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textspresso query

William Bug William.Bug at DrexelMed.edu
Wed Mar 28 14:26:50 PDT 2007


Mike is correct.  I'd recommend waiting for that upcoming release.   
Michael, Paul, et al. are working to make that release by May or  
June, I believe, and it does sound to be a significant step forward.

One thing to note when reviewing v1.0.0 (currently download at the  
GMOD.org site), regular expressions are no longer used in the  
indexing/markup process.  As Mike indicates, that's just the tip of  
the iceberg, so since you are just getting started on using  
TextPresso, waiting until a release of the new version is probably best.

That's just my sense of things.  You might also want to contact  
Michael Mueller directly on this issue.  He may have some preliminary  
docs he could pass on that provide more info on the changes.

Cheers,
Bill


On Mar 28, 2007, at 2:41 PM, Mike Cherry wrote:

> One thing to note is that a new version of Textpresso will be  
> released soon by Michael Mueller.  I suggest that you wait for this  
> new version.  There are several differences and so you will be  
> redoing some of your setup.  The new version is also faster.  With  
> that said it would be appropriate to look at the current textpresso  
> release because there are utilities that are needed by textpresso  
> that are not included.  You'll need to download and setup those  
> utilities.
>
> -Mike
>
>
> On Mar 28, 2007, at 10:33 AM, ranjana wrote:
>
>> Hello Carl and Fiona,
>> We use Textpresso routinely at WormBAse here for different kinds  
>> of curation including GO curation.  The team that developed  
>> Textpresso is also based here, making it convenient for us to  
>> pester them with questions!
>> The person to e-mail about Textpresso is Michael  
>> (mueller at caltech.edu).  PLease feel free to e-mail us curators  
>> too , if you have any questions.
>>
>> Cheers
>> Ranjana Kishore
>>
>> Fiona McCarthy wrote:
>>> Hi All,
>>>
>>> Carl Schmidt is a researcher at the University of Delaware who  
>>> has been
>>> doing a great deal of work to put together resources for avian
>>> researchers. He is interested in using Textpresso and would like to
>>> contact GO annotation groups that are using Textpresso and has  
>>> already
>>> done some preliminary work to look at using Textpresso for chicken
>>> literature.
>>> Could those of you who use Textpresso to assist with annotation  
>>> please
>>> contact Carl? His email is:
>>> schmidtc at udel.edu
>>>
>>> thanks,
>>> Fiona McCarthy
>>>
>>>
>>> AgBase Biomanager
>>> Department of Basic Sciences
>>> Box 6100
>>> MS 39762-6100 Mississippi State University
>>> USA
>>> Tel:   (+ 1) 662 325 5859
>>> Fax:  (+ 1) 662 325 1031
>>>
>>> http://www.agbase.msstate.edu/
>>>
>>> ----- Original Message -----
>>>
>>> 		Sunday, March 18, 2007 10:33:17 AM
>>> Message
>>> From:		Carl Schmidt <schmidtc at udel.edu>
>>> Subject:	textpresso
>>> To:		Fiona McCarthy
>>> Attachments:		Attach0.html		4K
>>>
>>> Hello Fi,
>>> We were wondering which other groups were using Textpresso to  
>>> support
>>> their ontology annotation efforts.
>>>
>>>
>>> Also, I prettyfied (sort of) and created links for the material  
>>> you added
>>> to the wiki gene mockup page. I need to sort out why I cannot  
>>> find the
>>> Ensembl Link and I am trying to get the chromosomal location to link
>>> directly to the appropriate coordinates in the Gbrowser.
>>> Carl
>>>
>>>
>>>
>>>
>>> Carl J. Schmidt
>>> Associate Professor
>>> Department of Animal & Food Sciences
>>> 051 Townsend Hall
>>> University of Delaware
>>> Newark, DE 19716-2150
>>>
>>>
>>> [ mailto:schmidtc at udel.edu ]schmidtc at udel.edu
>>> 302-831-1334
>>> Fax: 302-831-2822
>>> [ http://udel.edu/~schmidtc ]http://udel.edu/~schmidtc
>>>
>>>
>>> --
>>> This message is from the GOFriends moderated mailing list.  A  
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>>
>>
>> --
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>
>
> --
> This message is from the GOFriends moderated mailing list.  A list  
> of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner- 
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> request at geneontology.org
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Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug at DrexelMed.edu




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