.CellLine, ns.owl.equivalentClass, ns.wd.Q21014462)
# describe how CellLine classes relate in the universe
ns.describe(ns.cello.CellLine, ns.skos.closeMatch, "<http://purl.obolibrary.org/obo/CLO_0000031>")
ns.describe(ns.cello.CellLine, ns.skos.closeMatch, "<http://id.nlm.nih.gov/mesh/D002460>")
ns.describe(ns.cello.CellLine, ns.rdfs.seeAlso, "<https://www.cellosaurus.org/>")
ns.describe(ns.cello.CancerCellLine, ns.skos.closeMatch, f"<{ns.OBI.url}0001906>" )
ns.describe(ns.cello.EmbryonicStemCell, ns.skos.closeMatch, f"<{ns.BTO.url}0001581>" )
ns.describe(ns.cello.EmbryonicStemCell, ns.skos.closeMatch, f"<{ns.CLO.url}0037279>" )
ns.describe(ns.cello.FiniteCellLine, ns.skos.closeMatch, f"<{ns.CLO.url}0009829>" )
ns.describe(ns.cello.Hybridoma, ns.skos.closeMatch, f"<{ns.BTO.url}0001926>" )
ns.describe(ns.cello.Hybridoma, ns.skos.closeMatch, f"<{ns.CLO.url}0036932>" )
ns.describe(ns.cello.InducedPluripotentStemCell, ns.skos.closeMatch, f"<{ns.CLO.url}0037307>" )
ns.describe(ns.cello.StromalCellLine, ns.skos.closeMatch, f"<{ns.BTO.url}0005996>" )
ns.describe(ns.cello.TransformedCellLine, ns.skos.closeMatch, f"<{ns.OMIT.url}0003790>" )
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def get_onto_header(self, version="alpha"):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
lines = list()
# set last modification date for ontology
now = datetime.now()
date_string = now.strftime("%Y-%m-%d")
# set ontology URL
onto_url = "<" + self.get_onto_url() + ">"
# set ontology description
onto_descr = """The Cellosaurus ontology describes the concepts used to build the Cellosaurus knowledge resource on cell lines.
The Cellosaurus attempts to describe all cell lines used in biomedical research."""
# set ontology abstract
onto_abstract = onto_descr
# set preferred prefix for ontology
onto_prefix = "cls"
# set ontology introduction
onto_intro = onto_descr
# Note: all the prefixes are declared in namespace.py but not necessarily all the properties because used only once...
lines.append(onto_url)
lines.append(" a " + ns.owl.Ontology + " ;")
lines.append(" " + ns.rdfs.label + " " + ns.xsd.string("Cellosaurus ontology") + " ;")
lines.append(" " + ns.dcterms.created + " " + ns.xsd.date("2024-07-30") + " ;")
lines.append(" " + ns.dcterms.modified + " " + ns.xsd.date(date_string) + " ;")
lines.append(" " + ns.dcterms.description + " " + ns.xsd.string3(onto_descr) + " ;")
lines.append(" " + ns.dcterms.license + " <http://creativecommons.org/licenses/by/4.0> ;")
lines.append(" " + ns.dcterms.title + " " + ns.xsd.string("Cellosaurus ontology") + " ;")
lines.append(" " + ns.dcterms.hasVersion + " " + ns.xsd.string(version) + " ;")
lines.append(" " + ns.owl.versionInfo + " " + ns.xsd.string(version) + " ;")
lines.append(" " + ns.dcterms.abstract + " " + ns.xsd.string3(onto_abstract) + " ;")
lines.append(" " + ns.vann.preferredNamespacePrefix + " " + ns.xsd.string(get_onto_preferred_prefix()) + " ;")
#lines.append(" " + ns.bibo.status + " <http://purl.org/ontology/bibo/status/published> ;")
lines.append(" " + ns.bibo.status + " <http://purl.org/ontology/bibo/status/draft> ;")
lines.append(" " + ns.widoco.introduction + " " + ns.xsd.string3(onto_intro) + " ;")
lines.append(" " + ns.rdfs.seeAlso + " " + ns.help.IRI("index-en.html") + " ;")
lines.append(" " + ns.widoco.rdfxmlSerialization + " " + ns.help.IRI("ontology.owl") + " ;")
lines.append(" " + ns.widoco.ntSerialization + " " + ns.help.IRI("ontology.nt") + " ;")
lines.append(" " + ns.widoco.turtleSerialization + " " + ns.help.IRI("ontology.ttl") + " ;")
lines.append(" " + ns.widoco.jsonldSerialization + " " + ns.help.IRI("ontology.jsonld") + " ;")
lines.append(" " + ns.dcterms.contributor + " " + "<https://orcid.org/0000-0003-2826-6444>" + " ;")
lines.append(" " + ns.dcterms.contributor + " " + "<https://orcid.org/0000-0002-0819-0473>" + " ;")
lines.append(" " + ns.dcterms.contributor + " " + "<https://orcid.org/0000-0002-7023-1045>" + " ;")
lines.append(" " + ns.dcterms.creator + " " + "<https://orcid.org/0000-0002-7023-1045>" + " ;")
lines.append(" " + ns.dcterms.publisher + " " + "<https://www.sib.swiss>" + " ;")
lines.append(" " + ns.dcterms.bibliographicCitation + " " + ns.xsd.string("(to be defined)") + " ;")
# shacl declaration of prefixes for void tools
for elem in ns.namespaces:
lines.append(" " + ns.sh.declare + " [ ")
pfx = elem.pfx
if pfx == "": pfx = "cello"
lines.append(" " + ns.sh._prefix + " " + ns.xsd.string(pfx) + " ;")
lines.append(" " + ns.sh.namespace + " " + ns.xsd.string(elem.url) + " ;")
lines.append(" ] ;")
lines.append(" .")
lines.append("")
# lines.append("<https://orcid.org/0000-0003-2826-6444>")
# lines.append(" " + "<http://www.w3.org/ns/org#memberOf>" + " " + "<https://www.sib.swiss>" + " ;")
# lines.append(" " + "<http://xmlns.com/foaf/0.1/name>" + " " + ns.xsd.string("Amos Bairoch") + " ;")
# lines.append(" .")
# lines.append("")
# lines.append("<https://orcid.org/0000-0002-0819-0473>")
# lines.append(" " + "<http://www.w3.org/ns/org#memberOf>" + " " + "<https://www.sib.swiss>" + " ;")
# lines.append(" " + "<http://xmlns.com/foaf/0.1/name>" + " " + ns.xsd.string("Paula Duek") + " ;")
# lines.append(" .")
# lines.append("")
# lines.append("<https://orcid.org/0000-0002-7023-1045>")
# lines.append(" " + "<http://www.w3.org/ns/org#memberOf>" + " " + "<https://www.sib.swiss>" + " ;")
# lines.append(" " + "<http://xmlns.com/foaf/0.1/name>" + " " + ns.xsd.string("Pierre-André Michel") + " ;")
# lines.append(" .")
lines.extend(self.get_query_examples())
lines.append("")
return lines
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def get_topic_and_topic_annotations(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
text = """
# Topic individuals based on classes defined outside our ontology
cello:Biotechnology a owl:NamedIndividual, NCIt:C16351 ;
rdfs:label "Biotechnology"^^xsd:string ;
cello:name "Biotechnology"^^xsd:string ;
rdfs:comment "The field devoted to applying the techniques of biochemistry, cellular biology, biophysics, and molecular biology to addressing issues related to human beings and the environment."^^xsd:string ;
.
cello:DoublingTime a owl:NamedIndividual, NCIt:C94346 ;
rdfs:label "Doubling time"^^xsd:string ;
cello:name "Doubling time"^^xsd:string ;
rdfs:comment "In biology, the amount of time it takes for one cell to divide or for a group of cells (such as a tumor) to double in size. The doubling time is different for different kinds of cancer cells or tumors."^^xsd:string ;
.
cello:Omics a owl:NamedIndividual, NCIt:C205365 ;
rdfs:label "Omics"^^xsd:string ;
cello:name "Omics"^^xsd:string ;
rdfs:comment "The fields of research that use large scale sets of bioinformatics data to identify, describe and quantify the entire set of molecules and molecular processes that contribute to the form and function of cells, tissues and organisms."^^xsd:string ;
.
cello:Senescence a owl:NamedIndividual, NCIt:C17467 ;
rdfs:label "Senescence"^^xsd:string ;
cello:name "Senescence"^^xsd:string ;
rdfs:comment "PDL stands for Population Doubling Level. The process of growing old and showing the effects of time."^^xsd:string ;
.
cello:Virology a owl:NamedIndividual, NCIt:C17256 ;
rdfs:label "Virology"^^xsd:string ;
cello:name "Virology"^^xsd:string ;
rdfs:comment "The science that deals with the study of viruses."^^xsd:string ;
.
# Class for topic individuals defined in our ontology
cello:GeneralTopic a owl:Class ;
rdfs:label "General topic" ;
rdfs:subClassOf EDAM:topic_0003 ;
.
# Topic individuals based on classes defined within our ontology
cello:Characteristics a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Characteristics"^^xsd:string ;
cello:name "Characteristics"^^xsd:string ;
rdfs:comment "Production process or specific biological properties of the cell line"^^xsd:string ;
.
cello:Discontinuation a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Discontinuation"^^xsd:string ;
cello:name "Discontinuation"^^xsd:string ;
rdfs:comment "Discontinuation status of the cell line in a cell line catalog."^^xsd:string ;
.
cello:Miscellaneous a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Miscellaneous"^^xsd:string ;
cello:name "Miscellaneous"^^xsd:string ;
rdfs:comment "Miscellaneous remarks about the cell line."^^xsd:string ;
.
cello:Caution a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Caution"^^xsd:string ;
cello:name "Caution"^^xsd:string ;
rdfs:comment "Errors, inconsistencies, ambiguities regarding the origin or other aspects of the cell line."^^xsd:string ;
.
cello:Anecdotal a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Anecdotal"^^xsd:string ;
cello:name "Anecdotal"^^xsd:string ;
rdfs:comment "Anecdotal details regarding the cell line (its origin, its name or any other particularity)."^^xsd:string ;
.
cello:Misspelling a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Misspelling"^^xsd:string ;
cello:name "Misspelling"^^xsd:string ;
rdfs:comment "Identified misspelling(s) of the cell line name with in some case the specific publication or external resource entry where it appears."^^xsd:string ;
.
cello:DonorInfo a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "DonorInfo"^^xsd:string ;
cello:name "DonorInfo"^^xsd:string ;
rdfs:comment "Miscellaneous information relevant to the donor of the cell line."^^xsd:string ;
.
cello:Registration a owl:NamedIndividual, cello:GeneralTopic ;
rdfs:label "Registration"^^xsd:string ;
cello:name "Registration"^^xsd:string ;
rdfs:comment "Register or official list in which the cell line is registered."^^xsd:string ;
.
# Define cell line annotation topic class as a list of members (owl:oneOf)
cello:CellLineAnnotationTopic a owl:Class ;
rdfs:label "Cell line annotation topic"^^xsd:string ;
rdfs:subClassOf EDAM:topic_0003 ;
owl:equivalentClass [
owl:intersectionOf (
EDAM:topic_0003
[
rdf:type owl:Class ;
owl:oneOf (cello:Biotechnology cello:Senescence cello:DoublingTime cello:Virology cello:Omics cello:Characteristics
cello:Miscellaneous cello:Caution cello:Anecdotal cello:DonorInfo cello:Misspelling cello:Discontinuation cello:Registration) ;
]
)
]
.
# Define a topic data item
cello:VirologyComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Virology ;
]
)
] .
cello:BiotechnologyComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Biotechnology ;
]
)
] .
cello:SenescenceComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Senescence ;
]
)
] .
cello:DoublingTimeComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:DoublingTime ;
]
)
] .
cello:OmicsComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Omics ;
]
)
] .
cello:CharacteristicsComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Characteristics ;
]
)
] .
cello:DiscontinuationRecord a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Discontinuation ;
]
)
] .
cello:MiscellaneousInfoComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Miscellaneous ;
]
)
] .
cello:CautionComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Caution ;
]
)
] .
cello:AnecdotalComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Anecdotal ;
]
)
] .
cello:MisspellingRecord a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Misspelling ;
]
)
] .
cello:DonorInfoComment a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:DonorInfo ;
]
)
] .
cello:RegistrationRecord a owl:Class ;
rdfs:subClassOf IAO:0000027 ;
owl:equivalentClass [
owl:intersectionOf (
IAO:0000027
[ rdf:type owl:Restriction ;
owl:onProperty EDAM:has_topic ;
owl:hasValue cello:Registration ;
]
)
] .
"""
return text.split("\n")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def get_query_examples(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
lines = list()
px = get_onto_preferred_prefix()
lines.append("")
lines.append(px + ":Query_001 a sh:SPARQLExecutable ;")
lines.append(""" rdfs:comment "Count of cell lines" ; """)
lines.append(""" sh:select "select (count(*) as ?cnt) where { ?cl rdf:type / rdfs:subClassOf cello:CellLine . }" ; """)
lines.append(" .")
lines.append("")
lines.append(px +":Query_002 a sh:SPARQLExecutable ;")
lines.append(""" rdfs:comment "Count of publication citations" ; """)
lines.append(""" sh:select "select (count(*) as ?cnt) where { ?cl rdf:type / rdfs:subClassOf cello:Publication . }" ; """)
lines.append(" .")
lines.append("")
return lines
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def get_onto_url(self):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
onto_url = ns.cello.url