is_a complete biological process ontology

[Jennifer Clark]

Dear GO-Friends,

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.

The file:
http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/IsaComplete.obo

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 
accurate.

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 
by part_of.
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 
simply 'biological'.
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 
being caused.

Sincerely,

David, Jane, Jen, Midori and Tanya.
The GO Consortium.

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