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
- 5.1 Factors to consider in prioritization of projects
- 5.2 Retinoic Acid Pathway
- 5.3 Wnt signaling Pathway
- 5.4 Autophagy
- 5.5 Loop of Henle
- 5.6 RefG Heart Development co-curation
- 5.7 Signaling
- 5.8 Ageing
- 5.9 Cell cycle
- 5.10 DNA repair
- 5.11 Cell polarity and gastrulation
- 5.12 Cell motility
- 5.13 Ribosome
- 5.14 Protein amino acid N-linked glycosylation
- 5.15 Transcription
- 5.16 Basic energy metabolism
Annotation consistency, guidelines, and quality control
Directing Ontology development
Enable propagation of annotations via PAINT
Publicize the usefulness of the the Reference Genome initiative
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.
- 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, we can say more about ancient processes and we can cover basic biology
- Vertebrate biology (e.g. olfactory receptors)
- 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)
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
Selected genes involved in cardiovascular development (targeted to use terms developed by the recent Heart Ontology Content workshop): BHF-UCL
(GOA-UniProtKB; Rachael Huntley)
Cell polarity and gastrulation
(WormBase - Kimberly Van Auken)
Pascale and Petra
Pascale and Serenella
- Val, see 
- Karen Christie
Basic energy metabolism
- N-linked glycolsylation (Mike L)
- Emily? Judy?