From whetzel at stanford.edu Wed Mar 10 11:44:17 2010 From: whetzel at stanford.edu (Trish Whetzel) Date: Wed, 10 Mar 2010 08:44:17 -0800 Subject: [Gramene] [bioportal-announce] ALERT: Web service change - getAllTerms Message-ID: <5DB6049F-6187-4425-A48F-419E369960E3@stanford.edu> Dear Users, There will be a change to the Web service getAllTerms in both signature and content returned. This change will support speedier term retrieval and can be used for any version of an ontology accessible via the Web services. This Web service is scheduled to be pushed to production on Monday, March 15. For details on the change and to test updates to your code, see: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Changes_to_the_Get_all_terms_service . The BioPortal Team _______________________________________________ bioportal-announce mailing list bioportal-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioportal-announce From vbonnecarrere at lb.inia.org.uy Sun Mar 14 14:06:45 2010 From: vbonnecarrere at lb.inia.org.uy (Victoria Bonnecarrere) Date: Sun, 14 Mar 2010 15:06:45 -0300 Subject: [Gramene] question about map and ssr Message-ID: Hello I have selected 44 ssr from different maps that I am going to use in my study. I want to know if is possible to use gramene tool to draw a map with only these ssr . I could not find this option by myself Thank you very much Victoria Bonnecarrere -------------- next part -------------- An HTML attachment was scrubbed... URL: From christian.tobias at ARS.USDA.GOV Mon Mar 15 16:06:38 2010 From: christian.tobias at ARS.USDA.GOV (Christian Tobias) Date: Mon, 15 Mar 2010 13:06:38 -0700 Subject: [Gramene] switchgrass (Panicum virgatum) mapping study Message-ID: <1268683598.8280.19.camel@ctobias-laptop> Dear Gramene curators. My lab is focusing on the development of switchgrass genetic We have a paper that has been reviewed by Genetics on linkage mapping in switchgrass. One of the stipulations for publication is that all the data be available to the public. We have C-map data for the maps which are based on EST SSRs. We also have the raw genotypes. Can Gramene accept this data? Regards, Christian Tobias -- ================= Christian Tobias USDA-ARS Western Regional Research Center 800 Buchanan Street Albany CA 95125 ph: 510-559-6172 fax: 510-559-5818 From whetzel at stanford.edu Tue Mar 16 01:45:59 2010 From: whetzel at stanford.edu (Trish Whetzel) Date: Mon, 15 Mar 2010 22:45:59 -0700 Subject: [Gramene] [bioportal-announce] BioPortal 2.3.1 Released to Production Message-ID: <472A44A5-C41B-4947-B53F-9F17D7A5012E@stanford.edu> BioPortal 2.3.1 was released to production Monday, 3/15/10. The following new features were added in this release. New Features Get all terms service The 'Get all terms' service will be changing to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes. Documentation:http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Changes_to_the_Get_all_terms_service Instance service A new service has been added to retrieve information about an instance and its property/value pairs. Documentation:http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Instance_Services View Extraction The View Extraction service allows users to create branches of an ontology starting at a given concept. The service returns an OWL file that contains the branch. Documentation: http://www.bioontology.org/wiki/index.php/View_Extraction Logging Service Calls can now be made to the logging service remotely to track how users are interacting with various BioPortal interfaces (including the BioPortal UI, Search, Annotator, and Resource Index). Logging will be enabled on the BioPortal UI in the next few days. The BioPortal Team -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ bioportal-announce mailing list bioportal-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioportal-announce From lala at asiacongress.com Tue Mar 23 06:58:37 2010 From: lala at asiacongress.com (lala) Date: Tue, 23 Mar 2010 17:58:37 +0700 Subject: [Gramene] International Rice Congress 2010 Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: final_header_banner.jpg Type: image/jpeg Size: 126015 bytes Desc: not available URL: From erick.antezana at gmail.com Mon Mar 29 08:14:01 2010 From: erick.antezana at gmail.com (Erick Antezana) Date: Mon, 29 Mar 2010 14:14:01 +0200 Subject: [Gramene] xref_analog syntax issues, contributions? Message-ID: <8b6eced31003290514j313c0b76w2c5f5c69dd1632a2@mail.gmail.com> Hi, I came across a few syntax issues in the ontology file plant_trait.obo: xref_analog: EO:EO\:0007180 xref_analog: EO:EO\:0007183 xref_analog: EO:EO\:0007633 xref_analog: GO:GO\:0000278 xref_analog: GO:GO\:0007049 xref_analog: GO:GO\:0009809 xref_analog: GO:GO\:0010148 xref_analog: GO:GO\:0051321 The namespace is duplicated (e.g. GO:GO). It should be: xref_analog: EO:0007180 xref_analog: EO:0007183 xref_analog: EO:0007633 xref_analog: GO:0000278 xref_analog: GO:0007049 xref_analog: GO:0009809 xref_analog: GO:0010148 xref_analog: GO:0051321 Do you have any plans to adopt the OBO spec 1.2 (http://www.geneontology.org/GO.format.obo-1_2.shtml)? If case we would like to contribute new terms, who would be the key-contact person to discuss about it? or the procedure to follow? cheers, Erick From whetzel at stanford.edu Mon Mar 29 21:18:39 2010 From: whetzel at stanford.edu (Trish Whetzel) Date: Mon, 29 Mar 2010 18:18:39 -0700 Subject: [Gramene] [bioportal-announce] BioPortal Web interface updates Message-ID: <002b01cacfa6$ee20d3d0$ca627b70$@edu> We are pleased to announce updates to the BioPortal Web interface: . We have redesigned the Views tab for ontologies to provide greater ease of use: http://bioportal.bioontology.org/ontologies/42483#views . The Ontology Widgets (term-selection autocomplete, visualization, RSS feed, and Jump To BioPortal), developed in Javascript, are now fully compatible with Internet Explorer 8: http://bioportal.bioontology.org/ontologies/42483#widgets Bug fix: . Icons for OBO format ontologies to indicate is_a and part_of relationships are now visible The BioPortal Team -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ bioportal-announce mailing list bioportal-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioportal-announce