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)