From 8def29bb86f3fa7d02f4a72710481f573ca89a34 Mon Sep 17 00:00:00 2001 From: Jerven Bolleman Date: Thu, 23 May 2024 17:05:11 +0200 Subject: [PATCH] Fix some and remove TODO queries in Swiss-Lipids --- swisslipids/16.ttl | 17 ----------------- swisslipids/17.ttl | 17 ----------------- swisslipids/18.ttl | 17 ----------------- swisslipids/19.ttl | 16 ---------------- swisslipids/20.ttl | 15 --------------- swisslipids/21.ttl | 16 ---------------- swisslipids/22.ttl | 16 ---------------- swisslipids/23.ttl | 14 -------------- swisslipids/24.ttl | 16 ---------------- swisslipids/25.ttl | 16 ---------------- swisslipids/26.ttl | 17 +++++++++++++---- swisslipids/27.ttl | 21 +++++++++++++++------ swisslipids/28.ttl | 16 ---------------- swisslipids/29.ttl | 15 --------------- swisslipids/30.ttl | 15 --------------- swisslipids/31.ttl | 15 --------------- swisslipids/32.ttl | 15 --------------- swisslipids/33.ttl | 15 --------------- swisslipids/34.ttl | 18 +++++++++++++----- swisslipids/35.ttl | 19 +++++++++++++------ 20 files changed, 54 insertions(+), 272 deletions(-) delete mode 100644 swisslipids/16.ttl delete mode 100644 swisslipids/17.ttl delete mode 100644 swisslipids/18.ttl delete mode 100644 swisslipids/19.ttl delete mode 100644 swisslipids/20.ttl delete mode 100644 swisslipids/21.ttl delete mode 100644 swisslipids/22.ttl delete mode 100644 swisslipids/23.ttl delete mode 100644 swisslipids/24.ttl delete mode 100644 swisslipids/25.ttl delete mode 100644 swisslipids/28.ttl delete mode 100644 swisslipids/29.ttl delete mode 100644 swisslipids/30.ttl delete mode 100644 swisslipids/31.ttl delete mode 100644 swisslipids/32.ttl delete mode 100644 swisslipids/33.ttl diff --git a/swisslipids/16.ttl b/swisslipids/16.ttl deleted file mode 100644 index 43a5706bd..000000000 --- a/swisslipids/16.ttl +++ /dev/null @@ -1,17 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:16 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Mapping LipidX lipids to LIPID MAPS " ; - rdfs:comment """For a given list of LipidX lipid identifiers return the list of corresponding LIPID MAPS IDs. -Output should include LipidX ID, the corresponding SwissLipids ID and name, plus the LIPID MAPS ID. -This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies and from them the required LIPID MAPS identifiers. -Extends ID mapping to LipidX identifiers and by using the hierarchy. -extends ex:15"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO}""" . diff --git a/swisslipids/17.ttl b/swisslipids/17.ttl deleted file mode 100644 index 39feddb78..000000000 --- a/swisslipids/17.ttl +++ /dev/null @@ -1,17 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:17 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Mapping LipidX lipids to HMDB " ; - rdfs:comment """For a given list of LipidX lipid identifiers return the list of corresponding HMDB IDs. -Output should include LipidX ID, the corresponding SwissLipids ID and name, plus the HMDB ID. -This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies and from them the required HMDB identifiers. -Extends ID mapping to LipidX identifiers and by using the hierarchy. -extends ex:16"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO}""" . diff --git a/swisslipids/18.ttl b/swisslipids/18.ttl deleted file mode 100644 index 8ccbf9e3d..000000000 --- a/swisslipids/18.ttl +++ /dev/null @@ -1,17 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:18 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Mapping LipidX lipids to ChEBI" ; - rdfs:comment """For a given list of LipidX lipid identifiers return the list of corresponding ChEBI IDs. -Output should include LipidX ID, the corresponding SwissLipids ID and name, plus the HMDB ID. -This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the required ChEBI identifiers from them. -Extends ID mapping to LipidX identifiers and by using the hierarchy. -extends ex:15"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO}""" . diff --git a/swisslipids/19.ttl b/swisslipids/19.ttl deleted file mode 100644 index 1195d7732..000000000 --- a/swisslipids/19.ttl +++ /dev/null @@ -1,16 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:19 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Mapping LipidX lipids to possible enzymes" ; - rdfs:comment """For a given list of LipidX lipid identifiers return the list of possible structures and relevant enzymes. -Output should include the LipidX ID, the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the proteins. -This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies, and from them retrieves the list of reactions in which they participate, and the enzymes that catalyze them. -extends ex:16"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO}""" . diff --git a/swisslipids/20.ttl b/swisslipids/20.ttl deleted file mode 100644 index c3d5a3521..000000000 --- a/swisslipids/20.ttl +++ /dev/null @@ -1,15 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:20 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Lipid analyte composition of tissues" ; - rdfs:comment """Returns the list of lipid analytes identified in a list of tissues (UBERON lipid identifiers). -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the tissues. -A simple query which does not traverse the hierarchy."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO}""" . diff --git a/swisslipids/21.ttl b/swisslipids/21.ttl deleted file mode 100644 index 316667255..000000000 --- a/swisslipids/21.ttl +++ /dev/null @@ -1,16 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:21 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible lipid structure composition of tissues" ; - rdfs:comment """Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers). -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the tissues. -This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those. -Extends ex:20"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/22.ttl b/swisslipids/22.ttl deleted file mode 100644 index 369855780..000000000 --- a/swisslipids/22.ttl +++ /dev/null @@ -1,16 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:22 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible lipid structure composition of tissues – limited to published lipid structures" ; - rdfs:comment """Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers), but considers only those lipids associated with one or more publications. -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the tissues. -This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to at least one PMID. As that PMID does not necessarily reflect association to the tissue in question we don’t return that. -Extends ex:3, ex:23"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO}""" . diff --git a/swisslipids/23.ttl b/swisslipids/23.ttl deleted file mode 100644 index 0b09cb7f0..000000000 --- a/swisslipids/23.ttl +++ /dev/null @@ -1,14 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:23 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Lipid analyte composition of cellular compartments" ; - rdfs:comment """Returns the list of lipid analytes associated with a list of one or more subcellular locations (GO cellular components). -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the cellular components. """^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/24.ttl b/swisslipids/24.ttl deleted file mode 100644 index dde7d2138..000000000 --- a/swisslipids/24.ttl +++ /dev/null @@ -1,16 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:24 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible lipid structure composition of cellular compartments" ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components). -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the cellular components. -This query first retrieves SwissLipids identifiers for a given list of GO cellular component identifiers. It then retrieves the corresponding Isomeric subspecies and returns those. -Extends ex:25"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/25.ttl b/swisslipids/25.ttl deleted file mode 100644 index e4b6cd075..000000000 --- a/swisslipids/25.ttl +++ /dev/null @@ -1,16 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:25 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible lipid structure composition of cellular compartments – limited to published lipid structures" ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components), but considers only those lipids associated with one or more publications. -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the cellular components. -This query first identifies SwissLipids identifiers for a given list of GO cellular component identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to at least one PMID. As that PMID does not necessarily reflect association to the cellular compartment in question we don’t return that. -Extends ex:3, ex:25"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/26.ttl b/swisslipids/26.ttl index 272548a55..e51789a96 100644 --- a/swisslipids/26.ttl +++ b/swisslipids/26.ttl @@ -8,7 +8,16 @@ ex:26 a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; sh:prefixes _:sparql_examples_prefixes ; schema:target ; - rdfs:label "Lipid analyte composition of organisms" ; - rdfs:comment """Returns the list of lipid analytes associated with a list of one or more organisms (NCBI taxonomic IDs). -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the organisms."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . + rdfs:comment "Lipids produced in different organisms" ; + sh:select """SELECT ?swisslipid ?organism { + ?swisslipid owl:equivalentClass ?chebi . + SERVICE { + ?rhea rh:side/rh:contains/rh:compound ?compound . + ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?metabolite . + } + SERVICE { + ?catalyticActivityAnnotation up:catalyticActivity/up:catalyzedReaction ?rhea . + ?protein up:annotation ?catalyticActivityAnnotation ; + up:organism ?organism . + } +}""" . diff --git a/swisslipids/27.ttl b/swisslipids/27.ttl index a2b7f7bd3..9bd733563 100644 --- a/swisslipids/27.ttl +++ b/swisslipids/27.ttl @@ -8,9 +8,18 @@ ex:27 a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; sh:prefixes _:sparql_examples_prefixes ; schema:target ; - rdfs:label "Possible lipid structure composition of organisms" ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs). -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the organisms. -This query first identifies SwissLipids identifiers for a given list of NCBI taxonomic IDs. It then retrieves the corresponding Isomeric subspecies and returns those. -Extends ex:26"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . + rdfs:comment """Find the list of SwissLipids for all organisms and their Isomeric subspecies"""^^rdf:HTML ; + sh:select """SELECT ?swisslipid ?organism { + ?swisslipid owl:equivalentClass ?chebi . + SERVICE { + ?rhea rh:side/rh:contains/rh:compound ?compound . + ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?metabolite . + } + SERVICE { + ?catalyticActivityAnnotation up:catalyticActivity/up:catalyzedReaction ?rhea . + ?protein up:annotation ?catalyticActivityAnnotation ; + up:organism ?organism . + } + ?swisslipidIsomericSubpecies rdfs:subClassOf ?swisslipid ; + SWISSLIPID:rank SWISSLIPID:Isomeric_Subspecies . +}""" . diff --git a/swisslipids/28.ttl b/swisslipids/28.ttl deleted file mode 100644 index 21d39ecb0..000000000 --- a/swisslipids/28.ttl +++ /dev/null @@ -1,16 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:28 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible lipid structure composition of organisms – limited to published lipid structures" ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs), but considers only those lipids associated with one or more publications. -Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the organisms. -This query first identifies SwissLipids identifiers for a given list of NCBI taxonomic IDs. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to at least one PMID. As that PMID does not necessarily reflect association to the cellular compartment in question we don’t return that. -Extends ex:3, ex:28"""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/29.ttl b/swisslipids/29.ttl deleted file mode 100644 index 346afbc24..000000000 --- a/swisslipids/29.ttl +++ /dev/null @@ -1,15 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:29 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible LIPID MAPS lipid structure composition of tissues" ; - rdfs:comment """Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers), but considers only those lipids associated with LIPID MAPS identifers. -Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the tissues. -This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/30.ttl b/swisslipids/30.ttl deleted file mode 100644 index 138d525f5..000000000 --- a/swisslipids/30.ttl +++ /dev/null @@ -1,15 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:30 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible LIPID MAPS lipid structure composition of tissues" ; - rdfs:comment """Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers), but considers only those lipids associated with LIPID MAPS identifers. -Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the tissues. -This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/31.ttl b/swisslipids/31.ttl deleted file mode 100644 index 22ee4d01c..000000000 --- a/swisslipids/31.ttl +++ /dev/null @@ -1,15 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:31 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible LIPID MAPS lipid structure composition of cellular components " ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components), but considers only those lipids associated with LIPID MAPS identifers. -Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the subcellular locations (GO cellular components). -This query first retrieves SwissLipids identifiers for a given list of subcellular locations (GO cellular component identifiers). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/32.ttl b/swisslipids/32.ttl deleted file mode 100644 index 4882e8a00..000000000 --- a/swisslipids/32.ttl +++ /dev/null @@ -1,15 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:32 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible LIPID MAPS lipid structure composition of organisms" ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs) but considers only those lipids associated with LIPID MAPS identifers. -Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and NCBI taxonomic ID(s) of the organisms. -This query first retrieves SwissLipids identifiers for a given list of organisms (NCBI taxonomic IDs). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . diff --git a/swisslipids/33.ttl b/swisslipids/33.ttl deleted file mode 100644 index c1cb32e1a..000000000 --- a/swisslipids/33.ttl +++ /dev/null @@ -1,15 +0,0 @@ -prefix ex: -prefix up: -prefix sh: -prefix schema: -prefix rdf: -prefix rdfs: -ex:33 - a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; - sh:prefixes _:sparql_examples_prefixes ; - schema:target ; - rdfs:label "Possible LIPID MAPS lipid structure composition of cellular components " ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components), but considers only those lipids associated with LIPID MAPS identifers. -Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the subcellular locations (GO cellular components). -This query first retrieves SwissLipids identifiers for a given list of subcellular locations (GO cellular component identifiers). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """. diff --git a/swisslipids/34.ttl b/swisslipids/34.ttl index bc1d5a0c5..599cb8ef3 100644 --- a/swisslipids/34.ttl +++ b/swisslipids/34.ttl @@ -8,8 +8,16 @@ ex:34 a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; sh:prefixes _:sparql_examples_prefixes ; schema:target ; - rdfs:label "Possible LIPID MAPS lipid structure composition of organisms" ; - rdfs:comment """Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs) but considers only those lipids associated with LIPID MAPS identifers. -Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and NCBI taxonomic ID(s) of the organisms. -This query first retrieves SwissLipids identifiers for a given list of organisms (NCBI taxonomic IDs). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """ . + rdfs:comment "Lipids affected by human enzymes" ; + sh:select """SELECT ?swisslipid { + ?swisslipid owl:equivalentClass ?chebi . + SERVICE { + ?rhea rh:side/rh:contains/rh:compound ?compound . + ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|(rh:underlyingChebi/rh:chebi)) ?metabolite . + } + SERVICE { + ?catalyticActivityAnnotation up:catalyticActivity/up:catalyzedReaction ?rhea . + ?protein up:annotation ?catalyticActivityAnnotation ; + up:organism taxon:9606 . + } +}""" . diff --git a/swisslipids/35.ttl b/swisslipids/35.ttl index d9a343536..cc3417d2b 100644 --- a/swisslipids/35.ttl +++ b/swisslipids/35.ttl @@ -8,9 +8,16 @@ ex:35 a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; sh:prefixes _:sparql_examples_prefixes ; schema:target ; - rdfs:label "Lipids by fatty acid component and position" ; - rdfs:comment """Returns the list of isomeric subspecies containing a specific combination of fatty acids at defined positions. -If the user supplies a single fatty acid and position (e.g. hexadecanoate at sn1), find all lipids with that fatty acid at that position, irrespective of whether or not there are other fatty acids at positions (here sn2, sn3). -could generalize this query to allow logical combinations of fatty acids (e.g. hexadecanoate at sn1 AND (9Z)-octadecenoate at sn2, hexadecanoate at sn1 AND NOT (9Z)-octadecenoate at sn2, etc) -Output should include the corresponding SwissLipids ID(s) and name(s)."""^^rdf:HTML ; - sh:select """SELECT ?TODO WHERE {?TODO a ?TODO} """. + rdfs:comment "Lipids by fatty acid component (hexadecanoate) at position sn1" ; + sh:select """SELECT +?swisslipid +WHERE { + VALUES (?chebi) { + (CHEBI:7896) #hexadecanoate + } + ?swisslipidHexadeconate owl:equivalentClass ?chebi . + ?swisslipid SWISSLIPID:hasPart [ + SWISSLIPID:derived_from ?swisslipidHexadecanoate ; + SWISSLIPID:position SWISSLIPID:sn1 + ] +} """.