Ontology Meeting, Palo Alto, Jan 10 & 11, 1999

Participants:
SCD and Arabidopsis Databases
Mike Cherry, David Botstein, curators of SCD and Arabidopsis db.
=46lyBase
Michael Ashburner & Suzi Lewis
MGD
Janan Eppig, Joel Richardson, Judith Blake
Astra
Ken Fasman

1.  One or three? Answer is Three:
The first discussion reaffirmed that the Ontologies will be developed
independently.  In the future, we may explore edges between the independent
ontologies, but not now.
After stabilization and initial annotations of product to list terms, we
will see whether to combine all together, what the levels of annotation are
by species, and see about establishing edges between the three sets of
terms.
	- don't get into describing 'location' as part of 'function'
	- three ontologies are a) function b) process c) subcellular
location (but see below).

2. Gene Function vs. Gene Products?
Recognized confusion in gene product/complex listings in function list.
Agreed to move protein complexes and their components to the 'cellular'
list.  Renamed 'cellular location' to 'cellular components'.  Decided not
to create a fourth category, but rather to think of 'cellular' syntax as
'is located in' with synonym 'is subcomponent of'.  Recognized a subtle
distinction between something that is 'part of' a macromolecule and
something that is 'located in' i.e. 'part of' the nucleus. Still, decided
all would be placed in this category.  This is a system designed to deal
with a state of incomplete knowledge. Cell is composed of the whole set of
product complexes.

3. Define syntax:
	a.  function=8A 'is a' , hierarchical=8A
	b.  process=8A'is a subprocess of' but may also list 'is an instance
of', a DAG
c. component=8A'is located in' synonym: 'is subcomponent of' but may also
list 'is an instance of', a DAG.


 4. Specific function syntax=8A
a) Not for =8A Drop the 'Not for Mus, Not for Drosophila' distinctions
b) Precursors =8A receive function process annotation of mature protein.
c) Facultative/Obligatory=8A'maybe part of', 'sometimes part of', 'part of
>>under certain conditions'  some things present at sometimes, not at others=
,
or don't know.   Some things spend some of the time in one compartment and
some in the other (cell cycle proteins).  Decide not to annotate these
distinctions.  Decide function ontology will be a straight 'is a', no
qualifiers.

5)  Cell is a generic cell, will not divide by cell type. Generic gene
products will be listed as needed.
example:  Alpha tubulin=8A.yeast   has two, elegans has 6, some are there in
mitosis, some are not.
what are leaves of the trees? are they nodes representing genes from all
species? So, we've thrown out individual gene products except as needed,
but gene complexes still here. Not creating laundry list of gene products
of each species, but adding component parts as necessary.

     Example 1.
	a) cellular component:  gene product A, gene product B, gene product C
	b) function: alpha tubulin
	c) process:  mitosis, axonal transport

Not going to put in the relatedness between complex, process, and function
until we have some data and a better understanding of how this will work.


6) If you have process, function and localization, it's almost as good as
having a small paragraph about the gene.  (example of micro-array paper)

7) Implementation Plan
	a) Michael does revision of current version
b) All participants edit list very carefully
c) Suzi assigns GO numbers 'for real'
d) Start alpha annotations
 	e) Future terms added through 'ontology manager', currently Michael.


8) Immediate future
a) requires prototype funding (possibly from Astra via Ken Fasman, other
ideas too)
b) each database needs one curator for project
c) need overall curation manager (currently Michael, person would work with
Michael)
d) each database needs capitol money for computer 'kit'
e) need money for meetings/travel. two meetings/year, alternate coasts
f) need  programmer, ultimately 2, one for database DBA, when db created,
second for interface, tools.
Astra is buying our commitment to annotate our databases to the common
vocabulary=8Alooking for increased usability and searchability of each
individually and collectively.