Semantics for Biodiversity Symposium
at TDWG Conference 2013
October 28 - November 1, 2013 - Florence, Italy.
Symposium Description and Scope
This Symposium includes a series of three, 90 minute sessions at TDWG that together constitute a "Semantics for Biodiversity" track, focused on--
- Ontologies and formal models
- Technologies, Reasoning and Annotation methods
- Interoperability with genomic and ecological semantics
These sessions are not parallel tracked and they are placed on separate days to avoid saturation on the topic. Additionally, there will be an initial "primer/tutorial" session of 60 minutes, to provide basic background for TDWG participants about semantic technologies, and how these can help inform biodiversity research.
The conveners of this Symposium will be soliciting participation from diverse communities, including those from the biodiversity informatics and standards-development community per se, but also researchers interested in knowledge modeling and semantic application development in the biodiversity sciences, including relevant linkages to investigations in the ecological, genomic and phylogenetic sciences. These thematic areas recommend a stronger-than-usual outreach to the computer science community, as researchers in that community will be particularly attracted by the prospects of reporting their work in a planned (and approved) special issue of the Semantic Web Journal on "Semantics for Biodiversity". Multiple groups of informaticians and technologists are currently developing semantic technologies to enhance discovery, interpretation, and interoperability of biodiversity data, so the upcoming meeting will provide a signal opportunity to present and discuss these activities in a coordinated fashion before perhaps the most relevant community who can inform, critique, and contribute to these efforts. Further, it's anticipated that these sessions will significantly raise awareness among computer scientists and engineers relative to the informatics challenges confronting the biodiversity community, particularly among those developing generalized knowledge representation and reasoning technologies, and machine-learning approaches.
Submission due: September 4, 2013
Acceptance Notification: September 11, 2013
Symposium dates: October 29 - November 1, 2013
Primer on Semantic Technologies
Tuesday, Oct. 29, 16:00 - 17:00
Conveners: Mark Schildhauer, ...
Semantics of Biodiversity Symposium - Technologies
Wednesday, Oct. 30, 14:00 - 15:30
Conveners: John Deck*, Ben Adams*, Rob Guralnick, Reed Beaman, Steve Baskauf, Bob Morris, Mark Schildhauer, Norman Morrison
- Creating and working with RDF, linked open data, and semantically annotated information to enhance biodiversity data discovery and analyses.
- GUID solutions for creating persistent resources on the Semantic Web (e.g. DOI/ARK/LSID)
- Approaches to reasoning over Biodiversity data
- Mechanisms for semantically annotating Biodiversity data
- Semantic approaches to tracking Biodiversity data provenance
- Mining natural language resources for semantic content
This session will demonstrate working implementations of linked data, technologies that support linked data approaches, efforts affording advanced semantic reasoning, mechanisms for enrichment of data via semantic annotation, and natural language processing techniques for extracting semantic content about biodiversity data and topics. Much of the community activity to date has involved "linked data", with a focus on ontology development (for example, Semantics of Biodiversity workshop at KU, May 2012, Sample Ontology Workshop, Oxford 2012, and ongoing Darwin-SW development), instance identifier strategies (TDWG content discussions and community blogposts), and term reconciliation across domains ("RCN4GSC meeting reports", Standards in Genomic Sciences, vol 7, no1, 2012); with fewer examples of functional technologies to support these approaches, or discussion about the specific useful logical entailments that justify these efforts. Much as the potential of email and the World Wide Web was not widely recognized until early adopters demonstrated useful applications of these technologies, demonstrating working systems for linked data and the Semantic Web more generally now will help speed adoption by the biodiversity community in the future. This, in turn, will help realize the dream of linked data proponents: to conduct distributed, cross-domain, scientific analysis and object tracking. The content of the session will draw specifically on examples that connect Semantic Web standards with other standards, for both data and applications, and highlight the emerging tools and technology stacks that facilitate the creation of and operation on data that are semantically enriched.
Semantics of Biodiversity Symposium - Formal Models
Friday, Nov. 1, 09:00 - 10:30
Conveners: Ramona Walls*, Nico Franz*, Stan Blum, Rob Guralnick, Mark Schildhauer, Ben Adams, Steve Baskauf, Joel Sachs
- Semantics of observations, specimens, occurrences, samples, materials ("biomaterial"), plots, traits, and new forms of biodiversity evidence -- images, audio; etc (in a narrow biodiversity context)
- Knowledge Representation for Taxonomies and Nomenclatures
- RDF, OWL and alternative semantic models to support biodiversity information
- Issues in migrating Darwin Core, Audobon Core, etc. to semantic models
This session provides an overview of the state-of-the-art with respect to semantic modeling of biodiversity phenomena, by presenting some of the more prominent formal knowledge models being developed and used by the biodiversity community. There are a number of potential vocabularies and syntaxes that can be used for developing ontologies and other semantic representations of biodiversity phenomena and data, and details in their implementation can have strong implications for inferencing power and data interoperability. This session will also provide an opportunity to compare and contrast among potentially competing approaches, and encourage greater community consensus and sharing opportunities in advancing semantic approaches to describing biodiversity data.
Semantics of Biodiversity Symposium - Interoperability
Friday, Nov. 1, 11:00 - 12:30
Conveners: Mark Schildhauer*, Rob Guralnick*, Ben Adams, Norman Morrison, Evangelos Pafilis, Pelin Yilmaz
- Situating Biodiversity in the Environment -- unifying biodiversity information with semantic concepts from the earth sciences
- Critical semantics for linking genomic and metagenomic information to "Darwin Core" types of biodiversity information
Many research topics in Biodiversity science focus on understanding the evolutionary or ecological processes that give rise to, sustain or alter patterns in biodiversity. These investigations can often benefit from linking with semantically enriched data describing the local or regional environmental or ecological context; as well as from linking with semantically enriched data describing the phenotypes and functional traits associated with the underlying genomic and metagenomic sequences of the taxa or samples of interest. Both the Earth Sciences and Genomics Communities already have strong semantics efforts underway, so this panel will provide opportunities to report on these efforts, and especially how these might inform or harmonize with semantics efforts in the biodiversity sciences per se.
Symposium Format and Submissions
We invite abstract submissions (500 words maximum) for the three sessions, which will be dedicated to short presentations on the topics described in abstracts. We anticipate presentations will be for 20 minutes, with the possibility that these times will change depending on the number of quality submissions.
Abstract submissions should be made through EasyChair website at https://www.easychair.org/conferences/?conf=s4bdtdwg2013 by September 4th, 2013.
Organizers(alphabetic order by last name)
- Benjamin Adams, National Center for Ecological Analysis and Synthesis, USA
- Steve Baskauf, Vanderbilt University
- Stan Blum, California Academy of Sciences
- John Deck, University of California, Berkeley
- Nico Franz, Arizona State University
- Rob Guralnick, University of Colorado, Boulder
- Bob Morris, University of Massachusetts, Boston
- Norman Morrison, NEBC
- Evangelos Pafilis, Hellenic Center of Marine Research
- Joel Sachs, University of Maryland, Baltimore County
- Mark Schildhauer, National Center for Ecological Analysis and Synthesis, USA
- Ramona Walls, The iPlant Collaborative
- Pelin Yilmaz, Max-Planck-Institut fur Marine Mikrobiologie
Please feel free to contact the organizers for further questions at semantics4biodiversity @ nceas . ucsb . edu.