Difference between revisions of "Further reading"
(Created page with "==On taxonomic aggregators (global species lists) the aggregation process== ==On name and taxon identifiers== ==On the stability of taxonomies (names and taxonomic concepts)==") |
|||
| (14 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | ==On taxonomic aggregators (global species lists) the aggregation process== | + | (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 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 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] | ||
| + | |||
| + | 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] | ||
| + | |||
| + | 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]. | ||
| + | |||
| + | '''(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] | ||
| + | |||
| + | 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== | ||
| + | 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] | ||
| + | |||
| + | 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] | ||
| + | |||
==On the stability of taxonomies (names and taxonomic concepts)== | ==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 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 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 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 https://doi.org/10.3897/biss.3.38771] | ||
| + | |||
| + | ==OpenRefine== | ||
| + | |||
| + | 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 11:04, 6 August 2024
(Recent review publications - please also refer to references within)
Contents
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
