Supplementary material 1 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Supplementary information for: A continuous-score occupancy modeling framework for incorporating uncertain machine learning output in autonomous biodiversity surveys

Rhinehart, Tessa
Turek, Daniel
Kitzes, Justin

May 2022

Ecologists often study biodiversity by evaluating species occupancy and the relationship between occ...

Supplementary material 1 from: Townsend Peterson A, Asase A, Canhos D, de Souza S, Wieczorek J (2018) Data Leakage and Loss in Biodiversity Informatics. Biodiversity Data Journal 6: e26826. https://doi.org/10.3897/BDJ.6.e26826

Peterson, A. Townsend
Asase, Alex
Canhos, Dora
de Souza, Sidnei
Wieczorek, John

November 2018

This file offers detailed responses to two reviewers' comments, which were presented as very long, m...

Supplementary Information for 'Not all biodiversity richspots are climate refugia'

Kocsis, Ádám T.
Zhao, Qianshuo
Costello, Mark J.
Kiessling, Wolfgang

November 2021

Supplementary Information (pdf), supplementary data and code for the publication: Not all biodiversi...

Supplementary material 1 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Muñoz, Gabriel
Kissling, W. Daniel
van Loon, E. Emiel

January 2019

Biodiversity Observation User's manual. Follow this guide to upload literature and mine biodiversity...

Figure 3 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Muñoz, Gabriel
Kissling, W. Daniel
van Loon, E. Emiel

January 2019

Figure 3 Example of one text snippet resulting from running Biodiversity Observations Miner with O'F...

Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature

Muñoz, Gabriel
Kissling, W. Daniel
van Loon, E. Emiel

January 2019

A considerable portion of primary biodiversity data is digitally locked inside published literature ...

Supplementary material 1 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369

Underwood, Evelyn
Grace, Miriam

August 2017

The supplementary material provides additional detail on methods and data sources used in the case s...

Supplementary material 9 from: Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J (2020) Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodiversity Data Journal 8: e50124. https://doi.org/10.3897/BDJ.8.e50124

Bowser, Matthew
Brassfield, Rebekah
Dziergowski, Annie
Eskelin, Todd
Hester, Jennifer
Magness, Dawn
McInnis, Mariah
Melvin, Tracy
Morton, John
Stone, Joel

March 2020

This is the derived dataset created for the purpose of analysis. It includes only species-resolution...

Supplementary material 2 from: Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J (2020) Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodiversity Data Journal 8: e50124. https://doi.org/10.3897/BDJ.8.e50124

Bowser, Matthew
Brassfield, Rebekah
Dziergowski, Annie
Eskelin, Todd
Hester, Jennifer
Magness, Dawn
McInnis, Mariah
Melvin, Tracy
Morton, John
Stone, Joel

March 2020

These are the DNA extraction methods that were provided by RTL Genomics used for sweep-net samples o...

Supplementary material 2 from: Leidenberger S, Käck M, Karlsson B, Kindvall O (2016) The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research. Biodiversity Data Journal 4: e7644. https://doi.org/10.3897/BDJ.4.e7644

Leidenberger, Sonja
Käck, Martin
Karlsson, Björn
Kindvall, Oskar

March 2016

List of criteria that can be specified when searching for species observations in the Swedish LifeWa...

Supplementary material 8 from: Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J (2020) Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodiversity Data Journal 8: e50124. https://doi.org/10.3897/BDJ.8.e50124

Bowser, Matthew
Brassfield, Rebekah
Dziergowski, Annie
Eskelin, Todd
Hester, Jennifer
Magness, Dawn
McInnis, Mariah
Melvin, Tracy
Morton, John
Stone, Joel

March 2020

BOLD TaxonID Tree for SlikokOtu1170 generated by BOLD's Identification Engine, 26.December.201

Supplementary material 1: Global Biodiversity Information Facility: Taxa and Records from: Integrating and visualizing primary data from prospective and legacy taxonomic literature - Biodiversity Data Journal 3: e5063 (12 May 2015) https://doi.org/10.3897/BDJ.3.e5063

GBIF (5293459)

May 2018

All records in GBIF with taxonomic ranks (kingdom, phylum, class, order, and species), basis of reco...

Supplementary material 2 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059

Bingham, Heather,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Doudin, Michel,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Weatherdon, Lauren,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Despot-Belmonte, Katherine,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Wetzel, Florian,Museum fuer Naturkunde , Berlin, Germany
Groom, Quentin,Botanic Garden Meise, Meise, Belgium
Lewis, Edward,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Regan, Eugenie,The Biodiversity Consultancy, Cambridge, United Kingdom
Appeltans, Ward,Ocean Biogeographic Information System (OBIS), Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
Güntsch, Anton,Freie Universität Berlin, Berlin, Germany
Mergen, Patricia,Botanic Garden Meise, Meise, Belgium
Agosti, Donat,Plazi, Bern, Switzerland
Penev, Lyubomir,Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria
Hoffmann, Anke,Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
Saarenmaa, Hannu,University of Eastern Finland, Joensuu, Finland
Geller, Gary,Group on Earth Observations, Geneva, Switzerland
Kim, Kidong,National Institute of Ecology, Seocheon, Korea, South
Kim, HyeJin,National Institute of Ecology, Seocheon, Korea, South
Archambeau, Anne-Sophie,Global Biodiversity Information Facility France, Paris, France
Häuser, Christoph,Museum für Naturkunde, Berlin, Germany
Schmeller, Dirk,Environmental Research Center (UFZ) Halle, Leipzig, Germany
Geijzendorffer, Ilse,Tour du Valat, Research Institute for the conservation of Mediterranean Wetlands, Arles, France
García Camacho, Antonio,CSIC, Spanish Council for Scientific Research, Seville, Spain
Guerra, Carlos,Group on Earth Observations - Biodiversity Observation Network, Leipzig, Germany
Robertson, Tim,Global Biodiversity Information Facility, Copenhagen, Denmark
Runnel, Veljo,University of Tartu, Tartu, Estonia
Valland, Nils,Norwegian Biodiversity Information Centre, Trondheim, Norway
Martin, Corinne,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom

September 2017

Code used to generate Figures 1 - 3. Based on a script by Paul Kassebaum (https://uk.mathworks.com/m...

Supplementary material 3 from: Chapman AD, Belbin L, Zermoglio PF, Wieczorek J, Morris PJ, Nicholls M, Rees ER, Veiga AK, Thompson A, Saraiva AM, James SA, Gendreau C, Benson A, Schigel D (2020) Developing Standards for Improved Data Quality and for Selecting Fit for Use Biodiversity Data. Biodiversity Information Science and Standards 4: e50889. https://doi.org/10.3897/biss.4.50889

Chapman, Arthur
Belbin, Lee
Zermoglio, Paula
Wieczorek, John
Morris, Paul
Nicholls, Miles
Rees, Emily Rose
Veiga, Allan
Thompson, Alexander
Saraiva, Antonio
James, Shelley
Gendreau, Christian
Benson, Abigail
Schigel, Dmitry

March 2020

Counts of occurrence records in 2019-04-15 snapshot of GBIF-mediated data that fit the three categor...

Supplementary material 2 from: Townsend Peterson A, Asase A, Canhos D, de Souza S, Wieczorek J (2018) Data Leakage and Loss in Biodiversity Informatics. Biodiversity Data Journal 6: e26826. https://doi.org/10.3897/BDJ.6.e26826

Peterson, A. Townsend
Asase, Alex
Canhos, Dora
de Souza, Sidnei
Wieczorek, John

November 2018

These data are the summaries of data leaks in each of three dimensions for each of the bird and herb...

Supplementary information for: A continuous-score occupancy modeling framework for incorporating uncertain machine learning output in autonomous biodiversity surveys

Rhinehart, Tessa
Turek, Daniel
Kitzes, Justin

May 2022

Ecologists often study biodiversity by evaluating species occupancy and the relationship between occ...

Supplementary material 1 from: Townsend Peterson A, Asase A, Canhos D, de Souza S, Wieczorek J (2018) Data Leakage and Loss in Biodiversity Informatics. Biodiversity Data Journal 6: e26826. https://doi.org/10.3897/BDJ.6.e26826

Peterson, A. Townsend
Asase, Alex
Canhos, Dora
de Souza, Sidnei
Wieczorek, John

November 2018

This file offers detailed responses to two reviewers' comments, which were presented as very long, m...

Supplementary Information for 'Not all biodiversity richspots are climate refugia'

Kocsis, Ádám T.
Zhao, Qianshuo
Costello, Mark J.
Kiessling, Wolfgang

November 2021

Supplementary Information (pdf), supplementary data and code for the publication: Not all biodiversi...

Supplementary material 1 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Muñoz, Gabriel
Kissling, W. Daniel
van Loon, E. Emiel

January 2019

Biodiversity Observation User's manual. Follow this guide to upload literature and mine biodiversity...

Figure 3 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Muñoz, Gabriel
Kissling, W. Daniel
van Loon, E. Emiel

January 2019

Figure 3 Example of one text snippet resulting from running Biodiversity Observations Miner with O'F...

Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature

Muñoz, Gabriel
Kissling, W. Daniel
van Loon, E. Emiel

January 2019

A considerable portion of primary biodiversity data is digitally locked inside published literature ...

Supplementary material 1 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369

Underwood, Evelyn
Grace, Miriam

August 2017

The supplementary material provides additional detail on methods and data sources used in the case s...

Supplementary material 9 from: Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J (2020) Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodiversity Data Journal 8: e50124. https://doi.org/10.3897/BDJ.8.e50124

Bowser, Matthew
Brassfield, Rebekah
Dziergowski, Annie
Eskelin, Todd
Hester, Jennifer
Magness, Dawn
McInnis, Mariah
Melvin, Tracy
Morton, John
Stone, Joel

March 2020

This is the derived dataset created for the purpose of analysis. It includes only species-resolution...

Supplementary material 2 from: Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J (2020) Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodiversity Data Journal 8: e50124. https://doi.org/10.3897/BDJ.8.e50124

Bowser, Matthew
Brassfield, Rebekah
Dziergowski, Annie
Eskelin, Todd
Hester, Jennifer
Magness, Dawn
McInnis, Mariah
Melvin, Tracy
Morton, John
Stone, Joel

March 2020

These are the DNA extraction methods that were provided by RTL Genomics used for sweep-net samples o...

Supplementary material 2 from: Leidenberger S, Käck M, Karlsson B, Kindvall O (2016) The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research. Biodiversity Data Journal 4: e7644. https://doi.org/10.3897/BDJ.4.e7644

Leidenberger, Sonja
Käck, Martin
Karlsson, Björn
Kindvall, Oskar

March 2016

List of criteria that can be specified when searching for species observations in the Swedish LifeWa...

Supplementary material 8 from: Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J (2020) Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodiversity Data Journal 8: e50124. https://doi.org/10.3897/BDJ.8.e50124

Bowser, Matthew
Brassfield, Rebekah
Dziergowski, Annie
Eskelin, Todd
Hester, Jennifer
Magness, Dawn
McInnis, Mariah
Melvin, Tracy
Morton, John
Stone, Joel

March 2020

BOLD TaxonID Tree for SlikokOtu1170 generated by BOLD's Identification Engine, 26.December.201

Supplementary material 1: Global Biodiversity Information Facility: Taxa and Records from: Integrating and visualizing primary data from prospective and legacy taxonomic literature - Biodiversity Data Journal 3: e5063 (12 May 2015) https://doi.org/10.3897/BDJ.3.e5063

GBIF (5293459)

May 2018

All records in GBIF with taxonomic ranks (kingdom, phylum, class, order, and species), basis of reco...

Supplementary material 2 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059

Bingham, Heather,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Doudin, Michel,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Weatherdon, Lauren,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Despot-Belmonte, Katherine,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Wetzel, Florian,Museum fuer Naturkunde , Berlin, Germany
Groom, Quentin,Botanic Garden Meise, Meise, Belgium
Lewis, Edward,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom
Regan, Eugenie,The Biodiversity Consultancy, Cambridge, United Kingdom
Appeltans, Ward,Ocean Biogeographic Information System (OBIS), Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
Güntsch, Anton,Freie Universität Berlin, Berlin, Germany
Mergen, Patricia,Botanic Garden Meise, Meise, Belgium
Agosti, Donat,Plazi, Bern, Switzerland
Penev, Lyubomir,Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria
Hoffmann, Anke,Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
Saarenmaa, Hannu,University of Eastern Finland, Joensuu, Finland
Geller, Gary,Group on Earth Observations, Geneva, Switzerland
Kim, Kidong,National Institute of Ecology, Seocheon, Korea, South
Kim, HyeJin,National Institute of Ecology, Seocheon, Korea, South
Archambeau, Anne-Sophie,Global Biodiversity Information Facility France, Paris, France
Häuser, Christoph,Museum für Naturkunde, Berlin, Germany
Schmeller, Dirk,Environmental Research Center (UFZ) Halle, Leipzig, Germany
Geijzendorffer, Ilse,Tour du Valat, Research Institute for the conservation of Mediterranean Wetlands, Arles, France
García Camacho, Antonio,CSIC, Spanish Council for Scientific Research, Seville, Spain
Guerra, Carlos,Group on Earth Observations - Biodiversity Observation Network, Leipzig, Germany
Robertson, Tim,Global Biodiversity Information Facility, Copenhagen, Denmark
Runnel, Veljo,University of Tartu, Tartu, Estonia
Valland, Nils,Norwegian Biodiversity Information Centre, Trondheim, Norway
Martin, Corinne,UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom

September 2017

Code used to generate Figures 1 - 3. Based on a script by Paul Kassebaum (https://uk.mathworks.com/m...

Supplementary material 3 from: Chapman AD, Belbin L, Zermoglio PF, Wieczorek J, Morris PJ, Nicholls M, Rees ER, Veiga AK, Thompson A, Saraiva AM, James SA, Gendreau C, Benson A, Schigel D (2020) Developing Standards for Improved Data Quality and for Selecting Fit for Use Biodiversity Data. Biodiversity Information Science and Standards 4: e50889. https://doi.org/10.3897/biss.4.50889

Chapman, Arthur
Belbin, Lee
Zermoglio, Paula
Wieczorek, John
Morris, Paul
Nicholls, Miles
Rees, Emily Rose
Veiga, Allan
Thompson, Alexander
Saraiva, Antonio
James, Shelley
Gendreau, Christian
Benson, Abigail
Schigel, Dmitry

March 2020

Counts of occurrence records in 2019-04-15 snapshot of GBIF-mediated data that fit the three categor...

Supplementary material 2 from: Townsend Peterson A, Asase A, Canhos D, de Souza S, Wieczorek J (2018) Data Leakage and Loss in Biodiversity Informatics. Biodiversity Data Journal 6: e26826. https://doi.org/10.3897/BDJ.6.e26826

Peterson, A. Townsend
Asase, Alex
Canhos, Dora
de Souza, Sidnei
Wieczorek, John

November 2018

These data are the summaries of data leaks in each of three dimensions for each of the bird and herb...

Supplementary information for: A continuous-score occupancy modeling framework for incorporating uncertain machine learning output in autonomous biodiversity surveys

Rhinehart, Tessa
Turek, Daniel
Kitzes, Justin

May 2022

Ecologists often study biodiversity by evaluating species occupancy and the relationship between occ...

Supplementary material 1 from: Townsend Peterson A, Asase A, Canhos D, de Souza S, Wieczorek J (2018) Data Leakage and Loss in Biodiversity Informatics. Biodiversity Data Journal 6: e26826. https://doi.org/10.3897/BDJ.6.e26826

Peterson, A. Townsend
Asase, Alex
Canhos, Dora
de Souza, Sidnei
Wieczorek, John

November 2018

This file offers detailed responses to two reviewers' comments, which were presented as very long, m...

Supplementary Information for 'Not all biodiversity richspots are climate refugia'

Kocsis, Ádám T.
Zhao, Qianshuo
Costello, Mark J.
Kiessling, Wolfgang

November 2021

Supplementary Information (pdf), supplementary data and code for the publication: Not all biodiversi...

Supplementary material 1 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Abstract

Extracted data

Supplementary material 1 from: Muñoz G, Kissling W, van Loon E (2019) Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal 7: e28737. https://doi.org/10.3897/BDJ.7.e28737

Abstract

Extracted data

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