[tdwg] Semantics for Biodiversity special issue (updated submission date Feb. 28)

[Ben Adams]

*Semantics for Biodiversity -- call for papers*

*February 28, 2014 - Paper submission deadline (updated)*

The study of biodiversity examines the richness and variety of life on
Earth across multiple organizational and spatial scales, ranging from
genomic to organismal through populations and ecosystems; and from local to
global scales. Presently, biodiversity observational data are collected by
scientists around the world using a diverse set of methods and stored in a
variety of formats. Because the problems that biodiversity scientists are
investigating are time-critical, societally-relevant, and often global in
scale, there is a pressing need to enable scientists to better share,
discover, and synthesize biodiversity data from multiple sources. Modern
semantic technologies provide a promising way to accomplish this, by
capturing rich representations of biodiversity data in ways that afford
maximum interoperability and detailed description for re-use.

The goal of this special issue is to bring together a collection of papers
on biodiversity semantics - to present current state-of-the-art semantic
efforts in representing biodiversity data, to spur advances in semantic
technologies for biodiversity research, and to help define a common
strategy for advancing semantic approaches for describing biodiversity,
including considerations about the broader ecological and environmental
contexts that inform biodiversity investigations.

Semantic approaches for describing biodiversity data are currently being
explored on several fronts. The international-scope Biodiversity
Information Standards (TDWG) group has developed metadata standards such as
Darwin Core (specimen data), ABCD (biological collections), the Taxonomic
Concept Schema (names and concepts), and the proposed Audubon Core
(biodiversity multimedia). Darwin Core is very broadly accepted as a
transfer schema for sharing biodiversity data, and is the standard adopted
by GBIF, the Global Biodiversity Information Facility - that currently
aggregates over 400 million biodiversity records from collections around
the world. However, all current TDWG standards are lacking in semantic
expressivity and compatibility with reasoning requirements for effective
knowledge representation and reasoning (KRR), and tend to focus on
observations of specimens without descriptions of their environmental
context. In parallel, the Earth and environmental science community,
through emerging efforts like NSF's EarthCube, will be developing semantic
models for describing environmental systems and processes. The genomics
community also has a growing interest in linking biodiversity information
to genetic samples. For example, metagenomics research often involves
collection of aggregate samples of biodiversity, such as an amount of soil
or ocean water, where genetic sequencing then provides a characterization
of the variety of microbial and other life forms that are in the sample.
Under the banner term of phenotype ontologies, research communities
focusing on model organisms and (increasingly) broader taxonomic groups
have assembled structured vocabularies for anatomical features that permit
reasoning and integration with genomics and evolutionary analyses.
Clarifying the semantics of biodiversity will provide an essential linchpin
among investigations that enable us to understand how environmental
factors, both biotic and abiotic, influence phenotype, community
composition, and species' ranges and viability, as well as provide insights
into the evolutionary relationships among Earth's life forms.

This special issue calls for original papers describing the latest
developments, trends, and solutions for biodiversity semantics and its
applications. The topics of interests include, but are not limited to:

   - Formal models of biodiversity - specimens, occurrences, samples, etc.
   - Taxonomic and nomenclatural semantics, classification representation
   and provenance
   - Field observation and measurement semantics
   - Semantic approaches for enhancing discovery of biodiversity data
   - Interoperability of biodiversity with Earth and environmental science
   data
   - Linking taxonomic with trait and genomic data
   - Semantic representations of phylogenetic data
   - Semantic descriptions of biodiversity models and semantic approaches
   to support model-data confrontation
   - Integration of species, ecosystems, and genetic level data
   - Semantics of populations, communities, and ecosystem services
   - Data integration for critical zone studies
   - Geospatial semantics for biodiversity - locations, ranges,
   co-occurrences, etc.
   - Software for semantic annotation of biodiversity data
   - Bottom-up biodiversity ontology development
   - Ontology design patterns and methods for ontology evolution for
   biodiversity
   - Linked Open Data (LOD) for biodiversity
   - Representing provenance of biodiversity data
   - Limitations of, alternatives to, and extensions to Semantic Web
   languages and methodologies to serve biodiversity research needs

*Submissions*

*February 28, 2014 - Paper submission deadline (updated)*

Submissions shall be made through the Semantic Web journal website at
http://www.semantic-web-journal.net. Note that you need to request an
account on the website for submitting a paper. Please indicate in the cover
letter that it is for the *Semantics for Biodiversity* special issue.

Submissions are possible in all standing paper type of the journal, see
http://www.semantic-web-journal.net/authors for descriptions: full research
papers, surveys, linked dataset descriptions, ontology descriptions,
application reports, tool/systems reports.

*Guest editors*

Benjamin Adams (The University of Auckland, New Zealand)
Nico Franz (Arizona State University)
Birgitta König-Ries (Friedrich Schiller University Jena)
Deborah McGuinness (Rensselaer Polytechnic Institute)
Mark Schildhauer (NCEAS, University of California, Santa Barbara)
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