From cpetrach at uvic.ca  Thu Jun  2 18:37:33 2011
From: cpetrach at uvic.ca (Cassandra Petrachenko)
Date: Thu, 2 Jun 2011 15:37:33 -0700
Subject: [Gramene] [bioportal-announce] BioPortal User Survey
Message-ID: <BANLkTim2RBH5Y1X3D=W2gefav4upCvbFJA@mail.gmail.com>

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 Jun  3 11:21:19 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Fri, 3 Jun 2011 08:21:19 -0700
Subject: [Gramene] [bioportal-announce] BioPortal 3.0.1 Released
Message-ID: <97DCE1E0-0E1F-48C1-B043-DB91BC84AE07@stanford.edu>

We have released a patch update to fix an error in calculating metrics for OWL ontologies related to the number of classes that do not specify an author or definition property. In calculating these metrics, we use as defaults http://www.w3.org/2004/02/skos/core#definition and http://purl.org/dc/elements/1.1/creator. If your ontology uses different properties for this content, login to BioPortal and use the "Administer" link for your ontology to update this information. For any questions, email support at bioontology.org.

Best, 
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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From Julie.Leonard at SYNGENTA.COM  Mon Jun  6 13:13:41 2011
From: Julie.Leonard at SYNGENTA.COM (Julie.Leonard at SYNGENTA.COM)
Date: Mon, 6 Jun 2011 13:13:41 -0400
Subject: [Gramene] release date for version 2 release of MaizeCyc
Message-ID: <E6E983882972D447AF74D38898C1996310506E40D2@USETCMSXMB02.NAFTA.SYNGENTA.ORG>

Hi.  I'm writing to find out when you plan to deliver MaizeCyc version 2 (corresponding to genome version 5b.60).

Thanks,
Julie Leonard



message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. 
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From mmonaco at cshl.edu  Tue Jun  7 08:06:26 2011
From: mmonaco at cshl.edu (Monaco, Marcela)
Date: Tue, 7 Jun 2011 12:06:26 +0000
Subject: [Gramene] release date for version 2 release of MaizeCyc
In-Reply-To: <E6E983882972D447AF74D38898C1996310506E40D2@USETCMSXMB02.NAFTA.SYNGENTA.ORG>
References: <E6E983882972D447AF74D38898C1996310506E40D2@USETCMSXMB02.NAFTA.SYNGENTA.ORG>
Message-ID: <63413FB2-5C0C-4801-8991-3B3C0175EECF@cshl.edu>

Dear Julie,

I hope we are ready to release maizecyc within the next couple of weeks.  If you like, I could load the latest version we have available on our dev site. Inferred pathways are not likely to change very much, but the version is definitely not yet final.

Marcela



On Jun 6, 2011, at 1:19 PM, <Julie.Leonard at SYNGENTA.COM<mailto:Julie.Leonard at SYNGENTA.COM>>
 <Julie.Leonard at SYNGENTA.COM<mailto:Julie.Leonard at SYNGENTA.COM>> wrote:

Hi.  I?m writing to find out when you plan to deliver MaizeCyc version 2 (corresponding to genome version 5b.60).

Thanks,
Julie Leonard


________________________________
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. _______________________________________________
Gramene mailing list
Gramene at brie4.cshl.edu<mailto:Gramene at brie4.cshl.edu>
http://mail.gramene.org/mailman/listinfo/gramene




From whetzel at stanford.edu  Fri Jun 17 19:28:17 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Fri, 17 Jun 2011 16:28:17 -0700
Subject: [Gramene] [bioportal-announce] REMINDER: API Key requirement for
	NCBO Web services
Message-ID: <B938EB86-96E7-4F7A-B374-FD9F7B86CB6A@stanford.edu>

This is a reminder that the apikey parameter will be required at the end of June for all NCBO Web service calls. To obtain your API Key, login to BioPortal and go to your Account page where your API Key will be displayed. Web service calls that do not include the apikey parameter and a valid API key will no longer work after June. For more information on how to include this parameter within your Web service calls, see the NCBO Wiki [1]. 

Trish 

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services


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 nkaplin1 at swarthmore.edu  Tue Jun 21 22:07:32 2011
From: nkaplin1 at swarthmore.edu (Nick Kaplinsky)
Date: Tue, 21 Jun 2011 22:07:32 -0400 (EDT)
Subject: [Gramene] PLINK file information
In-Reply-To: <114900487.93536.1308708082495.JavaMail.root@zmmbox1.swarthmore.edu>
Message-ID: <115145458.93562.1308708452106.JavaMail.root@zmmbox1.swarthmore.edu>

Dear Gramene - 

I have downloaded the Arabidopsis diversity files in PLINK format.  In the PED files contained in each PLINK download each line represents a single ecotype with the ecotype specified in the second column.  For some of the PLINK files (i.e. the SNP discovery file) the ecotypes are described clearly as Col-O or Ler, for example.  For the other PLINK downloads the ecotypes are coded - for instance in the dbSNP file the ecotypes are numbered from 785 to 801.  For the PLINK files where the ecotype is not clear, how do I figure out which line refers to which ecotype?

Thanks in advance for your help,

Nick


From whetzel at stanford.edu  Fri Jun 24 13:52:21 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Fri, 24 Jun 2011 10:52:21 -0700
Subject: [Gramene] [bioportal-announce] REMINDER: NCBO User Group Webinar -
	June 27 at 12:00pm PT
Message-ID: <B15B661D-424E-4DDF-96BD-1801B9B76ADA@stanford.edu>

The next NCBO User Group Webinar will be held June 27 at 12:00pm PT and will focus on the Notes feature. 

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 
Access code:499 478 073  
Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=11067353&tollFree=0 


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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From jw12 at sanger.ac.uk  Tue Jun 28 08:46:35 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Tue, 28 Jun 2011 13:46:35 +0100
Subject: [Gramene] Old versions?
Message-ID: <9D78F272-D09E-4342-8A1A-EE9A75FF3616@sanger.ac.uk>

Hi

Do you still host old versions of gramene? if so where are they?
More specifically the DAS sources for say TAIR 9...7etc rather than  
TAIR 10? If they exist I can register them with the DAS Registry and  
they maybe useful for the DAS community and researchers?

Thanks in advance

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. 


From aloraine at uncc.edu  Tue Jun 28 10:26:33 2011
From: aloraine at uncc.edu (Loraine, Ann)
Date: Tue, 28 Jun 2011 10:26:33 -0400
Subject: [Gramene] TAIR9 vs TAIR10 - mixup on naming, was: RE: Old versions?
References: <9D78F272-D09E-4342-8A1A-EE9A75FF3616@sanger.ac.uk>
Message-ID: <8675A2F402711742A5D8AA8689D0068985B953@EXEVS02.its.uncc.edu>

Greetings all,

There is some confusion about the meaning of TAIR9 versus TAIR10.

TAIR9 is both a genome assembly release and a genome annotation release, meaning: it includes both new sequences for Arabidopsis chromosomes and some revised gene models.

TAIR10 is a genome annotation release only. The chromosomes did not change from TAIR9 to TAIR10 according to this README file:

ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/README_whole_chromosomes.txt

quote*Please note that the chromosome files have NOT CHANGED FROM TAIR9 to TAIR10*unquote

Thus, the gene structure annotations released in TAIR10 are using the same reference sequence as the gene structure annotations released with TAIR9.

I've noticed the DAS registry contains both TAIR9 and TAIR10 as reference assembles and that some data sets (looks like alignments) are referencing TAIR10 chromosomes. This is incorrect as there is no TAIR10 genome assembly. 

Also, I would like to suggest using a different term for the TAIR9 assembly in order to avoid future confusion. Please use the term: A_thaliana_Jun_2009. This is what we are using to designate this genome assembly in the Integrated Genome Browser QuickLoad and DAS systems. It would be great if the DAS registry could either recognize this as a synonym for TAIR9 or use this term instead so that people will not continue to be confused about the meaning of TAIR*.

Best wishes,

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



-----Original Message-----
From: Jonathan Warren [mailto:jw12 at sanger.ac.uk]
Sent: Tue 6/28/2011 8:46 AM
To: gramene at gramene.org
Subject: Old versions?
 
Hi

Do you still host old versions of gramene? if so where are they?
More specifically the DAS sources for say TAIR 9...7etc rather than  
TAIR 10? If they exist I can register them with the DAS Registry and  
they maybe useful for the DAS community and researchers?

Thanks in advance

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 jw12 at sanger.ac.uk  Tue Jun 28 12:13:32 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Tue, 28 Jun 2011 17:13:32 +0100
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming,
	was: RE: Old versions?
In-Reply-To: <8675A2F402711742A5D8AA8689D0068985B953@EXEVS02.its.uncc.edu>
References: <9D78F272-D09E-4342-8A1A-EE9A75FF3616@sanger.ac.uk>
	<8675A2F402711742A5D8AA8689D0068985B953@EXEVS02.its.uncc.edu>
Message-ID: <C9AD6A79-8DD1-4CD7-B2A6-0B211F0719C4@sanger.ac.uk>

Hi

The DAS Registry automatically takes it's information from the gramene  
DAS sources document http://dev.gramene.org/gramenedas/das/sources. If  
the reference coordinates are the same then the coordinate system  
should remain as TAIR 9. However if there are new sequences added then  
new entry_points need to be added to a the DAS reference sources. If  
the gramene sources document reverts to TAIR 9 then the registry will  
automatically reflect this. As all the data sources using the TAIR 10  
coordinate system are gramenes no other problems should arise.

On 28 Jun 2011, at 15:26, Loraine, Ann wrote:

> Greetings all,
>
> There is some confusion about the meaning of TAIR9 versus TAIR10.
>
> TAIR9 is both a genome assembly release and a genome annotation  
> release, meaning: it includes both new sequences for Arabidopsis  
> chromosomes and some revised gene models.
>
> TAIR10 is a genome annotation release only. The chromosomes did not  
> change from TAIR9 to TAIR10 according to this README file:
>
> ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/README_whole_chromosomes.txt
>
> quote*Please note that the chromosome files have NOT CHANGED FROM  
> TAIR9 to TAIR10*unquote
>
> Thus, the gene structure annotations released in TAIR10 are using  
> the same reference sequence as the gene structure annotations  
> released with TAIR9.
>
> I've noticed the DAS registry contains both TAIR9 and TAIR10 as  
> reference assembles and that some data sets (looks like alignments)  
> are referencing TAIR10 chromosomes. This is incorrect as there is no  
> TAIR10 genome assembly.
>
> Also, I would like to suggest using a different term for the TAIR9  
> assembly in order to avoid future confusion. Please use the term:  
> A_thaliana_Jun_2009. This is what we are using to designate this  
> genome assembly in the Integrated Genome Browser QuickLoad and DAS  
> systems. It would be great if the DAS registry could either  
> recognize this as a synonym for TAIR9 or use this term instead so  
> that people will not continue to be confused about the meaning of  
> TAIR*.
>
> Best wishes,
>
> Ann Loraine
> ____________________
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
>
>
>
> -----Original Message-----
> From: Jonathan Warren [mailto:jw12 at sanger.ac.uk]
> Sent: Tue 6/28/2011 8:46 AM
> To: gramene at gramene.org
> Subject: Old versions?
>
> Hi
>
> Do you still host old versions of gramene? if so where are they?
> More specifically the DAS sources for say TAIR 9...7etc rather than
> TAIR 10? If they exist I can register them with the DAS Registry and
> they maybe useful for the DAS community and researchers?
>
> Thanks in advance
>
> 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.
>
>

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 whetzel at stanford.edu  Tue Jun 28 12:32:04 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Tue, 28 Jun 2011 09:32:04 -0700
Subject: [Gramene] [bioportal-announce] Call for Participation: Last chance
	for advance registration for International Conference on
	Biomedical Ontology
Message-ID: <3A159EE4-7576-4311-A77B-30D56C4FD3F4@stanford.edu>

This year's ICBO conference will take place in Buffalo NY from July 28 to 30. The program of the conference and of the co-located workshops and tutorials is now complete.
  
Full details are available at http://icbo.buffalo.edu.

Please note that the advance registration discount is available only until July 1 and that there are limited places available.


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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From aloraine at uncc.edu  Tue Jun 28 14:02:39 2011
From: aloraine at uncc.edu (Ann Loraine)
Date: Tue, 28 Jun 2011 14:02:39 -0400
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming,
	was: RE: Old versions?
In-Reply-To: <C9AD6A79-8DD1-4CD7-B2A6-0B211F0719C4@sanger.ac.uk>
Message-ID: <CA2F8F7F.9A1E%aloraine@uncc.edu>

Okay, it sounds like gramene needs to correct this.

Probably the person at gramene who downloaded the Arabidopsis data wasn?t
aware that TAIR10 is really the same assembly as TAIR9. A lot of people get
confused about this. Or, they might have checked the actual data and
discovered a difference, despite what the documentation says.

Jonathan, since you are already providing validation services, could you
also provide some additional sanity checking of the data?

In this case, you could write something that determines whether two
reference assemblies with different names are in fact the same.

In addition, you could write something else that checks that two DAS sources
that serve the same genome sequence assemblies are indeed delivering the
same data. Confusion could easily arise if one source is delivering masked
sequence data but another one isn?t.

Best,

Ann

On 6/28/11 12:13 PM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:

> Hi
> 
> The DAS Registry automatically takes it's information from the gramene DAS
> sources document http://dev.gramene.org/gramenedas/das/sources. If the
> reference coordinates are the same then the coordinate system should remain as
> TAIR 9. However if there are new sequences added then new entry_points need to
> be added to a the DAS reference sources. If the gramene sources document
> reverts to TAIR 9 then the registry will automatically reflect this. As all
> the data sources using the TAIR 10 coordinate system are gramenes no other
> problems should arise.
> 
> On 28 Jun 2011, at 15:26, Loraine, Ann wrote:
> 
>>  
>>  
>> 
>> Greetings all,
>>  
>>  There is some confusion about the meaning of TAIR9 versus TAIR10.
>>  
>>  TAIR9 is both a genome assembly release and a genome annotation release,
>> meaning: it includes both new sequences for Arabidopsis chromosomes and some
>> revised gene models.
>>  
>>  TAIR10 is a genome annotation release only. The chromosomes did not change
>> from TAIR9 to TAIR10 according to this README file:
>>  
>>  
>> ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/README_whole_
>> chromosomes.txt
>>  
>>  quote*Please note that the chromosome files have NOT CHANGED FROM TAIR9 to
>> TAIR10*unquote
>>  
>>  Thus, the gene structure annotations released in TAIR10 are using the same
>> reference sequence as the gene structure annotations released with TAIR9.
>>  
>>  I've noticed the DAS registry contains both TAIR9 and TAIR10 as reference
>> assembles and that some data sets (looks like alignments) are referencing
>> TAIR10 chromosomes. This is incorrect as there is no TAIR10 genome assembly.
>>  
>>  Also, I would like to suggest using a different term for the TAIR9 assembly
>> in order to avoid future confusion. Please use the term: A_thaliana_Jun_2009.
>> This is what we are using to designate this genome assembly in the Integrated
>> Genome Browser QuickLoad and DAS systems. It would be great if the DAS
>> registry could either recognize this as a synonym for TAIR9 or use this term
>> instead so that people will not continue to be confused about the meaning of
>> TAIR*.
>>  
>>  Best wishes,
>>  
>>  Ann Loraine
>>  ____________________
>>  Ann Loraine
>>  Associate Professor
>>  Dept. of Bioinformatics and Genomics, UNCC
>>  North Carolina Research Campus
>>  600 Laureate Way
>>  Kannapolis, NC 28081
>>  704-250-5750
>>  www.transvar.org <http://www.transvar.org>
>>  
>>  
>>  
>>  -----Original Message-----
>>  From: Jonathan Warren [mailto:jw12 at sanger.ac.uk]
>>  Sent: Tue 6/28/2011 8:46 AM
>>  To: gramene at gramene.org
>>  Subject: Old versions?
>>  
>>  Hi
>>  
>>  Do you still host old versions of gramene? if so where are they?
>>  More specifically the DAS sources for say TAIR 9...7etc rather than
>>  TAIR 10? If they exist I can register them with the DAS Registry and
>>  they maybe useful for the DAS community and researchers?
>>  
>>  Thanks in advance
>>  
>>  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.
>>  
>>   
>>  
>>  
> 
>  
> 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.
> 

-- 
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


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From wspooner at cshl.edu  Wed Jun 29 12:26:00 2011
From: wspooner at cshl.edu (Spooner, Will)
Date: Wed, 29 Jun 2011 16:26:00 +0000
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming,	was: RE: Old
	versions?
In-Reply-To: <CA2F8F7F.9A1E%aloraine@uncc.edu>
References: <CA2F8F7F.9A1E%aloraine@uncc.edu>
Message-ID: <19996E93-DE27-469F-BCA2-71A3F5888334@cshl.edu>

Hi Ann, Jonathan,

Genome assembly names cause us endless problems, and we only look after a few of them!  

Ann; you would like us to use 'A_thaliana_Jun_2009' as the assembly name? If so I will patch the databases, and we will also need Dan Staines to do the same over at Ensembl Genomes.

Jonathan; as an 'independent' who has an interest in such things, what would your preference for assembly naming conventions be? Are there standards groups already considering this problem?

Best,

Will

On 28 Jun 2011, at 19:10, Ann Loraine wrote:

> Okay, it sounds like gramene needs to correct this. 
> 
> Probably the person at gramene who downloaded the Arabidopsis data wasn?t aware that TAIR10 is really the same assembly as TAIR9. A lot of people get confused about this. Or, they might have checked the actual data and discovered a difference, despite what the documentation says.
> 
> Jonathan, since you are already providing validation services, could you also provide some additional sanity checking of the data?
> 
> In this case, you could write something that determines whether two reference assemblies with different names are in fact the same.
> 
> In addition, you could write something else that checks that two DAS sources that serve the same genome sequence assemblies are indeed delivering the same data. Confusion could easily arise if one source is delivering masked sequence data but another one isn?t. 
> 
> Best,
> 
> Ann
> 
> On 6/28/11 12:13 PM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:
> 
>> Hi
>> 
>> The DAS Registry automatically takes it's information from the gramene DAS sources document http://dev.gramene.org/gramenedas/das/sources. If the reference coordinates are the same then the coordinate system should remain as TAIR 9. However if there are new sequences added then new entry_points need to be added to a the DAS reference sources. If the gramene sources document reverts to TAIR 9 then the registry will automatically reflect this. As all the data sources using the TAIR 10 coordinate system are gramenes no other problems should arise.
>> 
>> On 28 Jun 2011, at 15:26, Loraine, Ann wrote:
>> 
>>> 
>>>  
>>> 
>>> Greetings all,
>>>  
>>>  There is some confusion about the meaning of TAIR9 versus TAIR10.
>>>  
>>>  TAIR9 is both a genome assembly release and a genome annotation release, meaning: it includes both new sequences for Arabidopsis chromosomes and some revised gene models.
>>>  
>>>  TAIR10 is a genome annotation release only. The chromosomes did not change from TAIR9 to TAIR10 according to this README file:
>>>  
>>>  ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/README_whole_chromosomes.txt
>>>  
>>>  quote*Please note that the chromosome files have NOT CHANGED FROM TAIR9 to TAIR10*unquote
>>>  
>>>  Thus, the gene structure annotations released in TAIR10 are using the same reference sequence as the gene structure annotations released with TAIR9.
>>>  
>>>  I've noticed the DAS registry contains both TAIR9 and TAIR10 as reference assembles and that some data sets (looks like alignments) are referencing TAIR10 chromosomes. This is incorrect as there is no TAIR10 genome assembly.
>>>  
>>>  Also, I would like to suggest using a different term for the TAIR9 assembly in order to avoid future confusion. Please use the term: A_thaliana_Jun_2009. This is what we are using to designate this genome assembly in the Integrated Genome Browser QuickLoad and DAS systems. It would be great if the DAS registry could either recognize this as a synonym for TAIR9 or use this term instead so that people will not continue to be confused about the meaning of TAIR*.
>>>  
>>>  Best wishes,
>>>  
>>>  Ann Loraine
>>>  ____________________
>>>  Ann Loraine
>>>  Associate Professor
>>>  Dept. of Bioinformatics and Genomics, UNCC
>>>  North Carolina Research Campus
>>>  600 Laureate Way
>>>  Kannapolis, NC 28081
>>>  704-250-5750
>>>  www.transvar.org <http://www.transvar.org> 
>>>  
>>>  
>>>  
>>>  -----Original Message-----
>>>  From: Jonathan Warren [mailto:jw12 at sanger.ac.uk]
>>>  Sent: Tue 6/28/2011 8:46 AM
>>>  To: gramene at gramene.org
>>>  Subject: Old versions?
>>>  
>>>  Hi
>>>  
>>>  Do you still host old versions of gramene? if so where are they?
>>>  More specifically the DAS sources for say TAIR 9...7etc rather than 
>>>  TAIR 10? If they exist I can register them with the DAS Registry and 
>>>  they maybe useful for the DAS community and researchers?
>>>  
>>>  Thanks in advance
>>>  
>>>  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.
>>>  
>>>   
>>>  
>>>  
>> 
>>  
>> 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. 
>> 
> 
> -- 
> 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
> 
> _______________________________________________
> Gramene mailing list
> Gramene at brie4.cshl.edu
> http://mail.gramene.org/mailman/listinfo/gramene

William Spooner
wspooner at cshl.edu






From richard.sibout at versailles.inra.fr  Wed Jun 29 05:56:08 2011
From: richard.sibout at versailles.inra.fr (Richard Sibout)
Date: Wed, 29 Jun 2011 11:56:08 +0200
Subject: [Gramene] Brachypodium Workshop
Message-ID: <4E0AF6B8.2090407@versailles.inra.fr>

Dear webmasters and developers,

We would appreciate if you could advertize this workshop on your 
website. The "European Brachypodium Workshop" is open for registration at
>
> https://colloque.inra.fr/1st_european_brachypodium_workshop
>
This workshop is devoted to the use of Brachypodiumin plant biology as a 
model for grasses. The goal of this workshop is to bring together 
theBrachypodium community but also researchers interested in comparative 
genomics. Participants are invited to communicate on research but also 
to address relevant scientific question and technical problems with 
Brachypodium and other grasses.Themeeting will cover a large panel of 
plant biology: genetic transformation,physiology, germplasm and stock 
center, natural variation, database, molecular and bioinformatics 
tools...etc
> The workshop will be held at INRA in Versailles (France) from October 
> 19th to 21th (2011).
> Registrations and abstract submissions will end July 31th.
> Do not hesitate to communicate this email and to contact us for any 
> questions,
> We hope to see you in Versailles,
Please find flyers and poster in attachment,
> All the best,
>
> The Organizing Committee,
-- 

Richard Sibout
Institut Jean-Pierre Bourgin
UMR1318 INRA-AgroParisTech
Phone : 0033(1)30833065
Fax : 0033(1)30833099
http://www-ijpb.versailles.inra.fr/
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

European Brachypodium Workshop:
https://colloque.inra.fr/1st_european_brachypodium_workshop  



-- 

Richard Sibout
Institut Jean-Pierre Bourgin
UMR1318 INRA-AgroParisTech
Phone : 0033(1)30833065
Fax : 0033(1)30833099
http://www-ijpb.versailles.inra.fr/
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

European Brachypodium Workshop:
https://colloque.inra.fr/1st_european_brachypodium_workshop

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From dstaines at ebi.ac.uk  Thu Jun 30 06:33:29 2011
From: dstaines at ebi.ac.uk (Dan Staines)
Date: Thu, 30 Jun 2011 11:33:29 +0100
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming,	was: RE: Old
	versions?
In-Reply-To: <19996E93-DE27-469F-BCA2-71A3F5888334@cshl.edu>
References: <CA2F8F7F.9A1E%aloraine@uncc.edu>
	<19996E93-DE27-469F-BCA2-71A3F5888334@cshl.edu>
Message-ID: <4E0C50F9.7070402@ebi.ac.uk>


> Genome assembly names cause us endless problems, and we only look after a few of them!

Seconded from my end...

> Ann; you would like us to use 'A_thaliana_Jun_2009' as the assembly name? If so I will patch the databases, and we will also need Dan Staines to do the same over at Ensembl Genomes.
>
> Jonathan; as an 'independent' who has an interest in such things, what would your preference for assembly naming conventions be? Are there standards groups already considering this problem?

If someone can tell me a definitive assembly name to use, I'll be able 
to make the change, though the window for doing this in time for our 
next release (currently 12th July) is very tight.

Cheers,

Dan.

-- 
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  Thu Jun 30 09:48:32 2011
From: aloraine at uncc.edu (Ann Loraine)
Date: Thu, 30 Jun 2011 09:48:32 -0400
Subject: [Gramene] Re: TAIR9 vs TAIR10 - mixup on naming, was: RE: Old
	versions?
In-Reply-To: <4E0C50F9.7070402@ebi.ac.uk>
Message-ID: <CA31F6F0.9AC4%aloraine@uncc.edu>

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


On 6/30/11 6:33 AM, "Dan Staines" <dstaines at ebi.ac.uk> wrote:

> 
>> Genome assembly names cause us endless problems, and we only look after a few
>> of them!
> 
> Seconded from my end...
> 
>> Ann; you would like us to use 'A_thaliana_Jun_2009' as the assembly name? If
>> so I will patch the databases, and we will also need Dan Staines to do the
>> same over at Ensembl Genomes.
>> 
>> Jonathan; as an 'independent' who has an interest in such things, what would
>> your preference for assembly naming conventions be? Are there standards
>> groups already considering this problem?
> 
> If someone can tell me a definitive assembly name to use, I'll be able
> to make the change, though the window for doing this in time for our
> next release (currently 12th July) is very tight.
> 
> Cheers,
> 
> Dan.

-- 
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




