W08: Data Standards and Knowledge Sharing in Biodiversity -Tools and Applications

Submitted by cooperl on

ICBO2018 Workshop-W08

Date: Tuesday, August 07, 2018
Time: 1:30-3:30pm
Location: Elle Burlingham Room #111A-B

Organizer(s): Laurel Cooper, Planteome Project and Marie-Angélique Laporte, Bioversity International

Workshop Agenda:

Time Length (mins) Speaker Paper # Title
1:30 PM 5 Laurel Cooper n/a Welcome and Introduction    
1:35 PM 25 Hong Cui n/a Explorer of Taxon Concepts: Presentation and Demonstration
2:00 PM 15 Lorena Endara 50 A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a Focus on Flagellate Plants (remotely)
2:15 PM 15 Anne Thessen 75 ECOCORE: An ontology for core ecological concepts    
2:30 PM 15 Wasila Dahdul 62 Reasoning over anatomical homology in the Phenoscape KB    
2:45 PM 15 Ian Braun 58 Computational Classification of Phenologs Across Biological Diversity    
3:00 PM 15 Dennis Stevenson 21 From PO to GO and back    
3:15 PM 15 Discussion Panel n/a        


Workshop Abstract

Biodiversity research is the study of the variety and variability of life on Earth, and it encompasses a wide range of scales from local to global. Scientists have been collecting biodiversity data through observations and documentation for hundreds of years. Much of that information is currently stored in free text descriptions of specimens, data tables, and published papers. In keeping with the theme of ICBO 2018: Ontologies for Health, Food, Nutrition and Environment:A partnership with BIG-Data and Analytics, there is a need to enable scientists to leverage this data and improve sharing, discovery and interoperability. Only through this approach can we meet the needs of a growing population and changing climate. Recent advances in standards and semantics for biodiversity data include initiatives from such groups as The Global Biodiversity Information Facility (GBIF; http://www.gbif.org/), and Biodiversity Information Standards (TDWG; http://www.tdwg.org/) group. The GBIF is an international open data infrastructure which is encouraging the adoption of common standards, and provides access to data about all types of life on Earth. The TDWG focuses on the development of standards for the exchange of biological/biodiversity data such as the Darwin Core, and the Access to Biological Collections Data (ABCD).

The goals of this workshop are to bring together a set of researchers to present cutting-edge work in this area of biodiversity data representation and semantics. We will have presentations by invited speakers, followed by a short panel discussion.


This is an emerging area of plant biology research with rapid advances happening. Therefore, this workshop will attract a different set of researchers who would not normally come to the ICBO meeting, thus broadening the participation.

Planteome- NSF Award # IOS:1340112