Commit 157dcfc4 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Corrected and updated.

parent cc574fed
......@@ -62,13 +62,6 @@
There should not exist any relation between two terms belonging to
different namespaces.
For relation types that OBO defines as being reflexive and
anti-symmetric, we normalize the relation so that the child term
is more specific then the parent term (where this makes sense).
This means, for example, that we change all "A 'has_part' B" into
"B 'part_of' A". The 'has_part' relationship type is only present
in SO and is the only relationship type affected by this.
- closure
The 'closure' table contains the transitive closure over a
selection of transitive relation types. The transitive relation
......@@ -118,10 +111,9 @@
restricted to querying them for their basic attributes such as
the term accession, name, and definition, as well as relational
information such as their immediate parent and/or child terms.
Following a selection of relationship types (currently the
transitive relation types 'is_a' and 'part_of') we also provide fast
access to the set of all parent and/or child terms of any given
term.
For a selection of transitive relationship types (currently the
relation types 'is_a' and 'part_of') we also provide fast access
to the set of all parent and/or child terms of any given term.
The connection between the ontology terms and the genes,
transcripts, and translations of Ensembl is currently based on GO
......@@ -227,15 +219,15 @@
for help on usage, it's simple). The script lives in
ensembl/misc-scripts/ontology/scripts/
Optionally, also download the SO ontology from
5. Repeat steps 3 and 4 for the SO ontology. A recent version of
the ontology may be found at
http://song.cvs.sourceforge.net/viewvc/*checkout*/song/ontology/so.obo
and repeat the two previous steps.
5. Compute the transitive closure (the 'closure' table in the
6. Compute the transitive closure (the 'closure' table in the
database) by running the 'compute_closure.pl' in almost the same
way as in the last step. This step may take some time.
way as in step 4. This step may take some time.
6. Done.
7. Done.
$Id$
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment