Biodiversity Record Aggregators

ML Gaynor - Updated April 2020.

Are we missing a biodiversity aggregator? Let us know!

Warning - Some of these repositories feed into each other, duplicate records may exist among data aggregators. Methods to detect and remove duplicates for different research applications are available and/or in development.

It's important to note some of these feed off each other. The head of BISON spoke at UF once and showed this slide pic.twitter.com/4uCjTZI9bU

— Shawn Taylor (@dataEcologist) April 29, 2020

Table of Biodiversity Record Aggregators

Overview of a subset of biodiversity occurrence record aggregators, web portals are linked in the aggregators column. If a collection is stored or available in Darwin Core (DwC) format, a checkmark is indicated. Checkmarks also indicate that an Application Programming Interface (API) is available, R packages, or Python libraries are available, which streamlines access to data and standardizes formatting.

Aggregators	Focus	DwC	API	R packages	Python
ALA - Atlas of Living Australia	P, A	✓	✓	ALA4R1
Berkeley Ecoengine	P, A	✓	✓	Ecoengine2
CNABH	Br	✓
eBird	Bi	✓	✓	Auk3	ebird-api
FishNet2	F	✓	✓		fishnet
GBIF	B	✓	✓	Rgbif4	pygbif
iDigBio	B	✓	✓	Ridigbio5	idigbio
iNaturalist	P, A	✓	✓	Rinat6
LepNet	Lep	✓
Lichen Portal	Li	✓
Macaulay Library	Bi, F, Ap, Mm			WarbleR7
Macroalgal Herbarium Consortium Portal	Ma	✓
Mid-AtlanticHerbaria Consortium	P	✓
MyCoPortal	Fu	✓		RMyCoPortal8
OBIS	Pm, Am	✓	✓	Robis9
SEINet North American plant network	P	✓
SERNEC	P	✓
SCAN	At	✓
CNH	P	✓
Tri-Trophic Thematic Collections Network	P, At
BISON	P, A	✓	✓	Rbison10
VertNET	V	✓	✓	RVertNet11
Canadensys	B	✓	✓
Chinese virtual herbarium	P

Abbreviations: Aggregators- ALA (Atlas of Living Australia), CNABH (Consortium of North American Bryophyte Herbaria), GBIF (Global Biodiversity Information Facility), LepNet (Lepidoptera of North America Network), MyCoPortal (Mycology Collections data Portal), OBIS (Ocean Biogeographic Information System), SERNEC (Southeast Regional Network of Expertise and Collections), SCAN (Symbiota Collections of Arthropods Network), CNH (Consortium of Northeastern Herbaria), BISON (Biodiversity Information Serving Our Nation). Focus-A (Animals), Am (Marine Plants), Ap (amphibians), At (Arthropod​), B (Broad taxonomically), Br (Bryophytes), Bi (Birds), F (Fish), Fu (Fungus​), I (invertebrates), Lep (Lepidoptera​), Li (Lichen​), Ma (macroalgae) Mm (Mammals), P (Plants), Pm (Marine plants), V (Vertebrates).

References.

1

Raymond B, VanDerWal J, Belbin L. 2019. ALA4R: Atlas of Living Australia (ALA) data and resources in R. (14 May 2019; https://github.com/AtlasOfLivingAustralia/ALA4R).

2

Ram K. 2017. ecoengine: Programmatic Interface to the Web Service Methods Provided by UC Berkeley’s Natural History Data. R package version 1.11.0. (14 May 2019; https://CRAN.R-project.org/package=ecoengine). |

3

Strimas-Mackey M, Miller E, Hochachka W. 2017. auk: eBird Data Extraction and Processing with AWK. R package version. (14 May 2019; https://​github.com/​CornellLabofOrnithology/​auk).

4

Chamberlain S, Barve V, Mcglinn D, Oldoni D. 2018a. rgbif: Interface to the Global Biodiversity Information Facility API. R package version 1.1.0. (14 May 2019; https://CRAN.R-project.org/package=rgbif).

5

Michonneau F, and Collins M. 2017. ridigbio: Interface to the iDigBio Data API. R package version 0.3.5. (14 May 2019; https://CRAN.R-project.org/package=ridigbio).

6

Barve V, Hart E. 2014. rinat: Access iNaturalist data through APIs. R package version 0.1.4. [cited 16 May 2019].

7

Araya‐Salas M, Smith‐Vidaurre G. 2017. warbleR: An R package to streamline analysis of animal acoustic signals. Methods in Ecology and Evolution 8:184-191..

8

Krah FS, Bates ST, Miller AN. 2019. rMyCoPortal-an R package to interface with the Mycology Collections Portal. Biodiversity Data Journal 7..

9

Provoost P, Bosch S. 2019. “robis: R Client to access data from the OBIS API.” Ocean Biogegraphic Information System. Intergovernmental Oceanographic Commision of UNESCO. R package version 2.1.0. (14 May 2019; https://cran.r-project.org/package-robis).

10

Chamberlain S. 2019. rbison: Interface to the ‘USGS’ ‘BISON’ API. R package version 0.8.0. (14 May 2019; https://github.com/ropensci/rbison).

11

Chamberlain S. 2018. rvertnet: Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records. R package version 0.7.0. (14 May 2019; https://CRAN.R-project.org/package=rvertnet).