20th GO Consortium Meeting Minutes: Difference between revisions
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* place on wiki for requests that have gotten wedged? (suzi) | * 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)== | ==Function and process links (Harold)== | ||
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**** too many dbxrefs | **** too many dbxrefs | ||
**** things in the ont that are "corrent", but not always helpful to a given question for a human | **** 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. | ||
==Theory and examples of function and process (Jen)== | ==Theory and examples of function and process (Jen)== | ||
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* chris has been try to use reactome to make mappings between function and process | * chris has been try to use reactome to make mappings between function and process | ||
** xrefs not necessarily equivalent | ** 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) | (get her slides) | ||
Line 64: | Line 65: | ||
* eurie: cofactors... | * eurie: cofactors... | ||
* amelia: enzyme terms usually represent forward and backward, thus we need them as separate terms | * amelia: enzyme terms usually represent forward and backward, thus we need them as separate terms | ||
* harold: in | * harold: in general we try to use EC--sometimes opposite or different from what is expected | ||
** general agreement | ** general agreement | ||
* suzi: reactome and GO beginning and end of apoptosis are very different | * 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; | * 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. | * 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 | * 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 | * 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; | * 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? | * rex: when thay make changes, how do they get propagated so they don't break our system? | ||
* eurie: sometimes | * 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? | * judy: what descisions do we need to make? | ||
* add obvious part_of links; roll out | ===ACTION ITEMS=== | ||
* try mining pathways for | * add obvious part_of links; roll out regulates (feb) | ||
* try mining pathways for sometimes_part_of relationships | |||
* do glycolysis, nucleotide metabolism, apoptosis first | * do glycolysis, nucleotide metabolism, apoptosis first | ||
* agree on beginnings, middles, and ends | * agree on beginnings, middles, and ends of pathways/processes between Reactome and GO | ||
* examine impact on annotation priorities and implememntations | * 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' | * deferred: co-annotation 'has function as part of this process' | ||
==New relationship type (David)== | ==New relationship type (David)== | ||
Line 117: | Line 113: | ||
- Michael - are we overloading part-of? | - Michael - are we overloading part-of? | ||
*David: | * 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. | ||
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Regulation terms: reasoner looks at regulation terms and then at corresponding process terms, checks if the structures match or if relationships missing | 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 | * 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 | * we now have systematic ways of determining right, not just ad hoc | ||
Line 137: | Line 134: | ||
* midori: | * midori: | ||
* judy: test test test--2.0 means great | * judy: test test test--2.0 means great. Need a detailed testing protocol. | ||
==Reports (Jane)== | ==Reports (Jane)== | ||
Line 144: | Line 141: | ||
===PAMGO=== | ===PAMGO=== | ||
* | * This is an ongoing process. | ||
===Organization and biogenesis of cellular components=== | ===Organization and biogenesis of cellular components=== | ||
(has slides) | (has slides) | ||
ACTION: continue work on org and bio terms | ACTION: continue work on org and bio terms | ||
==Signaling (Jen)== | ==Signaling (Jen)== | ||
Line 156: | Line 152: | ||
===Future content meeting discussion=== | ===Future content meeting discussion=== | ||
* | * brenley: volunteer for virus terms | ||
* judy: maybe infetctious diease group? | * judy: maybe infetctious diease group? | ||
* midori: touches on every species | * midori: touches on every species | ||
* david: there should be specific venues; some of these are huges issues; | * 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 | ===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)== | ==Annotation checking by trigger file (Jen)== | ||
Line 172: | Line 171: | ||
** viral/bact ones should probably to be to host instead | ** viral/bact ones should probably to be to host instead | ||
ACTION | * 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 | |||
=General Annotation Issues= | =General Annotation Issues= |
Revision as of 15:04, 21 October 2008
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