GetProteinsAPI

From SPCTools

GetProteins is a CGI script which allows users to query the peptide atlas for one or more proteins of interest.

GetProteins offers a number of filters and options that are not easily set by external websites, so the most common usage is to 
specify a set of proteins and let the user define the other parameters and run the script. That said, the example query below 
provides enough information for the script to automatically run:
https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?organism=Human;biosequence_name_constraint=Q00987%3BP38398%3BP51587&presence_level_constraint=1&presence_level_constraint=2&redundancy_constraint=4&QUERY_NAME=AT_GetProteins&action=QUERY

This has the following parts:
Base URL: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins

Organism: organism=Human   # Could also specify an explicit build_id, e.g. atlas_build_id=393 - but these will change over time    
Protein(s): biosequence_name_constraint=Q00987%3BP38398%3BP51587
presence level: presence_level_constraint=1     # The presence and redundancy levels are are explained [http://tools.proteomecenter.org/wiki/index.php?title=Protein_identification_terminology  [here]]: 
                presence_level_constraint=2
redundancy: redundancy_constraint=4
query_name: QUERY_NAME=AT_GetProteins
run token: action=QUERY


# Unused parameters
upload_file=
tube_constraint=
sku_constraint=
biosequence_gene_name_constraint=
biosequence_desc_constraint=
n_observations_constraint=
n_distinct_peptides_constraint=
chromosome=
genetic_locus=
start_in_chromosome=
end_in_chromosome=
strand=
protein_probability_constraint=
protein_group_representative_constraint=