REST API

 
API overview
Most data in LncPlankton can be accessed using RESTful format API allowing for integration with other resources. The API is web browsable, and allows the users to retrieve information about lncRNA from LncPlankton. Thanks to the R package Plumber, the following APIs were implemented:
  - @get /lncRNA_details?id=id_transcript
- @get /species_content?name=name_species
- @get /phylum_content?name=name_phylum
- @get /lncRNA_species?name=name_species[& filter1 & filter2 & .. & filtern]
- @get /lncRNA_phylum?name=name_phylum[& filter1 & filter2 & .. & filtern]
GET /lncRNA_details
Description: Retrieve information on one specific lncRNA transcript.
Parameters:
      - id (required): A LncPlankton Transcript ID assigned to lncRNA, eg: "CAMNT_0013187459"
Values:
      - Species: the species name of lncRNA
      - Phylum: the group name of lncRNA
      - Transcript_length: length (in bp) of the sequence lncRNA
      - Peptide length: length (in aa) of the peptide sequence corresponding to the longest ORF encoded by lncRNA (if applicable)
      - fickett_score: fickett score of lncRNA
      - pI: the iso-electric point of lncRNA
      - Coverage_ORF: the coverage of the longest ORF encoded by lncRNA (if applicable)
      - GC: the content of G and C bases of the lncRNA sequence
      - Seq: the nucleotide sequence of lncRNA
      - Prob_maj: Coding potential probability as calculated by the majority voting pipeline
      - best_hit_pfam: the protein domain pfam matching to the peptide sequence encoded by lncRNA
      - e_value_pfam: the e-value of alignment as calculated by hmmscan
      - function_pfam: description of the protein family reported as significant by hmmscan
      - best_hit_blastp: the protein domain in swissprot matching to the peptide encoded by lncRNA
      - e_value_blastp: the e-value significance as calculated by the blastp program
      - similarity_blastp: the percentage similarity as calculated by the blastp program
Examples
Example API request
curl -H"Accept:application/json" http://localhost:8000/lncRNA_details?id=CAMNT_0013187459
or
wget -qO- --header='Accept:application/json' http://localhost:8000/lncRNA_details?id=CAMNT_0013187459
Example response
 
GET /species_content
Description: Retrieve the transcriptome content of a given species.
Parameters:
      - name (required): A LncPlankton Species name assigned to species, eg: "Amphiprora_paludosa"
Values:
      - Species: the species name of lncRNA
      - Phylum: the group name of lncRNA
      - Transcriptome_size: the transcriptome size in bp
      - N50: The N50 contig size of the transcriptome assembly in bp
      - Total contigs: the total number of assembled sequence contigs
      - Median length: the median length (bp) of assembled contigs
      - Mean GC: the mean GC content of assembled contigs
      - Entropy: The Shannon Entropy of the transcriptome assembly file
      - Coding: the number of transcripts classified as "coding"
      - sncRNA: the number of transcripts classified as "sncRNA"
      - lncRNA: the number of transcripts classified as "lncRNA"
      - high_confidence_lncRNA: the number of transcripts classified as "hc-lncRNA"
Examples
Example API request
curl -H"Accept:application/json" http://localhost:8000/species_content?name=Amphiprora_paludosa
or
wget -qO- --header='Accept:application/json' http://localhost:8000/species_content?name=Amphiprora_paludosa
Example response
 
LncPlankton Current Status
Phyla/Groups > 9
Species
Total transcripts
lncRNA-like
sncRNA-like
Coding-like
High-confidence lncRNAs