Difference between revisions of "RefG annotation priorities Sept 2009 (Retired)"

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'''Advantages'''
 
'''Advantages'''
- the group/curator heading a chosen project would have an invested interest  in helping to push forward the co-curation work; to help improve annotation consistency and the GO terms available.  These curators will therefore support Pascale's coordination efforts.
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- the group/curator heading a chosen project would have an invested interest  in helping 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.
 
- 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.

Revision as of 07:35, 9 February 2010

Background

There is a huge amount of potential that could be exploited from the co-curation activities made available via the RefGen project. Therefore would it be worth setting up a scheme whereupon GOC groups could 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? I have outlined some possible advantages to this idea below:

Advantages - the group/curator heading a chosen project would have an invested interest in helping 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 publications 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 could directly aid 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 could help to rapidly generate annotations that apply the newly created terms and ensure the new terms are appropriate for all species. If this work is carried out with a recent ontology development effort, then external experts involved in the content meeting may also still be interested in helping with questions arising from annotation discussions.

Possible requirements for these co-curation proposals

  1. project proposals should be designed to create annotations to targets that are of interest to human biomedical research
  1. 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
  1. 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.
  1. The annotation effort should, if possible encourage external collaborations to use and expand the information resource provided by the co-curation effort.

By using multiple focused, small annotation projects it would be hoped that more curators could become confident enough to be involved in ontology development efforts and that this may also help demonstrate to external users the usefulness of the the Reference Genome initiative; two points emphasized at the recent GOC meeting.

Proposal

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).

There is a huge amount of potential that could be exploited from the co-curation activities made available via the RefGen project. Therefore would it be worth setting up a scheme whereupon GOC groups could 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? I have outlined some possible advantages to this idea below:

Advantages - the group/curator heading a chosen project would have an invested interest in helping to push forward the co-curation work; to help improve annotation consistency and the GO terms available. These curators will therefore support Pascale's coordination efforts.

- 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 publications 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 could directly aid 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 could help to rapidly generate annotations that apply the newly created terms and ensure the new terms are appropriate for all species. If this work is carried out with a recent ontology development effort, then external experts involved in the content meeting may also still be interested in helping with questions arising from annotation discussions.

Requirements for these co-curation proposals:

  1. project proposals should be designed to create annotations to targets that are of interest to human biomedical research
  1. 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
  1. 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.
  1. The annotation effort should, if possible encourage external collaborations to use and expand the information resource provided by the co-curation effort.

By using multiple focused, small annotation projects it would be hoped that more curators could become confident enough to be involved in ontology development efforts and that this may also help demonstrate to external users the usefulness of the the Reference Genome initiative; two points emphasized at the recent GOC meeting.

Proposals

  • 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
  • Selected genes involved in lung development: MGI
  • 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.

Possible future Projects: Ageing, Cell cycle, DNA repair (GOA-UniProtKB; Rachael Huntley), Cell polarity and gastrulation (WormBase - Kimberly Van Auken)

  • 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
  • Selected genes involved in lung development: MGI
  • 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.

Possible future Projects: Ageing, Cell cycle, DNA repair (GOA-UniProtKB; Rachael Huntley), Cell polarity and gastrulation (WormBase - Kimberly Van Auken)

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