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
- maybe, but problems...
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?
- maybe 7, maybe even more...
- 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
- no complaints...
- 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
- no complaints...
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.