Biodiversity informatics describes integrating biological research, computational science, and software engineering to deal with biotic data. Biodiversity data is used for taxonomy, biogeography, ecology, conservation and more. Data is collected, standardized, digitized and published using Darwin Core and made available through organizations like GBIF. Key challenges include dealing with synonyms and standardizing data across sources.
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2018 04-03-shorthouse
1. Biodiversity Informatics
David P. Shorthouse
Assistant Collections Information Manager
Canadian Museum of Nature
@dpsSpiders
dshorthouse@nature.ca
4. What is biodiversity informatics?
How are biodiversity data used?
How are biodiversity data made available?
What are the key challenges?
What are its organizations?
Where can I go for more?
7. Biodiversity Informatics
Biodiversity informatics describes a new, synthetic
discipline that integrates biological research,
computational science, and software engineering to deal
with biotic data—their storage, integration, retrieval, and
use in analysis, prediction, and decision-making
8. History of “Biodiversity Informatics”
John S. Whiting
Canadian Biodiversity
Informatics Consortium (1993)
9. Johnson Norm F. 2007. Biodiversity
informatics. Annu Rev Entomol. 52:421-38.
DOI 10.1146/annurev.ento.52.110405.091259
13. Chapman, A. D. 2005. Uses of Primary
Species-Occurrence Data, version 1.0.
Report for the Global Biodiversity
Information Facility, Copenhagen.
http://www.gbif.org/resources/80545
14. 1 Taxonomy: research, indices, floras/faunas,
field guides, phylogenies
2 Biogeography: distributional atlases, species
distribution modeling, species decline
3 Life Histories and Phenologies
4 Endangered, Migratory, and Invasive Species
5 Impact of Climate Change
6 Ecology, Evolution and Genetics: habitat loss,
ecosystem function
7 Environmental Planning: impact assessments
Uses of Primary Occurrence Data
15. Uses of Primary Occurrence Data
8 Conservation Planning: rapid biodiversity assessments,
identifying priority areas, reserve selection, sustainable
use
9 Health and Public Safety: disease and disease vectors,
bioterrorism, biosafety, parasitology
10 Bioprospecting
11 Border Control and Wildlife Trade
12 Education and Public Outreach
13 Ecotourism
14 Society and Politics: data repatriation
15 Recreational activities
55. What about Canadian Organizations?
Canadian Biodiversity Information Facility
OBIS Canada
Canadensys
Alliance of Natural History Museums of Canada
Canadian Centre for DNA Barcoding
61. What is biodiversity informatics?
How are biodiversity data used?
How are biodiversity data made available?
What are the key challenges?
What are its organizations?
Where can I go for more?
Editor's Notes
The genus Drosophila was established in 1823 by Fallén, who included 12 species. Since then, several subgenera have been erected and today there are over 1000 species of Drosophila. Phylogenetic work, based largely on wing venation and meta analyses of all available literature (2008) has determined that Drosophila as currently defined is paraphyletic – there are several sister genera that have member species more closely related to species in the genus Drosophila than to each other. Solutions: sink all genera into one really large Drosophila (2250+ species), or spit them along natural clades. Unfortunately, D. melanogaster is not the type species for the genus and according to the International Code of Zoological Nomenclature, D. melanogaster would need to be renamed. In April 2010, ICZN ruled to keep D. funebris as the type species for the genus.
May 2017
it aids in sequencing and annotating genomes and their observed mutations.
Aids in development of biological and gene ontologies to organize and query biological data
plays a role in the analysis of gene and protein expression and regulation
Coined by John Whiting in 1992 to cover the activities of an entity known as the Canadian Biodiversity Informatics Consortium, a group involved with fusing basic biodiversity information with environmental economics and geospatial information in the form of GPS and GIS.
“I coined the term as part of a title for what was at first a loose affiliation between about five agencies (including myself, a firm specializing in GPS, and GIS firm, a firm specializing in database management, a firm specializing in environmental economics, and a representative of the Canadian Museum of Nature”
lost any obligate connection with the GPS/GIS world and be associated with the computerized management of any aspects of biodiversity information
Coined by John Whiting in 1992 to cover the activities of an entity known as the Canadian Biodiversity Informatics Consortium, a group involved with fusing basic biodiversity information with environmental economics and geospatial information in the form of GPS and GIS.
“I coined the term as part of a title for what was at first a loose affiliation between about five agencies (including myself, a firm specializing in GPS, and GIS firm, a firm specializing in database management, a firm specializing in environmental economics, and a representative of the Canadian Museum of Nature”
lost any obligate connection with the GPS/GIS world and be associated with the computerized management of any aspects of biodiversity information
Data on:
Who – the agents involved in collecting or curating the data
What – the characteristics of the data, the identity of the organism in the observation or the specimen
Where – what are the geographic coordinates , to what precision & what is the uncertainty in locality estimation
When – unit of time
Essentially all that is written on specimen labels