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go-perl-0.01
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/ map2slim

NAME

map2slim

SYNOPSIS

cd go map2slim.pl GO_Slims/generic.0208 ontology/* gene-associations/gene_association.fb

DESCRIPTION

Given a GO slim file, and a current ontology (in one or more files), this script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

The script can be used to either create a new gene association file, containing the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term

ARGUMENTS

-b bucket slim file

This argument adds bucket terms to the slim ontology; see the documentation below for an explanation. The new slim ontology file, including bucket terms will be written to bucket slim file

-outmap slim mapping file

This will generate a mapping file for every term in the full ontology showing both the most pertinent slim term and all slim terms that are ancestors. If you use this option, do NOT supply a gene-associations file

-c

This will force map2slim to give counts of the assoc file, rather than map it

-t

When used in conjunction with -c will tab the output so that the indentation reflects the tree hierarchy in the slim file

-o out file

This will write the mapped assocs (or counts) to the specified file, rather than to the screen

DOCUMENTATION

[this documentation needs to be viewed online for the graphics to be visible]

MAPPING ALGORITHM

GO is a DAG, not a tree. This means that there is often more than one path from a GO term up to the root Gene_Ontology node.

A hypothetical example blue circles show terms in the GO slim, and yellow circles show terms in the full ontology. The full ontology subsumes the slim, so the blue terms are also in the ontology.

  GO ID  MAPS TO SLIM ID        ALL SLIM ANCESTORS
  =====  ===============        ==================
  5      2+3                    2,3,1
  6      3 only                 3,1
  7      4 only                 4,3,1
  8      3 only                 3,1
  9      4 only                 4,3,1
  10     2+3                    2,3,1

The 2nd column shows the most pertinent ID(s) in the slim the direct mapping. The 3rd column shows all ancestors in the slim.

Note in particular the mapping of ID 9 although this has two paths to the root through the slim via 3 and 4, 3 is discarded because it is subsumed by 4.

On the other hand, 10 maps to both 2 and 3 because these are both the first slim ID in the two valid paths to the root, and neither subsumes the other.

The algorithm used is:

to map any one term in the full ontology: find all valid paths through to the root node in the full ontology

for each path, take the first slim term encountered in the path

discard any redundant slim terms in this set ie slim terms subsumed by other slim terms in the set

BUCKET TERMS

If you run the script with the -b option, bucket terms will be added. For any term P in the slim, if P has at least one child C, a bucket term P' will be created under P. This is a catch-all term for mapping any term in the full ontology that is a descendant of P, but NOT a descendant of any child of P in the slim ontology.

For example, the slim generic.0208 has the following terms and structure:

    %DNA binding ; GO:0003677
     %chromatin binding ; GO:0003682 
     %transcription factor activity ; GO:0003700, GO:0000130

After adding bucket terms, it will look like this:

   %DNA binding ; GO:0003677
    %chromatin binding ; GO:0003682
    %transcription factor activity ; GO:0003700 ; synonym:GO:0000130
    @bucket:Z-OTHER-DNA binding ; slim_temp_id:12

Terms from the full ontology that are other children of DNA binding, such as single-stranded DNA binding and its descendents will map to the bucket term.

The bucket term has a slim ID which is transient and is there only to facilitate the mapping. It should not be used externally.

The bucket term has the prefix Z-OTHER; the Z is a hack to make sure that the term is always listed last in the alphabetic ordering.

The algorithm is slightly modified if bucket terms are used. The bucket term has an implicit relationship to all OTHER siblings not in the slim.

GRAPH MISMATCHES

Currently map2slim does not flag graph mismatches; it takes the full ontology as being the real graph.

OUTPUT

In normal mode, a standard format gene-association file will be written. The GO ID column (5) will contain GO slim IDs. The mapping corresponds to the 2nd column in the table above. Note that the output file may contain more lines that the input file. This is because some full GO IDs have more than one pertinent slim ID.

COUNT MODE

map2slim can be run with the -c option, which will gives the counts of distinct gene products mapped to each slim term. There are actually two counts for every slim term the number of distinct gene products for which this is the most pertinent/direct slim ID, and the number of distinct gene products which are annotated to any descendant of this slim ID (or annotated directly to the slim ID). This corresponds to the 2nd and 3rd columns in the table above.

AUTHOR

Chris Mungall BDGP

SEE ALSO

http://www.godatabase.org/dev

GO::Parser GO::Model::Graph