fids_to_literature

We try to associate features and publications, when the publications constitute supporting evidence of the function. We connect a paper to a feature when we believe that an "expert" has asserted that the function of the feature is basically what we have associated with the feature. Thus, we might attach a paper reporting the crystal structure of a protein, even though the paper is clearly not the paper responsible for the original characterization. Our position in this matter is somewhat controversial, but we are seeking to characterize some assertions as relatively solid, and this strategy seems to support that goal. Please note that we certainly wish we could also capture original publications, and when experts can provide those connections, we hope that they will help record the associations.

Example:

    fids_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 fids_to_literature. It is documented as follows:

  $return = $obj->fids_to_literature($fids)

Parameter and return types

$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a pubrefs
fids is a reference to a list where each element is a fid
fid 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.