From huntley at ebi.ac.uk  Wed Mar  9 04:48:34 2011
From: huntley at ebi.ac.uk (Rachael Huntley)
Date: Wed, 09 Mar 2011 09:48:34 +0000
Subject: [Gramene] Use of the 'with' field in the Gramene GAF
Message-ID: <4D774CF2.90909@ebi.ac.uk>

Hello,

I am writing on behalf of the UniProtKB-GOA group at EBI to ask if it 
would it be possible for you to help us with some Gramene gene 
association file questions we have?

We're currently trying to improve the GO annotation we integrate into 
UniProtKB from external MODs, by looking at including the MOD 
identifiers used in the 'with' field (column 8) of externally generated 
annotations; at the moment we ignore any 'with' field data that doesn't 
use a GO identifier or UniProtKB accession, and so integrate these 
annotations into our set with an empty 'with' field, which obviously is 
not ideal.
Therefore we would very much like to include Gramene identifiers that 
match the following regular expressions:

(GR):([A-Z]\d[\d\w]{3}\d)
(GR_PROTEIN):([A-Z]\d[\d\w]{3}\d)

Do these look reasonable to you?

We have come across a couple of errors in the contents of the 'with' 
column of the Gramene gene association file, which I have listed below 
together with the reasons why they have been rejected.

Rejected:
[IPI  GR_protein:O24435]
[IPI  GR_protein:Q2XPP5]
Reason: The accessions shown are UniProtKB accessions and so should have 
a 'UniProtKB:' prefix.

Rejected:
[RCA  UniProt:Q69F95]
Reason:
The 'with' field should not be filled with an RCA annotation.

If you agree with these reasons, would you be able to make the changes 
to your file?

Your help in this is much appreciated.

Best wishes,
Rachael.

-- 
GOA and IntAct Curator
European Bioinformatics Institute
Welcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
UK

Tel: 01223 492515
Fax: 01223 494468
Email: huntley at ebi.ac.uk
GOA: http://www.ebi.ac.uk/GOA
IntAct: http://www.ebi.ac.uk/intact



From jaiswalp at science.oregonstate.edu  Wed Mar  9 14:15:32 2011
From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU))
Date: Wed, 09 Mar 2011 11:15:32 -0800
Subject: [Gramene] Use of the 'with' field in the Gramene GAF
In-Reply-To: <4D774CF2.90909@ebi.ac.uk>
References: <4D774CF2.90909@ebi.ac.uk>
Message-ID: <4D77D1D4.3090508@science.oregonstate.edu>


Rachel,

We will be looking at these issues and the WITH column in subsequent 
releases. Essentially we will be starting to move away from our Uniprot 
based annotation to the respective species genome based annotation, with 
gene/locus being the common denominator. Uniprot IDs would be mapped to 
the gene IDs.

On the other hand we have also realized that we are unable to submit our 
annotations regularly because of the stringency posted by GO annotation 
guidelines on IEAs and now IPI, IEA and RCAs. remember, not every genome 
database especially plants has enough number of hands to do manual 
curation. Now we have many more plant genomes than just the reference. 
Much of the work will remain in the IEA, IEP, IMP and IPI via genome 
scale interactomes.

Pankaj


On 3/9/2011 1:48 AM, Rachael Huntley wrote:
> Hello,
>
> I am writing on behalf of the UniProtKB-GOA group at EBI to ask if it
> would it be possible for you to help us with some Gramene gene
> association file questions we have?
>
> We're currently trying to improve the GO annotation we integrate into
> UniProtKB from external MODs, by looking at including the MOD
> identifiers used in the 'with' field (column 8) of externally generated
> annotations; at the moment we ignore any 'with' field data that doesn't
> use a GO identifier or UniProtKB accession, and so integrate these
> annotations into our set with an empty 'with' field, which obviously is
> not ideal.
> Therefore we would very much like to include Gramene identifiers that
> match the following regular expressions:
>
> (GR):([A-Z]\d[\d\w]{3}\d)
> (GR_PROTEIN):([A-Z]\d[\d\w]{3}\d)
>
> Do these look reasonable to you?
>
> We have come across a couple of errors in the contents of the 'with'
> column of the Gramene gene association file, which I have listed below
> together with the reasons why they have been rejected.
>
> Rejected:
> [IPI GR_protein:O24435]
> [IPI GR_protein:Q2XPP5]
> Reason: The accessions shown are UniProtKB accessions and so should have
> a 'UniProtKB:' prefix.
>
> Rejected:
> [RCA UniProt:Q69F95]
> Reason:
> The 'with' field should not be filled with an RCA annotation.
>
> If you agree with these reasons, would you be able to make the changes
> to your file?
>
> Your help in this is much appreciated.
>
> Best wishes,
> Rachael.
>



From u0044355 at biw.kuleuven.be  Mon Mar 14 14:34:43 2011
From: u0044355 at biw.kuleuven.be (Qiang FU)
Date: Mon, 14 Mar 2011 19:34:43 +0100
Subject: [Gramene] MaizeCyc Feedback: PLEASE TYPE YOUR OWN SUBJECT HERE
Message-ID: <4D7E5FC3.5010303@biw.kuleuven.be>


Please provide your area of interest and pathway feedback

Hello, dear Sir or madam,

Maizecyc website has done a great job to centralize various limited and 
scattered pathway information available for maize.
As for our on going research project, we are very interested in obtain 
and using the maize pathway information gathered on your site.
When we followed the link below to try to download the data.

ftp://ftp.gramene.org/pub/gramene/pathways/maizecyc/

however we could not find the data in Pathway Tools' tabular plain text 
format. 
(http://bioinformatics.ai.sri.com/ptools/flatfile-format.html#Tabular)
Hence, could you kindly provide the data in this format to be downloaded 
from your ftp? Your help will be highly appreciated.

Many thanks in advances and have a nice day.

-- 
Qiang FU
------------------------------------------
Centre of Microbial and Plant Genetics,
Katholieke Universiteit Leuven,
Kasteelpark Arenberg 20,
3001 Heverlee,
Belgium
qiang.fu at esat.kuleuven.be
Tel: +32 016 329686



From huntley at ebi.ac.uk  Wed Mar 16 07:16:30 2011
From: huntley at ebi.ac.uk (Rachael Huntley)
Date: Wed, 16 Mar 2011 11:16:30 +0000
Subject: [Gramene] Use of the 'with' field in the Gramene GAF
In-Reply-To: <4D77D1D4.3090508@science.oregonstate.edu>
References: <4D774CF2.90909@ebi.ac.uk>
	<4D77D1D4.3090508@science.oregonstate.edu>
Message-ID: <4D809C0E.6020503@ebi.ac.uk>

Hi Pankaj,

Sorry for the delay in responding. Thank you for letting us know your 
plans regarding your upcoming change to using gene/locus instead of 
UniProtKB accessions.

I'm sorry that you have been having problems with submitting your GO 
annotations, I'm not sure why this would be the case, so could you 
please give me some more details about what specific problems you have 
been facing and maybe we can assist you further. We are trying to 
improve our electronic annotation pipelines so that species that do not 
have resources for manual curation will be catered for, so this is 
something we are aware of and, hopefully, will be able to continually 
improve.

Best wishes,
Rachael.

On 09/03/2011 19:15, Pankaj Jaiswal (OSU) wrote:
>
> Rachel,
>
> We will be looking at these issues and the WITH column in subsequent 
> releases. Essentially we will be starting to move away from our 
> Uniprot based annotation to the respective species genome based 
> annotation, with gene/locus being the common denominator. Uniprot IDs 
> would be mapped to the gene IDs.
>
> On the other hand we have also realized that we are unable to submit 
> our annotations regularly because of the stringency posted by GO 
> annotation guidelines on IEAs and now IPI, IEA and RCAs. remember, not 
> every genome database especially plants has enough number of hands to 
> do manual curation. Now we have many more plant genomes than just the 
> reference. Much of the work will remain in the IEA, IEP, IMP and IPI 
> via genome scale interactomes.
>
> Pankaj
>
>
> On 3/9/2011 1:48 AM, Rachael Huntley wrote:
>> Hello,
>>
>> I am writing on behalf of the UniProtKB-GOA group at EBI to ask if it
>> would it be possible for you to help us with some Gramene gene
>> association file questions we have?
>>
>> We're currently trying to improve the GO annotation we integrate into
>> UniProtKB from external MODs, by looking at including the MOD
>> identifiers used in the 'with' field (column 8) of externally generated
>> annotations; at the moment we ignore any 'with' field data that doesn't
>> use a GO identifier or UniProtKB accession, and so integrate these
>> annotations into our set with an empty 'with' field, which obviously is
>> not ideal.
>> Therefore we would very much like to include Gramene identifiers that
>> match the following regular expressions:
>>
>> (GR):([A-Z]\d[\d\w]{3}\d)
>> (GR_PROTEIN):([A-Z]\d[\d\w]{3}\d)
>>
>> Do these look reasonable to you?
>>
>> We have come across a couple of errors in the contents of the 'with'
>> column of the Gramene gene association file, which I have listed below
>> together with the reasons why they have been rejected.
>>
>> Rejected:
>> [IPI GR_protein:O24435]
>> [IPI GR_protein:Q2XPP5]
>> Reason: The accessions shown are UniProtKB accessions and so should have
>> a 'UniProtKB:' prefix.
>>
>> Rejected:
>> [RCA UniProt:Q69F95]
>> Reason:
>> The 'with' field should not be filled with an RCA annotation.
>>
>> If you agree with these reasons, would you be able to make the changes
>> to your file?
>>
>> Your help in this is much appreciated.
>>
>> Best wishes,
>> Rachael.
>>


-- 
GOA and IntAct Curator
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
UK

Tel: 01223 492515
Fax: 01223 494468
Email: huntley at ebi.ac.uk
GOA: http://www.ebi.ac.uk/GOA
IntAct: http://www.ebi.ac.uk/intact



From whetzel at stanford.edu  Fri Mar 18 21:24:35 2011
From: whetzel at stanford.edu (Trish Whetzel)
Date: Fri, 18 Mar 2011 18:24:35 -0700
Subject: [Gramene] [bioportal-announce] ALERT: Change in Annotator Value
Message-ID: <543876F6-567D-49B4-90A0-D060D5B0ED86@stanford.edu>

Dear Annotator Users,

We plan to change a value for the XML element <contextName> from ISA_CLOSURE to CLOSURE on Wednesday, March 23. This change is in preparation for including traversal of the part_of hierarchy specified in OBO format ontologies.  

Trish
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