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Biodiversity Specimen Data

a collection of specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions

Biodiversity Record Aggregators

ML Gaynor - Updated April 2020.

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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.

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).



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


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; |


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


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;


Michonneau F, and Collins M. 2017. ridigbio: Interface to the iDigBio Data API. R package version 0.3.5. (14 May 2019;


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


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..


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


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;


Chamberlain S. 2019. rbison: Interface to the ‘USGS’ ‘BISON’ API. R package version 0.8.0. (14 May 2019;


Chamberlain S. 2018. rvertnet: Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records. R package version 0.7.0. (14 May 2019;