History
	We need to establish a FAQ page
	We need to arrange for introductory sessions for new groups

Status
Assumption built into this is that if a term is associated with a gene product it must
necessarily follow that all parent terms also are an accurate and truthful description
of that gene. The structure of the ontology is tested and validated continuously as 
the curators assure that the parents, parts and go terms are all true.
* Yeast 1800 genes associated to GO, represent half of the total number of yeast genes
  that have name, evidence code for almost all of them
* Fly, automated annotation at jamboree, but not submitted to GO until curators 
  validate them.
* Mouse mostly done automatically until now; see the handout for the numbers. When 
  conflicts arise they try not to change the ontology unless that have to. This is 
  done by going up to a broader term. Moving to hand annotation particularly for new 
  genes.

Tools and Common resources
* Now available, John's web browser (www.informatics.jax.org/~jpc/GO) modeled after 
  MESH and Brad's browser (www.fruitfly.org/~bradmars/cgi-bin/go.cgi) that is running 
  off the Informix database
* Database (Informix, MySQL, and Oracle?) implemented and there is a Perl object 
  methods in repository. We will be writing updates to the ontology in the database 
  after the fall meeting.
* Ontology editor, first priority. Suzi (et al.) to do by next meeting
* Mike C. to use Ian's scripts to automatically perform regular validation for text 
  version until editor is ready.
* Merge two html versions of browser (Brad and John)
* Suzi/John to fix Java browser and decide to either pull the plug or continue 
  development. Add link to Java help page
* Each organism database to provide a fasta file of protein sequences for those gene 
  products that have been annotated. Suzi (et al.) will set up blast search services 
  for GO
* API to be refined as applications are developed
* Steffan and Heather to work up prototype for next meeting of rules between the 
  separate ontologies
* Definitions, Michael is to contact Julian Dow for definitions from Dictionary of 
  Cell Biology
* Mike to e-mail style manual to Michael, who will then check it into CVS 
* Suzi/Brad to clean up XML version


Content
* Use part-of relationship to solve the 's/t/ protein kinase' (multipart protein) 
  problem. E.g.	%s/t protein kinase
<s/t protein kinase catalyst
<s/t protein kinase regulator

* TAIR to deal with plant specific terms from transport classification and Michael the
  rest (www-biology.uscd.edu/~msaier/transport/titlepage2.html)
* Rule for process include all processes that occur in more than one taxonomic Class
* Anatomy to be removed from process. The conjunction of anatomical and GO terms can 
  then be used for searching.
* Everyone to submit separate anatomy ontologies
* Michael to move "MEDLINE" xrefs from ontologies and put them into GO.defs
* GO.defs: If a definition changes the concept or meaning of a term then that term 
  must be made obsolete and a new term created. This is true even if the string
  'oldterm' is identical to the string 'newterm'. The older definition will still be
  retained, as well as the term itself.
* A new evidence criteria is to be added: Inferred by electronic annotation 
  [to database:ID] AKA IEA
* Add a new column to gene_associations.* for seqID (etc...). 
* Add a new column to gene_associations.* for negation
* There will be one row per unique reference-evidence pair
* Any given gene product can be annotated at multiple levels of granularity. The 
  reason is that evidence can only be available for a particular degree of refinement.

InterPro
* Long term model is that GO is restricted totally to model organisms (unlike SP that 
  covers everything): Mouse, zebra fish, maize, rice, human, Arabidopsis, worm, fly, 
  fugu, yeast, rat. The criterion is that there exists a serious well-funded community
  database.
* SP will use 0011001 to 0012500 as its GOid number range. SP will use these to 
  generate terms that are needed for annotating SP with GO terms for prokaryotes and 
  viruses (Suzi to send numbers) and submit them in batch.  They will also submit 
  terms needed for model organisms to the ''GO editor" (Michael and Midori).


Other databases
* Worm will be re-invited for the fall
* Malaria - no action from Altman yet
* Human - encourage Proteome Inc & Sue Povey (HUGO Nomenclature Cttee) to use GO but 
  as associates.
* Three levels of relationships: Friends, associates, consortium member. Friends are 
  anyone who wants to subscribe. Associates can get regular updates (like a user 
  group). Members have write access to the ontology. May - in future - have extra day
  for associates.
* TAIR
* Proposing to act as conduit between GO consortium and other plant databases; 
  MaizeDB, Rice, MedicagoDB, ClamyDB, Pine?, Cyanobacteria?. 
* 0009501 to 0011000 are the GOid number series for Tair
* Lenore and Sue to visit Midori to gain experience in extending the ontology. Mostly 
  conceptual, rather than the mechanics of editing the files. Kara to create a logic 
  guide by going through the old e-mails that can be used as a starting point. This is
  in addition to the style guide and the FAQ.
* Berkeley to do a clean up of flat file and Wolfgang to double check.

Other
* Companies only invited if they are contributing financially
* Send in abstract only to NAR by September
* Next meeting in Berkeley November 5-6
* Mike to add a what's new page link on the front web page
GO meeting June 30, 2000