From kottearachchins at yahoo.com  Sat Jan 19 08:24:09 2013
From: kottearachchins at yahoo.com (Kottearachchi Ns)
Date: Sat, 19 Jan 2013 05:24:09 -0800 (PST)
Subject: [Gramene] Fw: Re: [Gramene-dev] Live Site Feedback: let us know how
	to get the sequence of Rice SSR markers
Message-ID: <1358601849.25756.YahooMailClassic@web120302.mail.ne1.yahoo.com>



--- On Tue, 15/1/13, Kottearachchi Ns <kottearachchins at yahoo.com> wrote:

From: Kottearachchi Ns <kottearachchins at yahoo.com>
Subject: Re: [Gramene-dev] Live Site Feedback: let us know how to get the sequence of Rice SSR markers
To: "Pankaj Jaiswal" <jaiswalp at science.oregonstate.edu>
Received: Tuesday, 15 January, 2013, 8:51 AM






Dear Sir,?
?
Thank you very mch for the reply. Earlier (about one month back)??we were able to get any sequence of rice SSR from the link that you sent for us. But now primer?sequences are not?available???for those markers. As I remember, sequences were available in "Associations". But "Association" is not accessible.?For example I cannot receive the ?Rm242,? Rm500,? RM 7643, RM 24330 etc. So please be kind enough to look into this mater to rectify this problem as we cannot
 proceed our research without sequences. 
Thanks
?
Sincerely
?
Nisha Kottearachchi, PhD
Wayamba University of Sri Lanka

--- On Sun, 6/1/13, Pankaj Jaiswal <jaiswalp at science.oregonstate.edu> wrote:


From: Pankaj Jaiswal <jaiswalp at science.oregonstate.edu>
Subject: Re: [Gramene-dev] Live Site Feedback: let us know how to get the sequence of Rice SSR markers
To: kottearachchins at yahoo.com, gramene-dev at gramene.org
Cc: possible_feedback at www.gramene.org
Received: Sunday, 6 January, 2013, 11:26 PM


Please get it from
http://www.gramene.org/markers/microsat/

The link is available from the SSR Markers resource link on the webpage 
http://www.gramene.org/markers/

Sincerely
Pankaj

On 1/6/2013 3:01 PM, possible_feedback at www.gramene.org wrote:
> URL? ? ? ???: http://www.gramene.org/index.html
>
> Subject? ???: Live Site Feedback: let us know how to get the sequence of Rice SSR markers
>
> Name? ? ? ? : Dr. Nisha Kottearachchi
>
> Email? ? ???: kottearachchins at yahoo.com
>
>
 Organization: Wayamba University of Sri Lanka
>
> Comments? ? :
>
> Dear Sir,
>
> We are very much grateful, if you can let us know how to get the sequence of Rice SSR markers. we found that we cannot retrieve most of the primer sequences that were retrieved some time back.
>
> Thank you.
> Sincerely
> Dr. Nisha Kottearachchi
> Wayamba University of Sri Lanka
>
> http://www.warelab.org/bugs/view.php?id=4505
>
>
> _______________________________________________
> Gramene-dev mailing list
> Gramene-dev at gramene.org
> http://mail.gramene.org/mailman/listinfo/gramene-dev
>
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From amarasiv at science.oregonstate.edu  Sat Jan 19 19:05:28 2013
From: amarasiv at science.oregonstate.edu (amarasiv at science.oregonstate.edu)
Date: Sat, 19 Jan 2013 16:05:28 -0800
Subject: [Gramene] Fw: Re: [Gramene-dev] Live Site Feedback: let us know
 how to get the sequence of Rice SSR markers
In-Reply-To: <1358601849.25756.YahooMailClassic@web120302.mail.ne1.yahoo.com>
References: <1358601849.25756.YahooMailClassic@web120302.mail.ne1.yahoo.com>
Message-ID: <20130119160528.85257ria5izmznpc@webmail.oregonstate.edu>

Hello Nisha,

The primer sequences you are looking for can be found at

http://www.gramene.org/markers/microsat/ssr.html

regards,


Vindhya Amarasinghe
Curator
Gramene.org














Quoting Kottearachchi Ns <kottearachchins at yahoo.com>:

>
>
> --- On Tue, 15/1/13, Kottearachchi Ns <kottearachchins at yahoo.com> wrote:
>
> From: Kottearachchi Ns <kottearachchins at yahoo.com>
> Subject: Re: [Gramene-dev] Live Site Feedback: let us know how to  
> get the sequence of Rice SSR markers
> To: "Pankaj Jaiswal" <jaiswalp at science.oregonstate.edu>
> Received: Tuesday, 15 January, 2013, 8:51 AM
>
>
>
>
>
>
> Dear Sir,?
> ?
> Thank you very mch for the reply. Earlier (about one month back)??we  
> were able to get any sequence of rice SSR from the link that you  
> sent for us. But now primer?sequences are not?available???for those  
> markers. As I remember, sequences were available in "Associations".  
> But "Association" is not accessible.?For example I cannot receive  
> the ?Rm242,? Rm500,? RM 7643, RM 24330 etc. So please be kind enough  
> to look into this mater to rectify this problem as we cannot
>  proceed our research without sequences.
> Thanks
> ?
> Sincerely
> ?
> Nisha Kottearachchi, PhD
> Wayamba University of Sri Lanka
>
> --- On Sun, 6/1/13, Pankaj Jaiswal <jaiswalp at science.oregonstate.edu> wrote:
>
>
> From: Pankaj Jaiswal <jaiswalp at science.oregonstate.edu>
> Subject: Re: [Gramene-dev] Live Site Feedback: let us know how to  
> get the sequence of Rice SSR markers
> To: kottearachchins at yahoo.com, gramene-dev at gramene.org
> Cc: possible_feedback at www.gramene.org
> Received: Sunday, 6 January, 2013, 11:26 PM
>
>
> Please get it from
> http://www.gramene.org/markers/microsat/
>
> The link is available from the SSR Markers resource link on the webpage
> http://www.gramene.org/markers/
>
> Sincerely
> Pankaj
>
> On 1/6/2013 3:01 PM, possible_feedback at www.gramene.org wrote:
>> URL? ? ? ???: http://www.gramene.org/index.html
>>
>> Subject? ???: Live Site Feedback: let us know how to get the  
>> sequence of Rice SSR markers
>>
>> Name? ? ? ? : Dr. Nisha Kottearachchi
>>
>> Email? ? ???: kottearachchins at yahoo.com
>>
>>
>  Organization: Wayamba University of Sri Lanka
>>
>> Comments? ? :
>>
>> Dear Sir,
>>
>> We are very much grateful, if you can let us know how to get the  
>> sequence of Rice SSR markers. we found that we cannot retrieve most  
>> of the primer sequences that were retrieved some time back.
>>
>> Thank you.
>> Sincerely
>> Dr. Nisha Kottearachchi
>> Wayamba University of Sri Lanka
>>
>> http://www.warelab.org/bugs/view.php?id=4505
>>
>>
>> _______________________________________________
>> Gramene-dev mailing list
>> Gramene-dev at gramene.org
>> http://mail.gramene.org/mailman/listinfo/gramene-dev
>>
>



From lf259 at cornell.edu  Mon Jan 28 11:54:00 2013
From: lf259 at cornell.edu (Leila Feiz)
Date: Mon, 28 Jan 2013 16:54:00 +0000
Subject: [Gramene] Gramene search
Message-ID: <123D5C13E36C044E9CD75435A482561C011D02@BLUPRD0411MB401.namprd04.prod.outlook.com>

Hello,

I have s a list of proteins with the Gramene ID obtained by mass spect data. When I search them in Gramene, it shows "NO RESULT". For example one of them is GRMZM2G007263. Isn't this your Gene ID. Why can't I find the identity of this gene?

Thanks much

Leila Feiz post doc

BTI Cornell

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From whetzel at stanford.edu  Wed Jan 30 13:59:24 2013
From: whetzel at stanford.edu (Trish Whetzel)
Date: Wed, 30 Jan 2013 10:59:24 -0800
Subject: [Gramene] [bioportal-announce] NCBO Spring Developer Events
Message-ID: <10546CA0-A669-43B8-B68E-5F02DFC82A66@stanford.edu>

The National Center for Biomedical Ontology is hosting two developer events this spring: a Training Course on Building Applications with Biomedical Ontologies at the European Bioinformatics Institute (EBI) and an NCBO Hackathon at Stanford University.

The training course on Building Applications with Biomedical Ontologies will take place on April 18-19, 2013. This course will be taught by a team from EBI (James Malone and Simon Jupp) and a team from Stanford (Trish Whetzel and Paul Alexander). We will cover topics such as the OWL ontology language, working with RDF and SPARQL, and how to work with ontologies using NCBO Technology. Those attending the course should already have basic familiarity with both ontologies and programming in Java. Checkout the link below for more information and register soon since space is limited! 

http://www.ebi.ac.uk/training/course/biomedical-ontologies



The NCBO Hackathon will take place at Stanford University on April 29-30, 2013. This event will focus on projects in biomedical or clinical informatics that can benefit from use of ontology-based technology. The entire NCBO Team will be available to brainstorm application ideas and to answer development questions. We will also have separate sessions to provide training on the NCBO Web services, the BioPortal SPARQL endpoint, and other topics of interest requested by participants. If you are thinking of incorporating semantics into your software application, the Hackathon will provide a great opportunity to get a head start on your project. Register soon at the link below to hold your spot!


http://www.bioontology.org/wiki/index.php/NCBO_Hackathon_2013

 

Look forward to seeing you this Spring!

Trish 



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

"Like" NCBO on Facebook: http://on.fb.me/bioontology

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

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From whetzel at stanford.edu  Thu Jan 31 20:34:41 2013
From: whetzel at stanford.edu (Trish Whetzel)
Date: Thu, 31 Jan 2013 17:34:41 -0800
Subject: [Gramene] [bioportal-announce] CFP: ICBO 2013 - paper submission
	due date	extended to Feb. 15
Message-ID: <EC63FB28-2EF4-4168-98E2-7F6315A5E6E7@stanford.edu>


_____________________________________________________
This message is posted to several lists. Apologies for cross-posting.
Please forward it to everyone who might be interested.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ICBO 2013  Call for Participation

4th International Conference on Biomedical Ontologies 2013 (ICBO2013) 
Concordia University, Montreal, Quebec
July 7th - 9th 2013
http://www.unbsj.ca/sase/csas/data/ws/icbo2013/cfp.html
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Conference (long & short) paper submission deadline extended to Feb 15, 2013.

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience. The event is part of the Semantic Trilogy 2013 featuring:

       * International Conference on Biomedical Ontologies (ICBO 2013)
       * Canadian Semantic Web Symposium (CSWS 2013)
       * Data Integration in the Life Sciences (DILS 2013) 

web site:    http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/

Topics

Ontologies for biomedical research and clinical applications
Reports on ontologies for, and their application in high throughput omics data and systems biology, toxicology and environmental health, disorders, diseases, phenotypes and physiology, genetic variation and pharmacogenomics, translational research and personalized medicine, public health and electronic health care are invited..

Foundations and methodology
Papers on foundational and methodological issues pertaining to biomedical ontology are invited. Eligible topics are, though not limited to, the following; knowledge representation and reasoning, philosophical foundations of ontology, upper-level ontologies, topics in ontology engineering including design and life cycle, methodologies for knowledge elicitation and capture, ontology-oriented text mining techniques, ontology modularity, mapping, merging, and alignment of ontologies, and ontology evaluation.

Biomedical ontologies and the Semantic Web
Research on formal representation of biomedical knowledge using RDF and OWL, identifiers, mappings & normalization, biomedical research using linked data, integration strategies using the linked open data cloud, visualization and manipulation of ontology, federation of online resources, workflows and semantic web services for biomedical knowledge discovery.

Social aspects of biomedical ontologies
Perspectives from biomedical ontologists on community standards, adoption, and proliferation of semantics, use of semantic wikis, bio-curation & crowdsourcing techniques, user engagement and feedback, semantic publishing and provenance, governance, evolution and sustainability.


Submissions    http://www.easychair.org/conferences/?conf=icbo2013

All accepted submissions will be published as part of the Conference Proceedings. Papers are to be prepared using templates (available on website) and submitted via EasyChair. 

1. Long Research Paper (up to 6 pages) should satisfy the following criteria: original research; novelty in methodology and/or in research results; significant development with large potential for impact; theoretical soundness and/or strong evaluation with demonstration of utility in applications.

2. Short Research Paper (up to 4 pages) should satisfy the following criteria: original research; methodological soundness with either novel methodology & application, or demonstrated improvement over existing methods (with appropriate validation), or the use of existing methodology but in novel application. Short papers are appropriate for applied research or systems, or the development of new approaches.

3. Systems Paper (up to 2 pages) must describe the functionality, availability, and an application of the system. The system itself must be demonstrated at the conference.

4. Early Career Track (up to 4 pages) is to support the work of young investigators.
There will be an Early Career Track session for the presentation of the papers. The ECT paper review and acceptance criteria are the same as the short research papers. The staggered submission dates allows submissions (from young investigators) that are not accepted as long or short research papers to be revised and re-submitted; as well as allow first time submissions from young investigators to the Early Career Track directly.

5. Late Breaking Report (1 page) This track is for extended abstracts of posters. A limited set of the peer-reviewed reports will be selected to be presented as a flash talk. All reports must be presented as posters. Late breaking reports should address a clearly defined problem that is of interest to the ICBO community. A late breaking report is appropriate for interesting preliminary results; and systems updates.

6. Highlights (up to 500 words) This track highlights original peer-reviewed research with significant impact on data integration research or life sciences research that is published between May 1, 2012 and May 1, 2013. The submission is a short abstract highlighting the importance of the work for the ICBO community. If the publication is not open access, then the authors must make the paper available to the review committee.


7. Workshops
Workshops are half-day or full-day scientific events intended to provide a forum for the discussion of a specific topic through individual paper presentations. The workshop organizers will be responsible for advertising the workshop and reviewing and selecting the contributions. Workshops can be events focusing on a specific topic; they can also include interest group meetings, or meetings designed to disseminate the results of a research project on a specific topic.

8. Tutorials
Tutorials are educational events. They may be either for a full day or for a half day. They should focus on one specific topic presented by one or two experts and involve interaction with the audience. Tutorials can include hands-on training, in which case the proposal should specify the exact requirements (laptops, software to install, etc.).

Relevant dates    http://www.unbsj..ca/sase/csas/data/ws/icbo2013/dates.html

18 January 2013:      Workshop and tutorial proposal submission deadline
1 February 2013:    Notification of acceptance of workshops and tutorial proposals
15 February 2013: Conference (long & short) paper submission deadline
15 April 2013:  Notification of conference paper acceptance 
15 April 2013:  System, early career and workshop paper submission deadline
15 May 2013:  Notification of system, early career and workshop paper acceptance
20 May 2013:  Submission of late breaking reports and highlight track papers
1 June 2013:  Notification of acceptance of late breaking reports and highlight-track papers
15 June 2013:  Deadline for all camera-ready copies for the proceedings


Contact
For more information or to offer sponsorship, please send us a note at
         contact: icbo2013 at gmail.com

Organizing Committee
Co-Scientific Chair: Michel Dumontier
Co-Scientific Chair: Christopher Baker
Local Organizer: Gregory Butler
Programme Chair: Robert Hoehndorf
Workshop and Tutorial Chair: Chris Mungall
Poster and Demonstration Chair: Trish Whetzel
Proceedings and Special Issue Chair: Janna Hastings
Early Career Chair: Melissa Haendel
Sponsorship and Publicity Chair: Sivaram Arabandi 



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

"Like" NCBO on Facebook: http://on.fb.me/bioontology

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

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