REST API - Selectome

Rest API - General Information

A REST API allows to retrieve data/files directly via a simple web request GET to our Web Service.
It is currently accessible for the basic search as well as for the family-related information (with trees and alignments).

Basic Search

Results of the basic search are accessible directly in various output formats with this base URL:

https://selectome.org/timema/requests?out=FORMAT&query=QUERY_STRING

QUERY_STRING is the query your search for.
FORMAT is the output format you want:
- json: output the search query in JSON format
  e.g. https://selectome.org/euteleostomi/requests?out=json&query=ENSGGOG00000002312
- tsv: output the search query in TSV (tab-delimited) format
  e.g. https://selectome.org/euteleostomi/requests?out=tsv&query=ENSGGOG00000002312
- xmle: output the search query result count only in XML format
  e.g. https://selectome.org/euteleostomi/requests?out=xmle&query=ENSGGOG00000002312

Tree Requests

Return tree in various formats for a Selectome (sub-)family with this base URL:

https://selectome.org/timema/family/FAMILY_ID.FORMAT

FAMILY_ID is a family identifier
e.g. ENSGT00390000005194.1.Euteleostomi
FORMAT is the output format you want:
- nwk: tree in Newick format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.nwk
- nhx: tree in Newick-Extended format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.nhx
- phyloxml: tree in PhyloXML format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.phyloxml
- png: tree in PNG format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.png

MSA Requests

Return alignment in various formats for a Selectome (sub-)family with this base URL:

https://selectome.org/timema/family/FAMILY_ID.FORMAT

FAMILY_ID is a family identifier
e.g. ENSGT00390000005194.1.Euteleostomi
FORMAT is the output format you want:
- aa.fas: raw Amino-Acid alignment in fasta format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.aa.fas
- nt.fas: raw Nucleotide (codon) alignment in fasta format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.nt.fas
- aa_masked.fas: Masked Amino-Acid alignment in fasta format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.aa_masked.fas
- nt_masked.fas: Masked Nucleotide (codon) alignment in fasta format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.nt_masked.fas

Family Information

Return information in various formats for a Selectome (sub-)family with this base URL:

https://selectome.org/timema/family/FAMILY_ID.FORMAT

FAMILY_ID is a family identifier
e.g. ENSGT00390000005194.1.Euteleostomi
FORMAT is the output format you want:
- json: family information in JSON format
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.json
- zip: family information/trees/alignments in a ZIP archive
  e.g. https://selectome.org/euteleostomi/family/ENSGT00390000005194.1.Euteleostomi.zip