Provided by: libgo-perl_0.15-7_all bug


       map2slim - maps gene associations to a 'slim' ontology


         cd go
         map2slim GO_slims/goslim_generic.obo ontology/gene_ontology.obo gene-associations/gene_association.fb


       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

       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

       The association file format is described here:



       -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

           (Only works with -outmap)

           Show the names of the term in the slim mapping 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


       This script is part of the go-perl package, available from CPAN


       This script will not work without installing go-perl

       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; the path may intersect multiple terms in the slim
       ontology - which means that one annotation can map to multiple slim terms!

       (note you need to view this online to see the image below - if you are not viewing this on
       the site, you can look at the following URL:

       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.

         =====  ===============        ==================
         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

       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.

       Do I need bucket terms?

       Nowadays most slim files are entirely or nearly 'complete', that is there are no gaps.
       This means the the -b option will not produce noticeable different results. For example,
       you may see a bucket term OTHER-binding created, with nothing annotated to it: because all
       the children of binding in the GO are represented in the slim file.

       The bucket option is really only necessary for some of the older archived slim files,
       which are static and were generated in a fairly ad-hoc way; they tend to accumulate 'gaps'
       over time (eg GO will add a new child of binding, but the static slim file won't be up to
       date, so any gene products annotated to this new term will map to OTHER-binding in the

       Note that the slim ontology file(s) may be out of date with respect to the current

       Currently map2slim does not flag graph mismatches between the slim graph and the graph in
       the full ontology file; it takes the full ontology as being the real graph. However, the
       slim ontology will be used to format the results if you select -t -c as options.

       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.


       map2slim can be run with the -c option, which will gives the counts of distinct gene
       products mapped to each slim term. The columns are as follows

       GO Term
           The first column is the GO ID followed by the term name (the term name is provided as
           it is found in both the full GO and slim ontologies - these will usually be the same
           but occasionally the slim file will lage behind changes in the GO file)

       Count of gene products for which this is the most relevant slim term
           the number of distinct gene products for which this is the most pertinent/direct slim
           ID. By most direct we mean that either the association is made directly to this term,
           OR the association is made to a child of this slim term AND there is no child slim
           term which the association maps to.

           For most slims, this count will be equivalent to the number of associations directly
           mapped to this slim term. However, some older slim files are "spotty" in that they
           admit "gaps". For example, if the slim has all children of "biological process" with
           the exception of "behavior" then all annotations to "behavior" or its children will be
           counted here

           see example below

       Count of gene products inferred to be associated with slim term
           and the number of distinct gene products which are annotated to any descendant of this
           slim ID (or annotated directly to the slim ID).

       obsoletion flag
       GO ontology

       To take an example; if we use -t and -c like this:

         map2slim -t -c GO_slims/goslim_generic.obo ontology/gene_ontology.obo gene-associations/gene_association.fb

       Then part of the results may look like this:

        GO:0008150 biological_process (biological_process)     34      10025           biological_process
         GO:0007610 behavior (behavior)        632     632             biological_process
         GO:0000004 biological process unknown (biological process unknown)    832     832             biological_process
         GO:0007154 cell communication (cell communication)    333     1701            biological_process
          GO:0008037 cell recognition (cell recognition)       19      19              biological_process
       19 products were mapped to GO:0008037 or one of its children. (GO:0008037 is a leaf node in the slim, so the two counts are identical).

       On the other hand, GO:0008150 only gets 34 products for which this is the most relevant
       term. This is because most annotations would map to some child of GO:0008150 in the slim,
       such as GO:0007610 (behavior). These 34 gene products are either annotated directly to
       GO:0008150, or to some child of this term which is not in the slim. This can point to
       'gaps' in the slim. Note that running map2slim with the -b option will 'plug' these gaps
       with artificial filler terms.


       Chris Mungall BDGP