1
|
Sterner B, Witteveen J, Franz N. Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:8. [PMID: 32030540 DOI: 10.1007/s40656-020-0300-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or "settled" science.
Collapse
Affiliation(s)
- Beckett Sterner
- School of Life Sciences, Arizona State University, Tempe, USA.
| | - Joeri Witteveen
- Department of Science Education, Section for History and Philosophy of Science, University of Copenhagen, Copenhagen, Denmark
| | - Nico Franz
- School of Life Sciences, Arizona State University, Tempe, USA
| |
Collapse
|
2
|
Stucky BJ, Balhoff JP, Barve N, Barve V, Brenskelle L, Brush MH, Dahlem GA, Gilbert JDJ, Kawahara AY, Keller O, Lucky A, Mayhew PJ, Plotkin D, Seltmann KC, Talamas E, Vaidya G, Walls R, Yoder M, Zhang G, Guralnick R. Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. Biodivers Data J 2019; 7:e33303. [PMID: 30918448 PMCID: PMC6426826 DOI: 10.3897/bdj.7.e33303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/28/2019] [Indexed: 11/12/2022] Open
Abstract
Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.
Collapse
Affiliation(s)
- Brian J. Stucky
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | - James P. Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of AmericaRenaissance Computing Institute, University of North CarolinaChapel Hill, NCUnited States of America
| | - Narayani Barve
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | - Vijay Barve
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | - Laura Brenskelle
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | - Matthew H. Brush
- Oregon Health and Science University, Portland, OR, United States of AmericaOregon Health and Science UniversityPortland, ORUnited States of America
| | - Gregory A Dahlem
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, United States of AmericaDepartment of Biological Sciences, Northern Kentucky UniversityHighland Heights, KYUnited States of America
| | - James D. J. Gilbert
- Department of Biological and Marine Sciences, University of Hull, Hull, United KingdomDepartment of Biological and Marine Sciences, University of HullHullUnited Kingdom
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States of AmericaEntomology and Nematology Department, University of FloridaGainesville, FLUnited States of America
| | - Oliver Keller
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States of AmericaEntomology and Nematology Department, University of FloridaGainesville, FLUnited States of America
| | - Andrea Lucky
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States of AmericaEntomology and Nematology Department, University of FloridaGainesville, FLUnited States of America
| | - Peter J. Mayhew
- Department of Biology, University of York, York, United KingdomDepartment of Biology, University of YorkYorkUnited Kingdom
| | - David Plotkin
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | | | - Elijah Talamas
- Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States of AmericaFlorida Department of Agriculture and Consumer ServicesGainesville, FLUnited States of America
| | - Gaurav Vaidya
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | - Ramona Walls
- Bio5 and CyVerse, University of Arizona, Tucson, AZ, United States of AmericaBio5 and CyVerse, University of ArizonaTucson, AZUnited States of America
| | - Matt Yoder
- Species File Group, Illinois Natural History Survey, University of Illinois, Champaign, IL, United States of AmericaSpecies File Group, Illinois Natural History Survey, University of IllinoisChampaign, ILUnited States of America
| | - Guanyang Zhang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| | - Rob Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of AmericaFlorida Museum of Natural History, University of FloridaGainesville, FLUnited States of America
| |
Collapse
|