RefG annotation priorities Sept 2009 (Retired)

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Background

There is a huge amount of potential that could be exploited from the co-curation activities made available via the RefGen project. Therefore we encourage GOC groups to submit short proposals to the RefGen curation body, to suggest possible co-curation projects which the RefGen curators could choose to focus on for a specified amount of time.

Advantages - The group/curator heading a chosen project will be responsible to push forward the co-curation work; to help improve annotation consistency and the GO terms available. These curators will therefore support the coordination efforts of the reference genome group.

- 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.

- 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.

- 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.

- Those small annotation projects will help demonstrate to external users the usefulness of the the Reference Genome initiative.

Procedure for reference genome

  1. Projects leaders identify experts in the field.
  2. Project leaders prepare a summary of the area both to pick correct curation.

targets and to provide annotators with some basic background in the field.

  1. Projects leaders identify biologically coherent targets.
  2. Project leaders must ensure that the ontology is correctly developed and work

with experts to develop the ontology.

  1. MODs curators annotate gene products targets.
  2. Tree curators annotate families to the best of their understanding.
  3. Project leaders, tree curators and biological experts meet to finalize.

annotations and make sure the biology is well represented.

  1. Ideally, project can be published.

Requirements for these co-curation annotation projects

  1. Project proposals should be designed to create annotations to targets that are of interest to human biomedical research
  2. Proposals should incorporate a distinct time-requirement; i.e. a limited number of proteins should be proposed that would be possible to annotate in a period of approximately 3-4 months
  3. 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.
  4. The annotation effort should, if possible encourage external collaborations to use and expand the information resource provided by the co-curation effort.


Proposals

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

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

Cardiovascular development

Selected genes involved in cardiovascular development (targeted to use terms developed by the recent Heart Ontology Content workshop): BHF-UCL

Signaling

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.


Ageing

Cell cycle

DNA repair

(GOA-UniProtKB; Rachael Huntley)

Cell polarity and gastrulation

(WormBase - Kimberly Van Auken)

Cell motility

Pascale and Petra

Ribosome

Pascale and Serenella

Protein amino acid N-linked glycosylation



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