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From: Trish W. <plw...@gm...> - 2013-05-13 18:27:35
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The next NCBO Webinar will be presented by James Malone from the European Bioinformatics Institute on "Ontology Driven Annotation, Integration and Analysis of Gene Expression Data" at 10:00am PDT, Wednesday, May 15. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: Archiving, integrating, and adding semantic value to high-throughput gene-expression data present major challenges in bioinformatics. The data are both diverse, covering many species, disease, and tissue types, and the annotations need to be detailed enough to capture complex experimental nuance relating to experimental process and biology. The main challenges in annotating such data lie in identification of suitable ontologies, consistent application of ontologies to the data in the context of annotation tools, provision of context specific views of existing ontologies for query, and development of automated annotation pipelines to support curators. We describe in this talk our progress in addressing these challenges, specifically: the development of tools to help build ontologies for applications, the development of a linked data repository of annotation knowledge and the publication of our gene expression database as RDF linked data, connecting our ontology annotations to the data. Finally, we outline our future work in developing an analysis package for use with this semantically rich expression data enabling the generation and analysis of gene lists of biological relevance. We highlight how we utilise NCBO tools and the drivers we have identified as a result of this work. SPEAKER BIO: Dr. Malone is a Bioinformatician in the Functional Genomics Production Team at the European Bioinformatics Institute based in Cambridge, UK. He leads efforts to develop application ontologies and supporting ontology development tools for use in the annotation of biomedical data. He previously worked at the AIAI in University of Edinburgh on various joint commercial-academic projects in areas including biomedical intelligent system applications. He holds a PhD in Machine Learning in Bioinformatics, an MSc in Bioinformatics and a BSc in Computer Science. WEBEX DETAILS: ------------------------------------------------------- Meeting information ------------------------------------------------------- Date: May 15, 2013 Time: 10:00 am, Pacific Daylight Time (San Francisco, GMT-07:00) Meeting Number: 925 756 393 Meeting Password: ncbo ------------------------------------------------------- To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=171726072&UID=481527042&PW=NMzhlMDBjNzk0&RT=MiM0 ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=171726072&tollFree=0 Access code:925 756 393 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: Susanna-Assunta S. <sa....@gm...> - 2013-04-05 14:53:44
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Dear Colleagues, 1 week to submission deadline! What: Call for participation in the Bio-Ontologies SIG 2013 (www.bio-ontologies.org.uk) Where: July 20, 2013, Berlin, Germany. (Co-located with ISMB/ECCB 2013) When: Submissions Due: April 12th, 2013 (Fri) @ www.bio-ontologies.org.uk/submissions Notifications: May 10th, 2013 (Fri) Final Version Due: May 17th, 2013 (Fri) Please forward to everyone who might be interested. The Bio-Ontologies SIG provides a forum for discussion of the latest research in the application of ontologies and in the organisation, presentation and dissemination of knowledge in the life sciences. In its 15th year, Bio-Ontologies is one of the longest running SIG at ISMB. Papers are invited in areas, such as the applications of bio-ontologies, newly developed bio-ontologies, and the use of ontologies in data sharing standards. Example topics include (but not limited to): Applications of ontologies in bioinformatics Hypothesis Testing Platforms Use of Ontologies in Data Standards "Flash updates" on Newly Developed or Existing Bio-Ontologies Bio-Curation Platforms Automated Annotation Pipelines Efforts using ontologies for Bio-NLP or Information Retrieval Semantic Web Enabled Applications Advances in development of biomedical ontologies Collaborative Ontology Authoring and Peer-Review Mechanisms Automated Ontology Learning Mapping between Ontologies Research in Ontology Evaluation Using games for Ontology review and evaluation We invite three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated for a flash update on the poster. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Unsuccessful papers will automatically be considered for poster presentation. Best regards, SIG Organizers: Nigam Shah, Susanna Sansone, Michel Dumontier, Larisa Soldatova -- -- Susanna-Assunta Sansone, PhD skype: susanna-a.sansone uk.linkedin.com/in/sasansone University of Oxford e-Research Centre Associate Director, Principal Investigator www.isacommons.org|www.biosharing.org Nature Publishing Group Consultant, Scientific Data www.nature.com/scientificdata - |
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From: Susanna-Assunta S. <sa....@gm...> - 2013-03-14 17:34:24
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Dear Colleagues, 31 days to submission deadline! *What: Call for participation in the Bio-Ontologies SIG 2013 (www.bio-ontologies.org.uk <http://www.bio-ontologies.org.uk/>)* *Where:July 20, 2013, Berlin, Germany. (Co-located with ISMB/ECCB 2013) When: Submissions Due: April 12th, 2013 (Fri) @ www.bio-ontologies.org.uk/submissions <http://www.bio-ontologies.org.uk/submissions> * Notifications: May 10th, 2013 (Fri) * Final Version Due: May 17th, 2013 (Fri) * * Please forward to everyone who might be interested.* *The Bio-Ontologies SIG provides a forum for discussion of the latest research in the application of ontologies and in the organisation, presentation and dissemination of knowledge in the life sciences. In its 15th year, Bio-Ontologies is one of the longest running SIG at ISMB. Papers are invited in areas, such as the applications of bio-ontologies, newly developed bio-ontologies, and the use of ontologies in data sharing standards. Example topics include (but not limited to): Applications of ontologies in bioinformatics * Hypothesis Testing Platforms * Use of Ontologies in Data Standards * "Flash updates" on Newly Developed or Existing Bio-Ontologies * Bio-Curation Platforms * Automated Annotation Pipelines * Efforts using ontologies for Bio-NLP or Information Retrieval * Semantic Web Enabled Applications Advances in development of biomedical ontologies * Collaborative Ontology Authoring and Peer-Review Mechanisms * Automated Ontology Learning * Mapping between Ontologies * Research in Ontology Evaluation * Using games for Ontology review and evaluation We invite three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated for a flash update on the poster. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Unsuccessful papers will automatically be considered for poster presentation.* * * *Best regards,* SIG Organizers: Nigam Shah, Susanna Sansone, Michel Dumontier, Larisa Soldatova -- |
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From: Trish W. <plw...@gm...> - 2013-02-19 19:34:18
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The next NCBO Webinar will be presented by Andrew Su from The Scripps Research Institute on "Translating unstructured, crowdsourced content into structured data" at 10:00am PST, Wednesday, Feb. 20. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: The use of crowdsourcing in biology is gaining popularity as a mechanism to tackle challenges of massive scale. However, to maximize participation and lower the barriers to entry, contributions to crowdsourcing efforts are typically not well-structured, which makes computing on these data challenging and difficult. The presentation will discuss strategies for translating this unstructured content into structured data. Three vignettes (in varying degrees of completion) will be described, one each from our Gene Wiki [1], BioGPS [2], and serious gaming [3] initiatives. [1]: http://en.wikipedia.org/wiki/Portal:Gene_Wiki [2]: http://biogps.org [3]: http://genegames.org SPEAKER BIO: Andrew Su is an Associate Professor at The Scripps Research Institute. His group develops bioinformatics tools for biomedical research, focusing on harnessing the collective efforts of the biology community. The lab also applies these and other tools to a variety of projects in integrative genomics. Andrew previously led bioinformatics efforts at GNF from 2002 to 2011. Prior to that, he received his Ph.D. from the Scripps Research Institute and did his undergraduate studies at Northwestern University. WEBEX DETAILS: ------------------------------------------------------- Meeting information ------------------------------------------------------- Date: Wednesday, February 20, 2013 Time: 10:00 am, Pacific Standard Time (San Francisco, GMT-08:00) ------------------------------------------------------- To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=171726072&UID=481527042&PW=NMzhlMDBjNzk0&RT=MiM0 Meeting Number: 925 756 393 Meeting Password: ncbo ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=171726072&tollFree=0 Access code:925 756 393 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: Susanna-Assunta S. <sa....@gm...> - 2013-02-07 17:48:10
|
Dear Colleagues, *What: Call for participation in the Bio-Ontologies SIG 2013 (www.bio-ontologies.org.uk <http://www.bio-ontologies.org.uk>)* *Where:July 20, 2013, Berlin, Germany. (Co-located with ISMB/ECCB 2013) When: Submissions Due: April 12th, 2013 (Fri) @ www.bio-ontologies.org.uk/submissions <http://www.bio-ontologies.org.uk/submissions> * Notifications: May 10th, 2013 (Fri) * Final Version Due: May 17th, 2013 (Fri) * * Please forward to everyone who might be interested.* * The Bio-Ontologies SIG provides a forum for discussion of the latest research in the application of ontologies and in the organisation, presentation and dissemination of knowledge in the life sciences. In its 15th year, Bio-Ontologies is one of the longest running SIG at ISMB. Papers are invited in areas, such as the applications of bio-ontologies, newly developed bio-ontologies, and the use of ontologies in data sharing standards. Example topics include (but not limited to): Applications of ontologies in bioinformatics * Hypothesis Testing Platforms * Use of Ontologies in Data Standards * "Flash updates" on Newly Developed or Existing Bio-Ontologies * Bio-Curation Platforms * Automated Annotation Pipelines * Efforts using ontologies for Bio-NLP or Information Retrieval * Semantic Web Enabled Applications Advances in development of biomedical ontologies * Collaborative Ontology Authoring and Peer-Review Mechanisms * Automated Ontology Learning * Mapping between Ontologies * Research in Ontology Evaluation * Using games for Ontology review and evaluation We invite three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated for a flash update on the poster. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Unsuccessful papers will automatically be considered for poster presentation.* * * *Best regards,* SIG Organizers: Nigam Shah, Susanna Sansone, Michel Dumontier, Larisa Soldatova -- |
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From: Helen P. <par...@eb...> - 2012-10-29 09:03:02
|
Dear Anandhi there has been some activity on the W3C lists and we have some RDF representations of ArrayExpress data, I will reply to you off list and point you at those, best wishes Helen On 28/10/2012 01:23, John Matese wrote: > Dear Anandhi, > > You might also look at the encoding of that platform at ArrayExpress; > presumably that might be a guide on how one might represent it > (either adf or mage-ml). > http://www.ebi.ac.uk/arrayexpress/files/A-AFFY-33 > > [though as Chris mentioned, I don't think platform name or reporter > name was a property of the MGED Ontology, proper...] > > > Cheers, > John Matese > > On Oct 27, 2012, at 5:06 PM, Chris Stoeckert <sto...@pc... > <mailto:sto...@pc...>> wrote: > >> Dear Anandhi, >> Those are not available in the MGED Ontology. You might consider >> using OBI (Ontology for Biomedical Investigations; >> http://obi-ontology.org/page/Main_Page) instead. Most of the useful >> bits of the MGED Ontology have been incorporated into OBI. We even >> generated an FGED (functional genomics data) view available at >> http://bioportal.bioontology.org/ontologies/1123 under Views. >> Cheers, >> >> Chris Stoeckert, Ph.D. >> Research Professor, Dept. of Genetics >> 1415 Blockley Hall, Center for Bioinformatics >> 423 Guardian Dr., University of Pennsylvania >> Philadelphia, PA 19104 >> Ph: 215-573-4409 FAX: 215-573-3111 >> http://www.cbil.upenn.edu <http://www.cbil.upenn.edu/> >> >> >> On Oct 26, 2012, at 9:48 AM, Anandhi Iyappan >> <ana...@gm... <mailto:ana...@gm...>> wrote: >> >>> Hello, >>> >>> I am making use of the MGED ontology to make an RDF schema for my >>> project. I have problem finding the class and property that denotes >>> the "Platform name (eg:Affymetrix Human Genome U133A Array)" , >>> "platform_id" and the "probe_set_ids (eg: 1007_s_at)". Can you >>> please tell me the following? >>> >>> >>> 1. Resource and proerty for Platform Name >>> >>> 2. Resource and Property for Platform ID >>> >>> 3. Resource and Property for probe_set_ids >>> >>> It would be very helpful if you can guide me through these details!! >>> >>> Regards, >>> Anandhi >>> ------------------------------------------------------------------------------ >>> Everyone hates slow websites. So do we. >>> Make your web apps faster with AppDynamics >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________ >>> Mged-ontologies mailing list >>> Mge...@li... >>> <mailto:Mge...@li...> >>> https://lists.sourceforge.net/lists/listinfo/mged-ontologies >> >> ------------------------------------------------------------------------------ >> WINDOWS 8 is here. >> Millions of people. Your app in 30 days. >> Visit The Windows 8 Center at Sourceforge for all your go to resources. >> http://windows8center.sourceforge.net/ >> join-generation-app-and-make-money-coding-fast/_______________________________________________ >> Mged-ontologies mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-ontologies > > > > ------------------------------------------------------------------------------ > WINDOWS 8 is here. > Millions of people. Your app in 30 days. > Visit The Windows 8 Center at Sourceforge for all your go to resources. > http://windows8center.sourceforge.net/ > join-generation-app-and-make-money-coding-fast/ > > > _______________________________________________ > Mged-ontologies mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-ontologies -- Helen Parkinson, PhD Team Leader Functional Genomics Group EBI EBI 01223 494672 Skype: helen.parkinson.ebi www.ebi.ac.uk/fgpt/ |
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From: John M. <jcm...@ge...> - 2012-10-28 00:39:27
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Dear Anandhi, You might also look at the encoding of that platform at ArrayExpress; presumably that might be a guide on how one might represent it (either adf or mage-ml). http://www.ebi.ac.uk/arrayexpress/files/A-AFFY-33 [though as Chris mentioned, I don't think platform name or reporter name was a property of the MGED Ontology, proper...] Cheers, John Matese On Oct 27, 2012, at 5:06 PM, Chris Stoeckert <sto...@pc...> wrote: > Dear Anandhi, > Those are not available in the MGED Ontology. You might consider using OBI (Ontology for Biomedical Investigations; http://obi-ontology.org/page/Main_Page) instead. Most of the useful bits of the MGED Ontology have been incorporated into OBI. We even generated an FGED (functional genomics data) view available at http://bioportal.bioontology.org/ontologies/1123 under Views. > Cheers, > > Chris Stoeckert, Ph.D. > Research Professor, Dept. of Genetics > 1415 Blockley Hall, Center for Bioinformatics > 423 Guardian Dr., University of Pennsylvania > Philadelphia, PA 19104 > Ph: 215-573-4409 FAX: 215-573-3111 > http://www.cbil.upenn.edu > > > On Oct 26, 2012, at 9:48 AM, Anandhi Iyappan <ana...@gm...> wrote: > >> Hello, >> >> I am making use of the MGED ontology to make an RDF schema for my project. I have problem finding the class and property that denotes the "Platform name (eg:Affymetrix Human Genome U133A Array)" , "platform_id" and the "probe_set_ids (eg: 1007_s_at)". Can you please tell me the following? >> >> >> 1. Resource and proerty for Platform Name >> >> 2. Resource and Property for Platform ID >> >> 3. Resource and Property for probe_set_ids >> >> It would be very helpful if you can guide me through these details!! >> >> Regards, >> Anandhi >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________ >> Mged-ontologies mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-ontologies > > ------------------------------------------------------------------------------ > WINDOWS 8 is here. > Millions of people. Your app in 30 days. > Visit The Windows 8 Center at Sourceforge for all your go to resources. > http://windows8center.sourceforge.net/ > join-generation-app-and-make-money-coding-fast/_______________________________________________ > Mged-ontologies mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-ontologies |
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From: Chris S. <sto...@pc...> - 2012-10-27 21:06:54
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Dear Anandhi, Those are not available in the MGED Ontology. You might consider using OBI (Ontology for Biomedical Investigations; http://obi-ontology.org/page/Main_Page) instead. Most of the useful bits of the MGED Ontology have been incorporated into OBI. We even generated an FGED (functional genomics data) view available at http://bioportal.bioontology.org/ontologies/1123 under Views. Cheers, Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu On Oct 26, 2012, at 9:48 AM, Anandhi Iyappan <ana...@gm...> wrote: > Hello, > > I am making use of the MGED ontology to make an RDF schema for my project. I have problem finding the class and property that denotes the "Platform name (eg:Affymetrix Human Genome U133A Array)" , "platform_id" and the "probe_set_ids (eg: 1007_s_at)". Can you please tell me the following? > > > 1. Resource and proerty for Platform Name > > 2. Resource and Property for Platform ID > > 3. Resource and Property for probe_set_ids > > It would be very helpful if you can guide me through these details!! > > Regards, > Anandhi > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________ > Mged-ontologies mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-ontologies |
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From: Anandhi I. <ana...@gm...> - 2012-10-26 13:59:16
|
Hello, I am making use of the MGED ontology to make an RDF schema for my project. I have problem finding the class and property that denotes the "Platform name (eg:Affymetrix Human Genome U133A Array)" , "platform_id" and the "probe_set_ids (eg: 1007_s_at)". Can you please tell me the following? 1. Resource and proerty for Platform Name 2. Resource and Property for Platform ID 3. Resource and Property for probe_set_ids It would be very helpful if you can guide me through these details!! Regards, Anandhi |
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From: Anandhi I. <ana...@gm...> - 2012-10-26 13:48:46
|
Hello, I am making use of the MGED ontology to make an RDF schema for my project. I have problem finding the class and property that denotes the "Platform name (eg:Affymetrix Human Genome U133A Array)" , "platform_id" and the "probe_set_ids (eg: 1007_s_at)". Can you please tell me the following? 1. Resource and proerty for Platform Name 2. Resource and Property for Platform ID 3. Resource and Property for probe_set_ids It would be very helpful if you can guide me through these details!! Regards, Anandhi |
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From: Trish W. <plw...@gm...> - 2012-10-08 17:17:02
|
The next NCBO Webinar will be presented by Tania Tudorache and Matthew Horridge from Stanford University on "Editing and Publishing OWL 2 and OBO ontologies with WebProtégé and BioPortal" at 10:00am PDT, Wednesday, Oct. 10. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: WebProtégé is a collaborative ontology and knowledge base editor for the Web. In this talk, we will present the latest WebProtégé developments, including support for the editing of OWL 2 and OBO ontologies, the new OWL-API backend and the the various collaboration features. We will describe how WebProtégé can be customized as a domain-expert friendly tool and show the OBO specific user interface widgets that are optimized for editing components of OBO ontologies. We will demonstrate how users can upload and download ontologies, share them with collaborators, and simultaneously edit and comment on them. All ontology changes are recorded, and can be inspected by editors, curators or reviewers. We will also show how users can collaborate using the notes and discussions features, as well as the watches and notifications functionality. Finally, we will demonstrate how WebProtégé integrates with BioPortal services so that, for example, users can search for and reference terms in BioPortal ontologies at the click of a mouse. We will conclude with our plans for the future development of WebProtégé and its integration with BioPortal. SPEAKER BIOS: Tania Tudorache is a research scientist in the Stanford Center for Biomedical Informatics Research. Her main research interest is the collaborative development of ontologies applied to the biomedical domain. Dr. Tudorache has more than 9 years of experience with ontology development and Semantic Web technologies. She is also one of the key team member of the Protégé team. As a research scientist, Dr. Tudorache has done extensive work on the collaborative development of large biomedical terminologies and ontologies. She has also designed and implemented the initial versions of WebProtégé – a light-weight ontology and knowledge base editor for the Web. She is the lead person of the team developing the ICD Collaborative Authoring Tool (iCAT) - an adaptation of WebProtégé that the World Heath Organization is currently using to build the 11th revision of the International Classification of Diseases. Dr. Tudorache has organized and chaired several international Semantic Web conferences, and has served as a program committee member on numerous occasions. Matthew Horridge is a research software developer in the Biomedical Informatics Research Group at Stanford University. He works on the Protégé project, developing front and back end components for both WebProtégé and Protégé 4. In addition to this, Matthew has worked extensively on the design and implementation of the OWL API, which is the most popular API for dealing with OWL ontologies and underpins the latest versions of WebProtégé and Protégé 4. His research interests centre around the explanation of entailments in ontologies and he recently received a PhD from the University of Manchester in this area. WEBEX DETAILS: ------------------------------------------------------- To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=205918092&UID=481527042&PW=NMmEyZWM0YTg1&RT=MiM0 Meeting Number: 923 724 964 Meeting Password: ncbo ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=205918092&tollFree=0 Access code:923 724 964 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: Trish W. <plw...@gm...> - 2012-10-01 17:49:08
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The next NCBO Webinar will be presented by Maryann Martone, NIF/UCSD, Executive Director Force11 and Anita de Waard, Disruptive Technologies Director, Elsevier Labs, Force11 Exec Board member on "Force11: The Future of Research Communications and e-Scholarship: Past, Present, and Inviting Input for the Future" at 10:00am PDT, Wednesday, Oct. 3. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: Force11 (http://force11.org) is a community of scholars, librarians, archivists, publishers and research funders that has arisen organically to help facilitate the change toward improved knowledge creation and sharing. Individually and collectively, we aim to bring about a change in modern scholarly communications through the effective use of information technology which will also broaden to include, for example, the publication of software tools, research communication via social media channels, and sharing data and workflows in innovative ways. We see Force11 as a starting point for a community that we hope will grow and be augmented by individual and collective efforts by the participants and others. In our talk, we’ll discuss the background, goals, and plans we have for Force11. After this overview, we invite all participants to share ideas for future developments on which they would like FORCE11 to focus on. SPEAKER BIOS: Maryann Martone received her BA from Wellesley College in biological psychology and her Ph.D. in neuroscience in 1990 from the University of California, San Diego, where she is currently a Professor in the Department of Neuroscience. She is the principal investigator of the Neuroinformatics Framework project, a national project to establish a uniform resource description framework for neuroscience. Her recent work has focused on building ontologies for neuroscience for data integration. She just completed her tenure as the US scientific representative to the International Neuroinformatics Coordinating Facility (INCF), where she still heads a program on ontologies. Dr. Martone recently joined FORCE11, an organization dedicated to advancing scholarly communication and e-scholarship, as Executive Director. Anita de Waard is Disruptive Technologies Director at Elsevier Labs. She has a degree in experimental low-temperature physics from Leiden university, and worked at the Kapitza Institute in Moscow, before joining Elsevier as a physics publisher in 1988. Since 1997 she has worked on bridging the gap between science publishing and computational and information technologies, collaborating with different academic groups in Europe and the US. Her past work includes the application of Semantic Web technologies to scientific communication in the DOPE project, and the development of an Entity Identification database in the EU-funded OKKAM project. Other projects include co-organising a series of workshops with the goal of enunciating the key possibilities and main impediments to change scientific communications, including ‘Beyond the PDF’ and ‘FORCE11: The Future of Research Communications and E-Science’ http://force11.org. >From January 2006 onwards, de Waard has been working part-time as a researcher at the University of Utrecht on discourse analysis of biological text, with an emphasis on finding key rhetorical components that form a model of how biologists’ claims turn to facts. WEBEX DETAILS: ------------------------------------------------------- To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=175352027&UID=481527042&PW=NYjM4OTVlZTFj&RT=MiM0 Meeting Number: 925 343 903 Meeting Password: ncbo ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=175352027&tollFree=0 Access code:925 343 903 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: Trish W. <plw...@gm...> - 2012-09-17 23:35:50
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The next NCBO Webinar will be presented by Dr. Nigam Shah from Stanford University on "Do Proton Pump Inhibitors increase the risk of Myocardial Infarction? -- insights from mining clinical notes" at 10:00am PT, Wednesday, Sep. 19. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: The current state of the art in post-marketing drug surveillance utilizes voluntarily submitted reports of suspected adverse drug reactions. As adoption of electronic health records increases, we present an approach based on analyzing the unstructured clinical notes, which can enable rapid pharmacovigilance. Using this approach we find that proton pump inhibitors (PPIs) as a class appear strongly associated with major adverse cardiovascular events, increasing the risk of myocardial infarction by 20-50% depending upon the individual PPI. The association of PPIs with such events was hypothesized based on experimental results that show that PPIs, as a class, elevate plasma levels of asymmetric dimethylarginine, a disease marker and an independent predictor of major adverse cardiovascular events. We show that it is possible to investigate adverse drug event associations with high accuracy (72% sensitivity, 83% specificity) by analyzing textual notes in a clinical data warehouse using ontology-driven methods. We examine suspected associations for confounding via stratification and propensity score matching. We find that such an analysis of textual clinical notes could detect adverse drug events 2 years before the official alert. We argue that data-mining of unstructured clinical notes may expand meaningful use of the electronic health records for post-marketing drug surveillance and for rapid retrospective analysis of adverse event risk elucidated by experimental methods, such as in our case study on proton pump inhibitors. SPEAKER BIO: Dr. Nigam H. Shah is an Assistant Professor of Medicine (Biomedical Informatics) at the Stanford School of Medicine. Dr. Shah's research is focused on developing applications of bio-ontologies, specifically building novel approaches to annotate, index, integrate and analyze diverse information types available in biomedicine. Dr. Shah holds an MBBS from Baroda Medical College, India, a PhD from Penn State University, USA and completed post-doctoral training at the Stanford Medical School. WEBEX DETAILS: ------------------------------------------------------ To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=171726072&UID=481527042&PW=NMzhlMDBjNzk0&RT=MiM0 Meeting Number: 925 756 393 Meeting Password: ncbo ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=171726072&tollFree=0 Access code: 925 756 393 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: Jie Z. <jie...@pc...> - 2012-07-16 22:54:52
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Hi All, OBI 2012 summer release is out. The new version is on: http://purl.obolibrary.org/obo/obi.owl Highlight of this release: * 105 newly added classes, including - types of binding assays and related terms such as binding measurement data required by the IEDB group - types of assays related to ECO The newly added OBI classes are listed onhttp://obi.svn.sourceforge.net/viewvc/obi/releases/2012-07-01/docs/newClasses.html <http://obi.svn.sourceforge.net/viewvc/obi/releases/2012-03-29/docs/newClasses.html> The detailed release information can be found on: http://purl.obolibrary.org/obo/obi/release-notes.html The released OBI files can be loaded into Protege 4v and reasoned consistent using Hermit reasoner. It will be loaded into Ontobee (http://www.ontobee.org/) and Bioportal in 1-2 days. Jie & Carlo |
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From: jie z. <jie...@pc...> - 2012-06-17 21:23:13
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*Call for registration: 2012 ICBO tutorial on OBI: A shared ontology for representing biomedical studies and resources July 22nd 2012, Graz, Austria* Early registration rates for ICBO tutorials apply until July Ontology for Biomedical Investigations (OBI) developers will give a half day tutorial on ICBO 2012 (July 22th, 8:30 AM - 12:30 PM). The tutorial will contain three sessions: *Session 1: *(presented by Dr. Christian Stoeckert) Introduction To OBI Hands-on Exercises: Accessing and browsing OBI and associated resources *Session 2:*(presented by Dr. Jie Zheng) Representation Of Biomedical Investigations Using OBI Hands-on Exercises: Generate a community view of OBI for a specific application using Ontodog *Session 3:*(presented by Dr. Yongqun "Oliver" He) Ontology Development By Using OBI As A Source Ontology Hands-on Exercises: Reuse OBI terms in Vaccine Ontology (VO) based on MIREOT using OntoFox and add a set of new terms based on QTT using Ontorat For details of the tutorial, please visit the webpage: http://kr-med.org/icbofois2012/obi/index.htm For questions, please contact the tutorial organizers: Jie Zheng <jie...@pc...> Christian Stoeckert <sto...@pc...> Yongqun(Oliver) He <yon...@me...> We are looking forward seeing you on the ICBO OBI workshop. On behalf of the tutorial organizers, Jie Zheng Center for Bioinformatics Department of Genetics University of Pennsylvania Perelman School of Medicine |
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From: Trish W. <plw...@gm...> - 2012-06-04 17:55:10
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The next NCBO Webinar will be presented by Daniel Rubin from Stanford University on "Capturing and Computer Reasoning with Quantitative and Semantic Information in Radiology Images" at 10:00am PT, Wednesday, June 6. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: The use of semantic Web technologies to make the myriad of data in cyberspace accessible to intelligent agents is well established. However, a crucial type of information on the Web--and especially in life sciences--is imaging, which is largely being overlooked in current semantic Web endeavors. We are developing methods and tools to enable the transparent discovery and use of large distributed collections of medical images within hospital information systems and ultimately on the Web. Our approach is to make the human and machine descriptions of image content machine-accessible through "semantic annotation" using ontologies, capturing semantic and quantitative information from images as physicians view them in a manner that minimally affects their current workflow. We exploit new standards for making image contents explicit and publishable on the semantic Web. We will describe tools and methods we are developing and preliminary results using them for response assessment in cancer. While this work is focused on images in the life sciences, it has broader applicability to all images on the Web. Our ultimate goal is to enable semantic integration of images and all the related scientific data pertaining to their content so that physicians and basic scientists can have the best understanding of the biological and physiological significance of image content. SPEAKER BIO: Daniel L. Rubin, MD, MS is Assistant Professor of Radiology and Medicine (Biomedical Informatics Research) at Stanford University. He is a Member of the Stanford Cancer Center and the Bio-X interdisciplinary research program. His NIH-funded research program focuses on the intersection of biomedical informatics and imaging science, developing computational methods and applications to extract quantitative information and meaning from clinical, molecular, and imaging data, and to translate these methods into practice through applications to improve diagnostic accuracy and clinical effectiveness. He is Principal Investigator of one of the centers in the National Cancer Institute's recently-established Quantitative Imaging Network (QIN), Chair of the RadLex Steering Committee of the Radiological Society of North America (RSNA), and Chair of the Informatics Committee of the American College of Radiology Imaging Network (ACRIN). Dr. Rubin has published over 100 scientific publications in biomedical imaging informatics and radiology. WEBEX DETAILS: ------------------------------------------------------- To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=175352027&UID=481527042&PW=NYjM4OTVlZTFj&RT=MiM0 ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=175352027&tollFree=0 Access code:925 343 903 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: Trish W. <plw...@gm...> - 2012-05-01 17:30:34
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The next NCBO Webinar will be presented May 2 by Oliver He from the University of Michigan Medical School on "Vaccine Ontology (VO) and its application in literature mining of vaccine-gene interaction networks" at 10:00am PT, Wednesday, May 2. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: The Vaccine Ontology (VO, http://www.violinet.org/vaccineontology) is a community-based biomedical ontology in the domain of vaccine and vaccination. As of April 29, VO contains 5,578 ontology terms including 5,145 VO-specific terms, and the other terms are imported from over ten existing ontologies. VO represents over 1,000 licensed vaccines and vaccine candidates in clinical trials and in research. These vaccines have been developed against infections of various bacterial, viral, and parasitic pathogens as well as cancers in over 20 animal species. VO also represents all types of vaccine components (e.g., vaccine antigens and adjuvants) and vaccine preparations. In addition, various vaccine-induced immune responses and protection against specific disorders are being modeled in VO. We have developed VO-based natural language processing (NLP) approaches to retrieve and analyze vaccine-specific interaction networks of host or pathogen genes. Our use case studies demonstrated: (1) VO and centrality-based literature mining dramatically increased the identification of interferon-gamma (IFNG) and vaccine-associated human genes and gene interactions; (2) a NLP literature mining method based on VO and the Interaction Network Ontology (INO) allows the detection of significantly over- and under-represented gene-gene interactions in the IFNG network and IFNG-vaccine subnetwork; and (3) VO-based literature mining provided better performance than the MeSH-based PubMed approach in retrieving the interactions between vaccines and genes from Brucella (a bacterial pathogen). Novel scientific hypotheses have been generated through these ontology-based literature mining studies. SPEAKER BIO: Yongqun “Oliver” He is an associate professor in the Unit for Laboratory Animal Medicine, Department of Microbiology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center of the University of Michigan Medical School, Ann Arbor, MI, USA. He has initiated and led the development of several biomedical ontologies, including the community-based Vaccine Ontology (VO; http://www.violinet.org/vaccineontology) and Ontology of Adverse Events (OAE; http://www.oae-ontology.org). His group, through collaborations with others, has developed several ontology-oriented software programs including OntoFox (http://ontofox.hegroup.org) for importing and reusing individual ontology terms and Ontobee (http://www.ontobee.org) as a linked RDF data server for ontology term information retrieval and display. His group has also developed and applied ontology-based literature mining tools to study biological pathways with an emphasis on vaccine-associated gene interaction networks among host and pathogen genes. WEBEX DETAILS: ------------------------------------------------------- To start or join the online meeting ------------------------------------------------------- Go to https://stanford.webex.com/stanford/j.php?ED=175352027&UID=481527042&PW=NYjM4OTVlZTFj&RT=MiM0 Meeting Password: ncbo ------------------------------------------------------- Audio conference information ------------------------------------------------------- To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code. Call-in toll number (US/Canada): 1-650-429-3300 Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=175352027&tollFree=0 Access code:925 343 903 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: Jie Z. <jie...@pc...> - 2012-04-09 14:27:35
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Hi Bill, The issue caused by redirect from http protocol to https protocol. I have set the redirect using http protocol url. You can load OBI using URL http://purl.obolibrary.org/obo/obi.owl now. Thanks, Jie On 4/6/2012 12:24 PM, Bill Hogan wrote: > Folks, > > WHen I try to open the ontology from the URI, I get the following error: > > org.xml.sax.SAXParseException: White spaces are required between > publicId and systemId. > > I am using Protege 4.1 (Build 239) on a Windows PC. > > Bill > > > On Thu, Apr 5, 2012 at 3:51 PM, Jie Zheng<jie...@pc...> wrote: >> Hi All, >> >> OBI 2012 Spring version is released. The new version is on: >> http://purl.obolibrary.org/obo/obi.owl >> >> Highlight of this release: >> >> OBO format of OBI is available for this version >> (http://purl.obolibrary.org/obo/obi/obi.obo) >> >> The OBO format of OBI was generated using Oort, a OBO-OWL converter. >> >> 25 newly added classes, including >> - terms to represent metadate of sample required by BRC >> - types of binding assays and related terms such as binding measurement data >> required by the IEDB group >> >> The newly added OBI classes are listed on >> http://obi.svn.sourceforge.net/viewvc/obi/releases/2012-03-29/docs/newClasses.html >> >> fixed multiple asserted inheritance of NCBITaxon under organism branch >> caused by some errors occur during MIROET >> >> A static URL is given to OBI IEDB view ontology (view for IMMUNE EPITOPE >> DATABASE), http://purl.obolibrary.org/obo/obi/obi_IEDBview.owl >> >> The detailed release information can be found on: >> http://purl.obolibrary.org/obo/obi/release-notes.html >> >> The released OBI files can be loaded into Protege 4v and reasoned consistent >> using Hermit reasoner. It was loaded into Ontobee (http://www.ontobee.org/) >> and Bioportal. >> >> Notes: There are parsing errors shown in the Bioportal website. We are >> waiting for fixing. >> >> >> Jie >> >> >> ------------------------------------------------------------------------------ >> Better than sec? Nothing is better than sec when it comes to >> monitoring Big Data applications. Try Boundary one-second >> resolution app monitoring today. Free. >> http://p.sf.net/sfu/Boundary-dev2dev >> _______________________________________________ >> Obi-devel mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-devel >> |
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From: Jie Z. <jie...@pc...> - 2012-04-06 17:08:02
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Hi Bill, I have same issue when I opened OBI from url http://purl.obolibrary.org/obo/obi.owl This URL redirect to the file: https://obi.svn.sourceforge.net/svnroot/obi/releases/2012-03-29/merged/merged-obi-comments.owl If you use the above URL, everything worked fine. I have no idea about the error with Protege and cannot fix it by searching online. I will send the email to Protege mailing list. We have set this kind of redirect for each release. They all worked well. It might be some bug in the obi OWL file but I cannot find it. Will let you know when it get be fixed. You can use the link of the actually file located for OBI now. Thanks for reporting the error. Jie On 4/6/2012 12:24 PM, Bill Hogan wrote: > Folks, > > WHen I try to open the ontology from the URI, I get the following error: > > org.xml.sax.SAXParseException: White spaces are required between > publicId and systemId. > > I am using Protege 4.1 (Build 239) on a Windows PC. > > Bill > > > On Thu, Apr 5, 2012 at 3:51 PM, Jie Zheng<jie...@pc...> wrote: >> Hi All, >> >> OBI 2012 Spring version is released. The new version is on: >> http://purl.obolibrary.org/obo/obi.owl >> >> Highlight of this release: >> >> OBO format of OBI is available for this version >> (http://purl.obolibrary.org/obo/obi/obi.obo) >> >> The OBO format of OBI was generated using Oort, a OBO-OWL converter. >> >> 25 newly added classes, including >> - terms to represent metadate of sample required by BRC >> - types of binding assays and related terms such as binding measurement data >> required by the IEDB group >> >> The newly added OBI classes are listed on >> http://obi.svn.sourceforge.net/viewvc/obi/releases/2012-03-29/docs/newClasses.html >> >> fixed multiple asserted inheritance of NCBITaxon under organism branch >> caused by some errors occur during MIROET >> >> A static URL is given to OBI IEDB view ontology (view for IMMUNE EPITOPE >> DATABASE), http://purl.obolibrary.org/obo/obi/obi_IEDBview.owl >> >> The detailed release information can be found on: >> http://purl.obolibrary.org/obo/obi/release-notes.html >> >> The released OBI files can be loaded into Protege 4v and reasoned consistent >> using Hermit reasoner. It was loaded into Ontobee (http://www.ontobee.org/) >> and Bioportal. >> >> Notes: There are parsing errors shown in the Bioportal website. We are >> waiting for fixing. >> >> >> Jie >> >> >> ------------------------------------------------------------------------------ >> Better than sec? Nothing is better than sec when it comes to >> monitoring Big Data applications. Try Boundary one-second >> resolution app monitoring today. Free. >> http://p.sf.net/sfu/Boundary-dev2dev >> _______________________________________________ >> Obi-devel mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-devel >> |
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From: Jie Z. <jie...@pc...> - 2012-04-05 20:51:30
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Hi All, OBI 2012 Spring version is released. The new version is on: http://purl.obolibrary.org/obo/obi.owl Highlight of this release: * OBO format of OBI is available for this version (http://purl.obolibrary.org/obo/obi/obi.obo) o The OBO format of OBI was generated using Oort, a OBO-OWL converter. * 25 newly added classes, including - terms to represent metadate of sample required by BRC - types of binding assays and related terms such as binding measurement data required by the IEDB group The newly added OBI classes are listed onhttp://obi.svn.sourceforge.net/viewvc/obi/releases/2012-03-29/docs/newClasses.html * fixed multiple asserted inheritance of NCBITaxon under organism branch caused by some errors occur during MIROET * A static URL is given to OBI IEDB view ontology (view for IMMUNE EPITOPE DATABASE),http://purl.obolibrary.org/obo/obi/obi_IEDBview.owl The detailed release information can be found on: http://purl.obolibrary.org/obo/obi/release-notes.html The released OBI files can be loaded into Protege 4v and reasoned consistent using Hermit reasoner. It was loaded into Ontobee (http://www.ontobee.org/) and Bioportal. Notes: There are parsing errors shown in the Bioportal website. We are waiting for fixing. Jie |
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From: Trish W. <plw...@gm...> - 2012-04-04 07:43:58
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International Conference on Biomedical Ontology 2012, co-located with FOIS 2012, 21-25 July 2012; Graz, Austria. Call for Software Demonstrations and Posters Deadline: 15 April 2012 Conference Web site: http://purl.org/icbofois2012/ Submit via: https://www.easychair.org/conferences/?conf=icbo-2012 *** Software Demonstrations *** Software that create, manipulate and use biomedical ontologies will be an important feature of ICBO 2012. Without tools that use ontologies to help query, browse and analyse biomedical data the creation of all our biomedical ontologies is largely fruitless. So, come and show us your software that creates ontologies, manipulates ontologies, and is driven by ontologies. We want software demos to be first class citizens at ICBO, so submit your two-page software demonstration descriptions via our Easychair site at https://www.easychair.org/conferences/?conf=icbo-2012, track 'ICBO 2012 -- Software Demonstrations'. *** Poster Abstracts *** We also want posters sessions at ICBO that stimulate discussion about our domain - the ontologies you've created; the things you've done with ontologies; support and supplementary information about the papers you've written for ICBO or elsewhere. Again, we want ICBO posters to be first class citizens at the conference (they wil have "flash" slots at the conference), so get writing your ICBO poster abstracts. Submit your 1-page abstracts to https://www.easychair.org/conferences/?conf=icbo-2012, track 'ICBO 2012 -- Poster Abstracts'. *** Contact *** For more information or to offer sponsorship, please send us a note at con...@gm... *** Organizing Committee *** General Chairs: Ronald Cornet (Amsterdam, The Netherlands) and Robert Stevens (Manchester, UK) Workshops and Tutorials Chair: Melanie Courtot (Vancouver, Canada) Early Career Consortium Chair: Ludger Jansen (Rostock, Germany) Software Demonstration Chair: Trish Whetzel (Stanford, USA) Proceedings Chair: Janna Hastings (Geneva, Switzerland) Local Chair: Stefan Schulz (Graz, Austria) 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: jie z. <jie...@pc...> - 2012-04-03 16:50:19
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Apologies for duplicate postings: ICBO 2012 workshop on OBI: A shared ontology for representing biomedical studies and resources July 22nd 2012, Graz, Austria Ontology for Biomedical Investigations (OBI) developers will give a half day workshop on ICBO 2012 (July 22th, morning). OBI aims to represent all elements of investigations such as assays, instruments or subject enrollment criteria. This workshop will provide training on how to use OBI in specific applications and contribute to OBI development. The application use cases will cover both biological and medical investigations of interest to different communities. The workshop will have a hands-on session that allows attendees to practice tools and apply techniques (MIREOT, QTT, Ontology View) introduced in the use cases. The workshop webpage has been set up on the ICBO/FOIS website, including workshop outline, reading materials, software installation, etc: http://kr-med.org/icbofois2012/obi/index.htm We will update the page further as more details become available. For questions, please contact the workshop organizers: Jie Zheng <jie...@pc...> Christian Stoeckert <sto...@pc...> Yongqun(Oliver) He <yon...@me...> We are looking forward seeing you on the ICBO OBI workshop. On behalf of the workshop organizers, Jie Zheng Center for Bioinformatics Department of Genetics University of Pennsylvania Perelman School of Medicine |
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From: Susanna-Assunta S. <sa....@gm...> - 2012-04-02 11:25:23
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*What*: Call for participation in the Bio-Ontologies SIG 2012 *Where*: July 13 - 14, 2012, Long Beach, CA. (Co-located with ISMB 2012) *When*: Submissions Due: April 13th, 2012 (Fri) *URL*: www.bio-ontologies.org.uk <http://www.bio-ontologies.org.uk> Dear Colleagues, The Bio-Ontologies SIG provides a forum for discussion of the latest and innovative research in the application of ontologies and in the organisation, presentation and dissemination of knowledge in life sciences. Bio-Ontologies is one of the longest running SIG. We are interested in innovative approaches to organizing and consuming knowledge in life sciences and biomedicine. We invite papers in traditional areas, such as the biological applications of ontologies, reports on newly developed ones, and the use of ontologies in data sharing standards. In addition, we invite submissions on using ontologies for translational research as well as data-driven approaches to evaluate ontologies. See the full list of subject areas at: http://www.bio-ontologies.org.uk/call-for-participation. We are inviting three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the 2 days for at least one poster session. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation. 6-8 papers from the SIG are invited to submit an expanded version to a special issue of the open access Journal of Biomedical Semantics. The special issue with papers from 2011 (out at the end of April), will include: 1. Beisswanger E. et al .. Towards Valid and Reusable Reference Alignments - Ten Basic Quality Checks for Ontology Alignments and Their Application to Three Different Reference Data Sets 2. Ciccarese P. et al .. Open semantic annotation of scientific publications using DOMEO 3. Good B.M. et al .. Linking genes to diseases with a SNPedia-Gene Wiki mashup 4. Jupp S. et al .. Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations with OWL 5. LePendu P. et al .. Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes 6. Tcheremenskaia O. et al .. OpenTox Predictive Toxicology Framework: toxicological ontology and semantic media wiki-based OpenToxipedia 7. Tsatsaronis G. et al .. A Maximum-Entropy Approach for Accurate Document Annotation in the Biomedical Domain -- SIG Organizers http://www.bio-ontologies.org.uk/organizers -- |
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From: Trish W. <plw...@gm...> - 2012-03-19 19:48:46
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The next NCBO Webinar will be presented by Nicolas Le Novère from the European Bioinformatics Institute on "MIRIAM Registry and Identifiers.org - Robust and versatile identification in life sciences" at 10:00am PT, Wednesday, March 21. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series. ABSTRACT: MIRIAM Registry (http://www.ebi.ac.uk/miriam) provides unique, perennial and location-independent identifiers for data used in the biomedical domain. At its core is a shared catalogue of data collections, for each of which an individual namespace is created, and extensive metadata recorded. This namespace allows the generation of Uniform Resource Identifiers (URIs) to uniquely identify any record in a collection. Moreover, various services are provided to facilitate the creation and resolution of the identifiers. Since its launch in 2005, the system has evolved in terms of the structure of the identifiers provided, the software infrastructure, the number of data collections recorded, as well as the scope of the Registry itself. We describe here the new parallel identification scheme and the updated supporting software infrastructure. We also introduce the new Identifiers.org service (http://identifiers.org) that is built upon the information stored in the Registry and which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs). The flexibility of the identification scheme and resolving system allows its use in many different fields, where unambiguous and perennial identification of data entities are necessary. SPEAKER BIO: Nicolas Le Novère is group leader at the EMBL-EBI near Cambridge (UK). Besides his research activity, centred on modeling signal transduction in neurons, Le Novère develops community services that facilitate research in computational systems biology. In particular, he is coordinating efforts in encoding and annotating kinetic models in chemistry and cellular biology, including the languages SBML, SBGN, SED-ML, the reporting guidelines MIRIAM and MIASE, and the ontologies SBO, KiSAO and TEDDY. Le Novère also created BioModels Database, now the reference resource to share published mathematical models of biological interest. WEBEX DETAILS: ------------------------------------------------------- > To start or join the online meeting > ------------------------------------------------------- > Go to > https://stanford.webex.com/stanford/j.php?ED=171726072&UID=481527042&PW=NMzhlMDBjNzk0&RT=MiM0 > > Meeting Password: ncbo > > > ------------------------------------------------------- > Audio conference information > ------------------------------------------------------- > To receive a call back, provide your phone number when you join the > meeting, or call the number below and enter the access code. > Call-in toll number (US/Canada): 1-650-429-3300 > Global call-in numbers: > https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=171726072&tollFree=0 > > Access code:925 756 393 > > > > > 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: Susanna S. <sa....@gm...> - 2012-03-06 00:21:15
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*What*: Call for participation in the Bio-Ontologies SIG 2012 *Where*: July 13 - 14, 2012, Long Beach, CA. (Co-located with ISMB 2012) *When*: Submissions Due: April 13th, 2012 (Fri) *URL*: www.bio-ontologies.org.uk <http://www.bio-ontologies.org.uk> Dear Colleagues, The Bio-Ontologies SIG provides a forum for discussion of the latest and innovative research in the application of ontologies and in the organisation, presentation and dissemination of knowledge in life sciences. Bio-Ontologies is one of the longest running SIG. We are interested in innovative approaches to organizing and consuming knowledge in life sciences and biomedicine. We invite papers in traditional areas, such as the biological applications of ontologies, reports on newly developed ones, and the use of ontologies in data sharing standards. In addition, we invite submissions on using ontologies for translational research as well as data-driven approaches to evaluate ontologies. See the full list of subject areas at: http://www.bio-ontologies.org.uk/call-for-participation. We are inviting three types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the 2 days for at least one poster session. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation. 6-8 papers from the SIG are invited to submit an expanded version to a special issue of the open access Journal of Biomedical Semantics. The special issue with papers from 2011 (soon to be published!), will include: 1. Beisswanger E. et al .. Towards Valid and Reusable Reference Alignments - Ten Basic Quality Checks for Ontology Alignments and Their Application to Three Different Reference Data Sets 2. Ciccarese P. et al .. Open semantic annotation of scientific publications using DOMEO 3. Good B.M. et al .. Linking genes to diseases with a SNPedia-Gene Wiki mashup 4. Jupp S. et al .. Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations with OWL 5. LePendu P. et al .. Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes 6. Tcheremenskaia O. et al .. OpenTox Predictive Toxicology Framework: toxicological ontology and semantic media wiki-based OpenToxipedia 7. Tsatsaronis G. et al .. A Maximum-Entropy Approach for Accurate Document Annotation in the Biomedical Domain -- SIG Organizers http://www.bio-ontologies.org.uk/organizers |
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