About this tool
This is a
set of open-source tools
to dailycollect and serve consolidated taxonomic and occurrence data
from various open data sources
, perform geospatial analysis
that enable rapid risk assessmentof country-level biodiversity
, and allow simple and directed visualizationof the data and results.
How does this work
Specifically, the daily workflow goes as follows, mostly in parallel:
- Collect country taxonomic information from choosen checklists published in IPT
[TODO]Download and load into local IPT country occurrences from GBIF by families
- Collect from local and choosen IPTs occurrence datasets
- For each taxon:
- Consolidate occurrences from accepted name and synonyms
- Classify occurrences in groups
[TODO]Rate the quality of occurrences
- For each group of occurrences perform the following analysis
- Extent of occurrence (EOO)
- Area of occupancy with regular grid of 2km side (AOO-2km)
- Area of occupancy withh grid of variadic size (AOO-variadic)
- Subpopulations/Locations/Cluster of occurrences based on circular buffer of median distance
- Rapid Risk Assessment based on EOO, AOO and decline only
- Display the results and statistics.
Extent of occurrences (EOO)
Utilizes a convex-hull method to calculate the total extent of occurrence for the specie.
Area of Occupancy (AOO)
Using a world grid of 2km of side and of 10% of the maximum distance between occurrences, and matching those which have occurrences on it,
distincts them to calculate the area of occupancy of the specie.
Based on 10% of the maximum distance between the species occurrences (to be changed to a minimum-spaning-tree following Rapoport's approach), draws a buffer of this radius around them
and groups those that intersects.
Risk Assessment Analysis
Using IUCN category and criteria extinction risk assessment, but based only on geographical distribution and futher simplified.
|Number of records|| < 3||DD|
|Area of occupancy|| < 10km²||CR (B2)|
|Area of occupancy|| < 500km²||EN (B2)|
|Area of occupancy|| < 2000km²||VU (B2)|
|Extent of occurrence|| < 100km²||CR (B1)|
|Extent of occurrence|| < 5000km²||EN (B1)|
|Extent of occurrence|| < 20000km²||VU (B1)|
Decline and number of subpopulation might be taken into account as official guidelines suggest, if available.
Due to lack of a method for some extra information (specially locations and threats), the categories had to be simplified.
The methodology can be improved if we have easy access to such data.
Other informations and links
You can read the paper published at CSBC 2016 (WCAMA), entitled "Assessing the risk of extinction of Brazil’s flora: A computational approach based on micro-services and geospatial analysis", that describes the tools and methodolgies.
Follow the progress and participate on the public task manager.
You can also check the source code of the open source tools at github.
Any feedback you can get in contact by email: firstname.lastname@example.org.
All source code is available at gihub: