diff --git a/examples/Rhea/draft_human_metabolome.ttl b/examples/Rhea/19_draft_human_metabolome.ttl similarity index 96% rename from examples/Rhea/draft_human_metabolome.ttl rename to examples/Rhea/19_draft_human_metabolome.ttl index ca7ddf38d..4f5a96f41 100644 --- a/examples/Rhea/draft_human_metabolome.ttl +++ b/examples/Rhea/19_draft_human_metabolome.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:draft_human_metabolome a sh:SPARQLExecutable, +ex:19_draft_human_metabolome a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Generate a draft human metabolome"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/Rhea/search_chemical_names_in_japanese.ttl b/examples/Rhea/20_search_chemical_names_in_japanese.ttl similarity index 94% rename from examples/Rhea/search_chemical_names_in_japanese.ttl rename to examples/Rhea/20_search_chemical_names_in_japanese.ttl index 6c2edc4f0..e95da5023 100644 --- a/examples/Rhea/search_chemical_names_in_japanese.ttl +++ b/examples/Rhea/20_search_chemical_names_in_japanese.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:search_chemical_names_in_japanese a sh:SPARQLExecutable, +ex:20_search_chemical_names_in_japanese a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Search for Chemical names starting in Japanese, translated to english using allie"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_organelles_or_plasmids.ttl b/examples/UniProt/100_uniprot_organelles_or_plasmids.ttl similarity index 94% rename from examples/UniProt/uniprot_organelles_or_plasmids.ttl rename to examples/UniProt/100_uniprot_organelles_or_plasmids.ttl index 86b32ac81..33a671693 100644 --- a/examples/UniProt/uniprot_organelles_or_plasmids.ttl +++ b/examples/UniProt/100_uniprot_organelles_or_plasmids.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_organelles_or_plasmids a sh:SPARQLExecutable, +ex:100_uniprot_organelles_or_plasmids a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List the proteins encoded by a gene that is located in an organelle other than the nucleus, or on a plasmid rather than a chromosome. In these cases the gene location is stored with encodedIn properties. Note that if a plasmid has several names, they are listed as multiple rdfs:label properties."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_potential_isoforms.ttl b/examples/UniProt/101_uniprot_potential_isoforms.ttl similarity index 94% rename from examples/UniProt/uniprot_potential_isoforms.ttl rename to examples/UniProt/101_uniprot_potential_isoforms.ttl index 744008695..7556e078a 100644 --- a/examples/UniProt/uniprot_potential_isoforms.ttl +++ b/examples/UniProt/101_uniprot_potential_isoforms.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_potential_isoforms a sh:SPARQLExecutable, +ex:101_uniprot_potential_isoforms a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all human UniProtKB entries and their computationaly mapped potential isoforms."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_primary_accession.ttl b/examples/UniProt/102_uniprot_primary_accession.ttl similarity index 95% rename from examples/UniProt/uniprot_primary_accession.ttl rename to examples/UniProt/102_uniprot_primary_accession.ttl index a5f6b4e83..997478284 100644 --- a/examples/UniProt/uniprot_primary_accession.ttl +++ b/examples/UniProt/102_uniprot_primary_accession.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_primary_accession a sh:SPARQLExecutable, +ex:102_uniprot_primary_accession a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Extracting an UniProtKB primary accession from our IRIs. Is done with a bit of string manipulation. While UniProt primary accession are unique within UniProtKB they may be reused by accident or itentionally by other data sources. If we provided them as strings (not IRI) and if you used them in a query that way, you might accidentaly retrieve completely wrong records."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_proteome_location_of_gene.ttl b/examples/UniProt/103_uniprot_proteome_location_of_gene.ttl similarity index 93% rename from examples/UniProt/uniprot_proteome_location_of_gene.ttl rename to examples/UniProt/103_uniprot_proteome_location_of_gene.ttl index 9848f960a..4515ad6c4 100644 --- a/examples/UniProt/uniprot_proteome_location_of_gene.ttl +++ b/examples/UniProt/103_uniprot_proteome_location_of_gene.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_proteome_location_of_gene a sh:SPARQLExecutable, +ex:103_uniprot_proteome_location_of_gene a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List UniProtKB proteins with genetic replicon that they are encoded on using the Proteome data."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_recomended_protein_full_name.ttl b/examples/UniProt/104_uniprot_recomended_protein_full_name.ttl similarity index 91% rename from examples/UniProt/uniprot_recomended_protein_full_name.ttl rename to examples/UniProt/104_uniprot_recomended_protein_full_name.ttl index 3ae2a67aa..f0caae867 100644 --- a/examples/UniProt/uniprot_recomended_protein_full_name.ttl +++ b/examples/UniProt/104_uniprot_recomended_protein_full_name.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_recomended_protein_full_name a sh:SPARQLExecutable, +ex:104_uniprot_recomended_protein_full_name a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "The recommended protein full names for UniProtKB entries"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_recomended_protein_short_name.ttl b/examples/UniProt/105_uniprot_recomended_protein_short_name.ttl similarity index 91% rename from examples/UniProt/uniprot_recomended_protein_short_name.ttl rename to examples/UniProt/105_uniprot_recomended_protein_short_name.ttl index 94f5972e2..e577eac63 100644 --- a/examples/UniProt/uniprot_recomended_protein_short_name.ttl +++ b/examples/UniProt/105_uniprot_recomended_protein_short_name.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_recomended_protein_short_name a sh:SPARQLExecutable, +ex:105_uniprot_recomended_protein_short_name a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "The recommended protein short names for UniProtKB entries"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_reviewed_or_not.ttl b/examples/UniProt/106_uniprot_reviewed_or_not.ttl similarity index 92% rename from examples/UniProt/uniprot_reviewed_or_not.ttl rename to examples/UniProt/106_uniprot_reviewed_or_not.ttl index 48466e4f4..413e9db7d 100644 --- a/examples/UniProt/uniprot_reviewed_or_not.ttl +++ b/examples/UniProt/106_uniprot_reviewed_or_not.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_reviewed_or_not a sh:SPARQLExecutable, +ex:106_uniprot_reviewed_or_not a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all UniProtKB proteins and if they are reviewed (Swiss-Prot) or unreviewed (TrEMBL)"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_sequences_and_mark_which_is_cannonical_for_human.ttl b/examples/UniProt/107_uniprot_sequences_and_mark_which_is_cannonical_for_human.ttl similarity index 95% rename from examples/UniProt/uniprot_sequences_and_mark_which_is_cannonical_for_human.ttl rename to examples/UniProt/107_uniprot_sequences_and_mark_which_is_cannonical_for_human.ttl index 2c740a8de..4be9629bb 100644 --- a/examples/UniProt/uniprot_sequences_and_mark_which_is_cannonical_for_human.ttl +++ b/examples/UniProt/107_uniprot_sequences_and_mark_which_is_cannonical_for_human.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_sequences_and_mark_which_is_cannonical_for_human a sh:SPARQLExecutable, +ex:107_uniprot_sequences_and_mark_which_is_cannonical_for_human a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all human UniProtKB entries and their sequences, marking if the sequence listed is the cannonical sequence of the matching entry."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_signature_match_start_end.ttl b/examples/UniProt/108_uniprot_signature_match_start_end.ttl similarity index 95% rename from examples/UniProt/uniprot_signature_match_start_end.ttl rename to examples/UniProt/108_uniprot_signature_match_start_end.ttl index 35876d5e7..29b75946e 100644 --- a/examples/UniProt/uniprot_signature_match_start_end.ttl +++ b/examples/UniProt/108_uniprot_signature_match_start_end.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_signature_match_start_end a sh:SPARQLExecutable, +ex:108_uniprot_signature_match_start_end a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all InterPro member database signature match start and end for a specific UniProtKB protein."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_transporter_in_liver.ttl b/examples/UniProt/109_uniprot_transporter_in_liver.ttl similarity index 96% rename from examples/UniProt/uniprot_transporter_in_liver.ttl rename to examples/UniProt/109_uniprot_transporter_in_liver.ttl index a3bdcc86d..d9d01ab1b 100644 --- a/examples/UniProt/uniprot_transporter_in_liver.ttl +++ b/examples/UniProt/109_uniprot_transporter_in_liver.ttl @@ -5,7 +5,7 @@ @prefix sh: . @prefix spex: . -ex:uniprot_transporter_in_liver a sh:SPARQLExecutable, +ex:109_uniprot_transporter_in_liver a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find human transporter proteins in reviewed UniProtKB/Swiss-Prot, that are expressed in the liver (Uses Bgee and UBERON)."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_unamed_plasmids.ttl b/examples/UniProt/110_uniprot_unamed_plasmids.ttl similarity index 94% rename from examples/UniProt/uniprot_unamed_plasmids.ttl rename to examples/UniProt/110_uniprot_unamed_plasmids.ttl index 99b84abbc..205d35bd5 100644 --- a/examples/UniProt/uniprot_unamed_plasmids.ttl +++ b/examples/UniProt/110_uniprot_unamed_plasmids.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_unamed_plasmids a sh:SPARQLExecutable, +ex:110_uniprot_unamed_plasmids a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Sometimes it is known that a gene encoding a protein UniProtKB is located on a plasmid or an organelle, but the name of the plasmid is unknown."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/diseases_involving_enzymes.ttl b/examples/UniProt/62_diseases_involving_enzymes.ttl similarity index 94% rename from examples/UniProt/diseases_involving_enzymes.ttl rename to examples/UniProt/62_diseases_involving_enzymes.ttl index beb64d704..72bdf09cf 100644 --- a/examples/UniProt/diseases_involving_enzymes.ttl +++ b/examples/UniProt/62_diseases_involving_enzymes.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:diseases_involving_enzymes a sh:SPARQLExecutable, +ex:62_diseases_involving_enzymes a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find diseases that are thought to be related to enzymes"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/diseases_involving_enzymes_located_in_mitochondrion.ttl b/examples/UniProt/63_diseases_involving_enzymes_located_in_mitochondrion.ttl similarity index 93% rename from examples/UniProt/diseases_involving_enzymes_located_in_mitochondrion.ttl rename to examples/UniProt/63_diseases_involving_enzymes_located_in_mitochondrion.ttl index 1688ce60f..007359985 100644 --- a/examples/UniProt/diseases_involving_enzymes_located_in_mitochondrion.ttl +++ b/examples/UniProt/63_diseases_involving_enzymes_located_in_mitochondrion.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:diseases_involving_enzymes_located_in_mitochondrion a sh:SPARQLExecutable, +ex:63_diseases_involving_enzymes_located_in_mitochondrion a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find (Human genetic) diseases that are thought to be related to Enzymes, known to be located in the Mitochondrion"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/diseases_related_to_mutation_in_active_site.ttl b/examples/UniProt/64_diseases_related_to_mutation_in_active_site.ttl similarity index 96% rename from examples/UniProt/diseases_related_to_mutation_in_active_site.ttl rename to examples/UniProt/64_diseases_related_to_mutation_in_active_site.ttl index 09aaab6b9..503696b66 100644 --- a/examples/UniProt/diseases_related_to_mutation_in_active_site.ttl +++ b/examples/UniProt/64_diseases_related_to_mutation_in_active_site.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:diseases_related_to_mutation_in_active_site a sh:SPARQLExecutable, +ex:64_diseases_related_to_mutation_in_active_site a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find (Human Genetic) diseases, that are related to a natural variant on the active site of an enzyme."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/distinct_extinct_organisms_in_uniprotkb.ttl b/examples/UniProt/65_distinct_extinct_organisms_in_uniprotkb.ttl similarity index 93% rename from examples/UniProt/distinct_extinct_organisms_in_uniprotkb.ttl rename to examples/UniProt/65_distinct_extinct_organisms_in_uniprotkb.ttl index 9f9deb822..32fb82e34 100644 --- a/examples/UniProt/distinct_extinct_organisms_in_uniprotkb.ttl +++ b/examples/UniProt/65_distinct_extinct_organisms_in_uniprotkb.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:distinct_extinct_organisms_in_uniprotkb a sh:SPARQLExecutable, +ex:65_distinct_extinct_organisms_in_uniprotkb a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "How many distinct extinct organisms are represented in UniProtKB"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/distinct_rhea_transport_in_reviewed_uniprot.ttl b/examples/UniProt/66_distinct_rhea_transport_in_reviewed_uniprot.ttl similarity index 93% rename from examples/UniProt/distinct_rhea_transport_in_reviewed_uniprot.ttl rename to examples/UniProt/66_distinct_rhea_transport_in_reviewed_uniprot.ttl index 254080549..62a5b32a5 100644 --- a/examples/UniProt/distinct_rhea_transport_in_reviewed_uniprot.ttl +++ b/examples/UniProt/66_distinct_rhea_transport_in_reviewed_uniprot.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:distinct_rhea_transport_in_reviewed_uniprot a sh:SPARQLExecutable, +ex:66_distinct_rhea_transport_in_reviewed_uniprot a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Count number of unique Rhea transport reactions annotated in reviewed UniProtKB entries."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/draft_human_metabolome.ttl b/examples/UniProt/67_draft_human_metabolome.ttl similarity index 96% rename from examples/UniProt/draft_human_metabolome.ttl rename to examples/UniProt/67_draft_human_metabolome.ttl index ef6698732..8b6d2a48e 100644 --- a/examples/UniProt/draft_human_metabolome.ttl +++ b/examples/UniProt/67_draft_human_metabolome.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:draft_human_metabolome a sh:SPARQLExecutable, +ex:67_draft_human_metabolome a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Generate a draft human metabolome"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl b/examples/UniProt/68_drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl similarity index 100% rename from examples/UniProt/drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl rename to examples/UniProt/68_drosophila_enzymes_derived_from_at_least_two_mRNAs.ttl diff --git a/examples/UniProt/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl b/examples/UniProt/69_drosophila_proteins_derived_from_at_least_two_mRNAs.ttl similarity index 100% rename from examples/UniProt/drosophila_proteins_derived_from_at_least_two_mRNAs.ttl rename to examples/UniProt/69_drosophila_proteins_derived_from_at_least_two_mRNAs.ttl diff --git a/examples/UniProt/enzymes_interacting_with_molecules_similar_to_dopamine.ttl b/examples/UniProt/70_enzymes_interacting_with_molecules_similar_to_dopamine.ttl similarity index 94% rename from examples/UniProt/enzymes_interacting_with_molecules_similar_to_dopamine.ttl rename to examples/UniProt/70_enzymes_interacting_with_molecules_similar_to_dopamine.ttl index a47ab5aa3..0dd7d5f1f 100644 --- a/examples/UniProt/enzymes_interacting_with_molecules_similar_to_dopamine.ttl +++ b/examples/UniProt/70_enzymes_interacting_with_molecules_similar_to_dopamine.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:enzymes_interacting_with_molecules_similar_to_dopamine a sh:SPARQLExecutable, +ex:70_enzymes_interacting_with_molecules_similar_to_dopamine a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Look for enzymes catalyzing reactions with molecules similar to dopamine."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl b/examples/UniProt/71_enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl similarity index 94% rename from examples/UniProt/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl rename to examples/UniProt/71_enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl index 5c2c567b5..21b4ad8d6 100644 --- a/examples/UniProt/enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl +++ b/examples/UniProt/71_enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease a sh:SPARQLExecutable, +ex:71_enzymes_interacting_with_molecules_similar_to_dopamine_with_variants_related_to_disease a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Look for enzymes catalyzing reactions with molecules similar to dopamine, with natural variants related to a disease."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_mapping_to_PDB.ttl b/examples/UniProt/72_enzymes_mapping_to_PDB.ttl similarity index 95% rename from examples/UniProt/enzymes_mapping_to_PDB.ttl rename to examples/UniProt/72_enzymes_mapping_to_PDB.ttl index 2c1d5d18e..d3fbec944 100644 --- a/examples/UniProt/enzymes_mapping_to_PDB.ttl +++ b/examples/UniProt/72_enzymes_mapping_to_PDB.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix rdf: . -ex:enzymes_mapping_to_PDB a sh:SPARQLExecutable, +ex:72_enzymes_mapping_to_PDB a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment '''Select a mapping of UniProtKB enzymes to PDB entries using the UniProtKB cross-references to the PDB database.'''^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_related_to_protein.ttl b/examples/UniProt/73_enzymes_related_to_protein.ttl similarity index 95% rename from examples/UniProt/enzymes_related_to_protein.ttl rename to examples/UniProt/73_enzymes_related_to_protein.ttl index d8b5d274a..b287782fc 100644 --- a/examples/UniProt/enzymes_related_to_protein.ttl +++ b/examples/UniProt/73_enzymes_related_to_protein.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix rdf: . -ex:enzymes_related_to_protein a sh:SPARQLExecutable, +ex:73_enzymes_related_to_protein a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment '''Select Enzyme Classification (EC) classes that have a protein associated to them'''@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_with_at_least_two_transmembrane_domains.ttl b/examples/UniProt/74_enzymes_with_at_least_two_transmembrane_domains.ttl similarity index 93% rename from examples/UniProt/enzymes_with_at_least_two_transmembrane_domains.ttl rename to examples/UniProt/74_enzymes_with_at_least_two_transmembrane_domains.ttl index 923f3e6e5..7a7bb739b 100644 --- a/examples/UniProt/enzymes_with_at_least_two_transmembrane_domains.ttl +++ b/examples/UniProt/74_enzymes_with_at_least_two_transmembrane_domains.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:enzymes_with_at_least_two_transmembrane_domains a sh:SPARQLExecutable, +ex:74_enzymes_with_at_least_two_transmembrane_domains a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find Hydrolases (enzymes that catalyse the hydrolysis of various bonds) that have at least two transmembrane domains"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl b/examples/UniProt/75_enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl similarity index 94% rename from examples/UniProt/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl rename to examples/UniProt/75_enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl index 4cca979f1..fe54e3a58 100644 --- a/examples/UniProt/enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl +++ b/examples/UniProt/75_enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:enzymes_with_at_least_two_transmembrane_domains_PDB_xray a sh:SPARQLExecutable, +ex:75_enzymes_with_at_least_two_transmembrane_domains_PDB_xray a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find enzymes that have at least two transmembrane domains, whose 3D structure is elucidated through X-Ray analysis"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_with_mutagenesis_affecting_active_site.ttl b/examples/UniProt/76_enzymes_with_mutagenesis_affecting_active_site.ttl similarity index 96% rename from examples/UniProt/enzymes_with_mutagenesis_affecting_active_site.ttl rename to examples/UniProt/76_enzymes_with_mutagenesis_affecting_active_site.ttl index a0834fef4..54c00446f 100644 --- a/examples/UniProt/enzymes_with_mutagenesis_affecting_active_site.ttl +++ b/examples/UniProt/76_enzymes_with_mutagenesis_affecting_active_site.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:enzymes_with_mutagenesis_affecting_active_site a sh:SPARQLExecutable, +ex:76_enzymes_with_mutagenesis_affecting_active_site a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find enzymes, where the active site is a region affected by mutagenesis and show the comment regarding mutagenesis effect."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/enzymes_with_tyrosine_as_active_site.ttl b/examples/UniProt/77_enzymes_with_tyrosine_as_active_site.ttl similarity index 100% rename from examples/UniProt/enzymes_with_tyrosine_as_active_site.ttl rename to examples/UniProt/77_enzymes_with_tyrosine_as_active_site.ttl diff --git a/examples/UniProt/genetic_disease_related_proteins.ttl b/examples/UniProt/78_genetic_disease_related_proteins.ttl similarity index 94% rename from examples/UniProt/genetic_disease_related_proteins.ttl rename to examples/UniProt/78_genetic_disease_related_proteins.ttl index c20f41224..6328833e9 100644 --- a/examples/UniProt/genetic_disease_related_proteins.ttl +++ b/examples/UniProt/78_genetic_disease_related_proteins.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:genetic_disease_related_proteins a sh:SPARQLExecutable, +ex:78_genetic_disease_related_proteins a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all UniProtKB proteins annotated to be related to a genetic disease."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/mnemonic_also_known_as_id.ttl b/examples/UniProt/79_mnemonic_also_known_as_id.ttl similarity index 92% rename from examples/UniProt/mnemonic_also_known_as_id.ttl rename to examples/UniProt/79_mnemonic_also_known_as_id.ttl index 08eed2d27..08a846ee5 100644 --- a/examples/UniProt/mnemonic_also_known_as_id.ttl +++ b/examples/UniProt/79_mnemonic_also_known_as_id.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:mnemonic_also_known_as_id a sh:SPARQLExecutable, +ex:79_mnemonic_also_known_as_id a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all UniProtKB protein ID (mnemonic) for current UniProtKB entries."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/obsolete_mnemonic_also_known_as_id.ttl b/examples/UniProt/80_obsolete_mnemonic_also_known_as_id.ttl similarity index 92% rename from examples/UniProt/obsolete_mnemonic_also_known_as_id.ttl rename to examples/UniProt/80_obsolete_mnemonic_also_known_as_id.ttl index b4f3d67f8..f3a3f6189 100644 --- a/examples/UniProt/obsolete_mnemonic_also_known_as_id.ttl +++ b/examples/UniProt/80_obsolete_mnemonic_also_known_as_id.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:obsolete_mnemonic_also_known_as_id a sh:SPARQLExecutable, +ex:80_obsolete_mnemonic_also_known_as_id a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List all UniProtKB protein ID (mnemonic) that where used in the past for current UniProtKB entries."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/rhea_reactions_annotated_as_experimental_and_only_small_molecules.ttl b/examples/UniProt/81_rhea_reactions_annotated_as_experimental_and_only_small_molecules.ttl similarity index 94% rename from examples/UniProt/rhea_reactions_annotated_as_experimental_and_only_small_molecules.ttl rename to examples/UniProt/81_rhea_reactions_annotated_as_experimental_and_only_small_molecules.ttl index c1d231860..1a14452b1 100644 --- a/examples/UniProt/rhea_reactions_annotated_as_experimental_and_only_small_molecules.ttl +++ b/examples/UniProt/81_rhea_reactions_annotated_as_experimental_and_only_small_molecules.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:rhea_reactions_annotated_as_experimental_and_only_small_molecules a sh:SPARQLExecutable, +ex:81_rhea_reactions_annotated_as_experimental_and_only_small_molecules a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find all Rhea (only small molecule) that are used in UniProtKB where the annotation has a paper and is tagged having experimental evidence."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/rhea_reactions_associated_with_ec_in_uniprotkb.ttl b/examples/UniProt/82_rhea_reactions_associated_with_ec_in_uniprotkb.ttl similarity index 91% rename from examples/UniProt/rhea_reactions_associated_with_ec_in_uniprotkb.ttl rename to examples/UniProt/82_rhea_reactions_associated_with_ec_in_uniprotkb.ttl index 73ca362f0..7788b078d 100644 --- a/examples/UniProt/rhea_reactions_associated_with_ec_in_uniprotkb.ttl +++ b/examples/UniProt/82_rhea_reactions_associated_with_ec_in_uniprotkb.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:rhea_reactions_associated_with_ec_in_uniprotkb a sh:SPARQLExecutable, +ex:82_rhea_reactions_associated_with_ec_in_uniprotkb a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List Rhea reactions associated with an EC (enzyme classification)."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/rhea_reactions_not_associated_with_ec_in_uniprotkb.ttl b/examples/UniProt/83_rhea_reactions_not_associated_with_ec_in_uniprotkb.ttl similarity index 91% rename from examples/UniProt/rhea_reactions_not_associated_with_ec_in_uniprotkb.ttl rename to examples/UniProt/83_rhea_reactions_not_associated_with_ec_in_uniprotkb.ttl index ac62ad78d..b3a10a6b1 100644 --- a/examples/UniProt/rhea_reactions_not_associated_with_ec_in_uniprotkb.ttl +++ b/examples/UniProt/83_rhea_reactions_not_associated_with_ec_in_uniprotkb.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:rhea_reactions_not_associated_with_ec_in_uniprotkb a sh:SPARQLExecutable, +ex:83_rhea_reactions_not_associated_with_ec_in_uniprotkb a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List Rhea reactions that are not associated with an EC (enzyme classification)."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/taxonomy_hierarchy.ttl b/examples/UniProt/84_taxonomy_hierarchy.ttl similarity index 95% rename from examples/UniProt/taxonomy_hierarchy.ttl rename to examples/UniProt/84_taxonomy_hierarchy.ttl index 1fbcc61da..c4d774f97 100644 --- a/examples/UniProt/taxonomy_hierarchy.ttl +++ b/examples/UniProt/84_taxonomy_hierarchy.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:taxonomy_hierarchy a sh:SPARQLExecutable, +ex:84_taxonomy_hierarchy a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find all taxonomic records that describe species of the genus Homo."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/taxonomy_host.ttl b/examples/UniProt/85_taxonomy_host.ttl similarity index 94% rename from examples/UniProt/taxonomy_host.ttl rename to examples/UniProt/85_taxonomy_host.ttl index c0fe43bbc..9a65f241a 100644 --- a/examples/UniProt/taxonomy_host.ttl +++ b/examples/UniProt/85_taxonomy_host.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:taxonomy_host a sh:SPARQLExecutable, +ex:85_taxonomy_host a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find taxon records that are known to have part of their life cycle in other organisms (e.g. parasite, symbiont, infection)"^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/taxonomy_rank_and_scientific_name.ttl b/examples/UniProt/86_taxonomy_rank_and_scientific_name.ttl similarity index 93% rename from examples/UniProt/taxonomy_rank_and_scientific_name.ttl rename to examples/UniProt/86_taxonomy_rank_and_scientific_name.ttl index 8163c2f44..4c1a14075 100644 --- a/examples/UniProt/taxonomy_rank_and_scientific_name.ttl +++ b/examples/UniProt/86_taxonomy_rank_and_scientific_name.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:taxonomy_rank_and_scientific_name a sh:SPARQLExecutable, +ex:86_taxonomy_rank_and_scientific_name a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Retrieve the rank and the scientific name of an taxonomic record. Not all taxonomic records have a rank associated with them."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/taxonomy_with_at_least_one_swissprot.ttl b/examples/UniProt/87_taxonomy_with_at_least_one_swissprot.ttl similarity index 95% rename from examples/UniProt/taxonomy_with_at_least_one_swissprot.ttl rename to examples/UniProt/87_taxonomy_with_at_least_one_swissprot.ttl index 82f92589c..39657c10f 100644 --- a/examples/UniProt/taxonomy_with_at_least_one_swissprot.ttl +++ b/examples/UniProt/87_taxonomy_with_at_least_one_swissprot.ttl @@ -4,7 +4,7 @@ @prefix schema: . @prefix sh: . -ex:taxonomy_with_at_least_one_swissprot a sh:SPARQLExecutable, +ex:87_taxonomy_with_at_least_one_swissprot a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find taxon records for which one reviewed UniProtKB/Swiss-Prot entry exists. We might expect species, strains, subspecies and isolates in the taxon list."^^rdf:HTML ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniparc_linked_to_active_uniprot.ttl b/examples/UniProt/88_uniparc_linked_to_active_uniprot.ttl similarity index 93% rename from examples/UniProt/uniparc_linked_to_active_uniprot.ttl rename to examples/UniProt/88_uniparc_linked_to_active_uniprot.ttl index ab85141b1..8d50e50a1 100644 --- a/examples/UniProt/uniparc_linked_to_active_uniprot.ttl +++ b/examples/UniProt/88_uniparc_linked_to_active_uniprot.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniparc_linked_to_active_uniprot a sh:SPARQLExecutable, +ex:88_uniparc_linked_to_active_uniprot a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Show for a given UniParc accessions which active UniProtKB entries have the same amino acid sequence"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniparc_triples_directly_associated.ttl b/examples/UniProt/89_uniparc_triples_directly_associated.ttl similarity index 91% rename from examples/UniProt/uniparc_triples_directly_associated.ttl rename to examples/UniProt/89_uniparc_triples_directly_associated.ttl index d6808d99a..428fdad9b 100644 --- a/examples/UniProt/uniparc_triples_directly_associated.ttl +++ b/examples/UniProt/89_uniparc_triples_directly_associated.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniparc_triples_directly_associated a sh:SPARQLExecutable, +ex:89_uniparc_triples_directly_associated a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Predicates and objects, for a given UniParc accession as a subject"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_affected_by_metabolic_diseases_using_MeSH.ttl b/examples/UniProt/90_uniprot_affected_by_metabolic_diseases_using_MeSH.ttl similarity index 94% rename from examples/UniProt/uniprot_affected_by_metabolic_diseases_using_MeSH.ttl rename to examples/UniProt/90_uniprot_affected_by_metabolic_diseases_using_MeSH.ttl index 21ee5b007..b7772b9ad 100644 --- a/examples/UniProt/uniprot_affected_by_metabolic_diseases_using_MeSH.ttl +++ b/examples/UniProt/90_uniprot_affected_by_metabolic_diseases_using_MeSH.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:uniprot_affected_by_metabolic_diseases_using_MeSH a sh:SPARQLExecutable, +ex:90_uniprot_affected_by_metabolic_diseases_using_MeSH a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Proteins involved in metabolic diseases in UniProtKB. Using the MeSH concept as a root to find metabolic diseases in UniProt."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_alternative_protein_full_name.ttl b/examples/UniProt/91_uniprot_alternative_protein_full_name.ttl similarity index 91% rename from examples/UniProt/uniprot_alternative_protein_full_name.ttl rename to examples/UniProt/91_uniprot_alternative_protein_full_name.ttl index 837698050..d970541f8 100644 --- a/examples/UniProt/uniprot_alternative_protein_full_name.ttl +++ b/examples/UniProt/91_uniprot_alternative_protein_full_name.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_alternative_protein_full_name a sh:SPARQLExecutable, +ex:91_uniprot_alternative_protein_full_name a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Alternative protein full names for UniProtKB entries"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_bioregistry_iri_translation.ttl b/examples/UniProt/92_uniprot_bioregistry_iri_translation.ttl similarity index 94% rename from examples/UniProt/uniprot_bioregistry_iri_translation.ttl rename to examples/UniProt/92_uniprot_bioregistry_iri_translation.ttl index eddba7552..b3a6d5b88 100644 --- a/examples/UniProt/uniprot_bioregistry_iri_translation.ttl +++ b/examples/UniProt/92_uniprot_bioregistry_iri_translation.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:uniprot_bioregistry_iri_translation a sh:SPARQLExecutable, +ex:92_uniprot_bioregistry_iri_translation a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Translate the global unique identifier for a UniProtKB record into other options using the bioregistry translating endpoint."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_created_modified_updated.ttl b/examples/UniProt/93_uniprot_created_modified_updated.ttl similarity index 92% rename from examples/UniProt/uniprot_created_modified_updated.ttl rename to examples/UniProt/93_uniprot_created_modified_updated.ttl index f38b07022..be42f2852 100644 --- a/examples/UniProt/uniprot_created_modified_updated.ttl +++ b/examples/UniProt/93_uniprot_created_modified_updated.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_created_modified_updated a sh:SPARQLExecutable, +ex:93_uniprot_created_modified_updated a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List the created, last modified, and last sequence update dates for UniProtKB proteins."@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_encoding_gene.ttl b/examples/UniProt/94_uniprot_encoding_gene.ttl similarity index 92% rename from examples/UniProt/uniprot_encoding_gene.ttl rename to examples/UniProt/94_uniprot_encoding_gene.ttl index b8d8e0362..ac227937d 100644 --- a/examples/UniProt/uniprot_encoding_gene.ttl +++ b/examples/UniProt/94_uniprot_encoding_gene.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_encoding_gene a sh:SPARQLExecutable, +ex:94_uniprot_encoding_gene a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List UniProtKB proteins with their associated named gene"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_encoding_gene_alternative_names.ttl b/examples/UniProt/95_uniprot_encoding_gene_alternative_names.ttl similarity index 100% rename from examples/UniProt/uniprot_encoding_gene_alternative_names.ttl rename to examples/UniProt/95_uniprot_encoding_gene_alternative_names.ttl diff --git a/examples/UniProt/uniprot_encoding_gene_name.ttl b/examples/UniProt/96_uniprot_encoding_gene_name.ttl similarity index 93% rename from examples/UniProt/uniprot_encoding_gene_name.ttl rename to examples/UniProt/96_uniprot_encoding_gene_name.ttl index 250acd3e5..b94509349 100644 --- a/examples/UniProt/uniprot_encoding_gene_name.ttl +++ b/examples/UniProt/96_uniprot_encoding_gene_name.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_encoding_gene_name a sh:SPARQLExecutable, +ex:96_uniprot_encoding_gene_name a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List UniProtKB proteins with their associated gene and the gene's preffered name"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_encoding_gene_org_name.ttl b/examples/UniProt/97_uniprot_encoding_gene_org_name.ttl similarity index 91% rename from examples/UniProt/uniprot_encoding_gene_org_name.ttl rename to examples/UniProt/97_uniprot_encoding_gene_org_name.ttl index e06f73af2..d71b044f9 100644 --- a/examples/UniProt/uniprot_encoding_gene_org_name.ttl +++ b/examples/UniProt/97_uniprot_encoding_gene_org_name.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_encoding_gene_org_name a sh:SPARQLExecutable, +ex:97_uniprot_encoding_gene_org_name a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "List UniProtKB proteins with their associated gene and the gene's ORF label"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_entries_with_more_than_two_geneid_crossrefences.ttl b/examples/UniProt/98_uniprot_entries_with_more_than_two_geneid_crossrefences.ttl similarity index 92% rename from examples/UniProt/uniprot_entries_with_more_than_two_geneid_crossrefences.ttl rename to examples/UniProt/98_uniprot_entries_with_more_than_two_geneid_crossrefences.ttl index 5cc4ce484..85ebaca58 100644 --- a/examples/UniProt/uniprot_entries_with_more_than_two_geneid_crossrefences.ttl +++ b/examples/UniProt/98_uniprot_entries_with_more_than_two_geneid_crossrefences.ttl @@ -3,7 +3,7 @@ @prefix schema: . @prefix sh: . -ex:uniprot_entries_with_more_than_two_geneid_crossrefences a sh:SPARQLExecutable, +ex:98_uniprot_entries_with_more_than_two_geneid_crossrefences a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Find GeneID's crosslinked to more than one human or mouse UniProtKB entry"@en ; sh:prefixes _:sparql_examples_prefixes ; diff --git a/examples/UniProt/uniprot_identifiers_org_translation.ttl b/examples/UniProt/99_uniprot_identifiers_org_translation.ttl similarity index 94% rename from examples/UniProt/uniprot_identifiers_org_translation.ttl rename to examples/UniProt/99_uniprot_identifiers_org_translation.ttl index a0721ecc0..0d69d11f4 100644 --- a/examples/UniProt/uniprot_identifiers_org_translation.ttl +++ b/examples/UniProt/99_uniprot_identifiers_org_translation.ttl @@ -4,7 +4,7 @@ @prefix sh: . @prefix spex: . -ex:uniprot_identifiers_org_translation a sh:SPARQLExecutable, +ex:99_uniprot_identifiers_org_translation a sh:SPARQLExecutable, sh:SPARQLSelectExecutable ; rdfs:comment "Translate a selection of UniProtKB accession numbers into other options using the identifiers.org translating endpoint."@en ; sh:prefixes _:sparql_examples_prefixes ;