OSDB  OSDB Service Actions

Actions for Service: candygene

Action IDDescription
get_the_genomic_location_of_a_feature_identified_by_id_(e.g.,_gene,_exon/intron,_transcript_or_marker)Get the genomic location of a feature identified by ID (e.g., gene, exon/intron, transcript or marker).
Action options:

-f, --featureid <featureid>
	A value of type string that will substitute ?_featureid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_term_id(s)_for_a_trait_defined_in_several_trait_ontologiesGet term ID(s) for a trait defined in several trait ontologies.
Action options:

-t, --trait <trait>
	A value of type string that will substitute ?_trait in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_qtls_described_in_an_article_identified_by_idGet QTLs described in an article identified by ID.
Action options:

-p, --pmcid <pmcid>
	A value of type string that will substitute ?_pmcid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_qtls_associated_with_a_trait_identified_by_idGet QTLs associated with a trait identified by ID.
Action options:

-t, --traitid <traitid>
	A value of type string that will substitute ?_traitid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_orthologs_of_a_gene_identified_by_idGet orthologs of a gene identified by ID.
Action options:

-g, --geneid <geneid>
	A value of type string that will substitute ?_geneid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_genes_that_overlap_with_a_qtl_identified_by_idGet genes that overlap with a QTL identified by ID.
Action options:

-q, --qtlid <qtlid>
	A value of type string that will substitute ?_qtlid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-s, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
count_genomic_features_in_a_genome_graphCount genomic features in a genome graph.
Action options:

-g, --graph <graph>
	A value of type string (iri) that will substitute ?_graph_iri in the original query
	Required: yes
	Permitted values: http://plants.ensembl.org/Solanum_lycopersicum, http://plants.ensembl.org/Solanum_tuberosum, http://solgenomics.net/genome/Solanum_lycopersicum, http://solgenomics.net/genome/Solanum_pennellii, http://solgenomics.net/genome/Solanum_tuberosum
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_annotations_from_sgn,_ensembl_and_uniprot_given_a_gene_idGet annotations from SGN, Ensembl and UniProt given a gene ID.
Action options:

-g, --geneid <geneid>
	A value of type string that will substitute ?_geneid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
summarize_qtls_extracted_from_articlesSummarize QTLs extracted from articles.
Action options:

-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_genomic_features_given_an_intervalGet genomic features given an interval.
Action options:

-c, --chrom <chrom>
	A value of type string that will substitute ?_chrom_xsd_string in the original query
	Required: yes
-f, --feature <feature>
	A value of type string that will substitute ?_feature_xsd_string in the original query
	Required: yes
-e, --end <end>
	A value of type string that will substitute ?_end_xsd_integer in the original query
	Required: yes
-b, --begin <begin>
	A value of type string that will substitute ?_begin_xsd_integer in the original query
	Required: yes
-g, --graph <graph>
	A value of type string (iri) that will substitute ?_graph_iri in the original query
	Required: yes
	Permitted values: http://solgenomics.net/genome/Solanum_lycopersicum, http://solgenomics.net/genome/Solanum_pennellii, http://solgenomics.net/genome/Solanum_tuberosum
-h, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no
get_paralogs_of_a_gene_identified_by_idGet paralogs of a gene identified by ID.
Action options:

-g, --geneid <geneid>
	A value of type string that will substitute ?_geneid in the original query
	Required: yes
-e, --endpoint [endpoint]
	Alternative endpoint for SPARQL query
	Required: no
-u, --url_only [url_only]
	Return only the action URL, not the action results
	Required: no
-r, --response_format [response_format]
	Sets the response media type through an Accept header.
	Required: no
	Permitted values: application/json, text/csv, text/html
-q, --quality_values [quality_values]
	Quality value string. e.g. application/json;q=1.0,text/turtle;q=0.8,*/*;q=0.5. 
	--response_format takes precedence.
	Required: no