Difference between revisions of "Further reading"

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==On taxonomic aggregators (global species lists) and the aggregation process==
 
==On taxonomic aggregators (global species lists) and the aggregation process==
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Döring, M., Jeppesen, T., & Bánki, O. (2022). Introducing ChecklistBank: An index and repository for taxonomic data. Biodiversity Information Science and Standards, 6, e93938. doi: [https://doi.org/10.3897/biss.6.93938 https://doi.org/10.3897/biss.6.93938]
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Garnett, S. T., Christidis, L., Conix, S., Costello, M. J., Zachos, F. E., Bánki, O. S., Bao, Y., Barik, S. K., Buckeridge, J. S., Hobern, D. & Lien, A. (2020). Principles for creating a single authoritative list of the world’s species. PLoS Biology, 18(7), e3000736. doi: [https://doi.org/10.1371/journal.pbio.3000736 https://doi.org/10.1371/journal.pbio.3000736]
 
Garnett, S. T., Christidis, L., Conix, S., Costello, M. J., Zachos, F. E., Bánki, O. S., Bao, Y., Barik, S. K., Buckeridge, J. S., Hobern, D. & Lien, A. (2020). Principles for creating a single authoritative list of the world’s species. PLoS Biology, 18(7), e3000736. doi: [https://doi.org/10.1371/journal.pbio.3000736 https://doi.org/10.1371/journal.pbio.3000736]
 +
 +
Grenié M., Berti E., Carvajal-Quintero J., Dädlow G.M.L., Sagouis A. & Winter, M. 2022. Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices. Methods in Ecology and Evolution 14(1): 12-25. [https://doi.org/10.1111/2041-210X.13802 https://doi.org/10.1111/2041-210X.13802]
  
 
Hobern, D., Barik, S. K., Christidis, L., Garnett, S. T. Kirk, P., Orrell, T. M., Pape, T., Pyle, R. L., Thiele, K. R., Zachos, F. E., & Bánki, O. (2021). Towards a global list of accepted species VI. The Catalogue of Life checklist. Org Divers Evol. doi: [https://doi.org/10.1007/s13127-021-00516-w https://doi.org/10.1007/s13127-021-00516-w]
 
Hobern, D., Barik, S. K., Christidis, L., Garnett, S. T. Kirk, P., Orrell, T. M., Pape, T., Pyle, R. L., Thiele, K. R., Zachos, F. E., & Bánki, O. (2021). Towards a global list of accepted species VI. The Catalogue of Life checklist. Org Divers Evol. doi: [https://doi.org/10.1007/s13127-021-00516-w https://doi.org/10.1007/s13127-021-00516-w]
  
−
Döring, M., Jeppesen, T., & Bánki, O. (2022). Introducing ChecklistBank: An index and repository for taxonomic data. Biodiversity Information Science and Standards, 6, e93938. doi: [https://doi.org/10.3897/biss.6.93938 https://doi.org/10.3897/biss.6.93938]
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Lien, A., Banki, O., Barik, S. K., Buckeridge, J. S., Christidis, L., Cigliano, M. M., Conix, S., Costello, M. J., Hobern, D., Kirk, P. M., Kroh, A., Montgomery, N., Nikolaeva, S., Orrell, T. M., Pyle, R. L., Raz, L., Thiele, K., Thomson, S. A., van Dijk, P. P., Wambiji, N., Whalen, A., Zachos, F. E., Zhi-Qiang Zhang & Stephen T. Garnett (2023). Widespread support for a global species list with a formal governance system. PNAS 120(45), doi: [https://doi.org/10.1073/pnas.2306899120 https://doi.org/10.1073/pnas.2306899120]
  
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Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020 Jan 1;2020:baaa062. doi: [https://doi.org/10.1093/database/baaa062 10.1093/database/baaa062].
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Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I. (2020). NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020 Jan 1;2020:baaa062. doi: [https://doi.org/10.1093/database/baaa062 10.1093/database/baaa062].
 
   
 
   
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'''(Plants:)''' Borsch, T., Berendsohn, W., Dalcin, E., Delmas, M., Demissew, S., Elliott, A., Fritsch, P., Fuchs, A., Geltman, D., Güner, A., Haevermans, T., Knapp, S., le Roux, M. M., Loizeau, P.-A., Miller, C., Miller, J., Miller, J. T., Palese, R., Paton, A., & Zamora, N. (2020). World Flora Online: placing taxonomists at the heart of a definitive and comprehensive global resource on the world’s plants. Taxon, 69, 1311–1341. doi: [https://doi.org/10.1002/tax.12373 https://doi.org/10.1002/tax.12373]
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'''(Plants:)'''  
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 +
Borsch, T., Berendsohn, W., Dalcin, E., Delmas, M., Demissew, S., Elliott, A., Fritsch, P., Fuchs, A., Geltman, D., Güner, A., Haevermans, T., Knapp, S., le Roux, M. M., Loizeau, P.-A., Miller, C., Miller, J., Miller, J. T., Palese, R., Paton, A., & Zamora, N. (2020). World Flora Online: placing taxonomists at the heart of a definitive and comprehensive global resource on the world’s plants. Taxon, 69, 1311–1341. doi: [https://doi.org/10.1002/tax.12373 https://doi.org/10.1002/tax.12373]
  
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Govaerts, R., Nic Lughadha, E., Black, N., Turner, R. & Paton, A. 2021: The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci Data 8, 215 (2021). doi: [https://doi.org/10.1038/s41597-021-00997-6 https://doi.org/10.1038/s41597-021-00997-6]
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Govaerts, R., Nic Lughadha, E., Black, N., Turner, R. & Paton, A. (2021): The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci Data 8, 215. doi: [https://doi.org/10.1038/s41597-021-00997-6 https://doi.org/10.1038/s41597-021-00997-6]
  
 
==On name and taxon identifiers==
 
==On name and taxon identifiers==
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Anonymous 2023: Wikidata - List of taxon identifiers. [https://en.wikipedia.org/wiki/Template:Taxonbar/doc#Taxon_identifiers https://en.wikipedia.org/wiki/Template:Taxonbar/doc#Taxon_identifiers]
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Anonymous (2023): Wikidata - List of taxon identifiers. [https://en.wikipedia.org/wiki/Template:Taxonbar/doc#Taxon_identifiers https://en.wikipedia.org/wiki/Template:Taxonbar/doc#Taxon_identifiers]
  
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Page R. D. M. 2023: Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people
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Page R. D. M. (2023): Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people
 
doi: [https://doi.org/10.1101/2023.05.29.542697 https://doi.org/10.1101/2023.05.29.542697]
 
doi: [https://doi.org/10.1101/2023.05.29.542697 https://doi.org/10.1101/2023.05.29.542697]
  
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Pyle, R. L., Barik, S. K., Christidis, L., Conix, S., Costello, M. J., van Dijk, P. P., Garnett, S. T., Hobern, D., Kirk, P. M., Lien, A. M., Orrell, T. M., Remsen, D., Thomson, S. A., Wambiji, N., Zachos, F. E., Zhang, Z-Q., Thiele, K. R. (2021). Towards a global list of accepted species V. The devil is in the details. Organisms Diversity & Evolution. doi: [https://doi.org/10.1007/s13127-021-00504-0 https://doi.org/10.1007/s13127-021-00504-0]
 
Pyle, R. L., Barik, S. K., Christidis, L., Conix, S., Costello, M. J., van Dijk, P. P., Garnett, S. T., Hobern, D., Kirk, P. M., Lien, A. M., Orrell, T. M., Remsen, D., Thomson, S. A., Wambiji, N., Zachos, F. E., Zhang, Z-Q., Thiele, K. R. (2021). Towards a global list of accepted species V. The devil is in the details. Organisms Diversity & Evolution. doi: [https://doi.org/10.1007/s13127-021-00504-0 https://doi.org/10.1007/s13127-021-00504-0]
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 +
==Use cases==
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Islam, S., Papale, D., Vaira, L., Rosati, I. Peterseil, J. & Pichot, C. (2024): Navigating taxonomic complexity: A use-case report on FAIR scientific name-matching service usage in ENVRI Research Infrastructures. Research Ideas and Outcomes 10. doi: [https://doi.org/10.3897/rio.10.e121871 https://doi.org/10.3897/rio.10.e121871]
  
 
==Standards==
 
==Standards==
 
Döring, M., & Ower, G. D. (2019). The Catalogue of Life Data Package - A new format for exchanging nomenclatural and taxonomic information. Biodiversity Information Science and Standards, 3, e38711. [https://doi.org/10.3897/biss.3.38771 https://doi.org/10.3897/biss.3.38771]
 
Döring, M., & Ower, G. D. (2019). The Catalogue of Life Data Package - A new format for exchanging nomenclatural and taxonomic information. Biodiversity Information Science and Standards, 3, e38711. [https://doi.org/10.3897/biss.3.38771 https://doi.org/10.3897/biss.3.38771]
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 +
==OpenRefine==
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 +
GBIF course links: [https://docs.gbif.org/course-data-use/en/openrefine.html https://docs.gbif.org/course-data-use/en/openrefine.html]
 +
 +
Whitmire, A. & Mozzherin, D. (2023): Reconciling taxonomic names in OpenRefine via Global Names. URL: [https://github.com/gnames/gnverifier/wiki/OpenRefine-readme https://github.com/gnames/gnverifier/wiki/OpenRefine-readme]

Latest revision as of 10:04, 6 August 2024

(Recent review publications - please also refer to references within)

On taxonomic aggregators (global species lists) and the aggregation process

Döring, M., Jeppesen, T., & Bánki, O. (2022). Introducing ChecklistBank: An index and repository for taxonomic data. Biodiversity Information Science and Standards, 6, e93938. doi: https://doi.org/10.3897/biss.6.93938

Garnett, S. T., Christidis, L., Conix, S., Costello, M. J., Zachos, F. E., Bánki, O. S., Bao, Y., Barik, S. K., Buckeridge, J. S., Hobern, D. & Lien, A. (2020). Principles for creating a single authoritative list of the world’s species. PLoS Biology, 18(7), e3000736. doi: https://doi.org/10.1371/journal.pbio.3000736

Grenié M., Berti E., Carvajal-Quintero J., Dädlow G.M.L., Sagouis A. & Winter, M. 2022. Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices. Methods in Ecology and Evolution 14(1): 12-25. https://doi.org/10.1111/2041-210X.13802

Hobern, D., Barik, S. K., Christidis, L., Garnett, S. T. Kirk, P., Orrell, T. M., Pape, T., Pyle, R. L., Thiele, K. R., Zachos, F. E., & Bánki, O. (2021). Towards a global list of accepted species VI. The Catalogue of Life checklist. Org Divers Evol. doi: https://doi.org/10.1007/s13127-021-00516-w

Lien, A., Banki, O., Barik, S. K., Buckeridge, J. S., Christidis, L., Cigliano, M. M., Conix, S., Costello, M. J., Hobern, D., Kirk, P. M., Kroh, A., Montgomery, N., Nikolaeva, S., Orrell, T. M., Pyle, R. L., Raz, L., Thiele, K., Thomson, S. A., van Dijk, P. P., Wambiji, N., Whalen, A., Zachos, F. E., Zhi-Qiang Zhang & Stephen T. Garnett (2023). Widespread support for a global species list with a formal governance system. PNAS 120(45), doi: https://doi.org/10.1073/pnas.2306899120

Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I. (2020). NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020 Jan 1;2020:baaa062. doi: 10.1093/database/baaa062.

(Plants:)

Borsch, T., Berendsohn, W., Dalcin, E., Delmas, M., Demissew, S., Elliott, A., Fritsch, P., Fuchs, A., Geltman, D., Güner, A., Haevermans, T., Knapp, S., le Roux, M. M., Loizeau, P.-A., Miller, C., Miller, J., Miller, J. T., Palese, R., Paton, A., & Zamora, N. (2020). World Flora Online: placing taxonomists at the heart of a definitive and comprehensive global resource on the world’s plants. Taxon, 69, 1311–1341. doi: https://doi.org/10.1002/tax.12373

Govaerts, R., Nic Lughadha, E., Black, N., Turner, R. & Paton, A. (2021): The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci Data 8, 215. doi: https://doi.org/10.1038/s41597-021-00997-6

On name and taxon identifiers

Anonymous (2023): Wikidata - List of taxon identifiers. https://en.wikipedia.org/wiki/Template:Taxonbar/doc#Taxon_identifiers

Page R. D. M. (2023): Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people doi: https://doi.org/10.1101/2023.05.29.542697

On the stability of taxonomies (names and taxonomic concepts)

Thiele, K., Conix, S., Pyle, R. L., Barik, S. K., Christidis, L., Costello, M. J., van Dijk, P. P., Kirk, P., Lien, A., Thomson, S. A., Zachos, F. E., Zhang, Z.-Q., Garnett, S. T. (2021). Towards a global list of accepted species I. Why taxonomists sometimes disagree, and why this matters. Organisms Diversity & Evolution. doi: https://doi.org/10.1007/s13127-021-00495-y

Pyle, R. L., Barik, S. K., Christidis, L., Conix, S., Costello, M. J., van Dijk, P. P., Garnett, S. T., Hobern, D., Kirk, P. M., Lien, A. M., Orrell, T. M., Remsen, D., Thomson, S. A., Wambiji, N., Zachos, F. E., Zhang, Z-Q., Thiele, K. R. (2021). Towards a global list of accepted species V. The devil is in the details. Organisms Diversity & Evolution. doi: https://doi.org/10.1007/s13127-021-00504-0

Use cases

Islam, S., Papale, D., Vaira, L., Rosati, I. Peterseil, J. & Pichot, C. (2024): Navigating taxonomic complexity: A use-case report on FAIR scientific name-matching service usage in ENVRI Research Infrastructures. Research Ideas and Outcomes 10. doi: https://doi.org/10.3897/rio.10.e121871

Standards

Döring, M., & Ower, G. D. (2019). The Catalogue of Life Data Package - A new format for exchanging nomenclatural and taxonomic information. Biodiversity Information Science and Standards, 3, e38711. https://doi.org/10.3897/biss.3.38771

OpenRefine

GBIF course links: https://docs.gbif.org/course-data-use/en/openrefine.html

Whitmire, A. & Mozzherin, D. (2023): Reconciling taxonomic names in OpenRefine via Global Names. URL: https://github.com/gnames/gnverifier/wiki/OpenRefine-readme

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