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"""RDF utilities
This module is a collection of functions that handle SPARQL queries.
"""
from typing import Tuple
from string import Template
from urllib.parse import unquote
from urllib.parse import urlparse
from SPARQLWrapper import JSON, SPARQLWrapper
from gn3.monads import MonadicDict
RDF_PREFIXES = """PREFIX dct: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
PREFIX gn: <http://genenetwork.org/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX publication: <http://genenetwork.org/publication/>
PREFIX phenotype: <http://genenetwork.org/phenotype/>
PREFIX genotype: <http://genenetwork.org/genotype/>
"""
def sparql_query(
sparql_conn: SPARQLWrapper, query: str,
) -> Tuple[MonadicDict, ...]:
"""Run a SPARQL query and return the bound variables."""
def __add_value_to_dict(key, value, my_dict):
_values = set()
if key in my_dict:
if isinstance(my_dict[key], list):
_values = set(my_dict[key])
else:
_values = set([my_dict[key]])
_values.add(value)
if _values:
return list(_values)
return value
sparql_conn.setQuery(query)
sparql_conn.setReturnFormat(JSON)
parsed_response: dict = {}
results = sparql_conn.queryAndConvert()["results"]["bindings"] # type: ignore
if results:
for result in results:
if "s" in result: # A CONSTRUCT
key = get_url_local_name(
result["p"]["value"] # type: ignore
)
value = result["o"]["value"] # type: ignore
parsed_response[key] = __add_value_to_dict(
key, value, parsed_response
)
elif "key" in result: # A SELECT
parsed_response[
result["key"] # type: ignore
] = __add_value_to_dict(
result["key"], result["value"], # type: ignore
parsed_response
)
return (MonadicDict(parsed_response),)
def get_url_local_name(string: str) -> str:
"""Get the last item after a '/" from a URL"""
if string.startswith("http"):
url = urlparse(string)
return unquote(url.path).rpartition("/")[-1]
return string
def get_dataset_metadata(
sparql_conn: SPARQLWrapper, name: str
) -> MonadicDict:
"""Return info about dataset with a given NAME"""
__metadata_query = """
$prefix
CONSTRUCT {
gn:dataset ?datasetTerm ?datasetValue .
gn:dataset ?platformName ?platform_name .
gn:dataset gn:normalization ?normalization .
gn:dataset gn:investigatorName ?investigatorName .
gn:dataset gn:investigatorWebUrl ?investigatorWebUrl .
gn:dataset gn:tissueName ?tissueName .
gn:dataset gn:organism ?speciesDisplayName .
gn:dataset gn:organismUrl ?ncbiReference .
gn:dataset gn:inbredSetName ?inbredSetName .
gn:dataset gn:geoPlatformUrl ?geoPlatform .
gn:dataset gn:platformName ?platform_name .
} WHERE {
?subClass rdf:subClassOf gn:dataset .
?dataset rdf:type ?subclass ;
gn:name "$name";
?datasetTerm ?datasetValue .
OPTIONAL {
?dataset gn:datasetOfInvestigator ?investigator .
?investigator foaf:name ?investigatorName .
?investigator foaf:homepage ?investigatorWebUrl .
} .
OPTIONAL{
?dataset gn:normalization ?normalizationType .
?normalizationType gn:name ?normalization .
} .
OPTIONAL{
?dataset gn:datasetOfSpecies ?species .
?species gn:displayName ?speciesDisplayName .
?species gn:organism ?ncbiReference .
} .
OPTIONAL {
?dataset gn:datasetOfInbredSet ?inbredSet .
?inbredSet gn:binomialName ?inbredSetName .
?inbredSet gn:inbredSetOfSpecies ?species .
?species gn:displayName ?speciesDisplayName .
?species gn:organism ?ncbiReference .
} .
OPTIONAL{
?dataset gn:datasetOfPlatform ?platform .
?platform gn:name ?platform_name .
?platform gn:geoPlatform ?geoPlatform .
} .
OPTIONAL{
?dataset gn:datasetOfTissue ?tissue .
?tissue gn:name ?tissueName .
} .
VALUES ?datasetTerm {
dct:created gn:aboutCases gn:aboutDataProcessing gn:aboutPlatform
gn:aboutTissue gn:accessionId gn:acknowledgment gn:citation
gn:contributors gn:datasetGroup gn:datasetOfinvestigator
gn:experimentDesign gn:geoSeries gn:name gn:notes
gn:specifics gn:summary gn:title gn:publicationTitle
gn:datasetStatusName gn:datasetOfOrganization
}
}
"""
response: MonadicDict = MonadicDict()
for key, value in sparql_query(
sparql_conn,
Template(__metadata_query)
.substitute(
prefix=RDF_PREFIXES,
name=name
)
)[0].items():
response[key] = value
if isinstance(value, str) and not (
key.endswith("Url") or key == "geoSeries"
):
response[key] = value.map(get_url_local_name) # type: ignore
return response
def get_publication_metadata(
sparql_conn: SPARQLWrapper, name: str
):
"""Return info about a publication with a given NAME"""
__metadata_query = """
$prefix
CONSTRUCT {
gn:publication ?publicationTerm ?publicationValue .
gn:publication ?predicate ?subject .
} WHERE {
$name ?publicationTerm ?publicationValue .
?publication ?publicationTerm ?publicationValue .
OPTIONAL {
?subject ?predicate ?publication .
} .
VALUES ?publicationTerm {
gn:pubMedId gn:title gn:volume
gn:abstract gn:pages gn:month gn:year gn:author
}
VALUES ?predicate {
gn:phenotypeOfPublication
}
}
"""
response: MonadicDict = MonadicDict()
for key, value in sparql_query(
sparql_conn,
Template(__metadata_query)
.substitute(
prefix=RDF_PREFIXES,
name=name
)
)[0].items():
response[key] = value
if isinstance(value, str) and not key.endswith("pubMedId"):
response[key] = value.map(get_url_local_name) # type: ignore
return response
def get_phenotype_metadata(
sparql_conn: SPARQLWrapper, name: str
):
"""Return info about a phenotype with a given NAME"""
__metadata_query = """
$prefix
CONSTRUCT {
?phenotype ?pPredicate ?pValue .
?phenotype ?publicationTerm ?publicationValue .
?phenotype gn:speciesName ?speciesName .
?phenotype gn:inbredSetName ?inbredSetBinomialName .
?phenotype gn:datasetName ?datasetFullName .
} WHERE {
?phenotype ?pPredicate ?pValue .
OPTIONAL {
?phenotype gn:phenotypeOfPublication ?publication .
?publication ?publicationTerm ?publicationValue .
} .
OPTIONAL {
?phenotype gn:phenotypeOfDataset ?dataset .
?dataset gn:name ?datasetFullName .
?dataset gn:datasetOfInbredSet ?inbredSet .
?inbredSet gn:binomialName ?inbredSetBinomialName .
?inbredSet gn:inbredSetOfSpecies ?species .
?species gn:displayName ?speciesName .
} .
FILTER( ?phenotype = phenotype:$name ) .
MINUS {
?phenotype rdf:type ?pValue .
}
MINUS {
?publication rdf:type ?publicationValue .
}
}
"""
result: MonadicDict = MonadicDict()
for key, value in sparql_query(
sparql_conn,
Template(__metadata_query)
.substitute(name=name,
prefix=RDF_PREFIXES)
)[0].items():
result[key] = value
return result
def get_genotype_metadata(
sparql_conn: SPARQLWrapper, name: str
):
"""Return info about a phenotype with a given NAME"""
__metadata_query = """
$prefix
CONSTRUCT {
?genotype ?pPredicate ?pValue .
?genotype gn:speciesName ?speciesName .
?genotype gn:inbredSetName ?inbredSetBinomialName .
?genotype gn:datasetName ?datasetFullName .
} WHERE {
?genotype ?pPredicate ?pValue .
OPTIONAL {
?genotype gn:genotypeOfDataset ?dataset .
?dataset gn:fullName ?datasetFullName .
}.
OPTIONAL {
?genotype gn:genotypeOfDataset ?dataset .
?dataset gn:datasetOfInbredSet ?inbredSet .
?inbredSet gn:binomialName ?inbredSetBinomialName .
?inbredSet gn:inbredSetOfSpecies ?species .
?species gn:displayName ?speciesName .
} .
FILTER( ?genotype = genotype:$name ) .
MINUS {
?genotype rdf:type ?pValue .
}
}
"""
result: MonadicDict = MonadicDict()
for key, value in sparql_query(
sparql_conn,
Template(__metadata_query)
.substitute(name=name,
prefix=RDF_PREFIXES)
)[0].items():
result[key] = value
return result
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