Transitive closure

Calculating the transitive closure: the old way

See Schema notes

The old way was to ignore the relation in the GO graph and calculate a blind transitive closure. This works fine so long as GO consists of only a few relations like is_a and part_of. However, it results in false positives when used with regulates. These are not so serious as we had previously been treating regulates as part_of anyway. However, the relation does need to be taken into account for other relations, escpecially has_part

Calculating the transitive closure: the new way

The new way will take relations and semantics of those relations into account. See Category:Reasoning. This may more accurately be called the deductive closure

3rd party consumers of the GO will have the option of calculating the closure themselves, or using a pre-computed closure. The pre-computed closure will be available as:

1. A simple tab-delimited file
2. in the graph_path table in the database

Tab delimited file

This will mostly likely contain:

1. subject GO ID (i.e. child)
2. target GO ID (i.e. parent)
3. relation ID (e.g. part_of)
4. distance

graph_path table

The graph_path table is being extended to include the relation:

       --- @@ graph_path.relationship_type_id
       --- References an entry in the term table corresponding
       --- to the INFERRED relation that holds between term2 and term1.
       --- At this time the value is always NULL - a blind transitive closure
       --- is calculated, ignoring the relationship_type_id in term2term.
       --- However, in future we want to calculate different closures for
       --- different relations. [See
       --- ]
       relationship_type_id integer,

foreign key (relationship_type_id) references term(id),

How it's calculated

Currently the blind transitive closure is calculated using perl code in go-db-perl

This code will be retired - instead we will use a reasoner; most likely the OboEdit reasoner. See the OE reasoner paper (Category:Reasoning