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BioPortal Release 4.22 (November 2015)
Value sets are flat vocabularies consisting of a top concept (the name of the value set) and a set of terms. They are stored in BioPortal within ontologies that have a type indicating 'value set'; the nodes immediately under the root name the value sets contained in that value set ontology.
- New functionality at the REST API level in support of our collaboration with the CEDAR project:
- Added the ability to search for, and retrieve all value sets.
- Implemented search for value set items (example link).
- Implemented search for ontology classes and value set items (example link).
- Added the ability to exclude value set collections from search (example link).
- Added the ability to search for value set values across all value sets in an ontology.
- Ontologies are now sortable by creation date on the Admin page.
- Clicking the Add Comment and/or Add Proposal buttons in the Notes sections for ontologies will navigate unauthenticated users to the login page.
- Fixed an issue that caused Projects page load times in excess of 3 minutes.
- Fixed an issue that caused the UI to go blank after selecting the root node of the CCO ontology.
- Admin page: the ontologies table now refreshes after deleting an ontology.
- Fixed an issue that caused a 404 error when trying to view the DINTO ontology.
- Fixed an inconsistency in the metadata for the CHMO ontology that caused the parsing process to fail.
BioPortal Release 4.21 (October 2015)
- Fixed an issue that caused class trees to reload every time a class was selected.
- Fixed an issue with BioPortal's term selection widget that caused raw HTML to be displayed in search results.
- Fixed a problem in the REST API that caused an internal server error when accessing nonexistent users. The API now correctly displays a 404 not found message.
- Fixed a bug that prevented flat tree ontologies from displaying in BioPortal.
- Fixed an issue that prevented the latest versions of the Gazetteer and Chemical Entities of Biological Interest ontologies from parsing.
- Fixed a problem that prevented visualization from working with private ontologies (thanks go to Eric Verbeek for this).
BioPortal Release 4.20 (August 2015)
This release includes minor fixes from several previous releases.
- Released a new version of the Ontology Recommender. This version is more flexible than the previous version and allows users to assign weights to the scores for various factors that influence the recommendation. In addition, some edge cases in the old system that resulted in bad recommendations have been addressed. This new recommendation system was developed independently by Marcos Martinez and then incorporated into our base code.
- Instances (individuals) in an ontology can now be accessed through the API. Documentation for this is available at: http://data.bioontology.org/documentation#Instance.
- Components have been added to the Annotator UI to allow users to exercise additional options available through the API.
- Icons now indicate non-subclass relationships in OBO ontologies. Previously it was not possible to distinguish visually OBO subclass from other OBO relations displayed in the tree (such as OBO part-of).
- The UMLS MeSH vocabulary is now displayed hierarchically. Previously it was displayed as a flat list of terms because of some problems with the hierarchical relation in the source that we were using.
- The Search API now allows search-by-name of provisional classes assigned to an ontology.
- The UMLS ontologies have all been updated to the latest 2015AA release.
- A new version of BioMixer with a simpler user interface has been incorporated into the system. This work was done by our collaborators at the University of Victoria.
- Created both a REST service and a UI for BioPortal application administration. This interface is automatically visible to VM administrators.
- Updated the framework of our system from RAILS version 2 to version 4.
- Fixed many bugs, especially those causing failures when parsing an ontology.
BioPortal Release 4.14 (February 2015)
This release includes minor fixes from several previous releases.
- The ontology summary page for each ontology now has a graph of recent history of the level of user-interface (UI) web traffic (number of page views) for that ontology. This graph is available under the “Metrics” box. See, for example, http://bioportal.bioontology.org/ontologies/SNOMEDCT . The raw data is also available for download in CSV format from the same location.
- The BioPortal home page now has a link that displays all ontologies in the system and the number of UI views for each ontology. Previously usage of only the top 5 ontologies were available.
- Users of our virtual machine now have the ability to plug in alternate concept recognizers for use by the annotator. To support these custom annotators, arbitrary parameters can be passed via the rest interface to the underlying concept recognizer. Documentation for how to make use of this feature is available on GitHub. Previously the “mgrep” concept recognizer was hardwired into the system and code modifications were required to employ another recognizer.
- Ontologies views can now be used for annotation. Previously only top level ontologies were available for use by the annotation system.
- All of PubMed has been indexed for use by the Resource Index for all terms in all ontologies in BioPortal. Previously only 18 months of PubMed data was indexed.
- We now provide for download, for all resources in BioPortal, files containing counts for term occurrence and co-occurrence (occurrence of pairs of terms in a document). These files can be used for research in enrichment analysis. Documentation of the files and how they might be used is available on GitHub.
- The ontology browse page now has a faceted interface that allows the list of displayed ontologies to be narrowed as desired. Previously all ontologies appeared in an alphabetical list but this became unwieldy with the 400+ ontologies that we now have.
- There is now a user-interface for displaying all of the properties in an ontology. If the properties were created in a hierarchy then this hierarchy is displayed. Previously only the class hierarchy was displayed. Properties were available programmatically though the REST interface but this information was not surfaced in the UI.
- Ontologies defined using SKOS are now supported. For these ontologies, the hierarchy is determined by the SKOS “broader” and “narrower” properties.
- We now allow download of all publically available ontologies in RDF. UMLS ontologies with restrictive licenses are excluded.
- We fixed a number of non-parsing ontologies and removed a bunch of low-content (“test”) ontologies.
- The system now contains the latest versions (2014AB) of all UMLS ontologies.
- We now treat all OBO synonym types as a BioPortal synonyms. Previously only the OBO “exact” synonym type was treated as a BioPortal synonym.
- We now notify by email the ontology authors if the nightly pull of their ontology fails.
NCBO Scientific Advisory Board member Olivier Bodenreider, MD, PhD, Senior Scientist and Chief, Cognitive Sciences Branch, Lister Hill Center, has received the NLM 2014 Regents Award for Scholarship or Technical Achievement. He received the award “In recognition of his exceptional leadership in the dissemination of NLM drug information sources through graphical and programming interfaces.” Dr. Bodenreider’s work has greatly facilitated the use of standard drug terminology both in informatics research and in electronic health record systems.
Congratulations to Olivier on this well-deserved honor!
We are happy to announce the release of BioPortal 4.10. We have had a number of “silent releases” since the 4.6 release in late April. We are pleased to announce the latest BioPortal release and fill you in on features that have been released silently in the interim:
Over 30 individuals from across the US and Canada met at Stanford University for a two day NCBO-sponsored hackathon on April 26 and April 27. The hackathon brought together a new community together to develop a so-called Network of BioThings (proteins, genes, pathways, mutations, drugs, diseases) extracted from scientific research articles and integrated with public biomedical data. During the hackathon, we identified motivating use cases, developed shared, sustainable, multi-component infrastructures, implemented common data representations, ontology-based programmatic interfaces, and developed cool applications. Specifically, we received prize-winning submissions for building variant annotation hubs, multi-dataset traversal hubs, hypothesis explanation tools, natural language processing tools, and an ontology-driven application to semantically search PubMed. All in all, this event set the to develop nascent collaborations and group-based funding opportunities.
AAAI Fall Symposium on "Discovery Informatics: The Role of Artificial Intelligence in Innovating Scientific Processes"
CALL FOR PARTICIPATION
November 2-4, 2012
Addressing the ambitious research agendas put forward by many scientific disciplines requires meeting a multitude of challenges in intelligent systems, information sciences, and human-computer interaction. There are many aspects of the scientific discovery process that our community could help automate, facilitate, or make more efficient through artificial intelligence techniques. For example, although considerable efforts have been directed toward data modeling and integration, these activities continue to demand large investments of scientists’ time and effort. The scientific literature continues to grow and is becoming more and more unmanageable for researchers operating in the most active disciplines. Better interfaces for collaboration, visualization, and understanding would significantly improve scientific practice. Scientific data, publications, and tools could be published in open formats with appropriate semantic descriptions and metadata annotations to improve sharing and dissemination. Opportunities for broader participation in well-defined scientific tasks enable human contributors to provide large amounts of data, annotations, or complex processing results that could not otherwise be obtained. These are just some examples of areas where there are opportunities for artificial intelligent techniques could make a difference. Improvements and innovations across the spectrum of scientific processes and activities will have a profound impact on the rate of scientific discoveries.
This symposium provides a forum for researchers interested in understanding the role of AI techniques in improving or innovating scientific processes. The symposium will include invited talks, paper presentations, panel discussions, and plenary sessions. Six invited speakers will provide their personal perspectives on successes and challenges for Discovery Informatics. There will be seven full papers presented, interleaved with the invited talks. Two of the sessions will be panel discussions on current topics of interest, with panelists from a variety of perspectives including academia, funding agencies, and industry. The symposium will open and close with plenary sessions that will serve for exchange of general observations and synthesis of views for all attendees. AAAI will hold an evening reception as well as a joint session where major highlights of the other parallel symposia will be presented.
• Timothy W. Clark, Harvard University (bio)
• William Cohen, Carnegie Mellon University (bio)
• Lawrence Hunter, University of Colorado (bio)
• Chris Lintott, University of Oxford (bio)
• Hod Lipson, Cornell University (bio)
• Jude Shavlik, University of Wisconsin Madison (bio)
• Challenges in Big Data: Discoveries at the Fringe of Science
• Discovery Informatics: Innovating Science Practice one Scientist at a Time
Registration and hotel booking deadline is October 10, 2012.
• Will Bridewell, Stanford University
• Yolanda Gil, University of Southern California
• Haym Hirsh, Rutgers University
• Kerstin Kleese van Dam, Pacific Northwest National Laboratory
• Karsten Steinhaeuser, University of Minnesota
Semantic Tech & Business Conference - San Francisco - Early Bird Rates End April 26
Early bird rates for the Semantic Tech & Business Conference end on Thursday, April 26. Friends of NCBO should use discount code "BMIR15" to receive an extra 15% off of Gold Passports.
Also note that the next Protege-OWL short course will take place right before SemTech. You can combine two events in one trip.
This year’s conference, held in San Francisco on June 3-7, will feature:
· 130+ conference presentations
· 160+ expert speakers
· 25+ case studies
· 14 half-day workshops
· Major industry product announcements
· SemTechBiz Career Corner
· NEW for 2012: SemTechBiz Start-Up Competition
Sign up here today for substantial early bird discounts:
Baker's research is in the areas of computational biophysics, nanotechnology, and informatics. He currently serves as the chief scientist for Signature Sciences at PNNL and the laboratory's Signature Discovery Initiative. Signatures are distinguishing collections of features that identify, detect or predict a phenomena of interest, such as cyber intrusion, energy grid failure or disease progression.
Baker is actively involved in the development of new algorithms and software for computational biology and modeling in support of several research projects. He leads a National Cancer Institute activity called the caBIG Nanotechnology Working Group that is developing computational methods for the prediction of nanomaterial properties and the design of improved nanoparticles. He is also chair for an American Society for Testing and Materials (ASTM) subcommittee on nanotechnology informatics that is working to develop new standards for data sharing and analysis in nanotechnology. Baker is an editorial board member for the Biophysical Journal and editor-in-chief for Computational Science & Discovery.
After his research training at the University of California, San Diego, Baker joined the Department of Biochemistry and Molecular Biophysics at Washington University in St. Louis in 2002 and was promoted to associate professor with tenure in 2006. He joined PNNL in 2010. Baker earned a bachelor's degree from the University of Iowa and a doctorate from UC San Diego.
DATE: 21 September 2011
TIME: 9:00 - 17:00
PLACE: National Library of the Netherlands, The Hague
[Registration is available for this special day-long session only or for the full conference]
We are writing to invite you to participate in a Dublin Core special session being planned for DC-2011 at The Hague. The day-long pre-conference special session is intended as a forum for managers of structured data vocabularies as well as researches and practitioners working on metadata management and controlled vocabularies. The session will be focused on the shared needs for vocabulary management infrastructure, the policy issues surrounding vocabulary management, and the possibility of mapping between vocabularies. The topics listed are only suggestions--attendees will be able to influence the direction of discussion. A poll will be circulated to registrants prior to the meeting to gather additional background information and help set the agenda.
At DC-2010, Mike Bergman's keynote address strongly suggested that DCMI has a potential role in promoting co-operation among vocabulary managers and in providing best practices for vocabulary alignment and interoperability. The inevitable and useful proliferation of vocabularies emerging in the linked data space demonstrates a need for increased vocabulary reuse and tools to facilitate this reuse, as well as central reference vocabularies and tools to manage and encourage vocabulary mapping. The purpose of this day-long special session at DC-2011 is to explore the issues identified by Bergman among others and DCMI's potential role in supporting vocabulary alignment, interoperability and preservation across the metadata ecosystem.
If travel is not an option for any of you, remote participation may be possible through IRC. Please note that early-bird registration ends on 5 September.
We very much hope some or all of you may be able to attend what we expect to be a very useful event.
Tom Baker, DCMI, United States
Corey Harper, New York University, United States Diane Hillmann, DCMI, United States Gordon Dunsire, Consultant, United Kingdom Johannes Keizer, Food and Agriculture Organization of the United Nations (FAO), Italy Jon Phipps, Metadata Management Associates, United States
AMIA, the association for informatics professionals, invites your submission to the 2012 Joint Summits, March 19-23, 2012, in San Francisco. The Translational Bioinformatics (TBI) Summit opens the AMIA Joint Summits on Translational Science and will be followed by the Summit on Clinical Research Informatics (CRI) from March 21 23, 2012, at the same venue.
For TBI, we look forward to submissions that include innovative datacentric approaches that compute on large amounts of data to discover patterns and to make clinically relevant predictions that are the forte of Translational Bioinformatics. The changes in public policy, the availability of large datasets from multiple molecular level measurements, and increasing electronic heath record (EHR) adoption, coupled with recent advances in natural language processing, access to vast computing infrastructure, sophisticated ontologies, data-mining and machine learning tools that have all converged to enable Big Data mining in Translational Bioinformatics. This year, four tracks will cover research that takes the field from base pairs to bedside, with an emphasis on clinical implications of mining massive data-sets, and on bridging the latest multimodal measurement technologies with large amounts of healthcare data.
Concepts, Tools and Techniques for Translational Bioinformatics Integrative Analysis of multi modal measurements Base pairs to Bedside Informatics with Big Data Track details at: www.amia.org/jointsummits2012/tbi-submission
For CRI, we look forward to submissions that showcase leading-edge innovative methods and technologies that focus on accelerating all phases of translational science including study of conceptual design and simulation, patient identification and recruitment, data collection, integration and visualization, and data analysis, dissemination and knowledge transfer. We highlight four specific areas for special emphasis. But we invite submissions from across the CRI community to present the broad range of activities that are addressing translational research informatics needs.
Research and Resource Discovery, Collaboration and Sharing Bedside to Base Pairs -- From Clinical Observations to Genetic Discovery Clinical Care and Clinical Research Work Flow Integration Emerging Informatics Platforms for Integrated Translational Research Track details at: www.amia.org/jointsummits2012/cri-submission
Paper Proposals: due August 19, 2011
Panels, Posters, Podium Abstract Proposals: due October 21, 2011
Details on submission types: www.amia.org/jointsummits2012/types-proposals
We look forward to your submissions and hope that you will join us in San Francisco in March of 2012.
Nigam H. Shah, Stanford University
Chair, 2012 Scientific Program Committee TBI Summit
Michael Kahn, University of Colorado
Chair, 2012 Scientific Program Committee CRI Summit
The real challenge for Semantic Web technologies and ontologies lays in the adoption; although the need for this disruptive technology is clear, it has not yet been fully adopted by the mainstream. Ontologies: where, what for, how, when and why? Ontologies are being used in several applications, but is ontology engineering a mature discipline? Not only are we interested in practical realizations of the Semantic Web, but also in visions of technology that illustrate how SW technology and ontologies could change our experience of the Web
Interested in the OCAS Challenge?
Interested in submitting research papers or position statements to the OCAS Workshop?
Visit us: http://ocas.mywikipaper.org
Questions and issues addressed by OCAS:
- How are SW technologies and Ontologies being adopted by mainstream?
- Experience reports of the introduction of SW technologies and ontologies in corporate and government environments Once introduced in an environment, how do SW and ontology-based applications evolve?
- Ontologies in manufacturing and production chains Ontologies supporting CAD interoperability and feature extraction; towards smart CAD environments How could RDF(a) and ontologies be used to represent the knowledge encoded in scientific documents and in general-interest media publications?
- What ontologies do we need for representing structural elements in a document?
- How can we capture the semantics of rhetorical structures in scholarly communication, and of hypotheses and scientific evidence?
- What does a network of truly interconnected documents look like? How could interoperability across documents be enabled?
- Are decision support systems in the biomedical domain using ontologies? How?
- How are biomedical ontologies logically formalizing the rich set of lexical definitions gathered? How are these ontologies going beyond controlled vocabularies?
- Practical cases of successful and unsuccessful application of ontologies and SW technologies in application domains such as: financial, biomedical, e-business, engineering, law enforcement, document management, egovernment, legislative systems.
We would also like to have visionary papers addressing issues such as:
- Semantic Web + Ontologies + Ubiquitous Computing + Folksonomies =Visions of the future, how can technology make us look smart?
- Conceptualism vs Realism, how is this related to Ontology Engineering? How is this related to the realization of the Semantic Web?
- How are Semantic Web technologies and Ontologies shaping the intelligent layer of the Web?
OCAS can be summarized in a simple sentence, Ontologies and Semantic Web technology come of age, how is the Semantic Web changing our experience of the Web? Moving beyond theoretical frameworks and heading towards a significant impact in end user experience is at the core of OCAS. The overall objective of the challenge is to illustrate how ontologies and SW technologies are delivering novel user experiences.
First place: $2000 USD
Second place: $1000 USD
Three third prizes of $500 each
Selected projects will be funded through implementation by Protech Solutions Inc.
Projects are to focus on innovative uses of HPC and data mining in semantic technologies for HealthCare, Medical Informatics and Computer Security. Projects with high relevance to social networking, low-tech environments, and third-world countries are encouraged.
Those participating in the challenge should provide a three-page manuscript describing their software; from the manuscript it should be clear for judges:
- Software availability: judges and general public should be able to access the software. In most cases this means that the software, ontologies and/or infrastructure is freely accessible -free software is not compulsory.
- Semantic Web technology: how is this application making use of semantic web technology? How is this application making use of existing infrastructure? Data sources being used, etc.
- How is it delivering new layers of functionality based on semantic data sources (linked data, RDF stores, ontologies, etc).
- How is it delivering an intelligent interconnected experience to the end user?
- What is the added value?
- How is the Interconnectedness of semantic data sets being delivered to the end user?
- How are intelligence and interconnectivity being supported by the software or infrastructure?
- Does the software or infrastructure represent a fundamental change for the domain rather than just an incremental improvement or just one of many added new features?
- We would like to have applications from all domains. The GC is not limited to web based applications, mobile platforms for devices like iPAD, iphone, Galaxy, XOOM, HTC, etc are also encouraged. Authors submitting to other Challenges, workshops and conferences are welcome to also submit their work to the OCAS challenge.
For those who require high performance computing facilities our sponsor, http://protechsolutions.com/, will make them available free of charge.
Submission should be via Easychair https://www.easychair.org/conferences/?conf=ocas2011
All papers submitted for the OCAS Challenge should be formatted according to the LNCS format.
- Paper submission deadline: August 15
- Notification of acceptance or rejection: September 5
- Camera ready version due: September 16
Judging the Challenge:
Oscar Corcho, Ontology Engineering Group (OEG), UPM, Madrid, Spain
Pascal Hitzler, Dept. of Computer Science, Wright State University, Dayton, OH, USA
Alexander Garcia, University of Arkansas for Medical Sciences, USA.
Fabio Ciravegna, University of Sheffield, UK
Michel Dumontier, Carleton University, Canada
The NCBO team has performed a proof-of-concept study to demonstrate that text-mining patient records could be an effective way to gather information on safety, efficacy, and potential new drug indications.
The team presented the work earlier this month at the Bio-Ontologies Special Interest Group Meeting, held prior to the Intelligent Systems for Molecular Biology Conference.
The paper found that the anti-inflammatory drug rofecoxib, marketed by Merck as Vioxx, increased the risk of serious coronary heart disease. Merck withdrew the drug from the market voluntarily in 2004.
The International Biocuration Conferences is a unique event for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. For the 5th International Biocuration Conference (http://pir.georgetown.edu/biocuration2012.html), you are invited to submit your work for publication, with the possibility for an oral presentation at the Biocuration 2012 meeting. This call for papers is done in collaboration with Database: The Journal of Biological Databases and Curation (http://database.oxfordjournals.org/). This is a great occasion to enhance the recognition of our profession by the greater biological research communities.
There are seven topic sessions from which submitters are invited to select:
- Ontologies, standards and best practices, including gold standard datasets
- Protein annotation; sequence, structure, pathway
- Community annotation and Wikis
- Genomics and metagenomics data curation
- HTP data (focus on NGS and MS data) curation and presentation
- Literature collection, text mining and curation
- Tools to assist curation, including automated pipelines
Accepted papers will be given special consideration by the session chairs for selection as oral presentations. In the event that an accepted paper does not fit the scope of the session topics, it will still be considered for publication in DATABASE but may not be invited for a presentation at the conference.
Moreover, the DATABASE journal will create a virtual issue of papers presented at the Biocuration conference in Washington DC on April 2-4, 2012. This virtual issue will be printed and distributed to conference attendees.
The review process will be expedited for these papers and we will thus need to be firm on the submission deadline:
Call for papers: August 1, 2011
Submission deadline: October 15, 2011
First decisions: November 15, 2011
Deadline for revisions: December 15, 2011 Final decisions: January 10, 2012
Conference: April 2-4 2012
Authors wishing to submit to DATABASE for the 2012 Biocuration Virtual issue should go to the DATABASE home page (http://database.oxfordjournals.org/) and click on the "submit now" after having read the "Instructions to Authors". Authors should CLEARLY state that they are submitting this manuscript for consideration for the 2012 Annual Biocuration conference so that the DATABASE staff will ensure appropriate fast-track for inclusion in this meeting's proceedings.
In addition, in the database submission form, they should also select "Biocuration Conference Paper" as a manuscript type. We We look forward to your participation at the 5th International Biocuration Conference.
Biocuration 2012 Organizing Committee
*Submission deadline: October 1, 2011
* Notification: December 2011
* Final Version due: January 2012
* Publication: Early 2012
* Manuscript preparation - Instructions for Authors: http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/auth...
* Manuscript submission: http://ees.elsevier.com/jbi/
Aims and objectives
We are inviting submissions for a special issue of the Journal of Biomedical Informatics devoted to the topic of community-driven curation of ontologies and knowledge bases in Health Care and Life Sciences. The use of formal systems to define biomedical concepts and to represent and store biomedical knowledge has never been more important. In the past decade, ontologies have become central to the construction of intelligent decision-support systems, simulation systems, information-retrieval systems, and natural language systems. With the adoption of ontologies, especially by the broad biomedical community, the further development of ontologies and knowledge bases evolved into a community-driven process. This resulted in an increased number of knowledge bases published openly on the Web. Ontologies and knowledge bases are now authored/curated by more domain and knowledge experts than ever before. To ensure a high quality of the community-generated content, a well-defined curation process has to become a prominent and integral part of the life cycle of biomedical knowledge artifacts.
Several large biomedical projects are trying to apply the wisdom of the crowds model for building and curating their knowledge content. This model is already familiar to most experts (c.f. Web 2.0) and has already been proven successful in large community projects in other domains. The emergence of
different types of collaborative environments, such as, Wikis, content management systems, and collaborative ontology editors, enables novel ways of curating knowledge, hence transforming the workflow from being curator-centered to being community-driven. Such systems provide the means for communities of experts in different fields to collaboratively create, share and re-use knowledge. Their goal is to foster long term expansion and maximization of knowledge curation, extraction and reasoning, by creating live knowledge bases within their specific domains.
The collaborative aspect of curation raises a series of challenges ranging from specific initial design decisions to capturing and maintaining temporal and change elements of the knowledge content. The aim of this issue is to build upon and complement the research detailed in the Special Issue on Ontologies for Clinical and Translational Research (Vol. 44, Issue 1, 2011) by focusing on collaboration, its associated challenges and emerging methods for knowledge and ontology curation. The use of ontologies, as shared conceptualizations of a domain, has proved to provide support in diverse areas of biomedical informatics, such as the development of databases or biosample repositories. This issue intends to take a step back and analyze the foundational aspect of achieving and maintaining the shared (community-driven) agreement of the conceptualization (and of the resulting knowledge bases) by scrutinizing a series of intrinsic issues like design patterns, consistency or emerging knowledge discovery.
The issue is seeking, in particular, original methodological research papers, but will also consider survey papers, meant to provide a clear overview of the current state of the art in its specific themes of interest. Applications or system descriptions will be considered only as providing a context or use case for a detailed methodology, and not as individual (stand-alone) submissions. The topics of interest for the issue can be grouped into three main categories:
1. Challenges and experiences emerging from the collaborative aspects of knowledge capture in HealthCare and Life Sciences, including:
* design patterns
* workflows for knowledge capture or refinement
* managing change or revision of knowledge
* managing inconsistent knowledge
* hypotheses Ð representation, evaluation and validation
* using linked data to support knowledge capture
* user experience
2. Innovative methods for collaborative knowledge management, including:
* knowledge representation and reasoning
* knowledge discovery
* knowledge revision
* hypotheses management
* use of statistics in decision support systems
* intelligent knowledge-based retrieval
* knowledge integration from external sources
3. Evaluation methods and metrics for:
* the quality of the resulting curated knowledge
* collaborative knowledge acquisition
* collaborative knowledge discovery
* intelligent knowledge-based retrieval
School of ITEE, The University of Queensland, Australia
Stanford Center for Biomedical Informatics Research, Stanford University, USA
Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, Canada
NLM Express Research Grants in Biomedical Informatics (R01)
National Library of Medicine
Application Receipt/Submission Date(s): Multiple dates, see announcement.
Data Concepts and Terminology Standards for Clinical Research and Drug Development (R24)
Food and Drug Administration
Application Receipt/Submission Date(s): June 1, 2011; November 15, 2011; June 1, 2012; November 15, 2012, June 1,2013; November 15, 2013 http://grants.nih.gov/grants/guide/pa-files/PAR-11-209.html
CALL FOR PAPERS
OBML 2011 - 3rd Workshop on Ontologies in Biomedicine and Life Sciences
Berlin, Germany -- October 6-7, 2011
Co-located with INFORMATIK 2011
Submission of short papers (2-4 pages) due: June 30, 2011
Goals of the Workshop
The series "Ontologies in Biomedicine and Life Sciences" (OBML workshop) was initiated by the workgroup for OBML of the German Society for Computer
Science in 2009. The OBML aims to bring together scientists who are working in this area to exchange ideas and discuss new results, to start collaborations and to initiate new projects. The OBML workshop is held once annually and deals with all fundamental aspects of biomedical ontologies as well as additional "hot" topics.
Submissions are requested especially for the following topics:
* Ontologies and terminologies in biology, medicine, and clinical research;
* Ontologies for knowledge representation, methods of reasoning, integration and interoperability of ontologies;
* Methods and tools for the construction and management of ontologies; and
* Applications of the Semantic Web in biomedicine and the life sciences.
The focus of the OBML-2011 is "Phenotype ontologies in medicine and biomedical research".
Submission of papers June 30, 2011
Notification of review results August 10, 2011
Deadline for revised versions September 9, 2011
Workshop October 6-7, 2011
All papers will be printed in a proceedings volume (with ISBN or ISSN) that will be distributed during the workshop. A selection of these papers will be published in journal form.
Submissions to the workshop should comprise 2-4 pages and must be written in English.
* Peter Robinson, Charite Berlin "Phenotype Ontologies" (tentative title)
* Heinrich Herre, University of Leipzig (Coordinator)
* Robert Hoehndorf, University of Cambridge
* Frank Loebe, University of Leipzig
* Peter Robinson, Charite Berlin
* Robert Hoehndorf, University of Cambridge (Coordinator)
* Soeren Auer, University of Leipzig
* Franz Baader, Technical University Dresden
* Martin Boeker, University Medical Center Freiburg
* Patryk Burek, University of Leipzig
* Fred Freitas, University of Mannheim
* George Gkoutos, University of Cambridge
* Giancarlo Guizzardi, Federal University of Espirito Santo, Brazil
* Heinrich Herre, University of Leipzig
* Josef Ingenerf, University of Luebeck
* Ludger Jansen, University of Rostock
* Janet Kelso, Max Planck Institute for Evolutionary Anthropology, Leipzig
* Toralf Kirsten, University of Leipzig
* Frank Loebe, University of Leipzig
* Axel Ngonga-Ngomo, University of Leipzig
* Roberto Poli, University of Trento
* Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, Cambridge
* Peter Robinson, Charite Berlin
* Michael Schroeder, Dresden Technical University
* Stefan Schulz, Medical University Graz
* Luca Toldo, Merck KGaA
The workshop is a supported event of the International Association for Ontology and Its Applications (IAOA):
For further information, please see the workshop and the group websites:
Letter of Intent Due (optional): April 15, 2011
Submission Deadline: August 1, 2011
"Translating Standards into Practice: Experiences and Lessons Learned in Biomedicine and Health Care"
The increased interest and need for systematic approaches to organize, manage, and share data in biomedicine and health care has underscored the importance of standards. There is accordingly a need for detailed, experience-based discussions pertaining to the adoption and implementation of various types of standards, whether for knowledge representation and management, data integration and exchange, semantic interoperability, or other uses.
The goal of this special issue of the Journal of Biomedical Informatics is to provide a forum for describing advanced research and development in translating standards into practice. Papers submitted to the special issue should provide comprehensive descriptions of the methodologies employed and challenges encountered during the process of implementing a specific standard or set of standards in an operational setting. These experiences and lessons learned should aim to provide readers with a framework that can be generalized for adoption of standards in their settings. In addition to original research papers, one or more methodological review papers will be considered and submissions in this category are encouraged.
This special issue will not accept submissions that describe the development of new standards. Given the breadth of existing standards and related activities across domains from vocabularies (e.g., ICD, CPT, SNOMED CT, LOINC, RxNorm, and GO) to information models (e.g., HL7 RIM and CDA, and MIAME) to standards development organizations (e.g., ASTM, HL7, CEN, ISO, DICOM, NCPDP, IHE, IHTSDO, HITSP, CDISC, and GSC), papers may focus on a particular existing standard or cover a set of related standards.
Possible topics for research papers include, but are not limited to:
* Describing methods that have enabled existing standards to be implemented and/or evaluated for applications such as Electronic Health Records, Data Warehouses, Health Information Exchange, Decision Support, Quality Reporting, or Clinical Research (using vendor based or homegrown solutions);
* Discussing methods that have enabled existing standards to be used for improving data capture, integration, and/or sharing in various contexts (e.g., Biology, Imaging, Medicine, Nursing, Public Health, Translational Science, and Education); or,
* Providing methodological details (including empirical assessments) for specific customizations of standards to meet local, regional, national, or international needs (e.g., clinical and regulatory).
Potential methodological review topics may include:
* Comprehensive surveys of relevant standards to meet a particular biomedical or health care need;
* Comparing and contrasting specific related standards; or,
* Providing an overview of reference resources for standards in biomedicine and health care.
April 15, 2011 Letter of Intent Due (optional)
August 1, 2011 Submission Deadline
All submitted papers will go through a rigorous peer-review process (with at least two reviewers) that will include both programmatic relevance as well as scientific quality. The acceptance process will focus on those papers that address innovative methods for adopting and implementing standards in biomedicine and health care. All submissions should follow the guidelines for authors available at the Journal of Biomedical Informatics Web site (http://www.elsevier.com/locate/yjbin). JBI's editorial policy is also outlined on that page and will be strictly followed by special issue reviewers.
Optional letters of intent should be sent to firstname.lastname@example.org by April 15th, 2011. This will assist in assessing the number of likely submissions and in planning for the review process when papers are submitted. Authors must submit their papers via the online Elsevier Editorial System (EES) at http://ees.elsevier.com/jbi, no later than August 1st, 2011. Authors should register and upload their text, tables, and figures as well as subsequent revisions through this Web site, using the "Standards in Practice" paper category. Potential authors may contact the Publishing Services Coordinator in the journal's editorial office (email@example.com) if questions arise during the submission process.
Elizabeth S. Chen (University of Vermont)
Genevieve B. Melton (University of Minnesota)
Indra Neil Sarkar (University of Vermont)
- This search for new DBPs is nationwide.
- Any investigator with PI status is eligible to apply.
- The proposed project must be aligned with the overreaching goals of NCBO.
- The proposed project must provide a driving motivational biomedical problem.
- Specific Aims (The principal objective of the biomedical research; no more than one page)
- Background and Significance (Why is the biomedical research question important?)
- Prior Work (A succinct description of research results to date)
- Research Plan (The proposed research activities that will take place during the period of NCBO support)
- Proposed use of NCBO Technology (A summary of how existing and planned NCBO technology will contribute to the biomedical research plan; this is a key component of the proposal)
- Other collaborative considerations (Additional ways in which the DBP will contribute to the goals of the NCBO)
- Scientific merit
- Relevance of the proposal to the aims of the NCBO
- Approach and Innovation
- PI and Environment
- Plans to obtain support for the DBP’s work after July 31, 2013.
Bionomina is a new journal that offers an interdisciplinary forum for general discussions of terminology, naming practices, and concept use in different parts of biology. The journal is edited by biologists, historians and philosophers of biology, and solicits contributions from these groups of researchers.
Papers are directly submitted to an editor responsible for a certain subject area, such as 'Philosophy of (scientific) language', 'History & sociology of scientific language', or 'Terminology in evolutionary biology'. Details about the scope of the journal and the instructions for authors can be found at http://www.mapress.com/bionomina/
The second International Conference on Biomedical Ontology (ICBO 2011) will be held at University at Buffalo, NY on July 26-30, 2011.
The Elsevier sponsored 2010 Open Track Challenge winners were announced at the International Semantic Web Conference held in Shanghai, China, November 7-11, 2010. A jury of seven leading experts from academia and industry awarded the four best applications with cash prizes exceeding 3000 Euro total.
The semantic web is an exciting new direction in Artificial Intelligence, aiming to add meaning to information on a web-size scale. The field has been evolving over the last decade, and the Semantic Web Challenge showcases some of the most promising and exciting new applications emerging from this area.
Over the last eight years, the Challenge has attracted more than 140 entries. All submissions are evaluated rigorously by a jury composed of leading scientists and experts from industry in a 3 round knockout competition consisting of a poster session, oral presentations and live demonstrations.
Organized this year by Christian Bizer from the Freie Universität Berlin, Germany, and Diana Maynard from the University of Sheffield, UK, the Semantic Web Challenge consists of two categories: “Open Track” and “Billion Triples Track.” The Open Track requires that the applications can be used by ordinary people or scientists and must make use of the meaning of information on the web. The Billion Triples track requires applications to scale up to deal with huge amounts of information which has been gathered from the open web.
The winner of the 2010 Open Track Challenge was the NCBO team (Clement Jonquet, Paea LePendu, Sean M. Falconer, Adrien Coulet, Natalya F. Noy, Mark A. Musen, and Nigam H. Shah). Their entry provides clear benefits to the biomedical community bringing together knowledge from many different entities on the web with a large corpus of scientific literature though through the clever application of semantic web technologies and principles.
For info on additional talks about NCBO technology please click here.
The University at Buffalo, the National Center for Ontological Research (NCOR) and the National Center for Biomedical Ontology (NCBO) are sponsoring a one-day introductory training event on ontology building, which will be held in Buffalo, NY on Saturday, October 23, 2010.
Early registration fee due October 15, 2010.
The 2nd International Workshop on the Role of Semantic Web in Provenance Management (SWPM 2010) will be held at the 9th International Semantic Web Conference in Shanghai, China on November 7, 2010.
The growing eScience infrastructure is enabling scientists to generate scientific data on an industrial scale. Similarly, using the Web as the platform, the Linked Open Data (LOD) initiative has created a vast amount of information that can be leveraged by Semantic Web application in a variety of real world scenarios. The importance of managing various forms of metadata has long been recognized as critical in the Semantic Web. In this workshop we focus specifically on metadata that describes the origins of the data. The term provenance from the French word “provenir”, meaning “to come from", describes the lineage or origins of a data entity. Provenance metadata is essential to correctly interpret the results of a process execution, to validate data processing tools, to verify the quality of data, and to associate measures of trust to the data. The primary objective of this workshop is two-fold, (1) to explore the role of Semantic Web in addressing some of the critical challenges facing provenance management and (2) the role of provenance in real world Semantic Web applications.
Deborah McGuinness, RPI will be a keynote speaker.
Submission of papers due: August 27, 2010
The 1st International Workshop on Semantic Repositories for the Web (SERES 2010) will be held at the 9th International Semantic Web Conference in Shanghai, China on November 7, 2010.
Ontologies and Linked Data vocabularies are being actively developed and used by numerous applications. Several domains are making their vocabularies available for others to reuse. In addition, good practices when developing ontologies are often followed, particularly for producing reusable modules. The Semantic Web is a modular and highly federated environment of reusable knowledge sources; these provide the meaning so that SW applications change our experience of the web. Within this context, the need for repositories delivering the added value that makes the SW a concrete step beyond our current experience of the web is palpable. SERES addresses issues around semantic repositories within the context of the SW.
The AMIA 2011 Summit on Translational Bioinformatics (TBI) will be held in San Francisco, California on March 7-9, 2011. The American Medical Informatics Association (AMIA) is pleased to invite you to submit proposals for papers and panels for the 2011 Summit on Translational Bioinformatics (TBI). Submission of papers due: August 16, 2010 Submission of panels due: October 18, 2010 Submission of abstracts due: December 15, 2010 Website: http://jointsummits2011.amia.org
The AMIA 2011 Summit on Translational Bioinformatics (TBI) will be held in San Francisco, California on March 7-9, 2011.
The American Medical Informatics Association (AMIA) is pleased to invite you to submit proposals for papers and panels for the 2011 Summit on Translational Bioinformatics (TBI).
Submission of papers due: August 16, 2010
Submission of panels due: October 18, 2010
Submission of abstracts due: December 15, 2010
The 2nd Workshop of Ontologies in Biomedicine and Life Sciences (OBML) will be held in Mannheim, Germany on September 9-10, 2010. OBML will be co-located with GMDS 2010.
The second workshop of the OBML community aims at gathering people that work in the main areas of OBML for an exchange of ideas, the presentation of recent results and the stimulation of cooperation.
Submission of short papers (2-4 pages) due: July 1, 2010
The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 2.5, a Web-based platform for browsing, visualizing, mapping, and commenting on biomedical ontologies and terminologies. Our new release of BioPortal includes many new features, Web services, and bug fixes. BioPortal (http://bioportal.bioontology.org) is a comprehensive repository of biomedical ontologies that enables users to access and share ontologies that are actively used in biomedical communities. Users can publish their ontologies in BioPortal, link ontologies to each other, review ontologies and comment on specific terms, list projects that use ontologies, annotate textual metadata with ontologies, and use Web services to incorporate ontologies or their components into their software applications.
Major new features in this release include the following:
- Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms. BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.
- Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to firstname.lastname@example.org. We will have an interactive form to sign-up for notifications shortly.)
- A set of prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation  for details).
- A prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org
- A set of Web services for retrieving instance information for OWL ontologies . We are planning to release a user interface for viewing instances shortly.
- New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.
- A preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings
The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) will be held in Perth, Australia on October 12-15, 2010.
The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) will be held in Perth, Australia on October 12-15, 2010.
IEEE CBMS 2010 is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine.
Paper and tutorial submission due: June 24, 2010
NCBO will host a workshop on the Next steps for RDF. The goal of the workshop is to gather feedback from the Web community on whether and, if yes, in which direction RDF should evolve. One of the main issues the Workshop should help deciding is whether it is timely for W3C to start a new RDF Working Group to define and standardize a next version of RDF. The Resource Description Framework (RDF), including the general concepts, its semantics, and an XML Serialization (RDF/XML), have been published in 2004. Since then, RDF has become the core architectural block of the Semantic Web, with a significant deployment in terms of tools and applications.
NCBO will host a workshop on the Next steps for RDF. The goal of the workshop is to gather feedback from the Web community on whether and, if yes, in which direction RDF should evolve. One of the main issues the Workshop should help deciding is whether it is timely for W3C to start a new RDF Working Group to define and standardize a next version of RDF.
The Resource Description Framework (RDF), including the general concepts, its semantics, and an XML Serialization (RDF/XML), have been published in 2004. Since then, RDF has become the core architectural block of the Semantic Web, with a significant deployment in terms of tools and applications.
Barry Smith announced at the OBO Foundry workshop that the 2nd International Conference on Biomedical Ontologies will be held in Buffalo, New York, US on the July 29th-31st 2011. Note, this confirms that there will not be an ICBO 2010.
The 2010 ACM International Conference on Health Informatics (IHI 2010) will be held in Washinton, DC on November 11-12, 2010.
IHI 2010 is ACM's premier community forum concerned with the application of computer and information science principles and information and communication technology to problems in healthcare, public health, the delivery of healthcare services and consumer health as well as the related social and ethical issues.
The International Conference and Workshop on Enterprises *as* Systems: Theory and Theory in Action - 2010 will be held at Northern Illinois University, Hoffman Estates, IL on August 23-24, 2010.
Paper submission due: June 14, 2010
Web site: www.enterprisesystemtheory.net/estconference/estconference.html
The third edition of Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2010) will be held in Berlin on December 10th, 2010.
Following the request from last year participants for tutorial sessions and a longer workshop, we are open to organize related events in the one or two days preceding the workshop. If you are interested in presenting a tutorial, organizing an hackathon, a meetup please send a short proposal (half a page) to email@example.com by June 30th latest.
Paper submission due: October 18, 2010
The Third International Provenance and Annotation Workshop (IPAW2010) is part of International Provenance and Annotation Workshop Series (IPAW). It will further investigate the issues of data provenance, process documentation, data derivation, and data annotation.
Registration is now available at https://www.cs.rpi.edu/ipaw2010/register.html. Early Registration ends May 24th. A Facebook group, IPAW2010, has been created, and the hash tag #ipaw2010 will be used on Twitter.
Semantic Applications in Life Sciences at the 18th annual conference on Intelligent Systems for Molecular Biology (ISMB) 2010, July 9-13, Boston, MA
Semantic Applications in Life Sciences at the 18th annual conference on Intelligent Systems for Molecular Biology (ISMB) 2010, July 9-13, Boston, MA
Recognizing the increasing synergy in medical and biological ontology research and development, biomedical Knowledge Representation Working Group (KR-WG) of the American Medical Informatics Association (AMIA) has chosen the Bio-Ontologies SIG as the venue of the KR-WG's biannual knowledge representation in medicine meetings (KR-MED, www.kr-med.org). Bio-Ontologies 2010 will serve as host to KR-MED 2010 in the biannual meeting series. In order to attend the biannual KR-MED meeting, please register for the Bio-Ontology SIG.
Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organization, presentation and dissemination of knowledge in biology and life sciences. It has existed as a SIG at ISMB (http://www.iscb.org/ismb2010) for 12 years.
== Important Dates ==
Submissions Due: April 16th (Friday)
Notifications: May 7th (Friday)
Final Version Due: May 14th (Friday)
Workshop: July 9th-10th (Friday and Saturday)
The idea of a prize in ontology has become necessary at a time when philosophy is moving out of the confines of academia and making contributions to the better understanding and management of the wider world in fields such as social ontology, bioinformatics, intelligence analysis, and many more. The prize, which was designed especially by the artist Ugo Nespolo, is being awarded for the first time to Barry Smith, SUNY Distinguished Professor in the University at Buffalo and founder of IFOMIS, the Institute for Formal Ontology and Medical Information Science in Saarbrücken, Germany, which was the first to initiate a large-scale ontological research initiative in the biomedical sciences.
Smith has made groundbreaking contributions in practically all important areas of ontology. He is Director of the US National Center for Ontological Research, a founder of the Open Biomedical Ontologies (OBO) Foundry, and a lead scientist in the Ontology for General Medical Science (OGMS), Protein Ontology (PRO) and Infectious Disease Ontology (IDO) initiatives. He also works with the US Army Net-Centric Data Strategy Center of Excellence on ontology-based data integration and reasoning and with Hernando de Soto of the Institute for Liberty and Democracy in Lima, Peru on the role of documentation in social and economic development.
The award ceremony will be held on Thursday, April 15, 2010 at 4p.m. in the Aula of the Faculty of Humanities of the University of Turin. It will be followed by a lecture given by Barry Smith and a laudatio by Professor Maurizio Ferraris.
The Award was conceived by Maurizio Ferraris, who has made decisive contributions to social ontology through the foundation of LabOnt (the Laboratory of Ontology) in the University of Turin, and in particular through his development of the theme of "documentality", a theory of how social reality is intimately related to the systems of documents which underlie it. The title of Smith's lecture, "How to Do Things with Documents," fits exactly with this scheme.
Why dedicate the award to Paolo Bozzi? Paolo Bozzi (1930-2003) was professor of psychology at the University of Trieste. He was a proponent of radical ontological realism, who became the standard bearer of a philosophy that does not see the real world as dissolving into words, but actually gives it weight, autonomy and dignity, and thereby frees it from the stench and fluidity of postmodernism. Bozzi's life work demonstrates the need for an ontological reconstruction of philosophy exactly as manifested in initiatives such as IFOMIS and LabOnt.
Streaming video of prize ceremony is here:
Lecture by Barry Smith in English starts at about 35:45
OWL: Experiences and Directions
The Sixth International Workshop
June 21-22, San Francisco, California, USA
2010 Semantic Technology Conference (SemTech 2010)
W3C Workshop RDF Next Steps
The adoption of the W3C OWL Web Ontology Language in real-world
applications continues to grow as the research and tools for OWL mature.
The new version OWL 2 -- becoming a W3C recommendation late last year --
has been a positive factor in this direction. As the experience in using
OWL in different applications and domains increases, the strengths and
weaknesses of the language are discovered, resulting in new research
and development that further extends its reach.
The OWL: Experiences and Directions (OWLED) workshop series aims at
bringing users, implementors and researchers from academia and industry
together to describe applications of OWL, to share experience, and to
discuss extensions to the language for satisfying application
requirements. The workshop will allow the OWL community to set an
an agenda for research and deployment in order to incorporate OWL-based
technologies into new applications.
This year's OWLED workshop will be co-located with the 2010 Semantic
Technology Conference (SemTech) that will be held in San Francisco,
California on June 21-22. The W3C Workshop on RDF Next Steps will be
held near-by in Stanford, CA on June 26-27. Tutorials about OWL 2 and
related technologies may be organized for the larger SemTech community;
contact the chairs if you're interested.
As usual, the OWLED workshop will try to encourage participants to work
together and will give space for discussions on various topics to be
decided and published at some point in the future. There will also be
formal presentation of submissions to the workshop.
More information on the workshop is forthcoming. For more information
or to offer sponsorship, please send us a note at
== Important Dates ==
April 7, 2010 Titles and abstract due
April 14, 2010 Paper submissions due
May 14, 2010 Notifications of acceptance
June 4, 2010 Final versions of papers due
June 21-22, 2010 OWLED 2010 workshop
NCBO will present a panel on "Using Ontologies to Drive Biomedical Research" at the 2010 AMIA Summit on Translational Bioinformatics. Participants include Drs. Mark Musen and David Paik from Stanford University, Ida Sim from UCSF, Simon Twigger from the Medical College of Wisconsin, and Rai Winslow from Johns Hopkins University.
Session number and title: S13 (Panel): Using Ontologies to Drive Biomedical Research
Presentation type: Podium, 90 Minutes (15-20 minutes per presenter plus Q&A)
Date and Time: Thursday, March 11, 1:30 pm - 3:00 pm
Abstract: Biomedical research has become increasingly data intensive, making it difficult to effectively and efficiently utilize and integrate the vast amount and diversity of data. Computers can aid in the process of data analysis, however knowledge about the data and points of integration are needed. Ontologies provide this domain knowledge to drive data annotation, data integration, information retrieval, natural language processing, and decision support. This panel will demonstrate the use of biomedical ontologies to annotate electrocardiogram data, facilitating the use of machine learning algorithms to discover features to support diagnosis of heart disease and predict risk for Sudden Cardiac death; to automatically tag free text descriptions of microarray expression data with ontology terms, facilitating information retrieval; to describe the complex, multi-factorial components of nanoparticles facilitating decision support in the design of nanoparticles; and to provide structured knowledge representation to provide cognitive support to integrate complex data. Each panelist has participated as a Driving Biological Project of the National Center for Biomedical Ontology (NCBO) providing a feedback mechanism between the biomedical research objectives and development of NCBO technology.
Please check 2010 AMIA Summit for Translational Bioinformatics for further details.
Please check 2010 AMIA Summit for Translational Bioinformatics for further details.
Please check 2010 AMIA Summit for Translational Bioinformatics for further details.
Please check 2010 AMIA Summit for Translational Bioinformatics for further details.
Free registration is now available for the Symposium that marks the conclusion of our 3-month Ontology Summit 2010 - Creating the Ontologists of the Future. As most of you know, it will be held at the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, USA on March 15-16, 2010.
The registration page is at http://www.nist.gov/public_affairs/confpage/100315b.htm. Please note that registration closes on March 9th, a policy requirement because NIST is a U.S. Government facility. So please don’t delay in registering – there is no charge for this meeting.
You can find plenty of information about getting to NIST, including nearby hotels, at http://www.nist.gov/public_affairs/visitor/visitor.htm. Many of the hotels offer corporate and association discounts, so be sure to ask. Typical rates are around $150/night.
And of course, you can always keep updated on our ongoing discussions, surveys, and progress, at http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010. Our Summit surveys, which are a critical piece of collecting input from you, close on Thursday, February 25, 2010 (the day after tomorrow!), so please visit http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010_Survey if you haven’t already.
We are looking forward to what promises to be another productive and visible Ontology Summit. See you there!
Steven R. Ray and Barry Smith, Co-Chairs, Ontology Summit 2010
The 3rd International Provenance and Annotation Workshop (IPAW'2010)
Troy NY, USA, June 15-16, 2010
Interest in and needs for provenance are growing as data proliferates. Data is increasing in a wide array of application areas, including scientific workflow systems, logical reasoning systems, text extraction, social media, and linked data. As data increases and as applications become more hybrid and distributed in nature, there is increasing interest in where data came from and how it was produced in order to understand when and how to rely on it.
Provenance, or the origin or source of something, can capture a wide range of information. This includes, for example, who or what generated the data, history of data stewardship, manner of manufacture, place and time of manufacture, and so on. Annotation is tightly connected with provenance since data is often commented on, described, and referred to. These descriptions or annotations are often critical to the understandability, reusability, and reproducibility of data and thus are often critical components of today’s data and knowledge systems.
Provenance has been recognized to be important in a wide range of areas including databases, workflows, knowledge representation and reasoning, and digital libraries. Thus, many disciplines have proposed a wide range of provenance models, techniques, and infrastructure for encoding and using provenance. One timely challenge for the broader community is to understand the range of strengths and weaknesses of different approaches sufficiently to find and use the best models for any given situation. This also comes at a time when a new incubator group has been formed at the World Wide Web Consortium (W3C) to provide a state of the art understanding and develop a roadmap in the area of provenance for Semantic Web technologies, development, and possible standardization.
== Important Dates ==
* Abstract deadline: March 8, 2010
* Submission deadline (papers, demos & posters): March 15, 2010
* Notification to authors: April 22, 2010
* Camera-ready deadline: June 1, 2010
* Presentation deadline: June 13, 2010
* Workshop: June 15-16, 2010
Call for papers and system descriptions – DEADLINE EXTENDED TO March 7, 2010
The ORES 2010 Workshop is co-located with ESWC 2010 conference in Heraklion, Crete, Greece (May, 30th - June,3rd, 2010). The Extended Semantic Web Conference (EWSC 2010) brings together researchers and practioners dealing with different aspects of semantics on the Web.
== Topics ==
We would also like to announce the invited talk as part of the workshop, which
will be given by Nigam Shah from the Stanford Center for Biomedical Informatics
The growing number of online ontologies makes the availability of ontology
repositories, in which ontology practitioners can easily find, select and
retrieve reusable components, a crucial issue. The recent emergence of several
ontology repository systems is a further sign of this. However, in order for
these systems to be successful, it is necessary to provide a forum for
researchers and developers to discuss features and exchange ideas on the
realization of ontology repositories in general and to consider explicitly their
role in the ontology lifecycle. In addition, it is now critical to achieve
interoperability between ontology repositories, through common interfaces,
standard metadata formats, etc. ORES10 intends to provide such a forum.
Illustrating the importance of the problem, significant initiatives are now
emerging. One example is the Open Ontology Repositories (OOR) working group set
up by the Ontolog community. Within this effort regular virtual meetings are
organized and actively attended by ontology experts from around the world; The
Ontolog OOR 2008 meeting was held at the National Institute for Standards in
Technology (NIST), generating a joint communiqué outlining requirements and
paving the way for collaborations. Another example is the Ontology Metadata
Vocabulary (OMV) Consortium, addressing metadata for describing ontologies.
Despite these initial efforts, ontology repositories are hardly interoperable
amongst themselves. Although sharing similar aims (providing easy access to
Semantic Web resources), they diverge in the methods and techniques employed for
gathering these documents and making them available; each interprets and uses
metadata in a different manner. Furthermore, many features are still poorly
supported, such as modularization and versioning, as well as the relationship
between ontology repositories and ontology engineering environments (editors) to
support the entire ontology lifecycle.
We would like to bring together researchers and practitioners active in the design,
development and application of ontology repositories, repository-aware editors,
modularization techniques, versioning systems and issues around federated
ontology systems. We therefore encourage the submission of research papers,
position papers and system descriptions discussing some of the following
* How can ontology repositories “talk” to each other?
* How can the abundant and complex knowledge contained in an ontology
repository be made comprehensible for users?
* What is the role of ontology repositories in the ontology lifecycle?
* How can branching and versioning be managed in and across ontology
* How can ontology repositories interoperate with ontology editors, and other
applications and legacy systems?
* How can connections across ontologies be managed within and across ontology
* How can modularity be better supported in ontology repositories and editors?
* How can ontology repositories and editors use distributed reasoning?
* How can ontology repositories support corporate, national and domain specific
* How do ontology repositories support novel semantic applications?
* What measurements for describing and comparing ontologies can we use? How
could ontology repositories use these?
== Submission ==
Research papers are limited to 12 pages and position papers to 5 pages. For system descriptions, a 5 page paper should be submitted. All papers and system descriptions should be formatted according to the LNCS format. Proceedings of the workshop will be published online. Depending on the number and quality of the submission, authors might be invited to present their papers during a poster session.
Submissions can be realized through the easychair system at http://www.easychair.org/conferences/?conf=ores2010
== Important Dates ==
Papers and demo submission: March 7, 2010 (23:59 Hawaii Time)
Notification: April 5, 2010
Camera ready version: April 18, 2010
Workshop: May 30 or 31, 2010
The goal of the OBO Foundry initiative is to create an evolving group of biological and biomedical ontologies which will have the potential to cover a wide range of life science phenomena in a modular fashion. To realize this goal, we have subjected a number of candidate ontologies to a process of review, the first phase of which has now been completed. The following ontologies
CHEBI: Chemical Entities of Biological Interest
GO: Gene Ontology
PATO: Phenotypic Quality Ontology
PRO: Protein Ontology
XAO: Xenopus Anatomy Ontology
ZFA: Zebrafish Anatomy Ontology
have satisfied the OBO Foundry principles and are recommended as preferred targets for community convergence. More details concerning these recommendations, and also concerning the next steps in the OBO Foundry review process, have been published at:
See http://www.iscb.org/ismb2010-deadlines for the full list of ISMB deadlines.
Check out FriendFeed from CSHALS at: http://friendfeed.com/cshals-2010.
For more information on the conference see: http://www.iscb.org/cshals2010-home.
AAIM 2010 is the sixth conference of the AAIM series international conferences. Sponsored by National Natural Science Foundation of China, Montana State University (US), the University of Warwick (UK), and Shandong University (China), AAIM 2010 is undertaken by School of Computer Science and Technology, Shandong University. AAIM 2010 will be held in July 19 – 21, 2010 in Weihai, Shandong, China. Please refer to http://aaim2010.sdu.edu.cn for more information.
4th Int. Workshop on Modular Ontologies (WoMO)
Toronto, Canada, May 11, 2010
co-located with FOIS, KR, AAMAS, ICAPS, NMR, and DL
--- 1st Call for Papers ---
MODULARITY, as studied for many years in software engineering, allows
mechanisms for easy and flexible reuse, generalization, structuring,
maintenance, design patterns, and comprehension. Applied to ontology
engineering, modularity is central not only to reduce the complexity
of understanding ontologies, but also to facilitate ontology
maintenance and ontology reasoning.
Recent research on ontology modularity shows substantial progress in
foundations of modularity, techniques of modularization and modular
development, distributed reasoning and empirical evaluation. These
results provide a foundation for further research and development.
The workshop follows a series of successful events that have been an
excellent venue for practitioners and researchers to discuss latest
work and current problems, and is this time organised as a satellite
workshop of FOIS 2010, as well as being co-located with several other
relevant events, namely KR, AAMAS, ICAPS, NMR, and DL.
TOPICS include, but are not limited to:
- What is Modularity: Kinds of modules and their properties; modules
vs. contexts; design patterns; granularity of representation;
- Logical/Foundational Studies: Conservativity; modular ontology
languages (e.g., DDL, E-Connections, P-DL); reconciling
inconsistencies across modules; formal structuring of modules;
- Algorithmic Approaches: distributed reasoning; modularization and
module extraction; (selective) sharing and re-using, linking and
importing; hiding and privacy; evaluation of modularization
approaches; complexity of reasoning; reasoners or implemented systems;
- Applications: Semantic Web; Life Sciences; Bio-Ontologies; Natural
Language Processing; ontologies of space and time; Ambient
Intelligence; collaborative ontology development; etc.
Paper Submission: January 29, 2010
Notification: March 1, 2010
Camera ready: March 11, 2010
Workshop day: May 11, 2010
The workshop welcomes submission of high quality original and
previously unpublished papers.
Contributions should not exceed 13 pages in length and must be
formatted according to IOS Press style (see
Contributions should be prepared in PDF format and submitted not later
than January 29 2010 through the EasyChair Submission System (see
Submitted papers will be peer-reviewed by members of the program
committee. Accepted papers may be extended up to 16 pages and will be
published as chapters in an IOS Press book in the series 'Frontiers in
Artificial Intelligence and Applications'.
The authors of accepted papers are also welcome to submit
substantially extended versions to a planned special issue on
'Modularity in Ontologies' of the international journal 'Applied
Ontology' (IOS Press).
CALL FOR PAPERS
22nd International Conference on
Scientific and Statistical Database Management (SSDBM 2010)
June 30 - July 2, 2010
DEADLINES: Jan 8th (abstracts), Jan 15th (papers: regular, short/demo)
The SSDBM conference series focuses on concepts, tools, and techniques for scientific and statistical database applications. The 2010 meeting marks the 22nd time that scientific domain experts, database researchers, practitioners and developers will come together to share new insights and to discuss future research directions in a stimulating environment. The conference will consist of a single track of presentations, including invited talks, peer-reviewed papers, system and tool demonstrations, and panel discussions. The conference proceedings will be published as a volume in Springer's Lecture Notes in Computer Science (LNCS) series.
We solicit full papers (up to 18 pages LNCS style) describing original work not published or under review elsewhere. Papers selected after peer review will be included in the conference proceedings and presented orally at the conference. We also invite short papers (up to 9 pages LNCS style) describing systems and software demonstrations or discussing new ideas or work in an early stage. Accepted short papers will be featured in poster-and-demonstration sessions and also included in the proceedings!
Topics of particular interest include (but are not limited to):
* Modeling and representation of data, metadata, ontologies, and processes for scientific application domains
* Integration and exchange of scientific data
* Design, implementation, and optimization of scientific workflows
* Cyberinfrastructure architectures and components for scientific computing and eScience, including Web portals, repositories, and digital libraries
* System architectures in support of scientific data management and analysis, including distributed, parallel, and Grid architectures
* Management and querying of scientific data, including spatial, temporal, spatio-temporal, and streaming data
* Annotation and provenance of scientific and statistical data
* Mining and analysis of large-scale scientific datasets
* Security, privacy, and trust for scientific and statistical data
* Visualization and exploration of large-scale scientific datasets
* Case studies and applications related to scientific data management in all domains
January 8, 2010: Deadline for abstract submission
January 15, 2010: Deadline for paper submission
March 12, 2010: Notification of paper acceptance
April 9, 2010: Camera-ready version of accepted papers
Conference dates: June 30 - July 2, 2010
Andreas Reuter, European Media Laboratories Research gGmbH
Michael Gertz, University of Heidelberg
Tony Hey, Microsoft Research
Bertram Ludäscher, University of California at Davis
Local Organization Chair
Wolfgang Müller, European Media Laboratories Research gGmbH
ESWC2010 Ontology and Reasoning Track: CALL FOR PAPERS
Papers should be submitted through the EasyChair system:
7th Extended Semantic Web Conference | ESWC 2010 30 May - 3 June
2010 | Heraklion, Greece http://www.eswc2010.org/
ABOUT THE ESWC2010
The mission of the Extended Semantic Web Conference (ESWC2010) is to bring together researchers and practitioners dealing with
different aspects of semantics on the Web. ESWC2010 builds on the success of the former European Semantic Web Conference series, but
seeks to extend its focus by collaborating with other communities and research areas, in which web semantics play an important role
-- within and outside ICT. At the same time, ESWC2010 is a truly international conference, not only "European".
Semantics of web content, enriched with domain theories (ontologies), data about web usage, natural language processing,
etc. will enable a web that provides a qualitatively new level of functionality. It will weave together a large network of human
knowledge and make this knowledge machine-processable. Various automated services, based on reasoning with metadata and
ontologies, will help the users to achieve their goals by accessing and processing information in machine-understandable
form. This network of knowledge systems will ultimately lead to truly intelligent systems, which will be employed for various
complex decision-making tasks. Research about web semantics can benefit from ideas and cross-fertilization with many other areas:
Artificial Intelligence, Natural Language Processing, Database and Information Systems, Information Retrieval, Multimedia,
Distributed Systems, Social Networks, Web Engineering, and Web Science.
ESWC2010 will present the latest results in research and applications in its field. The research program will be organised
in targeted research tracks. In addition, the conference will feature a tutorial program, system descriptions and demos, a
posters track, a Ph.D. symposium, and a number of collocated workshops. The individual calls for these events can be found on
the conference Web site (http://www.eswc2010.org/).
Abstract Submission December 15, 2009 (compulsory)
Full Paper Submission December 22, 2009 (11:59 pm Hawaii time)
Notification February 24, 2010
Camera Ready March 10, 2010
ONTOLOGIES AND REASONING TRACK
The Ontologies and Reasoning programme involves the management of and reasoning with ontologies and rules, so as to support their
applications. The central idea of this vision is to use (1) ontologies to encode application data in a machine understandable
form, in order to be able to automatically integrate data from different sources and to be able to support semantic search for
information based on its meaning rather than its syntactic form, and (2) rules to perform conditional decision, event processing
and actions on behalf of the user.
In this track we invite high-quality submissions related (but not limited) to the following topics:
- Rules and ontology management (creation, evolution, reuse, evaluation, etc.)
- Searching, visualizing, navigating and browsing ontologies
- Ontology reasoning and query answering
- Approximate reasoning techniques for the Web
- Ontology usability
- Query languages and optimization for ontologies
- Combining rules and ontologies
- Declarative rule-based reasoning techniques
- Rule languages, standards, and rule systems
- Ontology-based search
- Ontology alignment (mapping, matching, merging, mediation and reconciliation)
- Ontology learning and metadata generation (e.g., HLT and ML approaches)
- Acquisition of rules and ontologies by knowledge extraction
- Corporate Semantic Web
- applications in enterprises and economic valuation
- Language extensions of OWL, ODM, RIF, RuleML, ...
Papers should be submitted through the Easychair system:
ESWC2010 welcomes the submission of original research and application papers dealing with all aspects of representing and
using semantics on the web. We encourage theoretical, methodological, empirical, and applications papers.
The proceedings of this conference will be published in Springer's Lecture Notes in Computer Science series. Paper submission and
reviewing for ESWC2010 will be electronic via the conference submissions site. Papers should not exceed fifteen (15) pages in
length and must be formatted according to the information for LNCS authors.
Papers must be submitted in PDF (Adobe's Portable Document Format) format and will *not* be accepted in any other format. Papers that
exceed 15 pages or do not follow the LNCS guidelines risk being rejected automatically without a review. Authors of accepted
papers will be required to provide semantic annotations for the abstract of their submission -- details of this process will be
provided on the conference Web page at the time of acceptance. At least one author of each accepted paper must register for the
BEST PAPER AWARD
An award will be given to the best paper (or papers) submitted to the conference as judged by the Program and Track Chairs in
collaboration with the Program Committee.
INFORMATION AND CONTACT
For further information please visit the conference website
(http://www.eswc2010.org) or contact firstname.lastname@example.org
ESWC2010 - brought to you by Semantic Technology Institute
The increasingly important role played by ontology in addressing the data integration needs of government, science and industry has brought a growing interest in the methods, tools and resources of ontology research and applications. The goal of the Interdisciplinary Ontology Conference of the Japanese Center for Ontological Research (JCOR) is to address the need for an international forum in the ontology domain and to provide a forum for the exchange of ideas and state-of-the-art technologies among researchers from around the world in ontology and related fields.
Submission instructions along with registration and logistics information will appear at the conference website
December 5: Deadline for submission of complete paper
By January 7, 2009: Notification of acceptance
January 28: Camera-ready copy due for on-site proceedings version
Submission instructions along with registration and logistics information will appear at the conference website
Werner Ceusters, Richard Scheuermann and Barry Smith are editing a special issue of the Journal of Biomedical Informatics on the topic of Ontologies for Clinical and Translational Research.
Some papers in the issue will be based on papers presented at the ICBO conference in Buffalo. However, this is an open call, and you
are invited to submit papers focusing on ways in which ontologies can contribute to breaking down the barriers between different sorts of
information relevant to the understanding and treatment of disease, ranging from information deriving from experimental biology and model
organism research to clinical trial data and information of the sort contained in electronic health records.
Deadline for submissions is October 31, 2009. Further details are available here: http://ontology.buffalo.edu/JBI/ontologies.pdf
The 5th Australasian Ontology Workshop (AOW 2009) to be held in Conjunction with the 22nd Australian Joint Conference on Artificial Intelligence (AI'09) on 1 December 2009, and the University of Melbourne, Melbourne, Australia.
AOW 2009 is the fifth in a series of workshops on ontologies held in the Australasian region.
The proceedings of the four previous workshops were published as volumes in the Conferences in Research and Practice in
Information Technology (CRPIT) series (http://crpit.com/), and this will again be the case for AOW 2009. As with the previous
workshops, we are investigating the possibility of extended versions of selected papers appearing in a special issue of a suitable journal.
Papers must be submitted via the EasyChair system at http://www.easychair.org/conferences/?conf=aow2009
Submission information such as format etc. can be found on the CRPIT website: http://crpit.com/AuthorsSubmitting.html. The page limit is 10 pages.
This year AOW 2009 will have a best paper award, with a prize of $250(AUD) being awarded to the author(s) of the best paper.
Paper submission deadline: 25 September 2009
Notification of acceptance/rejection: 23 October 2009
Camera-ready copies due: 13 November 2009
AOW 2009: 1 December 2009
Call for Abstracts - GPD-Rxn WORKSHOP: Genotype-Phenotype-Drug Relationship Extraction from Text, will be co-located with the Pacific Symposium on Biocomputing, January 4-8 2010, The Big Island of Hawaii. The aim of this workshop is to bring together researchers working on the automatic or semi-automatic extraction of relationships between biomedical entities from research literature. The workshop will focus particularly on methods for the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships and the use of the relationships for advancing pharmacogenomic research. Abstract Submission Deadline: September 15, 2009.
Deadline Extended on the Call for Papers to Aug 16th - 1st Workshop on Ontology Patterns (WOP2009). This workshop provides an arena for proposing and discussing good practices, patterns, pattern-based ontologies, systems etc. The aim is to broaden the pattern community that will develop its own “language” for discussing and describing relevant problems and their solutions. The workshop will be held in conjunction with ISWC2009 on October 25th. It will be a full-day workshop consisting of three parts; papers, posters, and “pattern writing” sessions.
CALL FOR PAPERS: The 5th International Workshop on Semantic Web Enabled Software Engineering (SWESE2009), will be located at the 8th International Semantic Web Conference (ISWC2009). A half day workshop is planned that will be before the main conference. The workshop will include paper presentations, invited talks, a panel and a poster session. Submission deadline: 10 Aug 2009.
Call for papers - Workshop on Semantic Web Applications in Scientific Discourse held in conjunction with The 8th International Semantic Web Conference (ISWC 2009), October 25-29, 2009. Paper Submissions due August 7, 2009.
Deadlines for OWLED 2009 have been extended one week. New Dates are as follows: July 31, 2009 - Titles and abstracts due. August 7, 2009 - Paper submissions due. September 1, 2009 - Paper acceptances sent out. OWLED 2009 will be held October 23-24, 2009, colocated with ISWC 2009 in Chantilly, Virginia, USA
The First International Workshop on Bio-Design Automation (IWBDA) will bring together researchers from the synthetic biology and design automation communities. The broad focus will be on concepts, methodologies and software tools for the automated synthesis of novel biological functions. A specific focus will be on the application of computational expertise from electronic circuit design to these areas. Abstracts submissions due May 22, 2009.
Visit the IWBDA website.
2nd International Conference on BioMedical Engineering and Informatics (BMEI 2009) and the 2nd International Congress on Image and Signal Processing (CISP 2009) will be jointly held in Tianjin, China, from October 17-19, 2009. Submit a paper and/or an exhibition. The submission deadline is 20 May 2009.
The theme of IJCAI-09 is "The Interdisciplinary Reach of Artificial Intelligence," with a focus on the broad impact of artificial intelligence on science, engineering, medicine, social sciences, arts and humanities. IJCAI-09 is sponsored jointly by IJCAI and AAAI.