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

[Twigger, Simon (MCW)]

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
>>> Biocurator at tairgroup.org
>>> http://mailman.tairgroup.org/mailman/listinfo/biocurator
>>
>
>
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