Difference between revisions of "20th GO Consortium Meeting Minutes"

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(Mike: Annotation Progress)
(David: RG from ont dev prespective)
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  (berkeley) automate mike's graph (as in proposal), need to be able to see progress through time
  (berkeley) automate mike's graph (as in proposal), need to be able to see progress through time
== David: RG from ont dev prespective ==
== Ref Genome impact on ontology development (David) ==
(has slides)
(has slides)
* we work through SF
David provided an update of the impact of Ref Genome curation on ontology development.
** RG request are prioritized
* 237 requests, 223 closed with 14 open
*** two flavors
* New requests tend to be two flavors: new term requests and problem areas in ontology
**** new term for RG
* New term requests turn around is fast
**** problem areas in ont
* Problem areas in ontology are slower because often lead to large-scale changes and are pointed out by multiple sources (curators and QC reports)
***** slower
* need annotors to get info about "response to" terms
* doing signalling now
* ...argh...
* please use SF and mark as RG
Current issues in progress that need curator comments.
* signaling
* detection of signal
* response to - how broad is this terms?  Is detection of something is part of the response or if it is separate?
* pascale: documentation and anno consis
** when doing big branch of ont, more discussion with RG group
* jen: doc for every big reorg, sometimes I don't know about a change
* debbie: def is sometimes unclear
** ex: ATP binding
** pascale: "binding", "regulating", ev--these are always a problem
** pascale: we need a group to make a proposal to get the defs down flat
** peter: ont distinguishes binding from catalysis
** kimberly: we're not consistant about how we use binding
** rex: documentation is the core issue
*** docs will solve all of the above
* ntrs turn around fairly quickly
And a reminder to make sure to mark all SourceForge items as the group "Ref Genome".
* ontology problems are slower
* David, what do you include in your response to terms.
** how broad is the "response to"?
** Is detection of something is part of the response or if it is separate?
* organization and biogenesis
* Debby: definition isn't always clear when to use to annotate to a certain term.  If it's a substrate of a reaction then do you use it or not?
* David/Harold: If the experiment shows that it binds, it binds.
* Peter: Interactions that occur for catalysis seem different than binding in the GO sense.
* Kimberley: We're not consistent in how we're using binding.
* Rex: Important issue of documentiaton and how documentation organize.  We cna have a working group for each of these issues but if the documentation is not clear and rationally planned out and indexed and easily accessible, it is not useful for current annotation and future annotation. 
* Ingrid: Look to definition of term, to have usage example in the comments.  This can link to somewhe re with a longer explanation.
* David: If ref genomes decides on how to use a term, then write to the editors to put a comment in
* Judy: no link from definition, conflict between use of resource by curators and use by the community.  Where do we provide this for the curators that doesn't impinge on the community.
* Seth: linkout to GONUTS to keep the information separate from the database.
* Richard: having examples of the use of the term has been valuable along with the definition. You might also want to include examples of improper uses.
* Pascale: already in the comments fields, there is already some informtation there we could extend.  We could also add another field called "curator information"
* Alex: This information can also be useful to the community and not just the curators.
* Jen: One place for documentation, and one search that just searches the documentation
* Mike: I don't think this should be private.  If it's useful for the curators on how to curate it, then it would be extremely useful for the user to know how the term was used.
* Debby: We're trying to do community annotation so for us the community are the curators. Comments, with linkouts to GONUTS that contains the history and the discussion of this term.
* Emily: There's only so much information in a public section that you can add.  Having the wiki would enable us not be limited by space.  Need to propagate these linkouts to child terms or related nodes such that they show up in different GO browsers.
* Jane: documentation goes out of date very quickly and there is a large overhead in maintaining it.
* David: it still comes down to curator judgement about what was shown in that paper and what term is appropriate.
Communication ontology changes is needed, particularly large rearrangements.  David suggested having a tutorial for annotators.
And there is a general issue of not being able to find documentation and when it's appropriate to use a term.  Particularly since some of this information is spread between the wiki, GO web page, meeting minutes, annotation camp minutes, etc.  This often leads to inconsistent usage - "binding" and "regulation" terms were brought up as examples.
Although the definition provides the core usage, it often is not enough.  Many people voiced support for examples of how to use the term, with PMIDs, as well as examples of cases when you wouldn't want to use it.  Seth and Debby suggested links to GONUTS from AmiGO.  Having a wiki would not limit the amount of space that's available.  A few were concerned about displaying this publicly but in general, there was support for making it public, particularly since E. coli is trying to have the community annotate.
==== ACTION ITEM ====
==== ACTION ITEM ====

Revision as of 13:39, 22 October 2008


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.


(everybody) 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.

Theory and examples of function and process links (Harold, Jen)

(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.

(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

David asked if every function should be a "part_of" process? In theory, there should be a link between each Molecular Function term to a Biological Process term. And there was general acceptance of this theory.

Eurie asked if MF enzyme terms made consistently in order to best make the links easy/consistent? Amelia pointed out there is also another issue that enzyme terms are usually forward and backward but we need separate terms. Harold also pointed out that we copied from EC but this may mean that two GO terms may exist solely on the basis of cofactors. So all these may contribute to issues in creating an automated mapping.

Suzi and Peter discussed that the definition of pathways between Go and Reactome are different, using apoptosis as an example. There are good examples where start and end may be different from organisms to an organism. Ingrid mentioned John Ingram (an experienced physiologist) said a metabolic pathway should begin and end with a central metabolite. Then pathways can feed into a common point that can then go to a central metabolite. But there is probably less consensus for models that are still being developed. All agree that a discussion needs to occur to work on coming to a common agreement.

Paul pointed out there we were discussing two extremes: an uncurated automated link and curated links. The curated links are the ultimate goal but there could be a compromise in the middle. The relationship linked between MF and BP go through KEGG, that evidence trail is documented. This is something better than "sometimes part_of". The concern with this is that changes other groups make need to be propagated.

There was a discussion about the impact on curation. With these inter-ontology links, you have to take the links in account as a true path rule. In addition, how much evidence do you need to make those annotations? That is why there is the "sometimes_part_of" but what if that pathway doesn't exist in your organism?


* Add obvious part_of links, like MF "kinase" and BP "phosphorylation"; will be rolled out after regulates is released in Feb 2009
* The sometimes_is_part relationship was agreed as a good idea. We should try mining pathways for sometimes_part_of relationships using 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)

New relationships will be released to the public in Feb 2009. This is the first cross-ontology links between BP and MF. It will occur between the BP "regulation of catalytic activity" and MF "catalytic activity". Those functions that regulate function terms will get the regulates relationship.

One major consequence is that all groups have to take into account relationships. The BP "negative regulation of kinase activity" is part_of "kinase activity", but the slimming will make them "kinase activity". Need to be careful about this.

Michael was concerned about whether the meaning of "part_of" was being overloaded. David replied that we probably are but practically, it may not matter because the child term really cannot be part of the both parents at the same time.

We will have to make sure that GO tools support these links. In addition, we need to make sure that users who develop tools are aware of these changes. Jane emphasized that we couldn't do testing for all tools but the users need to test.


(tanya) Send out function process email again.
(chris) Release examples of relationship usage for software development.

Quality Control (Tanya)

Much of the information is on the wiki. For regulation terms, the reasoner looks at regulation terms and then at corresponding process terms, checks if the structures match or if relationships missing. These were all reviewed.

Ontology developers will continue to review Chris' reports - it's becoming part of the process of ontology development since it is part of OBO-edit.

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. Lots of "regulates" terms.

Organization and biogenesis of cellular components

(has slides)

All "organization & biogeneis" terms will be changed to "organization" with the proposed high level structure:

-[i] assembly
-[i] disassembly
-[i] maintenance
-[i] morphogensis
-[p] assembly
-[p] part biosynthesis


(ontology dev) Continue work on "organization and biogenesis" terms.  Maybe biogenesis & organization should be switched at the higher level but this is up for discussion.

Signaling (Jen)

(has slides)

Is responding to the signal the same to the reception of the signal? Currently defined as within the realm of reception of the signal?

Future content meeting discussion

The discussion of signaling touches on every species. David pointed that some of these are huge issues - signaling alone can be roughly categorized into

  • g-protein coupled receptor signaling
  • calcium signaling
  • tyrosine kinase singaling
  • MAP kinase cascade


Pursue an ontology development meeting one or two:
   (Brenley, Kimberley, Candice, Michelle, Jane) Viral processes
   (Pascale, David, ???) GPCR
(?) A couple of GO meeting with major meetings on these topics
(?) Investigate funding sources

Annotation checking by trigger file (Jen)

(has slides)

Of 47,000 errors in the GOA file (0.14% of total), only 5 manual annotations were flagged suggesting that the graph may need improvement. The rest were IEAs.

Trigger file is being used by GOA and MGI for consistency. There was discussion whether this use should be expanded and run against all annotations when the files are submitted. This would address a QC aspect.

Emily said that it can be used as feedback to InterProt (for the InterProt to GO mappings) to update mappings because old mappings are causing problems. Dan also suggested that it could be integrated into QuickGO as a public resource.


(?) remove sensu synonyms
(Jen) Continue implementation of trigger system
(Dan) Make GOA quickgo checking available to the public
(?) write up for near future news letter

General Annotation Issues

Evidence code ontology (ECO) (Michelle)

Michelle is taking over managing the Evidence Code Ontology.


  • Correct incosistencies in the ECO with GO
    • ECO exists as its own and includes things other than GO and GO pulls from the ECO, using a subset

Mike asked is ECO the responsibility of this community? Michael says yes because we started it. We have not used it because we wanted to start out pretty easy. TAIR then wanted a much richer set of evidence codes. Michael and Sue did a mapping. But when TAIR reports to GO, they collapse the evidence codes down. Those arguments are still valid. If curators were faced with more evidence codes, it would take longer. IDA could be expanded to a zillion codes.

Michael thought we should integrate GO evidence codes into the ECO because other people might use them and that GO should use a subset/slim of ECO (i.e. the ones that we are using the ones we use now.) Judy agreed and said if an individual MOD wants to make use of the granular codes, they can, but they must be mapped up to the higher-level codes used by the GO.

Pascale asked if we needed to use the the more granular terms adopted by GO (ISM, ISO, ISA) or if we could keep to the higher level terms. This was deemed fine--Suzi pointed out you should annotate to the degree of knowledge available and this might end up being to the more general EV code. Also this allows for not having to retrofit older annotations as brought up by Harold.

Suzi brought up there could be various slim sets for various projects - AmiGO, Ref Genome, etc. for display purposes in the interfaces.

In response to a question from Eurie, it was stated that the GOC would only set standards for the GOC accepted codes, not all codes. Each database could have use more if they wanted, but would have to convert it into the standard set for the GA file.

Maybe EXP would be better when there is no consensus on which evidence code should be made. This may prevent spinning it. For use of ref genome, maybe have to have additional standards available. There were concerns from Peter about overloading the EXP term and/or losing accuracy. There is a lot of time spent debating which lower code to use and Rex would rather have people agree to EXP and spend more time annotating.

Any evidence code that is in the ECO could be submitted to the GOC for adoption. We could also explore writing software to slim the evidence codes used.


(suzi) We will use the ECO and create an EV code ontology tracker
(everybody) people can use the ECO in its entirety but they have to map up to the GO set of EV codes.

Separating annotation method from experimental method

In principle, most everyone was supportive of the idea to separate the evidence used to make the annotation and the curation method to make that annotation. There was, however, much discussion on the scope and implementation of this proposal.

Two implementation methods were proposed:

  1. A new column that contains a text describing the annotation process
  2. Creating a cross-product between the evidence code branch of the ECO and a methods branch of the ECO. This ID would be used in the GAF.

Because proposal 2 does not create a new column and is expandable to multiple combinations, it was favored.

Proposed methods were not agreed upon but words that were used to describe included

  • curator reviewed
  • not curator reviewed
  • electronic
  • manual

A direct consequence of this would be that IEA would go away. Emily proposed the following mappings:

  • Interpro2GO -> ISS/ISM, not reviewed
  • keyword mappings -> TAS, not reviewed

IEAs are stripped out after a year. How would those "not curator reviewed' be treated? Since the intent was to remove annotations based on sequences, maybe only those should be removed because they can be easily recomputed. Large-scale/high-volume/high-throughput experiments won't be repeated but still are experimental. We would have to consider exceptions for these.

There was some discussion about what users wanted and how users were taking advantage of the evidence codes. There is a range - some people just strip evidence codes and do not consider them. However, others would take advantage of additional levels of information. Both advisors mentioned that what users wanted was a level of confidence. This, however, would be difficult to do.

It was agreed that multiple issues need to be considered when dealing with this new qualifier of evidence codes:

  1. the experimental evidence
  2. was there judgement involved
  3. was there a review of the data


(Suzi, Michelle, Judy, Pascale, Emily, Eurie) Example cases of annotations and implementation into the ECO

PAMGO (Michelle/Candace)

Candance gives an overview of the new terms. Project is coming to an end - funding is coming to an end. New gene association files have been submitted.


  • PAMGO terms outside of PAMGO: viruses, c. albicans, p. falciparum, t. cruzi, t.brucei.


  • incorrect uses also.
  • there are a few terms where it is ambiguous whether or not the process is for the host or the virus side.

Future directions

  • fix virus terms
  • add comments
  • adopt more descriptive form for annotations.


  • missing taxon ids for dual taxons
  • need a way to capture "acted_upon" annotations

Dual taxon IDs

  • still not displayed in AmiGO due to technical issues


Check your annotations to terms under the 'symbiosis' and 'interaction with host' branches to make sure that there aren't any problems.

Cross products: Column 16 (Tanya)

Initially proposed in Jan 2007.

Reminder: this is extra information to combine multiple terms in a single annotation. These are GOIDs that we don't want to encode links in the ontology. If there is more than 1 localization, they can be piped and several different ontologies can be piped in the same row.

  • You are not restricted to one ontology in column 16
  • Column 16 is optional
  • Column 16 can also be used to identify a target i.e. regulation of transcription (Note that the current documentation states that column 16 is only for external ontologies.) or a chebi ID for a chemical when annotating "response to drug".

There were two proposed solutions on the table:

  • simple solution
  • expressive solution

No one had concerns about adding this column and a few people spoke up in favor of the expressive because it would allow for more information and no need to retrofit.


(everybody) go ahead with the implementation of the expressive model in column 16
  * get more examples 
  * get the documentation together

Transitive Relationships in GO

(has slides)

Relationships in terms, it's wrong to just slim terms given the different relationship types. Unless you're careful, you will violate true path rules.

  • The composition of is_a and part_of need to be taken into consideration for true path violations.
  • If you regulate a process, you regulate part of that process, not that whole process.
  • As you add more relationships, you need to create these transitive closures.
  • And as you take these into consideration, the slimming can become more sophisticated.

Judy proposed that we need a tool to help with this.

Reference Genome

How curators can use evo trees (Paul)

(has slides)

Paul presented a proposal for the new process. Highlights of new process include the following:

  • Trees will be overlayed with the OrthoMCL "ortholog clusters" to find "equivalogs" - the equivalent gene in all organisms.
  • Finding these groups will allow annotations to be inferred to the shared ancestor protein
  • Annotations can then be propagated to the extant protein so that annotations are concurrent and consistent in the context of the evolutionary tree.
  • There is an evidence trail that is documented.
  • The strength of this approach allows annotation of organisms where there are no curators. GOA could take these annotations.
  • Includes bacteria and archaeal sequences but horizontal transfer makes it harder.
  • The update would occur twice a year.

Paul showed screen shots of the tool that had GO annotations overlayed on the tree. The GO annotations displayed are mapped up the tree. Additional information can also be applied to the tree, such as bootstrap values or Interpro domains. This tool can be updated to reflect current GO annotation and GO tree structure.

The proposal also included a change to the gp2protein files. Most are complete but if genes are missing, they were supplemented with the ENSEMBL or Entrez Gene ID (based on the group). However, these genes are represented by a single representative protein sequence so this is not a long term solution. The proposal was to switch to the Swiss-Prot canonical protein sequence which is mapped to individual UniProt IDs and has instructions on how to generate all isoforms. There was agreement that two groups (MODs and SwissProt) should not work independently to create the same file and that they should communicate.

There was some concern that we were overloading the purpose of the gp2protein file. And that the GOC still needs additional files to keep track of all gene products in a genome as well as a mapping between genes and IDs for all isoforms.

The annotation process (Kara)

(has slides)

Kara then presented how this pipeline would work. The major points of the new pipeline include the following:

  • a new curator, known as a protein family curator, will suggest protein based on tree
  • MOD curators annotate all experimental data to completion
  • the protein family curator mediates/coordinates review of experimental based annotation review
  • the protein family curator also creates inferrence of annotations to equivalent genes

There was some initial discussion about how the interaction between the protein family curator and the MOD curator would work at each of the rounds. The process is intended to be an iterative process that requires feedback at each round. For example, curators may want to adjust experimental-based annotations after seeing another MOD's annotations. But there needs to be a fixed timeline to finish the experimental-based curation in order for propagation of annotation to occur in a timely fashion

This pipeline can generate reports to help get outlier annotations and other oddities. Automated checks can be done to alert groups when a MOD has added a new annotation or the equivalog tree has been updated or changed, particularly if a common ancestor has changed.

Kara also presented new features on P-POD:

  • multiple genes can be input in the search
  • tree display is based on Notung with an interactive applet
  • lists publications with functional complementation
  • has links to GO MGI and AmiGO graphs
  • if you have suggestions, please sent them along

Mechanics of incorporating ancestral inferences (Suzi)

(has slides)

There were two options proposed for inputting ancestrally inferred annotations:

  1. These annotations would be provided back to the MODs, and the MODs would incorporate them into their gene association submissions to the GO consortium
  2. They would be directly inputted into the GO database with a filtering script

Although it was brought up that a downside to the first option would be a delay in incorporation of annotations, people much preferred the first option for the following reasons:

  • it is consistent with the current policy of each MOD being the definitive source of annotations for their organisms.
  • most of the MODs also have systems in place to load external annotations (e.g. GOA).
  • it will ensure that annotations remain in sync between the MODs and the GO consortium files

This interaction should not be a part of the ejamboree but instead should be a one-on-one interaction between the MOD and the protein family curator. Also, feedback is only needed if there is a problem

Judy asked what the evidence code and source for the ancestrally inferred annotations would be. RefGenome was suggested as a source and this was considered favorably as it would increase visibility of the project. We could also version these annotations by the date. Suzi said the evidence code discussion should wait until there were annotations that could be discussed.


  • Draft a document about coordinating the GO gp2protein files with the UniProt proteome project (Paul/Kara). Look over it and bring it to Amos as a proposal (Michael A.).
  • For GO, generate a list of what files are needed (gp2protein, spliceforms, all gene products), define what these files should be, and build a file structure. (Paul/Kara)
  • Pascale will provide the seed genes for the annotation set at the first of every month, and the sets are to decided by Paul and Kara's trees.
  • If there are problems with the tree, the MODs will correspond with Paul and Kara. This will be done on a one-on-one as-needed basis.
  • Annotations made by ancestral inference will get fed back to the MODs in gaf format for them to incorporate into their sets to submit to the GO database. 'RefGenome' will become the source of these annotations.

Annotation Progress (Mike)

(has slides) Showed more graphs since people like them. Bottom line is that progress is being made. The numbers for the Ref Genome genes are a bit off since it's not easy to get the list of genes so current numbers are a bit off. Paul has number on his FTP site.


(berkeley) automate mike's graph (as in proposal), need to be able to see progress through time

Ref Genome impact on ontology development (David)

(has slides)

David provided an update of the impact of Ref Genome curation on ontology development.

  • 237 requests, 223 closed with 14 open
  • New requests tend to be two flavors: new term requests and problem areas in ontology
  • New term requests turn around is fast
  • Problem areas in ontology are slower because often lead to large-scale changes and are pointed out by multiple sources (curators and QC reports)

Current issues in progress that need curator comments.

  • signaling
  • detection of signal
  • response to - how broad is this terms? Is detection of something is part of the response or if it is separate?

And a reminder to make sure to mark all SourceForge items as the group "Ref Genome".

Communication ontology changes is needed, particularly large rearrangements. David suggested having a tutorial for annotators.

And there is a general issue of not being able to find documentation and when it's appropriate to use a term. Particularly since some of this information is spread between the wiki, GO web page, meeting minutes, annotation camp minutes, etc. This often leads to inconsistent usage - "binding" and "regulation" terms were brought up as examples.

Although the definition provides the core usage, it often is not enough. Many people voiced support for examples of how to use the term, with PMIDs, as well as examples of cases when you wouldn't want to use it. Seth and Debby suggested links to GONUTS from AmiGO. Having a wiki would not limit the amount of space that's available. A few were concerned about displaying this publicly but in general, there was support for making it public, particularly since E. coli is trying to have the community annotate.


come up with rational plan for documentation and indexing (including rational and examples)
  • suzi: we can ask the SAB about this as well
  • ingrid: i look at term def
  • how should we do this?
  • seth: why not GONuts and not muck-up the data
  • richard: examples would be very valuable, including counter examples
  • pascale: add more fields that didfferent people could see
  • alex: users should see the information
  • jen: wants one single information resource
  • mike: this curator info shouldn't be private--this is good stuff
  • debbie: seconds mike, and GONuts
  • emily: seconds
    • children as well
  • jen: graph can be weird
    • david: will fill in missing bits
  • jane: docs go bad over time need freshness
  • david: great defs vs. curator judgement--still an art
    • harold: seconds; always constrained by training

Discussion continued after lunch

  • PF will be responsible for some of the term usage
  • rex: we shoul
  • peter: sounds like w should use RG group, as they have he most concrete need
  • midori: GEO can help, but shouldn't be responsible--may not be able to give usful feedback
  • suzi: it is distibuted task, but it needs a coordinator
  • amelia: will put stuff up, but dont' want to manage content
  • suzi: salvage old content vs. getting new content; salvage would be one-off
  • pascal: who actually knows where this stuff is? probably web people and those who put it up
  • debbie: volunteer to help go through and look for documentation for certain terms
  • david: pascale's list of problem terms isn't cross with other materials
  • rex: there is a lot of salvagable material
    • indexed, consolidated, wikified


Amelia is point for documentation


pascale and kara for new content


debbie and brenlie will over salvage of existing


everyone will send examples and counter examples


GOE will add ...


GONuts, seth, amelia search, indexing, and wikification

Jane: helpdesk and newsletter

(has slides)

  • central email address
  • list rota
  • lotsa queries
    • response times decreasing
  • pie charts of query types
  • other avenues for help
    • faq
    • web docs
    • amigo help
    • suzi: how about a "was this page helpful" button
    • david: that slide shows that most work should be done on the faq


amelia will be documentation coord
  • newsletter
    • suzi: can do dynamic, RSS, etc.
    • judy: likes the PDFs and have different releases
    • eurie: it needs to be general enough for general consumption
    • eurie: it takes a lot of time to write this stuff;
    • pascale: maybe decrease frequency
      • suzi: frequency affects new features, so higher is better
    • jen:
    • suzi: the users are software, internal, and external


(jane) look into outsourcing newsletter construction


(?) separate newsletter into the above three listed sections
  • tools tool
    • will check all tools developers and see what's dead
    • will provide better information about the tools
    • mike: default will be to delete tools if we don't get a response

Michelle: PAMGO outreach workshop

(has slides)

  • .
  • jvci outreach
  • igs outreach
  • snippet from BRC II RFA
    • GO mentioned by name
  • talk of RFAs and BRCs

Tanya: TAIR and plant physiology collab

(has slides)

  • web interface
  • tracking results
    • not yet 100% compliance
  • only ask for info after it has been accepted
  • rex: haven't done spot checking?
    • no

Michael: swissprot

  • curation split three ways
    • there has been resistance in geneva to use GO terms
    • at last meeting in princeton, from now on, some will start using GO (~40)
    • EBI and (SID?) will work things out

Seth: AmiGO

(has slides)

  • ...

Michael: text-mining ontologies

(live demo)

  • ... [missed first few minutes]
  • OBO-Edit plugins
    • use of web resources for automated term generation
    • ...
  • indexing GO term MESH terms
  • workig onto gene symbols
  • gogene
    • ...
  • ...
  • suzi: it takes gene ident and goes to NCBI or somewhere, there is usually a pub--could that be used to boost results?
    • should be already indexed
  • ...
  • at the end, you'll always go back to the article to check if it was useful
  • would like GO curators to try this tool and see how good the results are
  • plugin should be in SVN soon
  • suzi: might be useful for AmiGO as well
    • usable for GOst

Michael: Next Meeting

  • Berlin
  • Cambridge, and then to berlin?
  • Maine
  • Eugene? Portland?
  • Texas


will setup doodle for next location


Look at action items from last meeting

  • push forward not dones
  • carry forward documentations issues

Previous Incomplete Action Items

Status Responsible Party Task Comments
In Progress Documentation working group Document annotation SOPs Another factor we have been tracking is when a curator judges that the curation of a gene is ‘comprehensive’, that is, that is accurately represents the biology (irrespective of the number of papers available or read). This appears in the spreadsheets. The guideline is that when there are few papers, all papers should be read; when there are many (a curator can judge what is too many), then a review should be read to find the important primary literature and decide what information needs to be captured. We don’t keep track of whether or not reviews have been read. Wormbase uses textpresso (PMID 15383839), that helps ensuring curators do not overlook information. The ‘comprehensive’ curation status doesn’t get invalidated when a newer paper is published; however, curators may (and are encouraged to) update the date when the newer literature is curated.
Chris Mungall Re-calculate with is_a only paths
Chris Mungall Re-calculate with experimental codes only generate several versions of the data classified by different evidence codes?
Chris Mungall Provide such reports on a regular basis
Judy Blake Contact NCBI/NLM/OMIM to link to reference genome genes
In progress Documentation working group Document Changes to Gene Association File (GAF) column 2 is canonical gene ID; column 17 is thing you are annotating (always required); column 12 matches column 17 and contains SO ID's; add header to gene association file
In progress Documentation working group Document Changes to gp2protein file includes complete gene index (except for pseudogenes and transposons); column 1 is canonical gene ID; column 2 is accession for sequence of longest form of protein from UniProtKB: or NCBI; syntax of gp2protein file will be provided by Mike and Chris
In progress (Jane) write notice of changes to GAF and gp2protein to users
In progress MODs + Ben Hitz make sure that their input matches new GAF and gp2protein requirements
Seth Carbon Have AmiGO show co-occurrency terms similar to function in QuickGO.
Seth Carbon & Val Wood SLIM by SLIM matrix Would be used to review intersections of different cellular processes and look for unexpected intersections which may identify possible errors. Try first applying to function and component terms; outline cells that you expect to be empty, Have these matrices generated automatically from the AmiGO database.
Ben & Mike Get isoforms into GO database
MODs & Chris Consistent use of IMP "with" column Chris will be talking to individual groups with how they use the with column for IMP. Each MOD groups needs to respond to this for Chris.
Michelle Implement Michelle's proposal decide whether to put 'response to drug' ID in column 16 or is separate IC annotation. Annotate to chemical term ‘response to cocaine’, co-annotate with chemical term for now, then later when available, put GO ID for “response to drug’ in column 16 (or separate IC annotation).
pending Midori, David, Chris, Mike Bada Chemical derivatives and metabolism terms Need input from Chris and Mike on how much can be automated; possibly also current and near-future state of ChEBI
MODs & Pascale All groups to check on how they use IGI and update annotations as per Princeton discussion.
Val Circulate draft doc on how contributes_to can & can't be used Will include: "Would this annotation make sense if this subunit was" ... [thought not finished; might be something like "viewed by itself"].
MODs & Pascale Check existing annotations for "contributes_to" with IDA We think only allow contributes_to with IDA. Look into adding to annotation checking script to flag contributes_to.
Jen Implement rules and software for sanity checking automated annotations (species-based trigger file).

New Items

Status Responsible Party Task Comments
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