GetProteinsAPI

From SPCTools

GetProteins is a CGI script which allows users to query the peptide atlas for one or more proteins of interest. Default export format is tab-separated values (TSV)

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


PATH parameter (base URI): https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins

Query parameters:
organism, string [required if no atlas_build_id]: e.g. Human        # Preferred as current best build will be used
atlas_build_id, integer [required if no organism]: e.g. 393   # Explicit, but may not be current best resource    
biosequence_name_constraint, string of (url-escaped)comma-separated identifiers: e.g. Q00987%3BP38398%3BP51587
query_name, string: QUERY_NAME=AT_GetProteins
run token, string: action=QUERY





# Optional parameters
presence_level_constraint, integer multiple      
redundancy_constraint, integer, multiple
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=

• The presence and redundancy levels are are explained [here]