REST API (Beta)

This REST API allows retrieval of basic lncRNA information from LNCipedia. Important: if a specific reference genome is prefered, this has to be be specified in the url. API endpoint:

http://lncipedia.org/api/

GET /api/transcript/:id

Retrieve information on one specific lncRNA transcript.

Parameters

  • :id (required): A LNCipedia Transcript ID. eg:

Fields

  • lncipediaTranscriptID: LNCipedia transcript ID. eg: 'lnc-A1BG-1:3'
  • lncipediaGeneID: LNCipedia gene ID. eg: 'lnc-A1BG-1'
  • chromosome: Chromosome. eg: 'chr10'
  • strand: Strand '+' or '-'
  • start: Start position
  • end: End position
  • exons: An array containing the start and end positions of the exons
  • nrExons: Number of exons
  • transcriptSize: Size of the transcript in nucleotides
  • sequence: RNA sequence
  • geneAliases: An array containing different aliases for the gene
  • transcriptAliases: An array containing different aliases for the transcript
  • class: Subclass. eg: 'intergenic'
  • refGenome: The reference genome use. eg: 'hg38'

Example

http://lncipedia.org/api/transcript/HOTAIR:1

GET /api/gene/:id

Retrieve information on one specific lncRNA gene.

Parameters

  • :id (required): A LNCipedia Gene ID. eg:

Fields

  • lncipediaGeneID: LNCipedia gene ID. eg: 'lnc-A1BG-1'
  • chromosome: Chromosome. eg: 'chr10'
  • strand: Strand '+' or '-'
  • start: Start position
  • end: End position
  • nrTranscripts: Number of transcripts
  • transcripts: An array containing the LNCipedia transcript IDs and start and end positions of the transcripts
  • refGenome: The reference genome use. eg: 'hg38'

Example

http://lncipedia.org/api/gene/HOTAIR

Search the LNCipedia database for lncRNA transcripts. If a specific chromosomal location is specified, all lncRNAs overlapping with that region (full or partial) are returned. A maximum of 20 records can be retrieved per request. Using the page parameter, one can traverse over all results. Page 0 is the first page and includes the 20 first results, page 1 includes results 21 to 40 etc. The nextPage field holds the URL to conveniently retrieve the next 20 results. When it is absent, no more results are available.

Parameters

  • id (optional): Any lncRNA identifier, internal or external. eg: 'ENSG00000228630'
  • chromosome (optional): Chromosome. eg: 'chr10'
  • start (optional): Start of region
  • end (optional): End of region
  • high_confidence_set (optional): Only retrieve lncRNAs in the high-confidence set. Default: false, set to 1 to enable
  • keyword (optional): A keyword in an abstract associated with the lncRNA. eg: 'cancer'
  • class (optional): Subclass. eg: 'intergenic'
  • page (optional): Specify the set of results to retrieve. Default is 0 and this corresponds to the 20 first results.

Fields

  • count: Total number of records found in the search
  • page: Zero based paginator
  • nextPage: URL to retrieve the next set of results
  • pages: Total number of pages with records available for this search
  • transcripts: An array containing the lncRNA transcripts, see GET /api/transcript/:id for a full description of the fields
  • refGenome: The reference genome use. eg: 'hg38'

Example

http://lncipedia.org/api/search?id=ENSG00000228630