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Improve turtle style #93

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Improve turtle style #93

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4189328
Improve turtle style
cthoyt Oct 18, 2023
79e956b
Merge remote-tracking branch 'upstream/master' into improve-turtle-style
cthoyt Oct 18, 2023
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181 changes: 87 additions & 94 deletions src/ncbitaxon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import zipfile
from collections import Counter, defaultdict
from datetime import date
from textwrap import dedent

oboInOwl = {
"SynonymTypeProperty": "synonym_type_property",
Expand Down Expand Up @@ -123,31 +124,32 @@ def convert_synonyms(tax_id, synonyms):
synonym = escape_literal(synonym)
predicate = predicates[name_class]
synonym_type = label_to_id(name_class)
output.append(
f"""
NCBITaxon:{tax_id} {predicate} "{synonym}"^^xsd:string .
[ a owl:Axiom
; owl:annotatedSource NCBITaxon:{tax_id}
; owl:annotatedProperty {predicate}
; owl:annotatedTarget "{synonym}"^^xsd:string
; oboInOwl:hasSynonymType ncbitaxon:{synonym_type}
] ."""
)
# todo skip adding axiom on synonym_type == "synonym"
output.append(dedent(f"""\
NCBITaxon:{tax_id} {predicate} "{synonym}"^^xsd:string .
[
a owl:Axiom;
owl:annotatedSource NCBITaxon:{tax_id} ;
owl:annotatedProperty {predicate} ;
owl:annotatedTarget "{synonym}"^^xsd:string ;
oboInOwl:hasSynonymType ncbitaxon:{synonym_type}
] .
"""))
return output


def convert_node(node, label, merged, synonyms, citations):
"""Given a node dictionary, a label string, and lists for merged, synonyms, and citations,
return a Turtle string representing this tax_id."""
tax_id = node["tax_id"]
output = [f"NCBITaxon:{tax_id} a owl:Class"]
first_row = f"\nNCBITaxon:{tax_id} a owl:Class ;"

label = escape_literal(label)
output.append(f'; rdfs:label "{label}"^^xsd:string')
output = [f'rdfs:label "{label}"^^xsd:string ;']

parent_tax_id = node["parent_tax_id"]
if parent_tax_id and parent_tax_id != "" and parent_tax_id != tax_id:
output.append(f"; rdfs:subClassOf NCBITaxon:{parent_tax_id}")
output.append(f"rdfs:subClassOf NCBITaxon:{parent_tax_id} ;")

rank = node["rank"]
if rank and rank != "" and rank != "no rank":
Expand All @@ -159,27 +161,33 @@ def convert_node(node, label, merged, synonyms, citations):
# WARN: This is a special case for backward compatibility
if rank in ["species_group", "species_subgroup"]:
output.append(
f"; ncbitaxon:has_rank <http://purl.obolibrary.org/obo/NCBITaxon#_{rank}>"
f"ncbitaxon:has_rank <http://purl.obolibrary.org/obo/NCBITaxon#_{rank}> ;"
)
else:
output.append(f"; ncbitaxon:has_rank NCBITaxon:{rank}")

gc_id = node["genetic_code_id"]
if gc_id:
output.append(f'; oboInOwl:hasDbXref "GC_ID:{gc_id}"^^xsd:string')
output.append(f"ncbitaxon:has_rank NCBITaxon:{rank} ;")

for merge in merged:
output.append(f'; oboInOwl:hasAlternativeId "NCBITaxon:{merge}"^^xsd:string')
output.append(f'oboInOwl:hasAlternativeId "NCBITaxon:{merge}"^^xsd:string ;')

for pubmed_id in citations:
output.append(f'; oboInOwl:hasDbXref "PMID:{pubmed_id}"^^xsd:string')
dbxrefs = [f"PMID:{pubmed_id}" for pubmed_id in citations]
gc_id = node["genetic_code_id"]
if gc_id:
dbxrefs.append(f"GC_ID:{gc_id}")

output.append('; oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string')
output.append(".")
if len(dbxrefs) == 1:
output.append(f'oboInOwl:hasDbXref "{dbxrefs[0]}"^^xsd:string ;')
else:
output.append(f'oboInOwl:hasDbXref "{dbxrefs[0]}"^^xsd:string ,')
for dbxref in dbxrefs[1:-1]:
output.append(f' "{dbxref}"^^xsd:string ,')
output.append(f' "{dbxrefs[-1]}"^^xsd:string ;')

output += convert_synonyms(tax_id, synonyms)
output.append('oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string .\n')

return "\n".join(output)
rows = [first_row]
rows.extend(f" {row}" for row in output)
rows.extend(convert_synonyms(tax_id, synonyms))
return "\n".join(rows)


def split_line(line):
Expand All @@ -201,60 +209,51 @@ def convert(taxdmp_path, output_path, taxa=None):
with open(output_path, "w") as output:
isodate = date.today().isoformat()
ncbi_date = date.today().replace(day=1)
output.write(
f"""@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix terms: <http://purl.org/dc/terms/> .
@prefix ncbitaxon: <http://purl.obolibrary.org/obo/ncbitaxon#> .
@prefix NCBITaxon: <http://purl.obolibrary.org/obo/NCBITaxon_> .
@prefix : <http://purl.obolibrary.org/obo/ncbitaxon.owl#> .

<http://purl.obolibrary.org/obo/ncbitaxon.owl> a owl:Ontology
; owl:versionIRI <http://purl.obolibrary.org/obo/ncbitaxon/{isodate}/ncbitaxon.owl>
; owl:versionInfo "{isodate}"^^xsd:string
; terms:title "NCBI organismal classification"
; terms:description "An ontology representation of the NCBI organismal taxonomy"
; terms:license <https://creativecommons.org/publicdomain/zero/1.0/>
; rdfs:comment "Built by https://github.com/obophenotype/ncbitaxon"^^xsd:string
; rdfs:comment "NCBI organismal taxonomy version {ncbi_date}"^^xsd:string
.

obo:IAO_0000115 a owl:AnnotationProperty
; rdfs:label "definition"^^xsd:string
.

ncbitaxon:has_rank a owl:AnnotationProperty
; obo:IAO_0000115 "A metadata relation between a class and its taxonomic rank (eg species, family)"^^xsd:string
; rdfs:label "has_rank"^^xsd:string
; rdfs:comment "This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored"^^xsd:string
; oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string
.
"""
)
output.write(dedent(f"""\
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix terms: <http://purl.org/dc/terms/> .
@prefix ncbitaxon: <http://purl.obolibrary.org/obo/ncbitaxon#> .
@prefix NCBITaxon: <http://purl.obolibrary.org/obo/NCBITaxon_> .
@prefix : <http://purl.obolibrary.org/obo/ncbitaxon.owl#> .

<http://purl.obolibrary.org/obo/ncbitaxon.owl> a owl:Ontology ;
owl:versionIRI <http://purl.obolibrary.org/obo/ncbitaxon/{isodate}/ncbitaxon.owl> ;
owl:versionInfo "{isodate}"^^xsd:string ;
terms:title "NCBI organismal classification";
terms:description "An ontology representation of the NCBI organismal taxonomy" ;
terms:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
rdfs:comment "Built by https://github.com/obophenotype/ncbitaxon"^^xsd:string ;
rdfs:comment "NCBI organismal taxonomy version {ncbi_date}"^^xsd:string .

obo:IAO_0000115 a owl:AnnotationProperty ;
rdfs:label "definition"^^xsd:string .

ncbitaxon:has_rank a owl:AnnotationProperty ;
obo:IAO_0000115 "A metadata relation between a class and its taxonomic rank (eg species, family)"^^xsd:string ;
rdfs:label "has_rank"^^xsd:string ;
rdfs:comment "This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored"^^xsd:string;
oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string .\n
"""))
for predicate, label in oboInOwl.items():
output.write(
f"""
oboInOwl:{predicate} a owl:AnnotationProperty
; rdfs:label "{label}"^^xsd:string
.
"""
)
output.write(dedent(f"""\
oboInOwl:{predicate} a owl:AnnotationProperty ;
rdfs:label "{label}"^^xsd:string .\n
"""))
for label, parent in predicates.items():
predicate = label_to_id(label)
parent = parent.replace("oboInOwl", "oio")
output.write(
f"""
ncbitaxon:{predicate} a owl:AnnotationProperty
; rdfs:label "{label}"^^xsd:string
; oboInOwl:hasScope "{parent}"^^xsd:string
; rdfs:subPropertyOf oboInOwl:SynonymTypeProperty
.
"""
)
dedent(f"""\
ncbitaxon:{predicate} a owl:AnnotationProperty ;
rdfs:label "{label}"^^xsd:string ;
oboInOwl:hasScope "{parent}"^^xsd:string ;
rdfs:subPropertyOf oboInOwl:SynonymTypeProperty .\n
"""))

with zipfile.ZipFile(taxdmp_path) as taxdmp:
with taxdmp.open("names.dmp") as dmp:
Expand All @@ -275,7 +274,7 @@ def convert(taxdmp_path, output_path, taxa=None):
print("WARN: Duplicate unique names", tax_ids, uniques)
for tax_id, unique in values:
labels[tax_id] = unique
# Reason for the line below
# Reason for the line below
# issue #56: https://github.com/obophenotype/ncbitaxon/issues/56
if name != 'environmental samples':
synonyms[tax_id].append(
Expand Down Expand Up @@ -329,30 +328,24 @@ def convert(taxdmp_path, output_path, taxa=None):
print(UNRECOGNIZED_RANKS)
# TODO: delnodes

output.write(
"""
<http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank> a owl:Class
; rdfs:label "taxonomic rank"^^xsd:string
; rdfs:comment "This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored."^^xsd:string
; oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string
.
"""
)
output.write(dedent("""
<http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank> a owl:Class ;
rdfs:label "taxonomic rank"^^xsd:string ;
rdfs:comment "This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored."^^xsd:string ;
oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string .
"""))
for label in ranks:
rank = label_to_id(label)
if rank in ["species_group", "species_subgroup"]:
iri = f"<http://purl.obolibrary.org/obo/NCBITaxon#_{rank}>"
else:
iri = f"NCBITaxon:{rank}"
output.write(
f"""
{iri} a owl:Class
; rdfs:label "{label}"^^xsd:string
; rdfs:subClassOf <http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank>
; oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string
.
"""
)
output.write(dedent(f"""
{iri} a owl:Class ;
rdfs:label "{label}"^^xsd:string ;
rdfs:subClassOf <http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank> ;
oboInOwl:hasOBONamespace "ncbi_taxonomy"^^xsd:string .
"""))


def main():
Expand Down