20th GO Consortium Meeting Minutes: Difference between revisions

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(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

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

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 -