jctoledo’s gists

jctoledo / gist:9222051

Created February 26, 2014 02:07

get the cycle uris of all cycles that have a part in a ligand neighbourhood

	select distinct ?a as ?cycle_uri
	from <http://bio2rdf.org/narf:rna_cycles_nr>
	where{
	?a a <http://bio2rdf.org/narf_vocabulary:cycle>.
	?a <http://bio2rdf.org/narf_vocabulary:has_part> ?b.
	?b a <http://bio2rdf.org/lighood_vocabulary:neighbor>.
	?lh <http://bio2rdf.org/lighood_vocabulary:has_member> ?b.
	}

jctoledo / gist:9357375

Created March 4, 2014 22:47

find the resolution of all pdbids in a graph

	select ?pdb_record ?aResolution
	from <http://bio2rdf.org/narf:rna_cycles_nr>
	where{
	?pdb_record <http://bio2rdf.org/pdb_vocabulary:hasPart> ?struct_deter.
	?struct_deter <http://bio2rdf.org/pdb_vocabulary:hasPart> ?refinement.
	?refinement <http://bio2rdf.org/pdb_vocabulary:hasLsDResHigh> ?res.
	?res a <http://bio2rdf.org/pdb_vocabulary:LsDResHigh>.
	?res <http://bio2rdf.org/pdb_vocabulary:hasValue> ?aResolution
	}

jctoledo / gist:9394011

Created March 6, 2014 16:47

get the cycle size distribution of level 1 cycles extracted from Aptamer base data

	select STR(?size) as ?cycle_size COUNT(?a) as ?frequency
	from <http://bio2rdf.org/narf:ab_rna_cycles>
	where{
	?a a <http://bio2rdf.org/narf_vocabulary:cycle>.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?c.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?d.
	?d a <http://bio2rdf.org/narf_vocabulary:cycle_size>.
	?d <http://bio2rdf.org/narf_vocabulary:has_value> ?size.
	?c a <http://bio2rdf.org/narf_vocabulary:cycle_profile_level_1> .
	?c <http://bio2rdf.org/narf_vocabulary:has_md5hash> ?ahash .

jctoledo / gist:9517428

Created March 12, 2014 22:03

find the pdbids of all structure files where the cycle 445c69d2714e43b727182b7496657eb1 occurs. Filter by resolution

	select distinct ?pdb_record
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?mcb <http://bio2rdf.org/narf_vocabulary:derived_from> ?pdb_record.
	?mcb <http://bio2rdf.org/narf_vocabulary:has_member> ?acycle.
	?acycle <http://bio2rdf.org/narf_vocabulary:has_attribute> ?a.
	?a <http://bio2rdf.org/narf_vocabulary:has_md5hash> ?ahash.
	FILTER regex(?ahash, "445c69d2714e43b727182b7496657eb1").
	?pdb_record <http://bio2rdf.org/pdb_vocabulary:hasPart> ?struct_deter.
	?struct_deter <http://bio2rdf.org/pdb_vocabulary:hasPart> ?refinement.

jctoledo / gist:9652461

Created March 19, 2014 22:06

list the name of all ligands used

	select distinct ?ares_label
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?ares a <http://bio2rdf.org/lighood_vocabulary:ligand>.
	?ares a <http://bio2rdf.org/pdb_vocabulary:Residue>.
	?ares <http://bio2rdf.org/pdb_vocabulary:isPartOf> ?cc.
	?extraction <http://bio2rdf.org/pdb_vocabulary:hasProduct> ?cc.
	?pdb_record <http://bio2rdf.org/pdb_vocabulary:hasPart> ?extraction.
	?ares rdfs:label ?ares_label
	}

jctoledo / gist:9761850

Created March 25, 2014 13:34

count the number of pdb structures in my study for which I computed MCBs

	select count (distinct ?a)
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?a a <http://bio2rdf.org/pdb_vocabulary:Experiment>.
	?mcb <http://bio2rdf.org/narf_vocabulary:derived_from> ?a.
	}

jctoledo / gist:9762002

Created March 25, 2014 13:40

get the total number of chains in my dataset

	select count (distinct ?chain)
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?a a <http://bio2rdf.org/pdb_vocabulary:Experiment>.
	?mcb <http://bio2rdf.org/narf_vocabulary:derived_from> ?a.
	?a <http://bio2rdf.org/pdb_vocabulary:hasPart> ?cse.
	?cse a <http://bio2rdf.org/pdb_vocabulary:ChemicalSubstanceExtraction>.
	?cse <http://bio2rdf.org/pdb_vocabulary:hasProduct> ?polymer.
	?polymer a <http://bio2rdf.org/pdb_vocabulary:Polymer>.
	?residue <http://bio2rdf.org/pdb_vocabulary:isPartOf> ?polymer.

jctoledo / gist:9762533

Created March 25, 2014 14:04

get the counts of backbones in my data

	select ?a count (distinct ?backbone) as ?c
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?a a <http://bio2rdf.org/pdb_vocabulary:Experiment>.
	?mcb <http://bio2rdf.org/narf_vocabulary:derived_from> ?a.
	?a <http://bio2rdf.org/pdb_vocabulary:hasPart> ?cse.
	?cse a <http://bio2rdf.org/pdb_vocabulary:ChemicalSubstanceExtraction>.
	?cse <http://bio2rdf.org/pdb_vocabulary:hasProduct> ?polymer.
	?polymer a <http://bio2rdf.org/pdb_vocabulary:Polymer>.
	?residue <http://bio2rdf.org/pdb_vocabulary:isPartOf> ?polymer.

jctoledo / gist:9762862

Created March 25, 2014 14:23

get the range of numbers of base pairs

	select ?a count (distinct ?bp) as ?c
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?a a <http://bio2rdf.org/pdb_vocabulary:Experiment>.
	?mcb <http://bio2rdf.org/narf_vocabulary:derived_from> ?a.
	?a <http://bio2rdf.org/pdb_vocabulary:hasPart> ?cse.
	?cse a <http://bio2rdf.org/pdb_vocabulary:ChemicalSubstanceExtraction>.
	?cse <http://bio2rdf.org/pdb_vocabulary:hasProduct> ?polymer.
	?polymer a <http://bio2rdf.org/pdb_vocabulary:Polymer>.
	?residue <http://bio2rdf.org/pdb_vocabulary:isPartOf> ?polymer.

jctoledo / gist:9762925

Created March 25, 2014 14:24

get the count of minimum cycles

	select count (distinct ?cyc)
	from <http://bio2rdf.org/rna_cycles_pdb>
	where{
	?a a <http://bio2rdf.org/pdb_vocabulary:Experiment>.
	?mcb <http://bio2rdf.org/narf_vocabulary:derived_from> ?a.
	?mcb <http://bio2rdf.org/narf_vocabulary:has_member> ?cyc.
	}

Jose Cruz-Toledo jctoledo