20th GO Consortium Meeting Minutes
- 1 Ontology content development
- 1.1 Overview (Midori)
- 1.2 Theory and examples of function and process links (Harold, Jennifer)
- 1.3 Function and process link discussion
- 1.4 New relationship type (David)
- 1.5 Quality Control (Tanya)
- 1.6 OBO-Edit (Amina)
- 1.7 Reports (Jane)
- 1.8 Signaling
- 1.9 Annotation checking by trigger file
- 2 General Annotation Issues
- 3 Reference Genome
- 4 User Advocacy and Outreach
- 4.1 GO helpdesk (Jane)
- 4.2 Newsletter (Jane)
- 4.3 Tools (Jane)
- 4.4 PAMGO outreach workshop (Michelle)
- 4.5 TAIR and Plant Physiology collaboration (Tanya)
- 4.6 Swissprot (Michael)
- 4.7 Seth: AmiGO
- 4.8 Obo-edit text mining plugin (Michael Schroeder)
- 4.9 Michael: Next Meeting
- 5 Final
- 6 Previous Incomplete Action Items
Ontology content development
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.
(Jennifer Deegan presenting: 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 "correct", but not always helpful to a given question for a human - like BP "carbohydrate metabolism"is linked to all glycolysis MF terms.
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 Jennifer 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.
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?
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.
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.
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.
This is an ongoing process. Lots of "regulates" terms.
Organization and biogenesis of cellular components
All "organization & biogeneis" terms will be changed to "organization" with the proposed high level structure:
organization -[i] assembly -[i] disassembly -[i] maintenance -[i] morphogensis biogenesis -[p] assembly -[p] part biosynthesis
(Jennifer Deegan presenting: 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
Annotation checking by trigger file
(Jennifer Deegan presenting: 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.
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.
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:
- A new column that contains a text describing the annotation process
- 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
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:
- the experimental evidence
- was there judgement involved
- was there a review of the data
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.
- 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
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.
Transitive Relationships in GO
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.
How curators can use evo trees (Paul)
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)
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)
There were two options proposed for inputting ancestrally inferred annotations:
- These annotations would be provided back to the MODs, and the MODs would incorporate them into their gene association submissions to the GO consortium
- 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.
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.
Ref Genome impact on ontology development and documentation (David)
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.
- 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. If there are links to a wiki page, they need to be propagated through to all children terms. 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.
The current documentation for GO is in many places and spans many many pages. It was agreed that there needed to be a central, consolidated repository for the documentation that was easily accessible and searchable. Jen brought up that these types of project works best when there is one person in charge of the technology and individuals take responsibility for sending that person up-to-date content. The GO editorial office can have oversight but would need input from all the groups. Peter pointed out that the RefGenome group already has a forum where examples and counterexamples with references are brought up and would be a natural group for providing documentation content.
User Advocacy and Outreach
GO helpdesk (Jane)
Highlights about the gohelp email address:
- increasing number of queries
- response time has gone down
- types of queries remain same
When checking usage for other avenues for help, FAQ is hit more than the rest of the web pages (~500/week vs. ~250/week). The FAQ is stale and needs to be cleaned up. The usage of the FAQ suggests that this should be the highest priority for clean up.
We are producing 4 newsletters a year but it is a lot of work, particularly formatting. Suggestions for additional outlets provided were;
- do it dynamically, like an RSS
- reduce frequency
The RSS could complement but not replace the newsletter. The PDF version is nice to take to meetings. Also, since we announce software changes in the newsletter for widespread dissemination, decreasing the frequency may impact release of new features.
There was some discussion about who actually reads the newsletter. Since the original intent of the newsletter was to make GO relevant to biologists, the newsletter needs to be general enough for general consumption. The users are GOC people, software developers, as well as biologists.
Upcoming plans to contact tools developers
- will check all tools developers and have them fill out a form
- goal will be to provide better information about the tools
- default will be to delete tools if we don't get a response
PAMGO outreach workshop (Michelle)
Michelle is doing annotation workshops at IGS, complementing JVCI workshops. GO was mentioned in the BRC RFA.
TAIR and Plant Physiology collaboration (Tanya)
A couple dozen GO annotations have been made from this effort. Not yet 100% compliance but increased after wording changed to "you are required to submit data". Authors are only asked for data after paper has been accepted. The papers are not curated at TAIR, authors make the annotations. There has been no spot checking of the annotations to check for accuracy.
Swissprot curators in Geneva are beginning to do GO annotations. There are about 40-50 curators. They will be trained by the EBI team and use their annotation software. They will only MF and BP because they use their own CC ontology. The CC ontology is mapped to GO by GOA.
AmiGO 1.5 Status
Most of the new work has been on speeding-up the input system for slimmer and term enrichment. We can now take input in the many thousands. Also, the 1.5 branch works with the new relationship. There have been many bug fixes and text updates, added as necessary.
AmiGO 1.6 Status
There is a publicly available beta/preview on ash
Initial community annotation support has been added by a round trip through GONuts . This will allow for real-time participation of our user community.
Initial Reference Genome support has also been added. This includes: full support for Reference Genome displays, links in from AmiGO through the gene product search page  (search for "pou5f") and gene product details page , as well as details  including details of evidence type, sortablility, and visualizations.
Given the complexity of some of the queries, there is now a caching mechanism in place for graph, images, and large pages.
There is also a summary  page that contains evidence type groups.
Future work in progress (visible in live beta)
- many different things, moving over to a new infrastructure
- most importantly probably: Lucene
- complex search
Obo-edit text mining plugin (Michael Schroeder)
Michael presented a tool that can help in ontology development by:
- Analyzing text to generate ontologies (Ontology Generation Tool)
- Suggesting definitions from doing a Yahoo! query to pick out text strings that appear to define the search term (Definition Generation)
- Add to Ontology
- The gopubmed tool also indexes GO terms and Mesh terms. All search results are filterable by several different parameters. The GoGene (www.gopubmed.org/gogene/) searches pubmed abstracts. Mutations and sequence searches are possible as well.
- All of the suggestions are automatically generated so it would be up to curators to go to the literature to verify.
- They would like annotators/editors to evaulate it, especially those who generate ontologies. The plugin will soon be in the SVN of Obo-edit. Michael and Chris will also discuss usages of this tool for AmiGO (GOst) as well.
Michael: Next Meeting
- Cambridge, and then to berlin?
- Eugene? Portland?
Table of action items for this meeting
|Ontology content development||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.|
|Function and process link discussion||Add obvious part_of links, like MF "kinase" and BP "phosphorylation"; will be rolled out after regulates is released in Feb 2009|
|Function and process link discussion||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|
|Function and process link discussion||Agree on beginnings, middles, and ends of pathways/processes between Reactome and GO|
|Function and process link discussion||Examine impact on annotation priorities and implememntations|
|Function and process link discussion||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)|
|Function and process link discussion||assign process to every molecular function.|
|Function and process link discussion||deferred: co-annotation 'has function as part of this process'|
|DONE - 10/28/08||New relationship type||Tanya||Send out function process email again.|
|New relationship type||Chris||Release examples of relationship usage for software development.|
|Organization and biogenesis of cellular components||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||J Deegan||Proposal agreed for implementation.|
|Future content meeting discussion||Brenley Kimberley Candice Michelle Jane Pascale David ???||Pursue an ontology development meeting one or two: (Brenley, Kimberley, Candice, Michelle, Jane) Viral processes (Pascale, David, ???) GPCR||(Jane: We have a wiki page for the viral term overhaul. Not much else so far.)|
|Future content meeting discussion||?||A couple of GO meeting with major meetings on these topics|
|Future content meeting discussion||?||Investigate funding sources|
|Annotation checking by trigger file||Jen||remove sensu synonyms|
|Annotation checking by trigger file||Jen||Continue implementation of trigger system|
|Annotation checking by trigger file||Dan||Make GOA quickgo checking available to the public|
|Annotation checking by trigger file||Jen||write up for near future news letter|
|Evidence code ontology (ECO)||suzi||We will use the ECO and create an EV code ontology tracker|
|Evidence code ontology (ECO)||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||Suzi Michelle Judy Pascale Emily Eurie||Example cases of annotations and implementation into the ECO|
|PAMGO||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||everybody||go ahead with the implementation of the expressive model in column 16||* get more examples * get the documentation together|
|In progress, see April 2009 minutes||Mechanics of incorporating ancestral inferences||Michael A.||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|
|In progress, see April 2009 minutes||Mechanics of incorporating ancestral inferences||Paul/Kara||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.|
|In progress, see April 2009 minutes||Mechanics of incorporating ancestral inferences||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.|
|In progress, see April 2009 minutes||Mechanics of incorporating ancestral inferences||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.|
|In progress, see April 2009 minutes||Mechanics of incorporating ancestral inferences||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||Berkeley||automate mike's graph (as in proposal), need to be able to see progress through time|
|Ref Genome impact on ontology development and documentation||Amelia||Amelia is the point person for the documentation project.|
|In progress||Ref Genome impact on ontology development and documentation||New content driven by Kara and Pascale as they go through the trees for the RefGenome project and see the usage of the terms|
|In progress||Ref Genome impact on ontology development and documentation||Debby and Brenley will be in charge of salvaging and consolidation of existing documentation|
|Not yet done||Ref Genome impact on ontology development and documentation||Everyone||Will send appropriate examples and counter-examples with PMIDs to the GO editorial office to add as comments to the GO terms and definitions|
|Not yet done||Ref Genome impact on ontology development and documentation||Seth Amelia||All documentation will be indexed and searchable on GONUTS|
|GO Helpdesk||Amelia||Amelia will be documentation coord.|
|Newsletter||Jane||look into outsourcing newsletter construction||(Jane: Newsletter has been discontinued. Soon to be replaced with a news feed. Someone will present at Eugene.)|
|Newsletter||Think about separating newsletter into the above three listed sections||(Jane: Newsletter has been discontinued. Soon to be replaced with a news feed. Someone will present at Eugene.)|
|AmiGO 1.6||Seth||work with RGWG to make displays correct for users|
|AmiGO 1.6||Seth||work out IDA bug that keeps coming (check with david for clarification of algorithm)|
|Next Meeting||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
|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).|