« Previous - Version 24/26 (diff) - Next » - Current version
Marta Bleda, 07/06/2012 04:01 pm


Regulatory RESTful WS API

URL pattern:

Category: regulatory

ws.bioinfo.cipf.es/cellbase/rest/{version}/{species}/ regulatory /{subcategory}/id/{resource|action}

Subcategories:

MicroRNA gene

Subcategory: mirna_gene

ws.bioinfo.cipf.es/cellbase/rest/{version}/{species}/regulatory/ mirna_gene / mirna_gene1,mirna_gene2 /{resource|action}

Resources/actions

  • help: get specifications for this subcategory.

Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_gene/help

  • info: Get information about a miRNA gene: name, accession, status and sequence.

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 target sites for 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.

Filters:

source: Filter by one or more of the data sources. (Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_gene/hsa-mir-150/target?source=miRecords,mirtarbase)

  • 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.

MicroRNA mature

Subcategory: mirna_mature

ws.bioinfo.cipf.es/cellbase/rest/{version}/{species}/regulatory/ mirna_mature / mirna_mature1,mirna_mature2 /{resource|action}

Resources/actions

  • help: get specifications for this subcategory.

Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/help

  • info: Get information about a miRNA mature: name, accession and sequence.

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/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/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/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.

  • taget: 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

Filters:

source: Filter by one or more of the data sources. (Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-150-3p/target?source=miRecords)

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/latest/hsa/regulatory/mirna_mature/hsa-miR-149-3p/disease

Output columns: miRBase ID, disease name, pubmed ID, description.

Transcription Factor

Subcategory: tf

ws.bioinfo.cipf.es/cellbase/rest/{version}/{species}/regulatory/ tf / tf1,tf2 /{resource|action}

Resources

  • help: get specifications for this subcategory.

Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/help

  • info: Get information about this transcription factor (TF).

Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/info

  • tfbs: Get all transcription factor binding sites (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.

Filters:

celltype: Filter by cellular type. (Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/tfbs?celltype=K562)

start, end: Filter TFBSs by a defined promoter region. By default the promoter region is defined from -2500bp to 500bp from the transcription start site.
(Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/SP1/tfbs?start=-1000&end=300)

  • gene: Get the gene that corresponds to 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.

  • 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/latest/hsa/regulatory/tf/USF1/pwm

Output columns: TF Name, type, frequency_matrix, description, source, length, jaspar_accession.