NAME

mapmaker.pl

SYNOPSIS

 mapmaker.pl -i go/ontology/gene_ontology.obo -s goslim_generic -o my_stuff/mapping-file.txt

DESCRIPTION

# must supply these arguments... or else! # INPUT -i || --ontology /path/to/<file_name> input file (ontology file) with path

# SPECIFYING A SUBSET -s || --subset <subset_name> name of the subset to extract or -t || --termfile /path/to/<file_name> an input file containing a list of terms ## termfile option not yet implemented

# OUTPUT -o || --output /path/to/<file_name> output file with path

#

# MISC SWITCHES -n || --show_names show term names in the mapping file

 -v || --verbose                         prints various messages


        Given a file where certain terms are specified as being in subset S, this
        script will produce a mapping of each term to its ancestors in subset S; the
        mapping indicates which ancestral terms are closest to the term.

        Relationships between terms are calculated by the inference engine.

        If the root nodes are not already in the subset, they are added to the graph.

        The slimming algorithm is 'relationship-aware', and finds the closest node
        for each relation (rather than just the closest term). For example, if we
        had the following relationships:

        A -i- B -i- C -p- D

        the slimmer would say that B was the closest node via the 'i' relation, and
        D was the closest via the 'p' relation.

        Note that there may be several different relationships between the same two
        terms in the slimmed file.

show_names

Show the names of the term in the slim mapping file

Output format

term ID(, term name [optional]) [tab] closest ancestral subset terms for each relationship [tab] all other ancestral terms

some sample lines:

GO:0000942, outer kinetochore of condensed nuclear chromosome is_a GO:0005575; part_of GO:0005634, part_of GO:0005694 part_of GO:0005575 GO:0000943, retrotransposon nucleocapsid is_a GO:0005575; part_of GO:0005634 part_of GO:0005575 GO:0001400, mating projection base is_a GO:0005575; part_of GO:0005575 GO:0001401, mitochondrial sorting and assembly machinery complex is_a GO:0005575; part_of GO:0005740, part_of GO:0016020 part_of GO:0005575, part_of GO:0005737, part_of GO:0005739 GO:0001405, presequence translocase-associated import motor is_a GO:0005575; part_of GO:0005740, part_of GO:0016020 part_of GO:0005575, part_of GO:0005737, part_of GO:0005739 GO:0001411, hyphal tip is_a GO:0030427; part_of GO:0005575 is_a GO:0005575 GO:0001518, voltage-gated sodium channel complex is_a GO:0005575; part_of GO:0005886 part_of GO:0005575, part_of GO:0016020 GO:0001520, outer dense fiber is_a GO:0005575; part_of GO:0005575 GO:0001527, microfibril is_a GO:0005575; part_of GO:0005576 part_of GO:0005575 GO:0001529, elastin obsolete