GetProteinsAPI

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Revision as of 15:25, 17 April 2014 Dcampbel (Talk | contribs) ← Previous diff		Current revision Dcampbel (Talk | contribs)
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	<pre>		<pre>
-	GetProteins is a CGI script which allows users to query the peptide atlas for one or more proteins of interest.	+	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)
	</pre>		</pre>
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	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		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	+	PATH parameter (base URI): https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins
-	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	+
		+	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
-	# Unused parameters	+
		+
		+
		+
		+	# Optional parameters
		+	presence_level_constraint, integer multiple
		+	redundancy_constraint, integer, multiple
	upload_file=		upload_file=
	tube_constraint=		tube_constraint=
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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]]

---

Current revision

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]