From elserj at science.oregonstate.edu Fri Oct 2 14:27:01 2009 From: elserj at science.oregonstate.edu (Justin Elser) Date: Fri, 02 Oct 2009 11:27:01 -0700 Subject: [Po-dev] (Bio)Informatics openings at Oregon State University Message-ID: <4AC645F5.8000505@science.oregonstate.edu> Bioinformatics and software programmer openings at the rank of Faculty Research Assistant are available in the Jaiswal lab at the Department of Botany and Plant Pathology to work on the Computational Biology and Bioinformatics projects. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in the Jaiswal lab (http://www.science.oregonstate.edu/bpp/faculty/jaiswal/). The positions are renewable annually. The projects involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining and biological ontology projects. The incumbent will have the necessary skills on developing the software in C, C++, Java, Perl, BioPerl, R, MATLAB, Shell, any other scientific programming language, etc.; and development of MySQL database driven web accessible applications, website coding in HTML, XML, JSP, PHP and computer science applications. To review the position description and apply, go to posting #0004776 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a Letter of Intent, and a Curriculum Vitae (including 3 references). Applications will be considered throughout the 2009-2010 fiscal year. The closing date is subject to change without notice to applicants. Oregon State University is an Affirmative Action/Equal Opportunity Employer and has a policy of being responsive to dual-career needs. -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Web: www.gramene.org www.plantontology.org -- ********************************************************** * * * Justin Elser * * Computational Biology Post Doc * * Dept. of Botany and Plant Pathology * * Oregon State University * * * * email: elserj at science.oregonstate.edu * * internet: www.science.oregonstate.edu/~elserj * * * ********************************************************** From cjm at berkeleybop.org Wed Oct 7 17:52:16 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Wed, 7 Oct 2009 14:52:16 -0700 Subject: [Po-dev] Re: [Obo-admin] po_anatomy file problem In-Reply-To: <4ACD0293.9010401@berkeleybop.org> References: <4ACD0293.9010401@berkeleybop.org> Message-ID: <1B2375CD-2BC7-4993-889A-5AA68B07BE5C@berkeleybop.org> seems to be just a problem with the /Poc/ directory. The other directories work fine. Any idea Pankaj? On Oct 7, 2009, at 2:05 PM, Seth Carbon wrote: > A problem has cropped up with po_anatomy. The following URL now fails: > > http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/po_anatomy.obo > > > Drilling down to that file from the top of the tree seems to cause > errors on their server, possible a permissions problem. Does anybody > have a contact over there? > > Cheers, > > -Seth > > _______________________________________________ > Obo-admin mailing list > Obo-admin at fruitfly.org > http://mail.fruitfly.org/mailman/listinfo/obo-admin > From elserj at science.oregonstate.edu Wed Oct 7 18:15:03 2009 From: elserj at science.oregonstate.edu (Justin Elser) Date: Wed, 07 Oct 2009 15:15:03 -0700 Subject: [Po-dev] Re: [Obo-admin] po_anatomy file problem In-Reply-To: <1B2375CD-2BC7-4993-889A-5AA68B07BE5C@berkeleybop.org> References: <4ACD0293.9010401@berkeleybop.org> <1B2375CD-2BC7-4993-889A-5AA68B07BE5C@berkeleybop.org> Message-ID: <4ACD12E7.7090604@science.oregonstate.edu> An HTML attachment was scrubbed... URL: From jaiswalp at science.oregonstate.edu Thu Oct 22 15:10:34 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu, 22 Oct 2009 12:10:34 -0700 Subject: [Po-dev] IPMB Gramene and Plant Ontology workshop Message-ID: <4AE0AE2A.1020501@science.oregonstate.edu> Dear IPMB Congress participants, We would like to invite the attendees of the 9th International Plant Molecular Biology (IPMB) Congress (http://www.ipmb2009.org/) to be held from October 25-30, 2009 in St. Louis, MO, USA to the Gramene Database and Plant Ontology Workshop. The workshop is free and open to everyone. Time: Monday October 26, 6-9pm Location: Room # 104/105 @ the meeting venue Workshop Title: Comparative Plant Genomics with the Gramene database and Plant Ontology project Schedule: 6-7pm: GRAMENE (www.gramene.org) -Get familiar with Gramene Database -How Gramene can help in your research -Questions and Answers 7-8pm: PLANT ONTOLOGY (www.plantontology.org) -Get familiar with Plant Ontology (PO) resource -How can PO resource help you -Questions and Answers 8-9pm: Discussion with the community of interested researchers and their participation in building community based curation network. - Plant Gene Wiki - Metabolic and regulatory Networks - Your feedback and interests. -- Pankaj Jaiswal Web: www.gramene.org www.plantontology.org From whetzel at stanford.edu Wed Oct 28 22:34:52 2009 From: whetzel at stanford.edu (Trish Whetzel) Date: Wed, 28 Oct 2009 19:34:52 -0700 Subject: [Po-dev] [bioportal-announce] BioPortal 2.2 Release Message-ID: <1517F8A7-9983-438B-81DE-C03D8B0BD95F@stanford.edu> The BioPortal team is pleased to announce the release of BioPortal 2.2 (http://bioportal.bioontology.org/). Release notes and known issues are listed below. New Features Ontology Views Views in BioPortal are subsets or other derivatives of ontologies in the repository that you can share with the community. You can upload views for any ontology, and review them, add notes, create mappings, and use REST Web services to access them programmatically. A view can also serve as a mechanism to define value sets, which are quite useful in combination with the BioPortal ontology-term selection widget. View generation and storage in BioPortal is the result of collaboration with Dr. Jim Brinkley?s group at the University of Washington. NCBO Resource Index We have initiated automated indexing of the contents of public databases using ontology terms. The indexing is done using the same workflow that drives the previously released Annotator web service. Currently we index the following public databases: Array Express, Biositemaps, caNanoLab, Conserved Domain Database, ClinicalTrials.gov, DrugBank, Gene Expression Omnibus, Online Mendelian Inheritance in Man, PharmGKB, Reactome, ResearchCrossroads (Grant funding database), Stanford Microarray Database, UniProt KB, and WikiPathways. The resulting annotations are accessible for browsing via the Resources tab corresponding to any ontology concept. The annotations can also be accessed programmatically: http://www.bioontology.org/wiki/index.php/Resource_Index . If you have recommendations on additional publicly accessible resources to index, let us know at support at bioontology.org. Search filter for Ontology Groups and Categories You can now limit your search to ontologies from a certain group (e.g., OBO Foundry, caBIG) or ontologies in a certain category (e.g., anatomy). New REST Web Services Services to access ontologies and ontology versions List all Categories List all Groups Download by virtual ontology identifier Services to access ontology views and ontology view versions List all Views of all Ontologies (lists the latest version) List all versions for a given View Concept services Get all concepts Search service ? parameter added to enable search within an ontology branch Service to access the NCBO Resource Index See http://www.bioontology.org/wiki/index.php/BioPortal_REST_services for the full list of BioPortal REST Web services. New Data: Mapping data generated by the LOOM algorithm are now in BioPortal (close to 1 million new lexical-based mappings). See http://www.bioontology.org/wiki/index.php/LOOM for more details about this tool. Selected UMLS ontologies are now available in BioPortal. Email support at bioontology.org to request loading of additional UMLS ontologies. Known Issues: The tree navigation shows ?Too many children? in cases where the number of siblings is greater than 500. Trish Whetzel, PhD Outreach Coordinator The National Center for Biomedical Ontology Ph: 650-721-2378 whetzel at stanford.edu http://www.bioontology.org -------------- 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