20th GO Consortium Meeting Minutes

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Revision as of 13:14, 21 October 2008 by Eurie (talk | contribs) (Theory and examples of function and process (Jen))

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Ontology content development

Overview (Midori)

Most of the report is on the wiki. A lot has been accomplished. Highlights include the following:

  • closed more SF items them opened since last meeting (~200)
  • peptidase reorg is finished: After SLC meeting, MEROPS database curators were contacted and they made recommendataions. Those recs have been acted upon and reorg is finished.

There still are ~200 open items. All those that are more than 6 months old have been assigned but maybe those should be reviewed to see if the priority should be changed. Also, David mentioned that many of the items are being taken care of the in large chunks with ontology changes, such as "biogenesis and organization" terms. Some are stuck because no consensus can be reached.

The majority of the ontology content section will talk about future work and the links that will be made between function and process ontologies.


  • SF items that cannot be closed due to lack of consensus should be put onto a wiki page so they can be resolved at an upcoming GOC meeting. Midori said to email the editors and they'll take care of it.

Biochemical pathway function and process links (Harold)

(get his slides)

Many groups have been working on systems for links trying to see how it works since it does represent biology. Harold showed examples of cross-products using biochemical pathways, defining a start and end, selecting paths, and using common resources. Done manually, the links looked OK but labor intensive. Could it be done automatically?

Problems with doing it automatically:

  • missing DBXREFs
  • too many DBXREFs
  • creates links in the ontology that are "corret", but not always helpful to a given question for a human - like BP "carbohydrate metabolism"is linked to all glycolysis MF annotations.

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.

Theory and examples of function and process (Jen)

(from chris' and Jen's talk)

So why should we even bother?

  • It will improve the GO because we need to be specific
  • It will help fill in annotation gaps - such as a MF "kinase activity" should be made to the BP "phoshorylation" - as well as provide ways to make suggestions new annotations.
  • It will allow better integration of pathway databases with GO.

Chris has been try to use Reactome to make mappings between function and process and has come across the following issues:

  • DBXREFs 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.

There are also gotchas from biology because there could be multiple variations for lysine biosynthesis that include mix-and-match reactions and variations of those reactions. A combinatorial explosion.

The proposal to deal with this:

  • When functions and process are closely related, like kinase and phosphorylation, can make a "part_of" annotation.
  • new relationship "sometimes part_of" when automated mappings are brought in which will avoid true path violations.

Function and process link 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 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?


  • 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


  • send out function process email again
  • we now have systematic ways of determining right, not just ad hoc

OBO-Edit (Amina)

(has slides)

Priority should be testing and bug fixes. This version doesn't need more features but all the new features need to be tested, tested, tested.

Reports (Jane)

(has slides)


  • 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


  • 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.


  • remove sensu synonyms
  • Make GOA quickgo checking available to the public
  • write up for near future news letter

General Annotation Issues