20th GO Consortium Meeting Minutes: Difference between revisions
(New page: ==David - Regulates relationships== Terms in MF that describe fns that regulate other fns - e.g. inhibitor activity TS regulator activity - describes fns that regulate processes Feb 200...) |
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Midori (most info 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) | |||
Harold: function and process links | |||
(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 | |||
Jen: theory of function and process | |||
(get her slides) | |||
(from chris' talk) | |||
* chris has been try to use reactome to make mappings between function and process | |||
** xrefs not necessarily equivalent | |||
** | |||
==Jen== | |||
(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... | |||
* sometimes_part_of if we bring in automatic | |||
* DISCUSSION | |||
* 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? | |||
=BREAK= | |||
* 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. | |||
=REGULATES= | |||
==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. | |||
==Tanya: QC== | |||
(info on wiki) | |||
* 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 | |||
==Amina: O-E== | |||
(has slides) | |||
* midori: | |||
* judy: test test test--2.0 means great | |||
==Jane: PAMGO== | |||
(has slides) | |||
* just a report | |||
==Jane: organization and biogenesis== | |||
(has slides) | |||
ACTION: continue work on org and bio terms | |||
* | |||
==Jen: Signalling transduction== | |||
(has slides) | |||
* 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 | |||
==Jen: annotation checking by trigger file== | |||
(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. | |||
==David - Regulates relationships== | ==David - Regulates relationships== | ||
Revision as of 13:21, 21 October 2008
Midori (most info 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)
Harold: function and process links (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...
Jen: theory of function and process (get her slides)
(from chris' talk)
- chris has been try to use reactome to make mappings between function and process
- xrefs not necessarily equivalent
Jen
(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...
- sometimes_part_of if we bring in automatic
- DISCUSSION
- 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?
BREAK
- 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.
REGULATES
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.
Tanya: QC
(info on wiki)
- 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
Amina: O-E
(has slides)
- midori:
- judy: test test test--2.0 means great
Jane: PAMGO
(has slides)
- just a report
Jane: organization and biogenesis
(has slides)
ACTION: continue work on org and bio terms
Jen: Signalling transduction
(has slides)
- 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
Jen: annotation checking by trigger file
(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.
David - Regulates relationships
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
==Tanya: QC
-Regulation terms: reasoner looks at regulation terms and then at corresponding process terms, checks if the structures match or if relationships missing -