These http://www.selleckchem.com/products/epz-5676.html workshops grew out of efforts sponsored by the NSF funded Resource Coordination Network (RCN) project for GSC [1] (RCN4GSC, hosted at UCSD, with John Wooley as PI) to reconcile terms from the Darwin Core (DwC) [2] vocabulary and with those in the MIxS family of checklists (Minimum Information about Any Type of Sequence) [3]. The original RCN4GSC meetings were able to align many terms between DwC and MIxS, finding both common and complementary terms. However, deciding exactly what constitutes the concept of a sample, a specimen, and an occurrence [4] to satisfy the needs of all use cases proved difficult, especially given the wide variety of sampling strategies employed within and between communities.

Further, participants in the initial RCN4GSC workshops needed additional guidance on how to relate these entities to processes that act upon them and the environments in which organisms live. These issues provided the motivation for the workshops described below. The two workshops drew largely from experiences of the Basic Formal Ontology (BFO) [5] and were led by Barry Smith, State University of New York at Buffalo. We chose to interact with Smith based on his successful interactions with the GSC in developing the Environment Ontology (EnvO) [6] and also, on the ability of BFO to unite previously disconnected ontologies in the medical domain [7]. The first workshop addressed term definitions in biodiversity informatics, working within the BFO framework, while the second workshop developed a prototype Bio-Collections Ontology, dealing with samples and processes acting on samples.

Concurrent with these workshops were two ongoing efforts involving data acquisition, visualization, and analysis that rely on a solid conceptual understanding of samples, specimens, and occurrences. These implementations are included in this report to show practical applications of term clarification. Finally, this report provides a discussion of some of the next steps discussed during the workshops. Workshops Semantics of Biodiversity Workshop [8], University of Kansas, Lawrence, Kansas USA, May 16-17, 2012 The Semantics of Biodiversity (SOB) workshop hosted at the University of Kansas Biodiversity Institute and sponsored by RCN4GSC, Morphbank [9], and BiSciCol [10], brought together a range of domain experts. On the morning of Day 1, Smith gave a background to ontologies, provided analogies Cilengitide from the biomedical domain, and led a discussion of the basic formal ontology (BFO), an upper-level ontology. BFO describes entities that have continuous existence through time (continuants), such as material objects or qualities, as well as entities which have temporal parts and unfold through time (occurrents), such as processes or temporal regions.