Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Last revision Both sides next revision
restful_web_services [2012/07/06 16:04]
mbleda [Regulatory category]
restful_web_services [2012/07/06 16:11]
mbleda
Line 11: Line 11:
 Sections in braquets are parameters, so they are variable entities: Sections in braquets are parameters, so they are variable entities:
  
-__Example__:​ [[http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​feature/​gene/​BRCA2/​tfbs]]+__Example__:​ [[http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​feature/​gene/​BRCA2/​tfbs]]
  
-As is explained in this documentation,​ this REST call will get all transcription factor binding sites (TFBSs) related to the gene BRCA2 of human in the version v1.+As is explained in this documentation,​ this REST call will get all transcription factor binding sites (TFBSs) related to the gene BRCA2 in human.
  
 **Note**: All sections in URL must be in **lower case!** **Note**: All sections in URL must be in **lower case!**
  
-^version|Versions are numbered as v1, v2, v3, etc consecutively. At this moment the public version is //v1//.|+^version|Versions are numbered as v1, v2, v3, etc consecutively. At this moment the public version is //v1//. Use //latest// to use the most updated version.|
 ^species|Currently,​ the supported species are human and mouse. Both, the abbreviated form (i.e: //​hsapiens//,​ //​mmusculus//​) and the 3-letter code (i.e: //hsa//, //mmu//) are accepted.| ^species|Currently,​ the supported species are human and mouse. Both, the abbreviated form (i.e: //​hsapiens//,​ //​mmusculus//​) and the 3-letter code (i.e: //hsa//, //mmu//) are accepted.|
 ^category|There are 3 main categories (**[[restful_web_services#​regulatory_category|regulatory]]**,​ **[[restful_web_services#​genomic_category|genomic]]** and **[[restful_web_services#​feature_category|feature]]**) that permit the access according to the nature of your query identifier (id).| ^category|There are 3 main categories (**[[restful_web_services#​regulatory_category|regulatory]]**,​ **[[restful_web_services#​genomic_category|genomic]]** and **[[restful_web_services#​feature_category|feature]]**) that permit the access according to the nature of your query identifier (id).|
Line 30: Line 30:
 Regulatory category refers to regulatory elements, such transcription factors and microRNAs. Regulatory category refers to regulatory elements, such transcription factors and microRNAs.
  
-**URL pattern:​**\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​**regulatory**/<​subcategory>/​id/<​resource|action>''​+**URL pattern:​**\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​**regulatory**/<​subcategory>/​id/<​resource>''​
  
 === Subcategories === === Subcategories ===
  
-**<fc #​007BA4>​tf</​fc>​**:​\\ URL pattern: ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​regulatory/​**tf**///​tf1,​ tf2///<​resource|action>''​\\ Format: HGNC Symbol, Ensembl gene, Ensembl TF Name.\\ Resources or actions:+**<fc #​007BA4>​tf</​fc>​**:​\\ URL pattern:\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​regulatory/​**tf**///​tf1,​ tf2///<​resource|action>''​\\ Format: HGNC Symbol, Ensembl gene, Ensembl TF Name.\\ Resources or actions:
 == == == ==
-  * **//​info//​**:​ Returns information about this transcription factor (TF).\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​tf/​USF1/​info\\ __Output columns__:+  * **//​info//​**:​ Returns information about this transcription factor (TF).\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​tf/​USF1/​info\\ __Output columns__:
  
-  * **//​tfbs//​**:​ Get all TFBSs for this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​tf/​USF1/​tfbs\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.+  * **//​tfbs//​**:​ Get all TFBSs for this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​tf/​USF1/​tfbs\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.
  
-  * **//gene//**: Get all genes regulated by this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​tf/​USF1/​gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.+  * **//target_gene//**: Get all genes regulated by this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​tf/​USF1/​target_gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.
  
-  * **//​pwm//​**:​ Get all position weight matrices associated to this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​tf/​USF1/​pwm\\ __Output columns__: TF Name, type, frequency_matrix,​ description,​ source, length, jaspar_accession.+  ​* **//​gene//​**:​ Get the corresponding gene for this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​tf/​USF1/​gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description. 
 + 
 +  ​* **//​pwm//​**:​ Get all position weight matrices associated to this TF.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​tf/​USF1/​pwm\\ __Output columns__: TF Name, type, frequency_matrix,​ description,​ source, length, jaspar_accession.
 === === === ===
  
  
-**<fc #​007BA4>​mirna_mature</​fc>​**:​\\ URL pattern: ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​regulatory/​**mirna_mature**///​mirna_mature1,​ mirna_mature2///<​resource|action>''​\\ Format: [[http://​www.mirbase.org/​help/​nomenclature.shtml|miRBase name/​identifier]].\\ Resources or actions:+**<fc #​007BA4>​mirna_mature</​fc>​**:​\\ URL pattern:\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​regulatory/​**mirna_mature**///​mirna_mature1,​ mirna_mature2///<​resource>''​\\ Format: [[http://​www.mirbase.org/​help/​nomenclature.shtml|miRBase name/​identifier]].\\ Resources or actions:
 == == == ==
-  * **//​info//​**:​ Returns information about a miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​info\\ __Output columns__: miRBase accession, miRBase ID, sequence.+  * **//​info//​**:​ Returns information about a miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​info\\ __Output columns__: miRBase accession, miRBase ID, sequence.
  
-  * **//​gene//​**:​ Get the gene associated to this miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.+  * **//​gene//​**:​ Get the gene associated to this miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.
  
-  * **//​mirna_gene//​**:​ Get the miRNA gene information associated to this miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​mirna_gene\\ __Output columns__: miRBase accession, miRBase ID, status, sequence, source.+  * **//​mirna_gene//​**:​ Get the miRNA gene information associated to this miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​mirna_gene\\ __Output columns__: miRBase accession, miRBase ID, status, sequence, source.
  
-  * **//​target_gene//​**:​ Get all genes that are regulated by this miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_mature/​hsa-miR-149/​target_gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.+  * **//​target_gene//​**:​ Get all genes that are regulated by this miRNA mature.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_mature/​hsa-miR-149/​target_gene\\ __Output columns__: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.
  
-  * **//​target//​**:​ Get all binding sites associated to this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_mature/​hsa-miR-149/​target\\ __Output columns__: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.+  * **//​target//​**:​ Get all binding sites associated to this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_mature/​hsa-miR-149/​target\\ __Output columns__: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.
  
-  * **//​disease//​**:​ Get all diseases related with this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​disease\\ __Output columns__: miRBase ID, disease name, pubmed ID, description.+  * **//​disease//​**:​ Get all diseases related with this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_mature/​hsa-miR-149-3p/​disease\\ __Output columns__: miRBase ID, disease name, pubmed ID, description.
 === === === ===
  
  
-**<fc #​007BA4>​mirna_gene</​fc>​**:​\\ URL pattern: ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​regulatory/​**mirna_gene**///​mirna_gene1,​ mirna_gene2///<​resource|action>''​\\ Format: [[http://​www.mirbase.org/​help/​nomenclature.shtml|miRBase name/​identifier]].\\ Resources or actions:+**<fc #​007BA4>​mirna_gene</​fc>​**:​\\ URL pattern:\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​regulatory/​**mirna_gene**///​mirna_gene1,​ mirna_gene2///<​resource|action>''​\\ Format: [[http://​www.mirbase.org/​help/​nomenclature.shtml|miRBase name/​identifier]].\\ Resources or actions:
 == == == ==
-  * **//​info//​**:​ Returns information about a miRNA gene.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​info\\ __Output columns__: ​ miRBase accession, miRBase ID, status, sequence, source.+  * **//​info//​**:​ Returns information about a miRNA gene.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​info\\ __Output columns__: ​ miRBase accession, miRBase ID, status, sequence, source.
  
-  * **//​target//​**:​ Get all binding sites associated to this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​target\\ __Output columns__: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.+  * **//​target//​**:​ Get all binding sites associated to this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​target\\ __Output columns__: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.
  
-  * **//​disease//​**:​ Get all diseases related with this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​disease\\ __Output columns__: miRBase ID, disease name, pubmed ID, description.+  * **//​disease//​**:​ Get all diseases related with this miRNA.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​disease\\ __Output columns__: miRBase ID, disease name, pubmed ID, description.
  
  
Line 75: Line 77:
 Genomic category makes reference to the coordinates necessary to place a position or a region in the genome. Using these coordinates,​ the user can query our database to retrieve any regulatory information within a position or region. Genomic category makes reference to the coordinates necessary to place a position or a region in the genome. Using these coordinates,​ the user can query our database to retrieve any regulatory information within a position or region.
  
-**URL pattern:** ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​**genomic**/<​subcategory>/​id/<​resource|action>''​+**URL pattern:**\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​**genomic**/<​subcategory>/​id/<​resource|action>''​
  
 === Subcategories === === Subcategories ===
Line 81: Line 83:
   * **<fc #​007BA4>​region</​fc>​**:​\\ URL pattern: ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​genomic/​**region**///​region1,​ region2///<​resource|action>''​\\ Chr. region format: //​chr:​start-end//​ (i.e.: 7:​245000-501560). Use the same start and end to indicate a position.\\ Resources or actions:   * **<fc #​007BA4>​region</​fc>​**:​\\ URL pattern: ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​genomic/​**region**///​region1,​ region2///<​resource|action>''​\\ Chr. region format: //​chr:​start-end//​ (i.e.: 7:​245000-501560). Use the same start and end to indicate a position.\\ Resources or actions:
 == == == ==
-  * **//​tfbs//​**:​ Returns all TFBSs located in the specified region.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​genomic/​region/​16:​3698105-3801105/​tfbs\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.+  * **//​tfbs//​**:​ Returns all TFBSs located in the specified region.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​genomic/​region/​16:​3698105-3801105/​tfbs\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.
  
-  * **//​mirna_binding_site//​**:​ Returns all miRNA binding sites located in the specified region.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​genomic/​region/​16:​3698105-3801105/​mirna_binding_site\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.+  * **//​mirna_binding_site//​**:​ Returns all miRNA binding sites located in the specified region.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​genomic/​region/​16:​3698105-3801105/​mirna_binding_site\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.
  
  
Line 89: Line 91:
 Feature category involve all elements which have a defined location on the genome. Feature category involve all elements which have a defined location on the genome.
  
-**URL pattern:** ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​**feature**/<​subcategory>/​id/<​resource|action>''​+**URL pattern:**\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​**feature**/<​subcategory>/​id/<​resource|action>''​
  
 === Subcategories === === Subcategories ===
  
-**<fc #​007BA4>​gene</​fc>​**:​\\ URL pattern: ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​feature/​**gene**///​gene1,​ gene2///<​resource|action>''​\\ Gene format: we accept all id formats.\\ Resources or actions:+**<fc #​007BA4>​gene</​fc>​**:​\\ URL pattern:\\ ''​ws.bioinfo.cipf.es/​cellbase/​rest/<​version>/<​species>/​feature/​**gene**///​gene1,​ gene2///<​resource|action>''​\\ Gene format: we accept all id formats.\\ Resources or actions:
 == == == ==
-  * **//​tfbs//​**:​ Returns all TFBSs located in the specified gene.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​feature/​gene/​BRCA2/​tfbs\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.+  * **//​tfbs//​**:​ Returns all TFBSs located in the specified gene.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​feature/​gene/​BRCA2/​tfbs\\ __Output columns__: TF name, target gene name, chromosome, start, end, cell type, sequence, score.
  
-  * **//​mirna_target//​**:​ Get all microRNA target sites for this gene.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​feature/​gene/​BRCA2/​mirna_target\\ __Output columns__: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.+  * **//​mirna_target//​**:​ Get all microRNA target sites for this gene.\\ __Example__:​ http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​feature/​gene/​BRCA2/​mirna_target\\ __Output columns__: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.
  
 \\ \\
Line 113: Line 115:
  
 ## define the query URL ## define the query URL
-my $url = '​http://​ws.bioinfo.cipf.es/​cellbase/​rest/​v1/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​disease';​+my $url = '​http://​ws.bioinfo.cipf.es/​cellbase/​rest/​latest/​hsa/​regulatory/​mirna_gene/​hsa-mir-149/​disease';​
  
 ## send request ## send request
restful_web_services.txt · Last modified: 2012/07/06 16:11 by mbleda
Driven by DokuWiki Recent changes RSS feed Valid XHTML 1.0 do yourself a favour and use a real browser - get firefox!!