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is_a complete biological process ontology
jclark at ebi.ac.uk
Fri Dec 29 14:41:25 PST 2006
As many of you will know, a few of us have been working steadily to
create an is_a path to the root for all Biological Process terms. We
have finally finished this project and have a draft ontology in the CVS
scratch directory called 'IsaComplete.obo'. We would like to commit this
file to the live GO on the 2nd January.
In many cases, the is_a complete path was made by simply creating is_a
relationships between existing terms. However, in some cases we have
made major changes to the ontologies to correct problems. None of our
changes should affect annotations; rather, they should only become more
We have also cleaned up a lot of ambiguous definitions by defining them
by where they were originally placed in the graph. Below we list some of
the major areas we worked on and some of the areas we will continue to
work on once the file is committed. Please have a look at areas that are
near and dear to your heart!
Areas worked on:
1. Processes are now organized under the major categories of
multicellular organismal processes, cellular processes (including
single-celled organisms), and multi-organism processes (formerly
'interaction between organisms'; there has been no change in meaning of
this term, only the name has changed). These categories are disjoint;
that is, no terms can have more than one of these terms as an is_a parent.
2. The major processes 'development' and 'metabolism' have been changed
to 'developmental process' and 'metabolic process' respectively. Most of
the child terms of 'metabolism' have also been changed to 'metabolic
process', likewise for biosynthesis and catabolism terms. This is
because these terms are groups of processes related by is_a, rather than
a set of processes that comprises e.g. the whole of development related
3. The term 'physiological process' has been merged into its parent
term, 'biological process', and all terms that included 'physiological'
have either had their names changed to remove this word, or have been
merged into their parent term. This is because we could find no
satisfactory way of defining 'physiological' that distinguished it from
4. Homeostasis has been reworked to reflect that it covers the
homeostasis of chemicals and homeostasis of cells, tissues, etc.
5. Pattern specification has been reworked.
6. Protein biosynthesis and translation have been merged into one term.
Areas that will be revised later:
1. Locomotion, movement and transport
2. Synaptic processes
If we do not hear any violent objections, we will commit the changes
(merged with the current GO) on 2nd January 2007. Please let us know if
this will cause any problems for you. We do not anticipate any problems
David, Jane, Jen, Midori and Tanya.
The GO Consortium.
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