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|} | |} | ||
- | The method for calculating these evidence codes in Perl can be found in the subroutine " | + | The method for calculating these evidence codes in Perl can be found in the subroutine "gpmdbProteinEvidence" in [ftp://ftp.thegpm.org/repos/gpmdb_rest/gpmdb_rest.pl gpmdb_rest.pl]. |
+ | |||
+ | The evidence code associated with any protein accession number can be retrieved using the GPMDB REST interface with a URL call, for example, the evidence code for the mouse protein NSMUSP00000026459 can be obtained at: | ||
+ | |||
+ | [http://gpmdb.thegpm.org/1/protein/evidence/acc=ENSMUSP00000026459 http://gpmdb.thegpm.org/1/protein/evidence/acc=ENSMUSP00000026459] | ||
The current version of the algorithm for a protein is summarized below. | The current version of the algorithm for a protein is summarized below. | ||
# Retrieve the lowest E-value assigned to the protein of interest; | # Retrieve the lowest E-value assigned to the protein of interest; | ||
- | # If that E-value is less than a threshold value (currently log(E) & | + | # If that E-value is less than a threshold value (currently log(E) < -13.5), report EC = 4; |
# Retrieve all of the observed E-values for peptides assigned to the protein of interest; | # Retrieve all of the observed E-values for peptides assigned to the protein of interest; | ||
# If none of the peptides have an observation with an E-value less than 0.01, report EC = 1; | # If none of the peptides have an observation with an E-value less than 0.01, report EC = 1; |
GPMDB uses an evidence code system to rate the current observation status of individual protein sequences. The same system is used for gene loci, where applicable. The ratings are as follows:
Code | Level | Meaning |
---|---|---|
black | 1 | no observation of a protein has reached a set scoring threshold |
red | 2 | at least one observation of a protein has exceeded the scoring threshold |
yellow | 3 | multiple observations of a protein have a set of common peptides and the distribution of scores for at least one peptide in that set exceeds a minimum test for non-randomness |
green | 4 | the set of common peptides contains at least one peptide with a scoring distribution that exceeds a stricter test for non-randomness |
The method for calculating these evidence codes in Perl can be found in the subroutine "gpmdbProteinEvidence" in gpmdb_rest.pl.
The evidence code associated with any protein accession number can be retrieved using the GPMDB REST interface with a URL call, for example, the evidence code for the mouse protein NSMUSP00000026459 can be obtained at:
http://gpmdb.thegpm.org/1/protein/evidence/acc=ENSMUSP00000026459
The current version of the algorithm for a protein is summarized below.