GetProteinsAPI

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	Organism: organism=Human # Could also specify an explicit build_id, e.g. atlas_build_id=393 - but these will change over time		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		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*: presence_level_constraint=1
	presence_level_constraint=2		presence_level_constraint=2
-	redundancy: redundancy_constraint=4	+	redundancy*: redundancy_constraint=4
	query_name: QUERY_NAME=AT_GetProteins		query_name: QUERY_NAME=AT_GetProteins
	run token: action=QUERY		run token: action=QUERY
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	protein_group_representative_constraint=		protein_group_representative_constraint=
	</pre>		</pre>
		+
		+	*The presence and redundancy levels are are explained [http://tools.proteomecenter.org/wiki/index.php?title=Protein_identification_terminology [here]]

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Revision as of 15:27, 17 April 2014

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      
                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=

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