OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system.

Background: The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies.

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.

Background: Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research.

Semantic annotation of mutable data.

Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology.

A decadal view of biodiversity informatics: challenges and priorities.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised.

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information.

The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a "non-commercial" (NC) condition.

XML schemas and mark-up practices of taxonomic literature.

We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of "taxon treatment" from the viewpoint of taxonomy mark-up into XML is discussed.

Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples.

The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.

Reactions of POxCly- ions with H and H2 from 298 to 500 K.

Rate constants and product branching ratios for POxCly- ions reacting with H and H2 were measured in a selected ion flow tube (SIFT) from 298 to 500 K. PO2Cl-, PO2Cl2-, POCl2-, and POCl3- were all unreactive with H2, having a rate constant with an upper limit of <5 x 10(-12) cm3 s(-1). PO2Cl2- did not react with H atoms either, having a similar rate constant limit of <5 x 10(-12) cm3 s(-1).

Retrospective pathology survey of green turtles Chelonia mydas with fibropapillomatosis in the Hawaiian Islands, 1993--2003.

We necropsied 255 stranded green turtles Chelonia mydas with fibropapillomatosis (FP) from the Hawaiian Islands, North Pacific, from August 1993 through May 2003. Of these, 214 (84 %) were euthanized due to advanced FP and the remainder were found dead in fresh condition. Turtles were assigned a standardized tumor severity score ranging from 1 (lightly tumored) to 3 (heavily tumored).