From dstaines at ebi.ac.uk  Fri Jul  1 05:58:06 2011
From: dstaines at ebi.ac.uk (Dan Staines)
Date: Fri, 01 Jul 2011 10:58:06 +0100
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming, was: RE: Old
	versions?
In-Reply-To: <CA31F6F0.9AC4%aloraine@uncc.edu>
References: <CA31F6F0.9AC4%aloraine@uncc.edu>
Message-ID: <4E0D9A2E.7050600@ebi.ac.uk>

Any news on this? As I've said, I'm happy to make a change, but the 
window for doing so in the next release is closing rapidly!

Many thanks,

Dan.

On 06/30/2011 02:48 PM, Ann Loraine wrote:
> I contacted TAIR to get their input.
>
> Probably I can give you a final answer as to what name to use later on
> today.
>
> Thanks for offering to make the change!

-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/


From aloraine at uncc.edu  Fri Jul  1 07:59:40 2011
From: aloraine at uncc.edu (Ann Loraine)
Date: Fri, 01 Jul 2011 07:59:40 -0400
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming, was: RE: Old
	versions?
In-Reply-To: <4E0D9A2E.7050600@ebi.ac.uk>
Message-ID: <CA332EEC.9B20%aloraine@uncc.edu>

Hi,

I have an answer.

I corresponded with curators at TAIR.

They would like the name of the genome release to be:

TAIR10

Note the letters are all caps and there is no space or underscore separating
the number and the R.

Quoting Eva Huala, PI of TAIR:

"I prefer to keep using TAIR10 for both the assembly and annotation although
no changes were made to the assembly for this release."

Sincerely,

Ann Loraine


On 7/1/11 5:58 AM, "Dan Staines" <dstaines at ebi.ac.uk> wrote:

> Any news on this? As I've said, I'm happy to make a change, but the
> window for doing so in the next release is closing rapidly!
> 
> Many thanks,
> 
> Dan.
> 
> On 06/30/2011 02:48 PM, Ann Loraine wrote:
>> I contacted TAIR to get their input.
>> 
>> Probably I can give you a final answer as to what name to use later on
>> today.
>> 
>> Thanks for offering to make the change!

-- 
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750 (office)
http://www.transvar.org




From dstaines at ebi.ac.uk  Fri Jul  1 08:15:23 2011
From: dstaines at ebi.ac.uk (Dan Staines)
Date: Fri, 01 Jul 2011 13:15:23 +0100
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming, was: RE: Old
	versions?
In-Reply-To: <CA332EEC.9B20%aloraine@uncc.edu>
References: <CA332EEC.9B20%aloraine@uncc.edu>
Message-ID: <4E0DBA5B.8010103@ebi.ac.uk>

So, no change then? TAIR10 is what we use as both assembly and 
genebuild, so I think it should be satisfactory.

Many thanks,

Dan.

On 07/01/2011 12:59 PM, Ann Loraine wrote:
> Hi,
>
> I have an answer.
>
> I corresponded with curators at TAIR.
>
> They would like the name of the genome release to be:
>
> TAIR10
>
> Note the letters are all caps and there is no space or underscore separating
> the number and the R.
>
> Quoting Eva Huala, PI of TAIR:
>
> "I prefer to keep using TAIR10 for both the assembly and annotation although
> no changes were made to the assembly for this release."
>
> Sincerely,
>
> Ann Loraine
>
>
> On 7/1/11 5:58 AM, "Dan Staines"<dstaines at ebi.ac.uk>  wrote:
>
>> Any news on this? As I've said, I'm happy to make a change, but the
>> window for doing so in the next release is closing rapidly!
>>
>> Many thanks,
>>
>> Dan.
>>
>> On 06/30/2011 02:48 PM, Ann Loraine wrote:
>>> I contacted TAIR to get their input.
>>>
>>> Probably I can give you a final answer as to what name to use later on
>>> today.
>>>
>>> Thanks for offering to make the change!
>

-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/


From jw12 at sanger.ac.uk  Fri Jul  1 09:32:04 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Fri, 1 Jul 2011 14:32:04 +0100
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming,
	was: RE: Old versions?
In-Reply-To: <CA332EEC.9B20%aloraine@uncc.edu>
References: <CA332EEC.9B20%aloraine@uncc.edu>
Message-ID: <703495A2-7CB7-49A5-8BB5-77D087326D50@sanger.ac.uk>

Thanks for clarifying this Anne

"_" between the authority and version number is a DAS coordinate  
convention, so for us that would stay the same.
This works ok for DAS as long as the clients people are using to  
access the Data allow people to attach DAS tracks to a different  
coodinate system.
It also relies on people knowing the difference between the two (or in  
this case lack of difference for the majority of mappings).

It maybe a good idea to have a mapping/pseudonym table and  
descriptions for coordinate systems in the DAS registry. This will  
still rely on people "in the know" putting data into these tables  
though. I've avoided pseudonyms as I think it makes things more  
complicated.

We are hoping to have the problem solved by the GCA accessions. http://www.ncbi.nlm.nih.gov/projects/genome/assembly/model.shtml

On 1 Jul 2011, at 12:59, Ann Loraine wrote:

> Hi,
>
> I have an answer.
>
> I corresponded with curators at TAIR.
>
> They would like the name of the genome release to be:
>
> TAIR10
>
> Note the letters are all caps and there is no space or underscore  
> separating
> the number and the R.
>
> Quoting Eva Huala, PI of TAIR:
>
> "I prefer to keep using TAIR10 for both the assembly and annotation  
> although
> no changes were made to the assembly for this release."
>
> Sincerely,
>
> Ann Loraine
>
>
> On 7/1/11 5:58 AM, "Dan Staines" <dstaines at ebi.ac.uk> wrote:
>
>> Any news on this? As I've said, I'm happy to make a change, but the
>> window for doing so in the next release is closing rapidly!
>>
>> Many thanks,
>>
>> Dan.
>>
>> On 06/30/2011 02:48 PM, Ann Loraine wrote:
>>> I contacted TAIR to get their input.
>>>
>>> Probably I can give you a final answer as to what name to use  
>>> later on
>>> today.
>>>
>>> Thanks for offering to make the change!
>
> -- 
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750 (office)
> http://www.transvar.org
>
>

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 
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From cpetrach at uvic.ca  Tue Jul  5 17:45:00 2011
From: cpetrach at uvic.ca (Cassandra Petrachenko)
Date: Tue, 5 Jul 2011 14:45:00 -0700
Subject: [Gramene] [bioportal-announce] REMINDER: BioPortal User Survey -
	closes July 15
Message-ID: <CAKuszcC2YikWEmKeaCSM1YokYeKwkf+qOhRdFyPOVURXPXv1Aw@mail.gmail.com>

Dear BioPortal User:

Thanks to everyone who has completed our survey!

The BioPortal User Survey will be open for one more week. If you have a few
minutes and haven't yet provided us with your feedback, we would appreciate
your help: http://www.surveymonkey.com/s/GX77Q5J


Regards,

Cassandra L. Petrachenko
*Research Associate
The CHISEL Group, University of Victoria
http://www.thechiselgroup.org
250-472-5775*



On Thu, Jun 2, 2011 at 3:37 PM, Cassandra Petrachenko <cpetrach at uvic.ca>wrote:

> Dear BioPortal User:
>
> My name is Cassandra and I am a Research Associate working with Dr.
> Margaret-Anne Storey at the University of Victoria, as well as with the NCBO
> project team. My current focus includes the BioPortal suite of tools.
>
> We are trying to understand more about how people use BioPortal, what
> ontologies they work with, and most importantly, what benefits people derive
> from BioPortal. To help with this, we have created a survey consisting of
> nine questions.
>
> If you have a few minutes, we would appreciate your help and ask that you
> complete the following survey:
> http://www.surveymonkey.com/s/GX77Q5J
>
> The survey is anonymous and your responses will be kept confidential. If
> you have any questions, please feel free to contact me directly.
>
>
> Regards,
>
> Cassandra L. Petrachenko
> *Research Associate
> The CHISEL Group, University of Victoria
> http://www.thechiselgroup.org
> 250-472-5775*
>
>
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From whetzel at stanford.edu  Fri Jul  8 21:48:25 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Fri, 8 Jul 2011 18:48:25 -0700
Subject: [Gramene] [bioportal-announce] BioPortal 3.1 Released
Message-ID: <B1A8EFB5-B7FC-4BFB-AF0A-B56603E519B7@stanford.edu>

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 3.1.  New features include updates to the Web interface and Web services:
Support for loading OWL 2 ontologies
Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. 
Browsing of ontologies that contain large numbers of sibling terms
Icons for is_a and part_of  are displayed for OBO format ontologies 
Display of the ?occurs_in? relationship used in the Extended version of the Gene Ontology 
Bug Fix ? Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response


Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org

 

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From whetzel at stanford.edu  Fri Jul 22 14:18:18 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Fri, 22 Jul 2011 11:18:18 -0700
Subject: [Gramene] [bioportal-announce] REMINDER: NCBO User Group Meeting -
	July 25 at 12:00pm PT
Message-ID: <1AA67C11-0BC1-42C0-96B9-30E908535B29@stanford.edu>

The next NCBO User Group Meeting will be held Monday, July 25 at 12:00pm PT. Monday's presentation will be on Bio-Mixer by Lars Grammel from the University of Victoria. 

Bio-Mixer is a web-based mashup environment for exploring biomedical ontologies from the NCBO repository. In the user group meeting, the Bio-Mixer features (e.g. searching for terms, using the graph viewer, using multiple views, storing and sharing workspaces, embedding views into external websites ) will be presented and explained. We are also hoping to elicit requirements and use cases to drive further Bio-Mixer development.

WebEx Details below:
Go to https://stanford.webex.com/stanford/j.php?ED=11067353&UID=481527042&PW=NM2NlMDZhMDI4&RT=MiM0 

Meeting Number: 499 478 073 
Meeting Password: ncbo 

Call-in toll number (US/Canada): 1-650-429-3300 
Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=11067353&tollFree=0 


Look forward to seeing you Monday!
Trish 


Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org

 

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