RefG annotation priorities Sept 2009 (Retired)
- 1 Rationale
- 2 Defining the Reference genome biocuration projects
- 3 Procedure for reference genome biocuration projects
- 4 Proposals
- 5 Possible future Projects
- 6 Factors to consider in prioritization of projects
- 7 Possible future Projects
- 7.1 Retinoic Acid Pathway
- 7.2 Wnt signaling Pathway
- 7.3 Autophagy
- 7.4 Loop of Henle
- 7.5 RefG Heart Development co-curation
- 7.6 Signaling
- 7.7 Ageing
- 7.8 Cell cycle
- 7.9 DNA repair
- 7.10 Cell polarity and gastrulation
- 7.11 Cell motility
- 7.12 Ribosome
- 7.13 Protein amino acid N-linked glycosylation
- 7.14 Transcription
- 7.15 Basic energy metabolism
Co-curation of gene families by the groups participating in the reference genome project makes several aspect of the GOC work more efficient, thus providing several advantages:
Annotation consistency, guidelines, and quality control
As the selected genes in a project will have a common theme, all curators from the different groups should generate an extended understanding of the biology in a particular area; this should help improve the consistency of annotations available for a particular system, and ontology development discussions.
Directing Ontology development
Focused co-curation will be coupled directly to ontology development work. For instance where an ontology development effort has recently generated new terms to describe a particular process, these could be provided to the group to be 'road tested' (with the understanding that terms need to be publicly available and that ontology developers are confident that a reasonable number of terms already exist in a usable state).
Where a recent ontology content meeting has generated a specific set of terms for an area of biology; co-ordinated curation work will help to rapidly generate annotations that apply the newly created terms and ensure the new terms are appropriate for all species. Annotation should be coordinated with ontology development so that external experts involved in the content meeting may also still be interested in helping with questions arising from annotation discussions.
Enable propagation of annotations via PAINT
Publicize the usefulness of the the Reference Genome initiative
Those small annotation projects will help demonstrate to external users the usefulness of the the Reference Genome initiative. Projects should aim to eventually generate targeted publications on usefulness of the GO resource with respect to a particular area of biology. For instance, a publication could compare the annotations generated for the same system across diverse species, exploring interesting differences/similarities in the data, perhaps linking up with external investigators in the chosen domain.
Defining the Reference genome biocuration projects
- The curation priorities of the reference genome group will be based on 'biological processes', that is, either a signaling pathway, the role of a molecular complex, etc.
- Each of those 'biocuration projects' will be lead by a 'reference genome biocuration project leader'. The project leader is a curator from a participating group that will be responsible for selecting the gene products and families involved in the selected process, provide some biological background to participating annotators, and ensure that ontology development is complete enough to undertake the project.
Requirements for these co-curation annotation projects
- Project proposals should be designed to create annotations to targets that are of interest to human biomedical research
- Proposals should include the time required for the completion of the project, aiming for a period of approximately 3-4 months. The project can be split into several subprojects if that time frame is not sufficient.
- At the end of this annotation period, the project should aim to generate a publication that demonstrates the usefulness of GO annotation resource and the value of the co-curation effort. The curators leading the co-curation exercise will be primary authors of such a publication as well as the Reference Genome group.
- The annotation effort should, if possible encourage external collaborations to use and expand the information resource provided by the co-curation effort.
- Some proposed projects can be found below: Strategy_for_establishing_RefG_annotation_priorities#Proposals.
Procedure for reference genome biocuration projects
- Once a project is agreed upon, the Projects Leader identify experts in the field.
- Project Leader prepares a summary of the area both to allow the selection of appropriate curation targets and to provide annotators with some basic background in the field.
- Project Leader identify biologically coherent targets.
- Project Leader must ensure that the ontology is correctly developed and work with experts to develop the ontology.
- MODs Curators annotate gene products targets.
- Tree Curators annotate families to the best of their understanding.
- Project leader, Tree Curators and Biological Experts meet (in person or through web-conferencing) to finalize annotations and make sure the biology is well represented.
- Ensure that the web presentation of the project is satisfactory
- Ideally, project can be published.
Please write the name of the person(s) that would be responsible for the project. Include estimated number of genes to annotate in the species of interest, and in what time frame the annotation might be done. Add any justification (medical interest, external groups interested in collaborating, coupling with ontology development, etc).
Lung branching morphogenesis: Li Ni, MGI
(Dec 2009-Feb 2010)
Possible future Projects
Factors to consider in prioritization of projects
- How old is the family, because we can say more about ancient processes and we can cover basic biology
- Vertebrate biology (e.g. olfactory receptors) which can be tied to particular diseases (and include experts in these diseases as advisors). In other words, the implications and potential impact.
- Things that happen within a single cell (molecular)
- Someone will devote the time to drive it forward
- There are external (i.e. outside GO, doing non-high-throughput lab work)
- Existence of a downstream reporter to measure whether the signal is coming through
Possible future Projects
Retinoic Acid Pathway
- Need to fix transcription factors in the ontology
Wnt signaling Pathway
Loop of Henle
The current Co-curation project for the Loop of Henle (this has been initiated by Yasmin for the Renal GO Initiative, and involves 4 curators annotating ~200 conserved orthologs found to be involved in the development of a kidney structure which differs greatly been species, see: http://wiki.geneontology.org/index.php/Loop_of_Henle_Cocuration): GOA-UniProtKB
- Project leader: Varsha Khodiar BHF-UCL
- Possible experts:
- Ontology status: Cardiovascular process GO ontology development workshop was held [dates]
When the GO editors are satisfied that the terms in this area satisfactory - curation groups could be asked to take a selection of different signaling pathways to test the structure of the ontology.
(GOA-UniProtKB; Rachael Huntley)
- Mismatch repair pathway
- Samir Acharya, Ohio State U, Columbus, OH 
Cell polarity and gastrulation
(WormBase - Kimberly Van Auken)
Pascale and Petra
Pascale and Serenella
- Val, see 
- Possible experts:
- Karen Christie
Basic energy metabolism
- N-linked glycolsylation (Mike L)
- Emily? Judy?