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)
- Email us and we'll find a place for it. (Midori)
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
- Moving forward, using the dbxrefs seems to be the way to go but we will have to go in manually to make them more complete.
- 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
- there are some reactions that always occur in a given process for a particular species and others that do not and this is more difficult to mine from reactome.
(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 general 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.
- Ingrid: John Ingram is an experienced physiologist. His idea of a metabolic pathway should begin and end with a central metabolite. There are pathways that feed into a common point that can then go to a central metabolite.
- Peter: manual curation will be necessary ; also, legacy clean-up problems; may be hard to get mutually ok; For metabolites, there is more consensus than something like apoptosis. We are also going to rediscover the 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 so they don't break our system?
- eurie: Annotations with links between function and process--sometimes you just don't have the evidence to make the annotation without breaking true path rules. It becomes an annotation issue when true path rules have to be considered.
- Jen: That's why we are asking for sometimes_part_of
- Kimberly: Would we have to use sometimes_part in all of these cases and couldn't we do better in cases where we have the information.
- judy: what descisions do we need to make?
ACTION ITEMS
- add obvious part_of links; roll out regulates (feb)
- try mining pathways for sometimes_part_of relationships
- do glycolysis, nucleotide metabolism, apoptosis first
- agree on beginnings, middles, and ends of pathways/processes between Reactome and GO
- examine impact on annotation priorities and implememntations
- Can we source our relationships as well as our term definitions.
- (david: this is about pushing the work onto the ontology developers and not the annotators)
- assign process to every molecular function.
- deferred: co-annotation 'has function as part of this process'
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: We've looked at everything in the BP that have more than one part_of parent. Gut feeling is 'yes', but practical feeling is 'it doesn't matter'. i.e. development of an anatomical structure.
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
- Emily: GO tools needing to adapt with the proliferation of the ontologies, it's in the OBO edit. Also, we shouldn't endorse tools that do not appropriately slim.
- Emily/Jane: We should continuously send out notices but it's the responsibility of the tool creator to take the initiative to test their tools.
- continue to review chris' reports--becoming part of the process
ACTION ITEM
- 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. Need a detailed testing protocol.
Reports (Jane)
(has slides)
PAMGO
- This is an ongoing process.
Organization and biogenesis of cellular components
(has slides)
ACTION: continue work on org and bio terms
Signaling (Jen)
(has slides)
Future content meeting discussion
- brenley: 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;
- focus: g-protein coupled receptors, calcium signaling, tyrosine kinase singaling, MAP kinase cascade
ACTION ITEMS
- pursue an ontology development meeting one or two
- viral processes (Brenley, Kimberley, Candice, Michelle, Jane)
- GPCR (Pascale, David, ??)
- Go to meetings on these topics and ask for experts to join meeting
- Investigate funding sources
Annotation checking by trigger file (Jen)
(has slides)
- problem IEAs
- viral/bact ones should probably to be to host instead
- Suzie: do we want all the groups submitting annotations run the triggers?
- Judy: we can do a monthly run with the trigger file
- Peter: Once it has run a few times, we can check for global issues from GA files.
- Michael A: What will you do about the GOA annotations where there is a confilct
- Emily: Can use to feed back to InterProt (for the InterProt to GO mappings) to update mappings because old mappings are causing problems.
ACTION ITEMS
- remove sensu synonyms
- Make GOA quickgo checking available to the public
- write up for near future news letter