2010 GO camp Meeting Logistics
The 3rd GO annotation camp (3 days) will be held from June 16-18, 2010 (Wednesday-Friday).
This annotation camp will be focused on updating and refining skills of existing GO biocurators including new GO biocurators in existing annotation groups and including the Swiss-Prot curation team. We hope members of each MOD will be represented.
- Deliverables: (1) final annotation documentation for each of the three annotation topics.
- There will be a special emphasis on the reference genome project. Deliverable: (2) annotation propagation rules for the reference genome project.
Swiss Institute for Bioinformatics (SIB), Geneva, Switzerland.
Not yet open.
To be announced.
To be announced.
Structure: There will be three (3) ‘focused annotation sessions’ where specific annotation issues will be discussed. Suggestion for discussion topics should be added to the GO camp agenda: 2010_GO_camp_Meeting_Logistics#Suggestions_for_annotation_issues_to_be_discussed
The agenda is not yet finalized.
Suggestions for annotation issues to be discussed
- Please add any concerns you have regarding specific GO annotation issues here, or add your comments to an existing annotation issue.
- As three topics will be selected for further discussion for the GO camp, please indicate which 3 issues are of most interest to you.
1. Binding and complexes
1.a. Binding documentation
The binding group presented annotation policy suggestions at the last GO Consortium meeting  These annotation guidelines should be finalized, and a full set of annotation guidelines on how annotation data is curated and presented in GAF files should be fully documented. For instance determine:
- that binding annotations, especially those where the GO term does not specify a particular binding partner, should where possible, indicate the interacting partner in the 'with' column
- fully describe the usage of pipes etc in the 'with' column.
- ask that protein binding annotations should be reciprocal - that if protein A is annotated as binding protein B, the reverse annotation should be provided
The use of column 16 to identify protein/gene targets of an molecular function GO annotation, could benefit this binding discussion.
Curators interested in discussing this topic at the GO Camp:
Emily, Donghui, Yasmin, Susan, Pascale, Ruth, Fiona, Lakshmi, Li
1.b. Annotation of complexes
- Can IPI be used to annotate molecular function? For example ribosomal subunits are annotated to 'structural constituent of ribosome' (a function)
- 'Structural components activity' function terms: some ribosome proteins are annotated to 'structural constituent of ribosome' by IDA (for example SGD:S000005760); but the paper (PMID: 18782943) only shows purification of the complex.
- Chromatin? See NIPBL discussion from Feb 22 jamboree. The general question is when is a protein part of a complex or organelle or when it binds to it?
- (Rama:) Interpretation of author statements: Authors very often use the word complex when two proteins are interacting, but there may not be enough evidence to show the existence of a stable complex. Should curators not add another layer of critiquing and request/annotate to the complex? How far should curators go with interpreting evidence and when should we let go thinking the reviewers are okay with that language, let us go with that.
Curators interested in discussing this topic at the GO Camp: Pascale, Stan, Manu, Li
2. Biological processes
2.a. Use of regulation
- This would include process beginning/end (maybe in the context of the new signaling terms)
- How to decide whether to annotate to 'regulates process x' or 'process x'?
Notes: How do groups decide on when to annotate to 'regulates process x' or 'process x'? For instance does SLIT regulate axon guidance or involved in the process of axon guidance? Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process. When should annotations be inherited up the regulates relationship?
Notes: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.
(Comment from Val: This is largely overlapping with the regulation issue. Where a process begins and ends is central to the decision to annotate directly to a process or to the regulation of a process )
(Comment from Pascale: 'regulation' and 'process beginning/end' have been merged now)
(Comment from Ruth: Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)
Curators interested in discussing this topic at the GO Camp
Emily, Donghui,Val, Stan, Pascale, Yasmin, Jane, Rachael, Susan, Rama, Ruth, Fiona, Lakshmi, Jodi
2.b. Response to terms, how will these relate to signaling terms and to final cellular effect
Curators interested in discussing this topic at the GO Camp
Varsha, Yasmin, Ruth, Becky, Manu
2.c. How is a downstream effect defined (i.e when not to capture phenotypes )
from 22nd Feb Jamboree call , Tanya: It's not uncommon for the initial publications to describe a mutant phenotype, with a developmental defect, and then later publications to describe much more explicit functions or processes. You should always annotate based on whatever evidence is available. Once you've done that, the question becomes, "When do we keep or remove the phenotype-based annotations?" At TAIR, their policy is to keep the developmental terms if they think that their users would expect to see them. Some participants suggested that one would expect all orthologs to have the same development-type annotations, across organisms. Others disagreed with this expectation.
Curators interested in discussing this topic at the GO Camp Donghui, Val, Rachael, Rama, Ruth, Fiona, Ranjana, Jodi
3. Use of column 16
Notes: The suggested use of Cell Type in column 16 seems to be progressing , and a date for GAF2.0 has been agreed for the 1st June. However this discussion needs to progress to decide how targets of a molecular function/biological process should be best captured in this field, as well as the linking of terms between different annotation lines.
Curators interested in discussing this topic at the GO Camp: Stan, Varsha, Michelle, Jane, Ruth, Fiona, Lakshmi, Ranjana, Li
Other suggestions for agenda items
- What is the bottle neck for manual annotations (with experimental evidence)? How can we step up manual curation? (Rama)
- How are the various annotating groups keeping with all the ontology development/changes (new relationships specifically)? (Rama)
|Name||Organization||Arrival Date/Time to Airport||Departure Date/Time from Airport|
|Rachael Huntley||GOA||June 15 16.35||June 18 20.05|
|Yasmin Alam-Faruque||GOA||June 15 16.35||June 18 20.05|
|Ruth Lovering||BHF-UCL||June 15 19:55||June 18 20.05|
We will try to provide Webex and Telephone Conferencing.
|Name||Organization||email (needed to set up your remote access)|
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