jctoledo’s gists

jctoledo / Q8

Created June 27, 2013 20:22

Q8: retrieve a gene that encodes for a certain kind of molecule using SO

	DL query: gene and (has_quality scRNA_encoding)

	# gene : http://semanticscience.org/resource/SIO_010035
	# has_quality : http://purl.obolibrary.org/obo/so_has_quality
	# scRNA_encoding : http://purl.obolibrary.org/obo/SO_0000575

jctoledo / Q7

Created June 27, 2013 20:21

Q7: retrieve a gene that encodes for a certain kind of molecule using SIO

	DL query: gene and (encodes some 'small cytoplasmic RNA (scRNA)')

	# gene : http://semanticscience.org/resource/SIO_010035
	# encodes : http://semanticscience.org/resource/SIO_010078
	# 'small cytoplasmic RNA (scRNA)' : http://semanticscience.org/resource/SIO_001231

jctoledo / Q6

Created June 27, 2013 20:18

Q6: retrieve organisms that have genes with an enzymatic activity that was not obtained by computational analysis

	DL query: 'Mammalia [taxid: 40674]' that inverse(has_taxid) some (gene that 'has function' some (function that inverse(go_term) some ('has evidence' some (not 'inferred from electronic annotation')))
	# 'Mammalia [taxon:40674]' : http://bio2rdf.org/taxon:40674
	# has_taxid : http://bio2rdf.org/geneid_vocabulary:has_taxid
	# gene : http://semanticscience.org/resource/SIO_010035
	# 'has function' : http://semanticscience.org/resource/SIO_000225
	# function : http://semanticscience.org/resource/SIO_000017
	# go_term : http://bio2rdf.org/geneid_vocabulary:go_term
	# 'has evidence' : http://semanticscience.org/resource/SIO_000772
	# 'inferred from electronic annotation' : http://purl.obolibrary.org/obo/ECO_0000501

jctoledo / Q5

Last active December 19, 2015 01:59

Q5: retrieve genes that are annotated with a specific function that was not inferred by computational analysis.

	DL query: gene that 'has function' some function that inverse(go_term) some ('has evidence' some (not 'inferred from electronic annotation'))
	# gene : http://semanticscience.org/resource/SIO_010035
	# 'has function' : http://semanticscience.org/resource/SIO_000225
	# function : http://semanticscience.org/resource/SIO_000017
	# go_term : http://bio2rdf.org/geneid_vocabulary:go_term
	# 'has evidence' : http://semanticscience.org/resource/SIO_000772
	# 'inferred from electronic annotation' : http://purl.obolibrary.org/obo/ECO_0000501

jctoledo / Q4

Created June 27, 2013 19:59

Q4: retrieve genes that are annotated with a specific enzymatic function:

	DL query: gene that 'has function' some 'acetylglucosaminyltransferase activity [go:0008375]'
	# gene : http://semanticscience.org/resource/SIO_010035
	# 'has function' : http://semanticscience.org/resource/SIO_000225
	# 'acetylglucosaminyltransferase activity [go:0008375]' : http://bio2rdf.org/go:0008375

jctoledo / Q3

Created June 27, 2013 19:56

Q3: retrieve genes that are from any mammal but human

	DL query: gene that has_taxid some ('Mammalia [taxid: 40674]' and not 'Homo sapiens [taxid:9606]')
	# gene : http://semanticscience.org/resource/SIO_010035
	# 'Mammalia [taxid: 40674]' : http://bio2rdf.org/taxon:40674
	# 'Homo sapiens [taxid:9606]' : http://bio2rdf.org/taxon:9606
	# has_taxid : http://bio2rdf.org/geneid_vocabulary:has_taxid

jctoledo / Q2

Last active December 19, 2015 01:59

Q2: Retrieve human genes

	DL query: gene that 'has_taxid' some 'Homo sapiens [taxid:9606]'
	# gene : http://semanticscience.org/resource/SIO_010035
	# 'has_taxid' : http://bio2rdf.org/geneid_vocabulary:has_taxid
	# 'Homo sapiens [taxid:9606]': http://bio2rdf.org/taxon:9606

jctoledo / Q1

Last active December 19, 2015 01:59

Q1: Retrieve transfer RNA genes

	DL query: tRNA-gene
	#tRNA-gene : http://bio2rdf.org/geneid_vocabulary:tRNA-gene

Jose Cruz-Toledo jctoledo