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Article ; Online: Global and national trends, gaps, and opportunities in documenting and monitoring species distributions.

Oliver, Ruth Y / Meyer, Carsten / Ranipeta, Ajay / Winner, Kevin / Jetz, Walter

2021 Volume 19, Issue 8, Page(s) e3001336

Abstract: Conserving and managing biodiversity in the face of ongoing global change requires sufficient evidence to assess status and trends of species distributions. Here, we propose novel indicators of biodiversity data coverage and sampling effectiveness and ... ...

Abstract	Conserving and managing biodiversity in the face of ongoing global change requires sufficient evidence to assess status and trends of species distributions. Here, we propose novel indicators of biodiversity data coverage and sampling effectiveness and analyze national trajectories in closing spatiotemporal knowledge gaps for terrestrial vertebrates (1950 to 2019). Despite a rapid rise in data coverage, particularly in the last 2 decades, strong geographic and taxonomic biases persist. For some taxa and regions, a tremendous growth in records failed to directly translate into newfound knowledge due to a sharp decline in sampling effectiveness. However, we found that a nation's coverage was stronger for species for which it holds greater stewardship. As countries under the post-2020 Global Biodiversity Framework renew their commitments to an improved, rigorous biodiversity knowledge base, our findings highlight opportunities for international collaboration to close critical information gaps.
MeSH term(s)	Animal Distribution ; Animals ; Artiodactyla ; Biodiversity ; Conservation of Natural Resources ; Ecology/methods ; Ecology/standards ; Ecology/trends ; Internationality ; Panthera
Language	English
Publishing date	2021-08-12
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001336
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A hierarchical inventory of the world's mountains for global comparative mountain science.

Snethlage, Mark A / Geschke, Jonas / Ranipeta, Ajay / Jetz, Walter / Yoccoz, Nigel G / Körner, Christian / Spehn, Eva M / Fischer, Markus / Urbach, Davnah

Scientific data

2022 Volume 9, Issue 1, Page(s) 149

Abstract: A standardized delineation of the world's mountains has many applications in research, education, and the science-policy interface. Here we provide a new inventory of 8616 mountain ranges developed under the auspices of the Global Mountain Biodiversity ... ...

Abstract	A standardized delineation of the world's mountains has many applications in research, education, and the science-policy interface. Here we provide a new inventory of 8616 mountain ranges developed under the auspices of the Global Mountain Biodiversity Assessment (GMBA). Building on an earlier compilation, the presented geospatial database uses a further advanced and generalized mountain definition and a semi-automated method to enable globally standardized, transparent delineations of mountain ranges worldwide. The inventory is presented on EarthEnv at various hierarchical levels and allows users to select their preferred level of regional aggregation from continents to small subranges according to their needs and the scale of their analyses. The clearly defined, globally consistent and hierarchical nature of the presented mountain inventory offers a standardized resource for referencing and addressing mountains across basic and applied natural as well as social sciences and a range of other uses in science communication and education.
Language	English
Publishing date	2022-04-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-022-01256-y
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Article ; Online: Camera trapping expands the view into global biodiversity and its change.

Oliver, Ruth Y / Iannarilli, Fabiola / Ahumada, Jorge / Fegraus, Eric / Flores, Nicole / Kays, Roland / Birch, Tanya / Ranipeta, Ajay / Rogan, Matthew S / Sica, Yanina V / Jetz, Walter

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2023 Volume 378, Issue 1881, Page(s) 20220232

Abstract: Growing threats to biodiversity demand timely, detailed information on species occurrence, diversity and abundance at large scales. Camera traps (CTs), combined with computer vision models, provide an efficient method to survey species of certain taxa ... ...

Abstract	Growing threats to biodiversity demand timely, detailed information on species occurrence, diversity and abundance at large scales. Camera traps (CTs), combined with computer vision models, provide an efficient method to survey species of certain taxa with high spatio-temporal resolution. We test the potential of CTs to close biodiversity knowledge gaps by comparing CT records of terrestrial mammals and birds from the recently released Wildlife Insights platform to publicly available occurrences from many observation types in the Global Biodiversity Information Facility. In locations with CTs, we found they sampled a greater number of days (mean = 133 versus 57 days) and documented additional species (mean increase of 1% of expected mammals). For species with CT data, we found CTs provided novel documentation of their ranges (93% of mammals and 48% of birds). Countries with the largest boost in data coverage were in the historically underrepresented southern hemisphere. Although embargoes increase data providers' willingness to share data, they cause a lag in data availability. Our work shows that the continued collection and mobilization of CT data, especially when combined with data sharing that supports attribution and privacy, has the potential to offer a critical lens into biodiversity. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.
MeSH term(s)	Animals ; Biodiversity ; Animals, Wild ; Mammals ; Birds ; Knowledge
Language	English
Publishing date	2023-05-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2022.0232
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Article ; Online: A cloud-based toolbox for the versatile environmental annotation of biodiversity data.

Li, Richard / Ranipeta, Ajay / Wilshire, John / Malczyk, Jeremy / Duong, Michelle / Guralnick, Robert / Wilson, Adam / Jetz, Walter

PLoS biology

2021 Volume 19, Issue 11, Page(s) e3001460

Abstract: A vast range of research applications in biodiversity sciences requires integrating primary species, genetic, or ecosystem data with other environmental data. This integration requires a consideration of the spatial and temporal scale appropriate for the ...

Abstract	A vast range of research applications in biodiversity sciences requires integrating primary species, genetic, or ecosystem data with other environmental data. This integration requires a consideration of the spatial and temporal scale appropriate for the data and processes in question. But a versatile and scale flexible environmental annotation of biodiversity data remains constrained by technical hurdles. Existing tools have streamlined the intersection of occurrence records with gridded environmental data but have remained limited in their ability to address a range of spatial and temporal grains, especially for large datasets. We present the Spatiotemporal Observation Annotation Tool (STOAT), a cloud-based toolbox for flexible biodiversity-environment annotations. STOAT is optimized for large biodiversity datasets and allows user-specified spatial and temporal resolution and buffering in support of environmental characterizations that account for the uncertainty and scale of data and of relevant processes. The tool offers these services for a growing set of near global, remotely sensed, or modeled environmental data, including Landsat, MODIS, EarthEnv, and CHELSA. STOAT includes a user-friendly, web-based dashboard that provides tools for annotation task management and result visualization, linked to Map of Life, and a dedicated R package (rstoat) for programmatic access. We demonstrate STOAT functionality with several examples that illustrate phenological variation and spatial and temporal scale dependence of environmental characteristics of birds at a continental scale. We expect STOAT to facilitate broader exploration and assessment of the scale dependence of observations and processes in ecology.
MeSH term(s)	Animals ; Biodiversity ; Birds/physiology ; Cloud Computing ; Databases as Topic ; Satellite Communications ; Seasons ; Spatio-Temporal Analysis ; Species Specificity ; Temperature ; Time Factors
Language	English
Publishing date	2021-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001460
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Article ; Online: A globally integrated structure of taxonomy to support biodiversity science and conservation.

Sandall, Emily L / Maureaud, Aurore A / Guralnick, Robert / McGeoch, Melodie A / Sica, Yanina V / Rogan, Matthew S / Booher, Douglas B / Edwards, Robert / Franz, Nico / Ingenloff, Kate / Lucas, Maisha / Marsh, Charles J / McGowan, Jennifer / Pinkert, Stefan / Ranipeta, Ajay / Uetz, Peter / Wieczorek, John / Jetz, Walter

Trends in ecology & evolution

2023 Volume 38, Issue 12, Page(s) 1143–1153

Abstract: All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We ... ...

Abstract	All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
MeSH term(s)	Biodiversity ; Classification ; Conservation of Natural Resources
Language	English
Publishing date	2023-09-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/j.tree.2023.08.004
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Country Compendium of the Global Register of Introduced and Invasive Species.

Pagad, Shyama / Bisset, Stewart / Genovesi, Piero / Groom, Quentin / Hirsch, Tim / Jetz, Walter / Ranipeta, Ajay / Schigel, Dmitry / Sica, Yanina V / McGeoch, Melodie A

Scientific data

2022 Volume 9, Issue 1, Page(s) 391

Abstract: The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien species, along with a designation of those species with evidence of impact at a country ... ...

Abstract	The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien species, along with a designation of those species with evidence of impact at a country level. The Compendium provides a baseline for monitoring the distribution and invasion status of all major taxonomic groups, and can be used for the purpose of global analyses of introduced (alien, non-native, exotic) and invasive species (invasive alien species), including regional, single and multi-species taxon assessments and comparisons. It enables exploration of gaps and inferred absences of species across countries, and also provides one means for updating individual GRIIS Checklists. The Country Compendium is, for example, instrumental, along with data on first records of introduction, for assessing and reporting on invasive alien species targets, including for the Convention on Biological Diversity and Sustainable Development Goals. The GRIIS Country Compendium provides a baseline and mechanism for tracking the spread of introduced and invasive alien species across countries globally. Design Type(s) Data integration objective ● Observation design Measurement Type(s) Alien species occurrence ● Evidence of impact invasive alien species assessment objective Technology Type(s) Agent expert ● Data collation Factor Type(s) Geographic location ● Origin / provenance ● Habitat Sample Characteristics - Organism Animalia ● Bacteria ● Chromista ● Fungi ● Plantae ● Protista (Protozoa) ● Viruses Sample Characteristics - Location Global countries.
MeSH term(s)	Biodiversity ; Ecosystem ; Eukaryota ; Fungi ; Introduced Species ; Plants
Language	English
Publishing date	2022-07-09
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-022-01514-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A globally integrated structure of taxonomy to support biodiversity science and conservation

Sandall, Emily L. / Maureaud, Aurore A. / Guralnick, Robert / McGeoch, Melodie A. / Sica, Yanina V. / Rogan, Matthew S. / Booher, Douglas B. / Edwards, Robert / Franz, Nico / Ingenloff, Kate / Lucas, Maisha / Marsh, Charles J. / McGowan, Jennifer / Pinkert, Stefan / Ranipeta, Ajay / Uetz, Peter / Wieczorek, John / Jetz, Walter

Trends in Ecology & Evolution.

2023

Abstract: All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on coordination and organization of taxonomic data. We assess ... ...

Abstract	All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
Keywords	biodiversity ; evolution ; taxonomy ; taxonomic backbone ; integrative science ; data linkage ; social infrastructure ; biodiversity conservation
Language	English
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/j.tree.2023.08.004
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A suite of global, cross-scale topographic variables for environmental and biodiversity modeling.

Amatulli, Giuseppe / Domisch, Sami / Tuanmu, Mao-Ning / Parmentier, Benoit / Ranipeta, Ajay / Malczyk, Jeremy / Jetz, Walter

Scientific data

2018 Volume 5, Page(s) 180040

Abstract: Topographic variation underpins a myriad of patterns and processes in hydrology, climatology, geography and ecology and is key to understanding the variation of life on the planet. A fully standardized and global multivariate product of different terrain ...

Abstract	Topographic variation underpins a myriad of patterns and processes in hydrology, climatology, geography and ecology and is key to understanding the variation of life on the planet. A fully standardized and global multivariate product of different terrain features has the potential to support many large-scale research applications, however to date, such datasets are unavailable. Here we used the digital elevation model products of global 250 m GMTED2010 and near-global 90 m SRTM4.1dev to derive a suite of topographic variables: elevation, slope, aspect, eastness, northness, roughness, terrain roughness index, topographic position index, vector ruggedness measure, profile/tangential curvature, first/second order partial derivative, and 10 geomorphological landform classes. We aggregated each variable to 1, 5, 10, 50 and 100 km spatial grains using several aggregation approaches. While a cross-correlation underlines the high similarity of many variables, a more detailed view in four mountain regions reveals local differences, as well as scale variations in the aggregated variables at different spatial grains. All newly-developed variables are available for download at Data Citation 1 and for download and visualization at http://www.earthenv.org/topography.
Language	English
Publishing date	2018-03-20
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/sdata.2018.40
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Article ; Online: Location, location, location

Ranipeta Ajay / Wieczorek John / Beaman Reed / Flemons Paul / Guralnick Robert / Hill Andrew W / Chavan Vishwas / Remsen David

BMC Bioinformatics, Vol 10, Iss Suppl 14, p S

utilizing pipelines and services to more effectively georeference the world's biodiversity data

2009 Volume 3

Abstract: Abstract Background Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions ... ...

Abstract	Abstract Background Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions associated with biodiversity records that are often heterogeneous and not in a map-ready format. The biodiversity informatics community has developed best practices and tools that provide the means to do retrospective georeferencing (e.g., the BioGeomancer toolkit), a process that converts heterogeneous descriptions into geographic coordinates and a measurement of spatial uncertainty. Even with these methods and tools, data publishers are faced with the immensely time-consuming task of vetting georeferenced localities. Furthermore, it is likely that overlap in georeferencing effort is occurring across data publishers. Solutions are needed that help publishers more effectively georeference their records, verify their quality, and eliminate the duplication of effort across publishers. Results We have developed a tool called BioGeoBIF, which incorporates the high throughput and standardized georeferencing methods of BioGeomancer into a beginning-to-end workflow. Custodians who publish their data to the Global Biodiversity Information Facility (GBIF) can use this system to improve the quantity and quality of their georeferences. BioGeoBIF harvests records directly from the publishers' access points, georeferences the records using the BioGeomancer web-service, and makes results available to data managers for inclusion at the source. Using a web-based, password-protected, group management system for each data publisher, we leave data ownership, management, and vetting responsibilities with the managers and collaborators of each data set. We also minimize the georeferencing task, by combining and storing unique textual localities from all registered data access points, and dynamically linking that information to the password protected record information for each publisher. Conclusion We have developed one of the first examples of services that can help create higher quality data for publishers mediated through the Global Biodiversity Information Facility and its data portal. This service is one step towards solving many problems of data quality in the growing field of biodiversity informatics. We envision future improvements to our service that include faster results returns and inclusion of more georeferencing engines.
Keywords	Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	306
Language	English
Publishing date	2009-11-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data.

Hill, Andrew W / Guralnick, Robert / Flemons, Paul / Beaman, Reed / Wieczorek, John / Ranipeta, Ajay / Chavan, Vishwas / Remsen, David

BMC bioinformatics

2009 Volume 10 Suppl 14, Page(s) S3

Abstract: Background: Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions associated ... ...

Abstract	Background: Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions associated with biodiversity records that are often heterogeneous and not in a map-ready format. The biodiversity informatics community has developed best practices and tools that provide the means to do retrospective georeferencing (e.g., the BioGeomancer toolkit), a process that converts heterogeneous descriptions into geographic coordinates and a measurement of spatial uncertainty. Even with these methods and tools, data publishers are faced with the immensely time-consuming task of vetting georeferenced localities. Furthermore, it is likely that overlap in georeferencing effort is occurring across data publishers. Solutions are needed that help publishers more effectively georeference their records, verify their quality, and eliminate the duplication of effort across publishers. Results: We have developed a tool called BioGeoBIF, which incorporates the high throughput and standardized georeferencing methods of BioGeomancer into a beginning-to-end workflow. Custodians who publish their data to the Global Biodiversity Information Facility (GBIF) can use this system to improve the quantity and quality of their georeferences. BioGeoBIF harvests records directly from the publishers' access points, georeferences the records using the BioGeomancer web-service, and makes results available to data managers for inclusion at the source. Using a web-based, password-protected, group management system for each data publisher, we leave data ownership, management, and vetting responsibilities with the managers and collaborators of each data set. We also minimize the georeferencing task, by combining and storing unique textual localities from all registered data access points, and dynamically linking that information to the password protected record information for each publisher. Conclusion: We have developed one of the first examples of services that can help create higher quality data for publishers mediated through the Global Biodiversity Information Facility and its data portal. This service is one step towards solving many problems of data quality in the growing field of biodiversity informatics. We envision future improvements to our service that include faster results returns and inclusion of more georeferencing engines.
MeSH term(s)	Biodiversity ; Computational Biology/methods ; Databases, Factual ; Humans
Language	English
Publishing date	2009-11-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-10-S14-S3
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