[Annotation] [Biocurator] possible data submission at publication model

[Alan Ruttenberg]

Thanks Tanya and Judy for clarifying. I think this approach makes  
very practical sense -  minimal hassle for the author and trained  
people doing the curation. It would be a great deal for the  
publishers, I think.  Now that I understand the approach, I'll think  
some more about possibilities. One thing that comes to mind is that  
there may be different curator groups that could curate different  
aspects of the paper, working from the same source. For instance, OBI  
is interested in protocols and reagents, Science Commons is  
interested in materials that might be made available to other  
researchers, and there was mention of PDB in an earlier response. So  
you can imaging multiple curation groups feeding off the same  
information.

BTW, although the Pubmed id may not exist, the DOI may have been  
allocated already and this would serve as an adequate identifier and  
can be later mapped to the Pubmed id. It would be interesting to know  
whether it is available from the publishers at the stage that the  
form filling would be done. If so, perhaps they could supply the form  
to authors with that already filled out.

Another thought is that you might be able to use Phenote for the data  
collection as it is quite configurable and will give, for any  
sections that are reasonable to offer controlled vocabulary, term  
completion.

-Alan


On Mar 21, 2008, at 7:08 AM, Judith Blake wrote:

>
> Alan,
>
> We do not expect authors to understand or be able to easily pick  
> the right term from an controlled vocabulary such as the GO.  Their  
> colloquial terminology will, we think, be pretty easily interpreted  
> by trained curators who are biologists skilled in the use of bio- 
> ontologies.
>
> The primary and highly useful aspect of this approach is the  
> indexing of the paper by taxon ID and geneID.  This is a royal  
> hassle for curators to have to do and something the authors should  
> have at hand.
> Judy
>
>
> Alan Ruttenberg wrote:
>> If there is no control on the vocabulary, is it intended that  
>> someone on the journal staff curate these, or are you suggesting  
>> that they be published, as is, and the picked up by external  
>> curators.
>> -Alan
>>
>> On Mar 20, 2008, at 4:41 PM, Judith Blake wrote:
>>
>>> Hi all,
>>>
>>> Here's a mock-up of what we are starting to present to some  
>>> journals.  I would appreciate any feedback.  these are just some  
>>> screen shots with no commentary, but you can see where this is  
>>> going I think.  It would be melded into the publication process  
>>> somewhere.  One thing to notice is that there is no requirement  
>>> for cho0sing any particular term for the annotation.  It justs  
>>> asks for what the author would propose.  The idea is that it  
>>> would be up to the curator to use this as appropriate in the  
>>> curation of the paper particularly as a clue to what the author  
>>> is thinking.
>>>
>>> One thing of course is that as 'author submission' forms, there  
>>> would be no pubmed ID yet.   Also, we may swap the GO taxon table  
>>> for a MOD taxon table...really meant to reflect the most common  
>>> taxonIDs for the work published in that journal.
>>>
>>> notice that if you want to add data for more than one gene, you  
>>> click at the bottom and a new annotation table opens from the  
>>> same form.  You can choose for a different taxon here if you want  
>>> to.
>>>
>>> I would welcome any comments.
>>>
>>> Judy<JournalMetadataSubmission.ppt>_________________________________ 
>>> ______________
>>> Biocurator mailing list
>>> Biocurator at tairgroup.org
>>> http://mailman.tairgroup.org/mailman/listinfo/biocurator
>>
>
>