News
Submitted by admin on March 13, 2009 - 13:33
To view past news, click here.
Recent News
January 23, 2012
NCBO News
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.
September 13, 2011
Call for Participation
Semantic technologies have become a well-established field of computer science. However, the field is continuously evolving: the number of semantic technologies is constantly increasing, standards evolve and new ones are defined; and, in this scenario, the problem of how to compare and evaluate the various approaches becomes crucial.
The consistent evaluation of semantic technologies is critical not only for future scientific progress, by identifying research goals and allowing a rigorous examination of research results, but also for their industrial adoption, by allowing objective measurement and comparison of these technologies and enabling their certification.
Semantic technology evaluation must, on the one hand, be supported by strong methodological approaches and relevant test data and, on the other hand, satisfy the differing needs of developers, researchers and adopters by addressing those quality characteristics that are relevant to each target group.
Nevertheless, numerous issues must be faced when evaluating semantic technologies. On the one hand, because of the fast evolution of the semantic field, previous evaluation methods and techniques need to be adapted and extended and new ones have to be developed. On the other hand, the cost of defining new evaluations methods or reusing existing ones can be prohibitive, so facilitating the understanding of such methods or their automated processing becomes highly significant.
The goal of this special issue is to present current advances and trends in semantic technology evaluation (theories and models, methods and techniques, evaluation campaigns, technology comparison, etc.). Therefore we solicit papers that improve evaluation paradigms of semantic technologies. At the same time papers that evaluate a particular method, technology or system without investigating the evaluation regime itself will be considered out of scope and will be returned to the authors with no review.
Topics of interest
Relevant topics for the special issue include, but are not limited to, the following:
- Semantic technology evaluation methods
- Test data for semantic technology evaluation
- Automation of semantic technology evaluation
- Evaluation of semantic technologies in real world scenarios
- Evaluation of linked data technologies
- Quality requirements for semantic technologies
- Semantic technology certification
- Maturity models for semantic technologies
- Semantic technology selection
- Semantic technology quality estimation
- Interoperability and conformance of semantic technologies
- Semantic technology efficiency and scalability
- Usability of semantic technologies
Important dates
We will aim at an efficient publication cycle in order to guarantee prompt availability of the published results. To this end, we encourage submissions well before the submission deadline.
Submission deadline February 29, 2012
Author notification May 31, 2012
Final version July 31, 2012
Publication Fall 2012
Instructions for submission
Please see the author guidelines for detailed instructions before you submit:
Submissions should be conducted through Elseviers Electronic Submission System (http://ees.elsevier.com/jws/). More details on the Journal of Web Semantics can be found on its homepage: http://www.elsevier.com/locate/websem
Editors
- Ral Garca-Castro (contact), Universidad Politcnica de Madrid
- Heiner Stuckenschmidt, University of Mannheim
- Stuart Wrigley, University of Sheffield
- Jeff Heflin, Lehigh University
Dr. Ral Garca Castro
http://delicias.dia.fi.upm.es/~rgarcia/
Ontology Engineering Group
Dpto. de Lenguajes y Sistemas Informticos e Ingeniera de Software
Universidad Politcnica de Madrid
Campus de Montegancedo, s/n - Boadilla del Monte - 28660 Madrid
Phone: +34 91 336 36 70 - Fax: +34 91 352 48 19
______________________________________________
Project SEALS - News
Seals-news@listas.fi.upm.es
September 6, 2011
Call for Participation
DATE: 21 September 2011
TIME: 9:00 - 17:00
PLACE: National Library of the Netherlands, The Hague
REGISTRATION: http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/registration-2011
[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.[1] 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.[2] 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.
Cordially,
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
[1] http://purl.org/dcevents/dc-2011
[2] http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/specialSessions-2011
August 12, 2011
Call for Participation
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
Key dates:
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
August 12, 2011
Call for Participation
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 Challenge
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.
Prizes
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.
IMPORTANT DATES
- 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
July 28, 2011
Call for Participation
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.
Kind regards,
Biocuration 2012 Organizing Committee
July 18, 2011
Call for Participation
Important Dates
*Submission deadline: October 1, 2011
* Notification: December 2011
* Final Version due: January 2012
* Publication: Early 2012
Submission Guidelines
* 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
Guest Editors
Tudor Groza
School of ITEE, The University of Queensland, Australia
Tania Tudorache
Stanford Center for Biomedical Informatics Research, Stanford University, USA
Michel Dumontier
Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, Canada
April 11, 2011
Call for Participation
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.
Important Dates:
April 15, 2011 Letter of Intent Due (optional)
August 1, 2011 Submission Deadline
Peer-Review Process:
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.
Submission Process:
Optional letters of intent should be sent to liz.chen@uvm.edu 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 (jbi@elsevier.com) if questions arise during the submission process.
Guest Editors:
Elizabeth S. Chen (University of Vermont)
Genevieve B. Melton (University of Minnesota)
Indra Neil Sarkar (University of Vermont)