proteins_to_literature

The routine proteins_to_literature can be used to extract the list of papers we have associated with specific protein sequences. The user should note that in many cases the association of a paper with a protein sequence is not precise. That is, the paper may actually describe a closely-related protein (that may not yet even be in a sequenced genome). Annotators attempt to use best judgement when associating literature and proteins. Publication references include [pubmed ID,URL for the paper, title of the paper]. In some cases, the URL and title are omitted. In theory, we can extract them from PubMed and we will attempt to do so.

Example:

proteins_to_literature [arguments] < input > output

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the identifer. If another column contains the identifier use

-c N

where N is the column (from 1) that contains the subsystem.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Documentation for underlying call

This script is a wrapper for the CDMI-API call proteins_to_literature. It is documented as follows:

$return = $obj->proteins_to_literature($proteins)

Parameter and return types

$proteins is a proteins
$return is a reference to a hash where the key is a protein and the value is a pubrefs
proteins is a reference to a list where each element is a protein
protein is a string
pubrefs is a reference to a list where each element is a pubref
pubref is a reference to a list containing 3 items:
	0: a string
	1: a string
	2: a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added.

Input lines that cannot be extended are written to stderr.