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

[Judith Blake]

Simon,

This is a good suggestion.  I too was wondering how to make it more 
explicit.  I will incorporate somehow.

Judy


Twigger, Simon (MCW) wrote:
> Hi Judy,
>
> For the list of functions/process, etc. and the method description, do 
> these go in pairs? In other words I might put 'kinase' in box 1 and 
> then 'enzyme assay' in the Method box 1 to indicate that I thought 
> this gene was a kinase because I did an enzyme assay? If this is the 
> case, it might be worth making it more explicit that the two go hand 
> in hand, otherwise people might enter a whole list of things in the 
> function/process boxes and nothing in the methods, or the function 
> keyword might not match up with the right method, etc.
>
> Again, assuming the boxes go in pairs, you could rearrange these boxes 
> as sentences to help people enter data and perhaps allow them to 
> specify if they are entering a function/process/location/interacting 
> partner using a drop down menu - this would make subsequent parsing 
> easier and might help the user enter more appropriate information:
>
> For example it might look something like this (the drop down menu 
> options are separated by a pipe '|' )
>
> "A [function this gene has | process this gene is involved in | 
> location this gene is found in | protein this gene interacts with] is 
> [insert function/process/partner here] and the method I used in my 
> paper to determine this is [Insert method here]"
>
> You could create more rows as desired if people wanted to add more 
> facts. Its a bit more wordy than the two boxes you have now but might 
> help the researcher's know what was expected and enter relevant 
> information.
>
> Is location meant to be cellular location or can it be any location 
> (subcellular, organ, tissue, cell type, etc?). I would imagine 
> location means different things to different scientists so we'd need 
> to be more precise as to what was expected or anticipate a wide 
> variety of input.
>
> Simon,
>
>
> -- 
>
> Simon N. Twigger, Ph.D.
> Assistant Professor, Department of Physiology
> Medical College of Wisconsin
> 8701 Watertown Plank Road,
> Milwaukee, WI, USA
> tel: 414-456-8802
> fax: 414-456-6516
> AIM/iChat: simontatmcw
>
>
>
> On Mar 21, 2008, at 6:08 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
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>>>
>>
>>
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