20th GO Consortium Meeting Minutes

Ontology content development

Overview (Midori)

Mostly on wiki. ontology development

• closed more SF items them opened since last meeting (~200)
  • done over time? (judy)
  • we should look at priorities
  • we may be able to take care of the in large chunks with ontology changes (david)

• actually a lot accomplished
  • will make links between function and process ontologies

• place on wiki for requests that have gotten wedged? (suzi)

Function and process links (Harold)

(get his slides)

• many groups have been working on systems for links trying to see how it works

• life depends on cross-products

• biochemical pathways
  • selected paths and used common resources
  • manually linked a set using GO
    • looked OK
  • could this be done automatically?
    • maybe, but problems...
      • missing dbxrefs
      • too many dbxrefs
      • things in the ont that are "corrent", but not always helpful to a given question for a human
    • hope using more complete dbxrefs

Theory and examples of function and process (Jen)

(get her slides)

(from chris' talk)

• chris has been try to use reactome to make mappings between function and process
  • xrefs not necessarily equivalent

(get her slides)

• manual cross-products (lysine biosynthesis example)
  • maybe 7, maybe even more...
    • combinatorial explosion
  • where do they start and end?

• if there were two isoforms...
• let's continue...

Discussion

• sometimes_part_of if we bring in automatic

• david: is every function a "part_of" process?
  • no complaints...
    • peter: counter-example
    • suzi: sounds like a lot of clean-up
  • david: we can just try a little and see

• suzi: never really done annotations to conjuntive annotations
• eurie: cofactors...
• amelia: enzyme terms usually represent forward and backward, thus we need them as separate terms
• harold: in gernela we try to use EC--sometimes opposite or different from what is expected
  • general agreement
• suzi: reactome and GO beginning and end of apoptosis are very different
• peter: what do we mean by pathway? need to be very specific; may be different in different organisms;
• suzi: proposal: let's get argreement on what beginnings and are, even if they are arbitrary.
• ???: things that degrade...
• ???: manual curation will be necessary ; also, legacy clean-up problems; may be hard to get mutually ok ; also, sensu problem
• let's explore how good can common start and ends can be created in the GO
• judy: we need a process to work towards a shared start and end, but respect the dfferences; we should just get the ones where we can get the overlaps first
• paul: is there a compromise argreement for the interim? saw two extremes (some has part and hash part with sublasses); external layer between function and process, start with a sampling that are more specific;
• rex: when thay make changes, how do they get propagated?
• eurie: sometimes there just isn't the evidence to make an annotation to both func and proc
• judy: what descisions do we need to make?

• add obvious part_of links; roll out after regulates (feb)
• try mining pathways for sometimes part of

(** not just reactome)

• do glycolysis, nucleotide metabolism, apoptosis first
• agree on beginnings, middles, and ends
• examine impact on annotation priorities and implememntations

(* david: this is about pushing the work onto the ontology developers and not the annotators)

• deferred: co-annotation 'has function as part of this process'
• can we source our our relationships as well as terms?

• david: is every function a "part_of" process?
  • no complaints...
    • peter: counter-example
    • suzi: sounds like a lot of clean-up
  • david: we can just try a little and see

ACTION ITEM: assign process to every molecular function.

New relationship type (David)

• there will be problems with slimming if they don't think about relationships
• ACTION: software, release examples of relationship usage
• michael: are we overloading part_of
  • david: yes we are, but it probably doesn't matter.

Terms in MF that describe fns that regulate other fns - e.g. inhibitor activity

TS regulator activity - describes fns that regulate processes

Feb 2009 - regulates relationships going into the db full tilt

• big impact on SLIMMING activities
• simple slimming is not a good idea
• will have to enforce community awareness of relationships
• test case for whether inter-ontology links will break software or not
• will provide backups for those not up to date with relationships

- Michael - are we overloading part-of?

• David: different types of part-of in the ontologies but doesn't matter ATM

Quality Control (Tanya)

(info on wiki)

Regulation terms: reasoner looks at regulation terms and then at corresponding process terms, checks if the structures match or if relationships missing

• continue to review chris' reports--becoming part of the process

• multiple aprt_of parents...
• need to push to users...

ACTION: send out function process email again

• we now have systematic ways of determining right, not just ad hoc

OBO-Edit (Amina)

(has slides)

• midori:
• judy: test test test--2.0 means great

Reports (Jane)

(has slides)

PAMGO

• just a report

Organization and biogenesis of cellular components

(has slides)

ACTION: continue work on org and bio terms

Signaling (Jen)

(has slides)

Future content meeting discussion

• brenlie: volunteer for virus terms
• judy: maybe infetctious diease group?
• midori: touches on every species
• david: there should be specific venues; some of these are huges issues;
  • separate meetings
• judy:

ACTION: pursue an ontology dev meeting one or two (around viral prcesses); ACTION: around signalling as well

Annotation checking by trigger file (Jen)

(has slides)

• problem IEAs
  • viral/bact ones should probably to be to host instead

ACTION: sensu must go ACTION: Make GOA quickgo checking available to the public ACTION: write up for near future news letter.