├── .gitignore ├── logo.png ├── docs ├── schema.pdf ├── schema.png ├── schemaNU.pdf ├── schemaNU.png ├── material_citations_formatting_guide.pdf ├── publishing-guide-txtree.md └── publishing-guide.md ├── examples └── normalised-authors │ ├── distribution.tsv │ ├── taxon-property.tsv │ ├── species-estimate.tsv │ ├── species-interaction.tsv │ ├── taxon-concept-relation.tsv │ ├── media.tsv │ ├── synonym.tsv │ ├── default.yaml │ ├── vernacular-name.tsv │ ├── type-material.tsv │ ├── name-relation.tsv │ ├── taxon.tsv │ ├── metadata.yaml │ ├── author.tsv │ ├── reference.bib │ └── name.tsv ├── data ├── species-interaction.tsv ├── default.yaml ├── taxon-concept-relation.tsv ├── synonym.tsv ├── species-estimate.tsv ├── vernacular-name.tsv ├── media.tsv ├── distribution.tsv ├── name-relation.tsv ├── treatments │ ├── Jarvis2007.html │ └── Hind2013.txt ├── type-material.tsv ├── taxon.tsv ├── reference.tsv └── name.tsv ├── templates ├── CoLDP flat.xlsx ├── CoLDP flat.accdb ├── CoLDP nameusage.xlsx ├── CoLDP nameusage.accdb ├── CoLDP parent-child.xlsx ├── CoLDP parent-child.accdb ├── schema-pg.sql └── schema-pg-enum.sql ├── CHANGES.md ├── metadata.json ├── metadata.yaml └── README.md /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | -------------------------------------------------------------------------------- /logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/logo.png -------------------------------------------------------------------------------- /docs/schema.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/docs/schema.pdf -------------------------------------------------------------------------------- /docs/schema.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/docs/schema.png -------------------------------------------------------------------------------- /docs/schemaNU.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/docs/schemaNU.pdf -------------------------------------------------------------------------------- /docs/schemaNU.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/docs/schemaNU.png -------------------------------------------------------------------------------- /examples/normalised-authors/distribution.tsv: -------------------------------------------------------------------------------- 1 | taxonID areaID gazetteer status referenceID 2 | -------------------------------------------------------------------------------- /examples/normalised-authors/taxon-property.tsv: -------------------------------------------------------------------------------- 1 | taxonID property value referenceID remarks 2 | -------------------------------------------------------------------------------- /examples/normalised-authors/species-estimate.tsv: -------------------------------------------------------------------------------- 1 | taxonID estimate type referenceID remarks 2 | -------------------------------------------------------------------------------- /examples/normalised-authors/species-interaction.tsv: -------------------------------------------------------------------------------- 1 | taxonID relatedTaxonID type referenceID 2 | -------------------------------------------------------------------------------- /examples/normalised-authors/taxon-concept-relation.tsv: -------------------------------------------------------------------------------- 1 | taxonID relatedTaxonID type referenceID 2 | -------------------------------------------------------------------------------- /data/species-interaction.tsv: -------------------------------------------------------------------------------- 1 | taxonID relatedTaxonID type referenceID 2 | 1001 hybrid epiphyte of 3 | -------------------------------------------------------------------------------- /data/default.yaml: -------------------------------------------------------------------------------- 1 | Name: 2 | code: botanical 3 | Taxon: 4 | extinct: false 5 | environment: terrestrial -------------------------------------------------------------------------------- /data/taxon-concept-relation.tsv: -------------------------------------------------------------------------------- 1 | taxonID relatedTaxonID type referenceID 2 | Hind2013 Jarvis2007 equals 3 | -------------------------------------------------------------------------------- /examples/normalised-authors/media.tsv: -------------------------------------------------------------------------------- 1 | taxonID url type format title created creator license link remarks 2 | -------------------------------------------------------------------------------- /templates/CoLDP flat.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/templates/CoLDP flat.xlsx -------------------------------------------------------------------------------- /templates/CoLDP flat.accdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/templates/CoLDP flat.accdb -------------------------------------------------------------------------------- /templates/CoLDP nameusage.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/templates/CoLDP nameusage.xlsx -------------------------------------------------------------------------------- /templates/CoLDP nameusage.accdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/templates/CoLDP nameusage.accdb -------------------------------------------------------------------------------- /templates/CoLDP parent-child.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/templates/CoLDP parent-child.xlsx -------------------------------------------------------------------------------- /templates/CoLDP parent-child.accdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/templates/CoLDP parent-child.accdb -------------------------------------------------------------------------------- /examples/normalised-authors/synonym.tsv: -------------------------------------------------------------------------------- 1 | taxonID nameID status remarks 2 | sp1 sp2 synonym 3 | sp1 sp3 synonym 4 | spy2 spy1 synonym 5 | -------------------------------------------------------------------------------- /docs/material_citations_formatting_guide.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CatalogueOfLife/coldp/HEAD/docs/material_citations_formatting_guide.pdf -------------------------------------------------------------------------------- /examples/normalised-authors/default.yaml: -------------------------------------------------------------------------------- 1 | Name: 2 | code: botanical 3 | Taxon: 4 | provisional: false 5 | extinct: false 6 | environment: terrestrial -------------------------------------------------------------------------------- /data/synonym.tsv: -------------------------------------------------------------------------------- 1 | taxonID nameID status remarks 2 | 1 2 synonym 3 | 10 11 synonym 4 | 1006 1006-s1 synonym 5 | 1006 1006-s2 synonym 6 | 1006 1006-s3 synonym 7 | -------------------------------------------------------------------------------- /data/species-estimate.tsv: -------------------------------------------------------------------------------- 1 | taxonID estimate type referenceID remarks 2 | 10 32913 living TPL-Asteraceae number of living and described species 3 | 10 27000 living Fu2016 4 | -------------------------------------------------------------------------------- /data/vernacular-name.tsv: -------------------------------------------------------------------------------- 1 | taxonID name transliteration language country lifeStage sex referenceID 2 | 1001 Baker's hawksbeard eng wp1 3 | hybrid Heritage® Hybrid Oak eng heritage -------------------------------------------------------------------------------- /data/media.tsv: -------------------------------------------------------------------------------- 1 | taxonID url type format title created creator license link 2 | 1001 https://plants.usda.gov/gallery/pubs/crba2_001_pvp.jpg IMAGE image/jpeg June 7, 2009 Gary A. Monroe https://plants.usda.gov/java/largeImage?imageID=crba2_001_avp.tif 3 | -------------------------------------------------------------------------------- /examples/normalised-authors/vernacular-name.tsv: -------------------------------------------------------------------------------- 1 | taxonID name language country preferred lifeStage sex referenceID remarks 2 | sp11 June grass English United States false x 3 | sp11 Kentucky blue grass English Canada true x 4 | sp11 smooth meadow grass English Pakistan false x 5 | -------------------------------------------------------------------------------- /examples/normalised-authors/type-material.tsv: -------------------------------------------------------------------------------- 1 | ID nameID status citation locality country date collector institutionCode catalogNumber referenceID page link remarks 2 | LINN-87.17 sp10 lectotype LINN (NO. 87.17, right-hand plant) 1753 Linné 87.17 Jarvis_2000 254 https://tropicos.org/specimen/100983611 right-hand plant 3 | -------------------------------------------------------------------------------- /examples/normalised-authors/name-relation.tsv: -------------------------------------------------------------------------------- 1 | nameID relatedNameID type referenceID page remarks 2 | goch sectoch BASIONYM 3 | sp11 gpoa type Hitchcock_1929 Type discussion: Reference article Hitchcock, A. S. 1920. The genera of grasses of the United States. U.S.D.A. Bull. (1915-23) 772: 41. 4 | spy2 spy1 REPLACEMENT_NAME Ye_2021 494 -------------------------------------------------------------------------------- /data/distribution.tsv: -------------------------------------------------------------------------------- 1 | taxonID areaID gazetteer status referenceID 2 | 1001a US-CA ISO native wp1 3 | 1001a US-NV ISO native wp1 4 | 1001a US-OR ISO native wp1 5 | 1001a US-WA ISO native wp1 6 | 1001b US-CA ISO native wp1 7 | 1001b US-OR ISO native wp1 8 | 1001b US-UT ISO native wp1 9 | 1001c US-CA ISO native wp1 10 | 1001c US-ID ISO native wp1 11 | -------------------------------------------------------------------------------- /data/name-relation.tsv: -------------------------------------------------------------------------------- 1 | nameID relatedNameID type referenceID remarks 2 | 1006 1006-s3 basionym 3 | fake hybrid SPELLING_CORRECTION rel a relation remark 4 | fake hybrid BASED_ON rel another relation remark 5 | fake hybrid REPLACEMENT_NAME rel yet another relation remark 6 | hybrid fake LATER_HOMONYM rel yet another relation remark 7 | hybrid fake SUPERFLUOUS rel yet another relation remark 8 | -------------------------------------------------------------------------------- /examples/normalised-authors/taxon.tsv: -------------------------------------------------------------------------------- 1 | ID parentID nameID alternativeID crutinizer scrutinizerID scrutinizerDate lifezone link remarks 2 | p p x x x x x x 3 | c1 p c1 x x x x x x 4 | c2 c1 c2 x x x x x x 5 | c3 c2 c3 x x x x x x 6 | c4 c3 c4 x x x x x x 7 | op c4 op x x x x x x 8 | fp op fp x x x x x x 9 | sfp fp sfp x x x x x x 10 | tp sfp tp x x x x x x 11 | stp tp stp x x x x x x 12 | gpoa stp gpoa wfo:wfo-4000030438 x x x 13 | gpan stp gpan x x x x x x x 14 | gc stp gc x x x x x x 15 | sp1 gc sp1 wfo:wfo-0000860245 x x x x x x 16 | sp10 gpoa sp10 wfo:wfo-0000860245 x x x x x x 17 | sp11 gpoa sp11 wfo:wfo-0000860245 x x x x x x 18 | sfb fp sfb x x x x x x 19 | ta sfb ta x x x x x x 20 | gy ta gy x x x x x x 21 | spy2 gy spy2 x x x x x x -------------------------------------------------------------------------------- /data/treatments/Jarvis2007.html: -------------------------------------------------------------------------------- 1 |
2 |

Gundelia tournefortii Linnaeus, Species Plantarum 2: 814. 1753.

3 |

"Habitat in Armenia, Syria." RCN: 6724.

4 |

Lectotype (Vitek & Jarvis in Annalen Nat. Hist. Mus. Wien, B, in press): [icon] " Silybum dioscoridis s. Hacub alcardeg serapionis " in Rauwolf, Aigent. Beschr. Morgenl.: 74, t. 74. 1583. - Epitype (Vitek & Jarvis in Annalen Nat. Hist. Mus. Wien, B, in press): Herb. Rauwolf 4: 81 (L).

5 |

Generitype of Gundelia Linnaeus.

6 |

Current name: Gundelia tournefortii L. (Asteraceae).

7 |

Note: See Burtt (in Karaca Arbor. Mag. 6: 59, f. 12. 2001; 6: 139, f. 4. 2002) on Tournefort’s account of this plant, including a reproduction of Tournefort’s illustration.

8 |
-------------------------------------------------------------------------------- /data/type-material.tsv: -------------------------------------------------------------------------------- 1 | ID nameID status citation locality country date collector link 2 | NDG65570 1001 holotype U.S.A.; California, (Modoc Co.); June 1894; Rebecca M. Austin; lava beds, under juniper trees; NDG 65570 California, (Modoc Co.) US 1894-06 https://plants.jstor.org/stable/10.5555/al.ap.specimen.ndg65570 3 | GH00006265 1001c holotype United States; Valley of the Clearwater River; 30th May 1892; J.H.Sandberg, D. T. MacDougal & A. A. Heller; GH 00006265 Valley of the Clearwater River US 1892-05-30 J.H.Sandberg, D. T. MacDougal & A. A. https://plants.jstor.org/stable/10.5555/al.ap.specimen.gh00006265 4 | MIN1000737 1001c isotype United States; Idaho, Nes Perces; May 1892; J.H.Sandberg; Dry hillsides; MIN 1000737 Idaho, Nes Perces US May 1892 J.H.Sandberg https://plants.jstor.org/stable/10.5555/al.ap.specimen.min1000737 5 | -------------------------------------------------------------------------------- /examples/normalised-authors/metadata.yaml: -------------------------------------------------------------------------------- 1 | # yaml-language-server: $schema=https://raw.githubusercontent.com/CatalogueOfLife/coldp/master/metadata.json 2 | 3 | identifier: 4 | col: 272998 5 | 6 | title: ColDP Full Example 7 | alias: ColDP 8 | 9 | description: Strongly normalised ColDP test dataset that tries to cover most fields for testing API & UI. 10 | keyword: 11 | - example 12 | - coldp 13 | issued: 2023-11-11 14 | version: "0.1" 15 | 16 | contact: 17 | given: Markus 18 | family: Döring 19 | email: mdoering@gbif.org 20 | 21 | creator: 22 | - given: Markus 23 | family: Döring 24 | email: mdoering@gbif.org 25 | orcid: 0000-0001-7757-1889 26 | 27 | # Any Open Definition license ID: https://licenses.opendefinition.org/licenses/groups/all.json 28 | # For ChecklistBank please use only CC0-1.0, CC-BY-4.0 or CC-BY-NC-4.0 29 | # Must be CC0-1.0 or CC-BY-4.0 to be used by COL !!! 30 | license: CC0-1.0 31 | url: https://github.com/CatalogueOfLife/coldp 32 | -------------------------------------------------------------------------------- /examples/normalised-authors/author.tsv: -------------------------------------------------------------------------------- 1 | ID alternativeID given family suffix abbreviationBotany alternativeNames sex country birth birthPlace death interest link remarks 2 | 12653 ipni:12653-1,wikidata:Q1043 Carl Linnaeus L. Linn.|Carl von Linné male Sweden 1707 Råshult 1778 botany,zoology 3 | 492 ipni:492-1 John Hendley Barnhart Barnhart US 1871 1949 Spermatophytes 4 | 18271 ipni:18271-1 Barthélemy Charles Joseph Dumortier Dumort. Du Mortier Belgium 1797 1878 Bryophytes, Spermatophytes, Mycology, Algae 5 | 9229 ipni:9229-1 Hildemar Wolfgang Scholz H.Scholz Germany 1928 2012 Mycology, Spermatophytes Eponymy: Lolium scholzii Greuter (2012) 6 | 307 ipni:307-1,wikidata:Q61290,viaf:59388161 Paul Friedrich August Ascherson Asch. Germany 1834-06-04 Berlin 1913-03-06 Spermatophytes 7 | 3308 ipni:3308-1 Karl Otto Robert Peter Paul Graebner Graebn. Germany 1871 1933 Spermatophytes, Pteridophytes 8 | 27136 ipni:27136-1,wikidata:Q78630 Otto Stapf Stapf Austria 1857 1933 Spermatophytes, Bryophytes 9 | 974 ipni:974-1,wikidata:Q4026914 Norman Loftus Bor Bor Ireland 1893 Tramore,Ireland 1972 Spermatophytes 10 | 1792 ipni:1792-1 Thomas Arthur Cope Cope UK 1949 Spermatophytes 11 | 12 | -------------------------------------------------------------------------------- /data/taxon.tsv: -------------------------------------------------------------------------------- 1 | ID parentID nameID provisional accordingToID scrutinizer scrutinizerDate lifezone link remarks 2 | 1 1 false M.Döring 2005-01-21 3 | 10 1 10 false M.Döring 2015-03-11 4 | 20 10 20 false M.Döring 2015-03-11 5 | 30 20 30 false M.Döring 2015-04-22 6 | 31 20 31 false M.Döring 2015-04-22 7 | 100 20 100 false M.Döring 2019-07-21 8 | 101 30 101 false M.Döring 2019-07-21 9 | 102 30 102 false M.Döring 2019-07-21 10 | 110 31 110 false M.Döring 2019-07-21 11 | 1000 100 1000 false M.Döring 2019-07-21 12 | 1001 101 1001 false M.Döring 2019-07-21 https://en.wikipedia.org/wiki/Crepis_bakeri 13 | 1002 101 1002 false M.Döring 2019-07-21 14 | 1005 102 1005 false M.Döring 2019-07-21 15 | 1006 102 1006 false M.Döring 2019-07-21 16 | 1010 110 1010 false M.Döring 2019-07-21 17 | 1011 110 1011 false M.Döring 2019-07-21 18 | 1001a 1001 1001a false https://en.wikipedia.org/wiki/Crepis_bakeri 19 | 1001b 1001 1001b false https://en.wikipedia.org/wiki/Crepis_bakeri 20 | 1001c 1001 1001c false https://en.wikipedia.org/wiki/Crepis_bakeri 21 | fake 1 fake true M.Döring 2018 terrestrial,brackish https://herbaria.plants.ox.ac.uk/bol/plants400/profiles/OP/Paulownia unclear classification 22 | hybrid 1 hybrid false Shin Vac 2003-03-21 terrestrial,freshwater my favorite hybrid 23 | Hind2013 110 1011 false Hind2013 https://www.jstor.org/stable/45066252 24 | Jarvis2007 110 1011 false Jarvis2007 http://tb.plazi.org/GgServer/html/24BF99B096BF897134A192EB740A13F7 25 | -------------------------------------------------------------------------------- /data/reference.tsv: -------------------------------------------------------------------------------- 1 | ID citation type author title version issued publisher containerTitle volume issue page doi isbn link 2 | wp1 webpage Crepis bakeri 2018 Wikipedia https://en.wikipedia.org/wiki/Crepis_bakeri 3 | greene1895 Greene, Edward Lee 1895. Erythea 3(5) article-journal Greene, Edward Lee 1895 Erythea 3 5 4 | fna Greene (2018) Crepis bakeri, Flora of North America chapter Greene Crepis bakeri 2018 Flora of North America http://www.efloras.org/florataxon.aspx?flora_id=1&taxon_id=250066440 5 | ulloa article Ulloa Ulloa, C.; P. Acevedo-Rodríguez; S. G. Beck; M. J. Belgrano; R. Bernal; P. E. Berry; L. Brako; M. Celis; G. Davidse; S. R. Gradstein; O. Hokche; B. León; S. León-Yánez; R. E. Magill; D. A. Neill; M. H. Nee; P. H. Raven; Stimmel, Heather; M. T. Strong; Villaseñor Ríos, José L.; J. L. Zarucchi; F. O. Zuloaga & P. M. Jørgensen An integrated assessment of vascular plants species of the Americas 2017-12-22 Science 358 6370 1614–1617 10.1126/science.aao0398 6 | frank motion picture James Whale The Bride of Frankenstein 1935 Universal Pictures https://www.imdb.com/title/tt0026138/ 7 | heritage webpage Heritage® Hybrid Oak Heritage seedlings & liners, inc. http://www.heritageseedlings.com/page_608_40/quercus-heritage-q.-robur-x-q.-macrocarpa-clemons 8 | rel Personal communications J.P.Sartre (1967) 9 | Hind2013 Hind, N. (2013). 763. GUNDELIA TOURNEFORTII: Compositae. Curtis's Botanical Magazine, 30(2), 114-138. article Hind, Nicholas 763. GUNDELIA TOURNEFORTII: Compositae 2013 Curtis's Botanical Magazine 30 2 114-138 doi:10.2307/45066252 10 | Jarvis2007 book Jarvis, Charlie Order out of Chaos. Linnaean Plant Types and their Types 2007-12-31 Linnaean Society of London in association with the Natural History Museum 10.5281/zenodo.291971 978-0-9506207-7-0 11 | TPL-Asteraceae dataset Species of Compositae contained within The Plant List 1.1 2013 http://www.theplantlist.org/1.1/browse/A/Compositae/ 12 | Fu2016 article-journal Fu, Zhi-Xi and Jiao, Bo-Han and Nie, Bao and Zhang, Guo-Jin and Gao, Tian-Gang and China Phylogeny Consortium A comprehensive generic-level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae 2016 Journal of Systematics and Evolution 54 4 doi: 10.1111/jse.12216 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12216 13 | -------------------------------------------------------------------------------- /examples/normalised-authors/reference.bib: -------------------------------------------------------------------------------- 1 | @book{Ascherson_1896, 2 | doi = {10.5962/bhl.title.35810}, 3 | url = {https://doi.org/10.5962%2Fbhl.title.35810}, 4 | year = 1896, 5 | publisher = {W. Engelmann}, 6 | author = {Paul Ascherson and Paul Graebner and Paul Graebner}, 7 | title = {Synopsis der mitteleuropaïschen flora} 8 | } 9 | 10 | @article{Jarvis_2000, 11 | doi = {10.2307/1223839}, 12 | url = {https://doi.org/10.2307%2F1223839}, 13 | year = 2000, 14 | month = {may}, 15 | publisher = {Wiley}, 16 | volume = {49}, 17 | number = {2}, 18 | pages = {239--260}, 19 | author = {Charles E. Jarvis and Nicholas J. Turland}, 20 | editor = {Steve Cafferty}, 21 | title = {Typification of Linnaean plant names in the $\less$i$\greater$Poaceae$\less$/i$\greater$ ($\less$i$\greater$Gramineae$\less$/i$\greater$)}, 22 | journal = {{TAXON}} 23 | } 24 | 25 | @book{SpPl1, 26 | url = {https://www.biodiversitylibrary.org/page/358012}, 27 | year = 1753, 28 | month = {may}, 29 | volume = {1}, 30 | author = {Carl Linnaeus}, 31 | title = {Species Plantarum} 32 | } 33 | 34 | @incollection{Hitchcock_1929, 35 | author = {A.S. Hitchcock and M.L. Green}, 36 | title = {Standard species of Linnean [sic] genera of Phanerogamae (1753-54).}, 37 | booktitle = {International Botanical Congress. Cambridge (England), 1930. Nomenclature. Proposals by British Botanists}, 38 | url = {https://bibdigital.rjb.csic.es/viewer/13040/?offset=#page=111&viewer=picture}, 39 | publisher = {London}, 40 | year = {1929}, 41 | month = {august}, 42 | pages = {111--195}, 43 | } 44 | 45 | @article{Ye_2021, 46 | doi = {10.1016/j.pld.2021.03.001}, 47 | url = {https://doi.org/10.1016%2Fj.pld.2021.03.001}, 48 | year = 2021, 49 | month = {dec}, 50 | publisher = {Elsevier {BV}}, 51 | volume = {43}, 52 | number = {6}, 53 | pages = {492--501}, 54 | author = {Xia-Ying Ye and Yu-Xiao Zhang and De-Zhu Li}, 55 | title = {Two new species of Yushania (Poaceae: Bambusoideae) from South China, with a taxonomic revision of related species}, 56 | journal = {Plant Diversity} 57 | } 58 | 59 | @article{Yang_2013, 60 | year = 2013, 61 | volume = {32}, 62 | number = {5}, 63 | author = {T.P. Yi and L. Yang}, 64 | title = {Two new species of Yushania Keng f. (Poaceae) from Guizhou, China and the name about Bashania faberi (Rendle) Yi}, 65 | title = {5--8}, 66 | journal = {J. Bamboo Res.} 67 | } -------------------------------------------------------------------------------- /data/name.tsv: -------------------------------------------------------------------------------- 1 | ID scientificName authorship rank genus specificEpithet infraspecificEpithet referenceID publishedInPage code status link remarks 2 | 1 Plantae kingdom botanical 3 | 2 Viridae kingdom botanical 4 | 10 Asteraceae family botanical 5 | 11 Compositae family botanical 6 | 20 Cichorioideae subfamily botanical 7 | 30 Cichorieae tribe botanical 8 | 31 Gundelieae tribe botanical 9 | 100 Platycarpha genus botanical 10 | 101 Crepis L. genus botanical 11 | 102 Leontodon genus botanical 12 | 110 Gundelia L. genus botanical 13 | 1000 Platycarpha glomerata (Thunberg) A. P. de Candolle species Platycarpha glomerata botanical 14 | 1001 Crepis bakeri Greene species Crepis bakeri greene1895 73 botanical https://beta.ipni.org/n/69325-2 15 | 1002 Crepis occidentalis Nutt. species Crepis occidentalis botanical 16 | 1005 Leontodon anomalus species Leontodon anomalus botanical 17 | 1006 Leontodon taraxacoides (Vill.) Mérat species Leontodon taraxacoides botanical 18 | 1006-s1 Leontodon leysseri species Leontodon leysseri botanical 19 | 1006-s2 Leontodon saxatilis species Leontodon saxatilis botanical 20 | 1006-s3 Leonida taraxacoida Vill. species Leonida taraxacoida botanical 21 | 1010 Gundelia rosea L. species Gundelia rosea botanical 22 | 1011 Gundelia tournefortii L. species Gundelia tournefortii botanical 23 | 1001a Crepis bakeri subsp. bakeri subspecies Crepis bakeri bakeri botanical 24 | 1001b Crepis bakeri subsp. cusickii (Eastw.) Babc. & Stebbins subspecies Crepis bakeri cusickii botanical 25 | 1001c Crepis bakeri subsp. idahoensis Babc. & Stebbins subspecies Crepis bakeri idahoensis botanical 26 | fake Paulownia × tomentosa subsp. tella f. pasta (Carl & Ruth) Frankenstein ex Semmelrogge forma frank 87 botanical conserved https://herbaria.plants.ox.ac.uk/bol/plants400/profiles/OP/Paulownia Unclear name origin 27 | hybrid Quercus robur x Q. macrocarpa species botanical LEGITIMATE http://www.heritageseedlings.com/page_608_40/quercus-heritage-q.-robur-x-q.-macrocarpa-clemons commercial seeds 28 | virus Acanthocystis turfacea chlorella virus 1 virus 29 | cult Clematis 'Sapphire Indigo' species http://plants.thegrowingplace.com/12120014/Plant/6164/Sapphire_Indigo_Clematis/ 30 | -------------------------------------------------------------------------------- /examples/normalised-authors/name.tsv: -------------------------------------------------------------------------------- 1 | ID alternativeID scientificName authorship rank uninomial genus infragenericEpithet specificEpithet infraspecificEpithet combinationAuthorshipID combinationExAuthorshipID combinationAuthorshipYear basionymAuthorshipID basionymExAuthorshipID basionymAuthorshipYear referenceID publishedInYear publishedInPage publishedInPageLink gender genderAgreement originalSpelling status link etymology remarks 2 | p Plantae kingdom Plantae 3 | c1 Tracheophytes Tracheophytes 4 | c2 Angiosperms Angiosperms 5 | c3 Monocot Monocot 6 | c4 Commelinids Commelinids 7 | op Poales order Poales 8 | fp Poaceae Barnhart family Poaceae 492 9 | sfp Pooideae subfamily Pooideae 10 | tp Poeae tribe Poeae 11 | stp Poinae Dumort. subtribe Poinae 18271 12 | gpoa ipni:18760-1 Poa L. genus Poa 12653 Benth. & Hook. f. Gen. Pl. iii. 1196. ALLAGOSTACHYUM, Nees, ex Steud. Nom. ed.II. i. 50 (1840). ARCTOPHILA, Rupr. in Beitr. Pfl. Russ. Reich. ii. 62 (1845).POIDIUM, Nees, in Lindl. Introd. Nat. Syst. ed. II. 450 (1836). PLOTIA, Schreb.ex Steud. Nom. ed. II. ii. 356 (1841). 13 | goch ipni:77075709-1 Ochlopoa (Asch. & Graebn.) H.Scholz genus Ochlopoa 9229 307,3308 x 14 | sectoch ipni:77075450-1 Poa sect. Ochlopoa Asch. & Graebn. section Poa Ochlopoa 307,3308 Ascherson_1896 1900 387 https://www.biodiversitylibrary.org/page/11278031 Syn. Mitteleur. Fl. [Ascherson & Graebner] 387 (1900). 15 | gpan Panicularia Keng genus Panicularia 16 | gc Cleistogenes Heist. ex Fabr. genus Cleistogenes 1759 nom. superfl. 17 | sp1 ipni: Cleistogenes gatacrei (Stapf) Bor species Cleistogenes gatacrei 974 27136 x 18 | sp2 ipni: Diplachne gatacrei Stapf species Diplachne gatacrei 27136 x 19 | sp3 ipni: Kengia gatacrei (Stapf) Cope species Kengia gatacrei 1792 27136 x 20 | sp10 ipni:320035-2 Poa annua L. species Poa annua 12653 SpPl1 1753 68 https://www.biodiversitylibrary.org/page/358087 female x 21 | sp11 ipni:417792-1 Poa pratensis L. species Poa pratensis 12653 SpPl1 1753 67 https://www.biodiversitylibrary.org/page/358086 female x 22 | sfb Bambusoideae subfamily Bambusoideae 23 | ta Arundinarieae tribe Arundinarieae 24 | gy Yushania P.C. Keng genus Yushania 1957 25 | spy1 ipni:77297577-1 Yushania microphylla T.P. Yi & L. Yang species Yushania microphylla Yang_2013 2013 5 https://www.biodiversitylibrary.org/page/358087 female nom. illeg. x 26 | spy2 ipni:77297575-1 Yushania weiningensis D.Z. Li & X.Y. Ye species Yushania weiningensis Ye_2021 2021 494 https://www.biodiversitylibrary.org/page/358087 female nom. nov. x 27 | -------------------------------------------------------------------------------- /docs/publishing-guide-txtree.md: -------------------------------------------------------------------------------- 1 | # Text-Tree publishing guide 2 | This guide tries to provide help in publishing ColDP compliant data with the help of simple [text trees](https://github.com/gbif/text-tree). 3 | TextTree is a very simple format, but can be extended in a flexible way: 4 | 5 | > Abies alba Mill. [species] {PUB=Miller2019 ENV=terrestrial,marine REF=Döring2021,Banki2022 VERN=de:Traubeneiche,fr:Chêne rouvre,dk:Vintereg,nl:Wintereik} 6 | > †Kalloprion kilmisteri [species] {PUB=Eriksson_2006 ENV=marine CHRONO=Llandovery-Wenlock} 7 | 8 | This guide provides conventions how to share additional information using TextTree. 9 | For interoperability with [ChecklistBank](https://www.checklistbank.org) and other taxonomic systems we encourage to use some common information keys and value formats. 10 | 11 | ### Value restrictions 12 | Values are not allowed to contain whitespace or commas! 13 | Instead of a space an underscore is allowed in most fields, which should be decoded into a regular space upon reading. 14 | 15 | ### Multi values 16 | The comma is used to delimit multiple values. 17 | If you need to use a commo in the value itself, double it: ```,,``` 18 | 19 | ### Information keys 20 | The following keys do use verbatim values without underscore decoding: 21 | - **ID**: The identifier for the name usage. 22 | - **PUB**: The key of a reference for the original publication of the name. The key should resolve to a reference given in an additional reference.[bib](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#reference-bibtex) or [json](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#reference-json-csl) file. See [ColDP](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#reference) for more information. 23 | - **REF**: A list of reference keys to support the taxonomic opinion, concatenated by a comma. 24 | - **LINK**: A [URL](/docs/README.md#link-3) linking to a webpage from the source with this name 25 | 26 | The following keys must use an underscore `_` instead of a space: 27 | - **ENV**: A list of [environments](/docs/README.md#environment) the species occurrs in, concatenated by a comma: ```ENV=marine,brackish``` 28 | - **VERN**: A list of vernacular names, concatenated by a comma, each given as languageCode:name. Example: ```VERN=de:Traubeneiche,fr:Chêne rouvre,dk:Vintereg``` 29 | - **DIST**: A list of range distributions, concatenated by a comma. Each given as gazetteer:areaID:status. Example: ```DIST=iso:de:native,iso:fr:native``` 30 | - **CHRONO**: A geochronological time range for the earliest-latest appearance of the taxon. The range is delimited by a hyphen, e.g. `CHRONO=Jurassic-Cretaceous` 31 | - **CODE**: [nomenclatural code](/docs/README.md#code) of the name: ```CODE=zoology``` 32 | - **NOM**: [nomenclatural status](/docs/README.md#status) of the name, e.g. ```NOM=nom.cons.``` 33 | - **TYPE**: Type species or genus name, e.g. ```TYPE=Aster_amellus``` 34 | - **TM**: [Type material](/docs/README.md#typematerial) for the name as typeStatus:specimenCitation, multi value concatenated by '|' . Remember to replace spaces with underscores: ```TM=holotype:Montana;CM_9380``` 35 | - **EST**: Species estimate. Can be just a number for living species estimate, prefixed with the dagger symbol for extinct estimates or both: ```EST=45000,†340``` 36 | 37 | Any other keys for accepted names will be treated as generic taxon properties. 38 | 39 | 40 | ## References 41 | A `reference.bib` BibText or `reference.json` CSL-JSON file should accompany the text tree file 42 | to define the reference keys used in `PUB` or `REF` variables. 43 | 44 | BibTex content can be retrieved from CrossRef for most DOIs when known. 45 | For example by using curl on the terminal like this: 46 | > curl --location --silent --header "Accept: application/x-bibtex" https://doi.org/10.1080/11035890601282097 47 | 48 | ``` 49 | @article{Eriksson_2006, 50 | doi = {10.1080/11035890601282097}, 51 | url = {https://doi.org/10.1080%2F11035890601282097}, 52 | year = 2006, 53 | month = {jun}, 54 | publisher = {Informa {UK} Limited}, 55 | volume = {128}, 56 | number = {2}, 57 | pages = {97--101}, 58 | author = {Mats E. Eriksson}, 59 | title = {Polychaete jaw apparatuses and scolecodonts from the Silurian Ireviken Event interval of Gotland, Sweden}, 60 | journal = {{GFF}} 61 | } 62 | ``` 63 | -------------------------------------------------------------------------------- /CHANGES.md: -------------------------------------------------------------------------------- 1 | # ColDP Release Notes 2 | 3 | ColDP adheres to [semantic versioning](http://semver.org/): 4 | - **patch** changes (1.0.x) do not alter the exchange schema at all. No more fields or entities will be renamed, removed or added. The documentation and enumeration of values are allowed to change. 5 | - **minor** changes (1.x.0) preserve backwards compatability. Fields or entities can be added, but not renamed or removed. 6 | - **major** changes (x.0.0) break backwards compatability. Fields or entities can be renamed, removed, added or changed in semantics. 7 | 8 | 9 | ## unreleased v2 10 | 11 | ## v1.2.0 12 | [Released](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.2.0) on 2025-10-30, [Milestone 1.2](https://github.com/CatalogueOfLife/coldp/issues?q=is%3Aissue+milestone%3A%22Version+1.2%22+) 13 | - adding feedbackUrl to metadata, see https://github.com/CatalogueOfLife/coldp/issues/80 14 | - Allow TypeMaterial.nameID and TypeMaterial.status to be multi valued 15 | - Accept JSON Lines in `reference.jsonl`, see https://github.com/CatalogueOfLife/coldp/issues/87 16 | - remove taxonomicScopeInEnglish from metadata 17 | - remove Distribution.status in favor of new fields 18 | - extend Distribution class with 19 | - establishmentMeans 20 | - degreeOfEstablishment 21 | - pathway 22 | - threatStatus 23 | - year 24 | - season 25 | - lifeStage 26 | 27 | 28 | ## v1.1.0 29 | [Released](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.1.0) on 2024-09-26, [Milestone 1.1](https://github.com/CatalogueOfLife/coldp/issues?q=is%3Aissue+milestone%3A%22Version+1.1%22+) 30 | - Add conversion.description & url to metadata: https://github.com/CatalogueOfLife/coldp/issues/82 31 | - Taxon.accordingToPage & Taxon.accordingToPage: https://github.com/CatalogueOfLife/coldp/issues/60 32 | - add modified, modifiedBy to all entities: https://github.com/CatalogueOfLife/coldp/issues/73 33 | - nomenclatural relation & TypeMaterial.page 34 | - Add urlFormatter to metadata 35 | - Name.etymology 36 | - Name.originalSpelling 37 | - Name.gender & genderAgreement: https://github.com/CatalogueOfLife/coldp/issues/69 38 | - VernacularName.preferred: https://github.com/CatalogueOfLife/coldp/issues/70 39 | - Add Author entity: https://github.com/CatalogueOfLife/coldp/issues/77 40 | + [Name.combinationAuthorshipID](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#combinationAuthorshipID) 41 | + [Name.combinationExAuthorshipID](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#combinationExAuthorshipID) 42 | + [Name.basionymAuthorshipID](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#basionymAuthorshipID) 43 | + [Name.basionymExAuthorshipID](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#basionymExAuthorshipID) 44 | + Reference.authorID 45 | + Reference.editorID 46 | + Reference.containerAuthorID 47 | + Reference.collectionEditorID 48 | - Structured authorships: https://github.com/CatalogueOfLife/coldp/issues/75 49 | + [combinationAuthorship](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#combinationAuthorship) 50 | + [combinationExAuthorship](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#combinationExAuthorship) 51 | + [combinationAuthorshipYear](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#combinationAuthorshipYear) 52 | + [basionymAuthorship](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#basionymAuthorship) 53 | + [basionymExAuthorship](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#basionymExAuthorship) 54 | + [basionymAuthorshipYear](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#basionymAuthorshipYear) 55 | - titleShort and containerTitleShort added to Reference: https://github.com/CatalogueOfLife/coldp/issues/74 56 | - Add default.yaml: https://github.com/CatalogueOfLife/coldp/issues/44 57 | - Add TaxonProperty entity: https://github.com/CatalogueOfLife/coldp/issues/76 58 | - Add metadata keywords: https://github.com/CatalogueOfLife/coldp/issues/67 59 | - Best practises for misapplied names 60 | - Change enum links to point to checklistbank.org not catalogue.life 61 | - Add alternativeID for version 1.1: https://github.com/CatalogueOfLife/coldp/issues/61 62 | - Mark additions in readme as v1.1 63 | - Update temporal range docs to accept Ma values 64 | - Add missing type material fields for EJT guidelines: https://github.com/CatalogueOfLife/coldp/issues/64 65 | - Explain CSV & TSV format in more detail 66 | - Recommend to include changelog file 67 | - Include logo.png in readme 68 | - remove Distribution.pageReferenceID and VernacularName.pageReferenceID from readme, which were never present in the schema 69 | - link to identifiers.org 70 | 71 | ## v1.0.1 72 | [Released](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.0.1) on 2022-04-07 73 | - Smaller documentation fixes, updates 74 | - Fix NameUsage diagram, add missing NameUsage.nameRemarks 75 | - Link to csltype vocabulary 76 | 77 | ## v1.0.0 78 | [Released](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.0.0) on 2021-10-25 79 | Initial release -------------------------------------------------------------------------------- /templates/schema-pg.sql: -------------------------------------------------------------------------------- 1 | -- Postgres ColDP schema 2 | 3 | CREATE TABLE reference ( 4 | id TEXT PRIMARY KEY, 5 | alternative_id TEXT[], 6 | source_id TEXT, 7 | citation TEXT, 8 | type TEXT, 9 | author TEXT, 10 | editor TEXT, 11 | title TEXT, 12 | title_short TEXT, 13 | container_author TEXT, 14 | container_title TEXT, 15 | container_title_short TEXT, 16 | issued TEXT, 17 | accessed TEXT, 18 | collection_title TEXT, 19 | collection_editor TEXT, 20 | volume TEXT, 21 | issue TEXT, 22 | edition TEXT, 23 | page TEXT, 24 | publisher TEXT, 25 | publisher_place TEXT, 26 | version TEXT, 27 | isbn TEXT, 28 | issn TEXT, 29 | doi TEXT, 30 | link TEXT, 31 | remarks TEXT 32 | ); 33 | 34 | CREATE TABLE name_usage ( 35 | id TEXT PRIMARY KEY, 36 | alternative_id TEXT[], 37 | name_alternative_id TEXT[], 38 | source_id TEXT, 39 | parent_id TEXT REFERENCES name_usage, 40 | ordinal INTEGER, 41 | branch_length NUMERIC, 42 | basionym_id TEXT REFERENCES name_usage, 43 | status TEXT, 44 | scientific_name TEXT NOT NULL, 45 | authorship TEXT, 46 | rank TEXT, 47 | uninomial TEXT, 48 | generic_name TEXT, 49 | infrageneric_epithet TEXT, 50 | specific_epithet TEXT, 51 | infraspecific_epithet TEXT, 52 | cultivar_epithet TEXT, 53 | notho TEXT, 54 | original_spelling BOOLEAN, 55 | combination_authorship TEXT, 56 | combination_ex_authorship TEXT, 57 | combination_authorship_year TEXT, 58 | basionym_authorship TEXT, 59 | basionym_ex_authorship TEXT, 60 | basionym_authorship_year TEXT, 61 | name_phrase TEXT, 62 | name_reference_id TEXT REFERENCES reference, 63 | name_published_id_year INTEGER, 64 | name_published_id_page TEXT, 65 | name_published_id_page_link TEXT, 66 | gender TEXT, 67 | gender_agreement BOOLEAN, 68 | code TEXT, 69 | name_status TEXT, 70 | according_to_id TEXT REFERENCES reference, 71 | scrutinizer TEXT, 72 | scrutinizer_id TEXT, 73 | scrutinizer_date TEXT, 74 | reference_id TEXT[], 75 | extinct BOOLEAN, 76 | temporal_range_start TEXT, 77 | temporal_range_end TEXT, 78 | environment TEXT[], 79 | link TEXT, 80 | name_remarks TEXT, 81 | remarks TEXT 82 | ); 83 | 84 | CREATE TABLE name_relation ( 85 | name_id TEXT NOT NULL REFERENCES name_usage, 86 | related_name_id TEXT REFERENCES name_usage, 87 | source_id TEXT, 88 | type TEXT NOT NULL, 89 | reference_id TEXT REFERENCES reference, 90 | remarks TEXT 91 | ); 92 | 93 | CREATE TABLE type_material ( 94 | id TEXT PRIMARY KEY, 95 | source_id TEXT, 96 | name_id TEXT NOT NULL REFERENCES name_usage, 97 | citation TEXT, 98 | status TEXT, 99 | institution_code TEXT, 100 | catalog_number TEXT, 101 | reference_id TEXT REFERENCES reference, 102 | locality TEXT, 103 | country CHARACTER(2), 104 | latitude DECIMAL, 105 | longitude DECIMAL, 106 | altitude INTEGER, 107 | host TEXT, 108 | sex TEXT, 109 | "date" TEXT, 110 | collector TEXT, 111 | associated_sequences TEXT, 112 | link TEXT, 113 | remarks TEXT 114 | ); 115 | 116 | CREATE TABLE distribution ( 117 | taxon_id TEXT NOT NULL REFERENCES name_usage, 118 | source_id TEXT, 119 | area TEXT NOT NULL, 120 | area_id TEXT, 121 | gazetteer TEXT, 122 | status TEXT, 123 | reference_id TEXT REFERENCES reference, 124 | remarks TEXT 125 | ); 126 | 127 | CREATE TABLE media ( 128 | taxon_id TEXT NOT NULL REFERENCES name_usage, 129 | source_id TEXT, 130 | url TEXT NOT NULL, 131 | type TEXT, 132 | format TEXT, 133 | title TEXT, 134 | created TEXT, 135 | creator TEXT, 136 | license TEXT, 137 | link TEXT, 138 | remarks TEXT 139 | ); 140 | 141 | CREATE TABLE treatment ( 142 | taxon_id TEXT NOT NULL REFERENCES name_usage, 143 | source_id TEXT, 144 | document TEXT NOT NULL, 145 | format TEXT 146 | ); 147 | 148 | 149 | CREATE TABLE vernacular_name ( 150 | taxon_id TEXT NOT NULL REFERENCES name_usage, 151 | source_id TEXT, 152 | name TEXT NOT NULL, 153 | transliteration TEXT, 154 | language CHARACTER(3), 155 | preferred BOOLEAN, 156 | country CHARACTER(2), 157 | area TEXT, 158 | sex TEXT, 159 | reference_id TEXT REFERENCES reference, 160 | remarks TEXT 161 | ); 162 | 163 | CREATE TABLE species_estimate ( 164 | taxon_id TEXT NOT NULL REFERENCES name_usage, 165 | source_id TEXT, 166 | estimate INTEGER NOT NULL, 167 | type TEXT NOT NULL, 168 | reference_id TEXT REFERENCES reference, 169 | remarks TEXT 170 | ); 171 | 172 | CREATE TABLE taxon_property ( 173 | taxon_id TEXT NOT NULL REFERENCES name_usage, 174 | source_id TEXT, 175 | property TEXT NOT NULL, 176 | value TEXT NOT NULL, 177 | reference_id TEXT REFERENCES reference, 178 | page TEXT, 179 | ordinal INTEGER, 180 | remarks TEXT 181 | ); 182 | 183 | CREATE TABLE species_interaction ( 184 | taxon_id TEXT NOT NULL REFERENCES name_usage, 185 | related_taxon_id TEXT REFERENCES name_usage, 186 | source_id TEXT, 187 | related_taxon_scientific_name TEXT, 188 | type TEXT NOT NULL, 189 | reference_id TEXT REFERENCES reference, 190 | remarks TEXT 191 | ); 192 | 193 | CREATE TABLE taxon_concept_relation ( 194 | taxon_id TEXT NOT NULL REFERENCES name_usage, 195 | related_taxon_id TEXT REFERENCES name_usage, 196 | source_id TEXT, 197 | type TEXT NOT NULL, 198 | reference_id TEXT REFERENCES reference, 199 | remarks TEXT 200 | ); 201 | -------------------------------------------------------------------------------- /metadata.json: -------------------------------------------------------------------------------- 1 | { 2 | "description": "JSON schema for COL Data Package (ColDP) metadata", 3 | "$schema": "https://json-schema.org/draft/2020-12/schema", 4 | "$id": "https://raw.githubusercontent.com/CatalogueOfLife/coldp/master/metadata.json", 5 | "type": "object", 6 | "properties": { 7 | "doi": { 8 | "$ref": "#/definitions/doi" 9 | }, 10 | "identifier": { 11 | "type": "object", 12 | "properties": { 13 | "col": {"type": "integer"}, 14 | "gbif": {"type": "string"}, 15 | "plazi": {"type": "string"} 16 | }, 17 | "additionalProperties": { 18 | "type": "string" 19 | } 20 | }, 21 | "title": { 22 | "type": "string" 23 | }, 24 | "alias": { 25 | "type": "string" 26 | }, 27 | "version": { 28 | "type": "string" 29 | }, 30 | "issued": { 31 | "$ref": "#/definitions/isodate" 32 | }, 33 | 34 | "creator": { 35 | "items": { 36 | "$ref": "#/definitions/Agent" 37 | }, 38 | "type": "array" 39 | }, 40 | "editor": { 41 | "items": { 42 | "$ref": "#/definitions/Agent" 43 | }, 44 | "type": "array" 45 | }, 46 | "publisher": { 47 | "$ref": "#/definitions/Agent" 48 | }, 49 | "contact": { 50 | "$ref": "#/definitions/Agent" 51 | }, 52 | "contributor": { 53 | "items": { 54 | "$ref": "#/definitions/Agent" 55 | }, 56 | "type": "array" 57 | }, 58 | 59 | "description": { 60 | "type": "string" 61 | }, 62 | 63 | "keyword": { 64 | "items": { 65 | "type": "string" 66 | }, 67 | "type": "array" 68 | }, 69 | "taxonomicScope": { 70 | "type": "string" 71 | }, 72 | "temporalScope": { 73 | "type": "string" 74 | }, 75 | "geographicScope": { 76 | "type": "string" 77 | }, 78 | 79 | "completeness": { 80 | "type": "integer" 81 | }, 82 | "confidence": { 83 | "type": "integer" 84 | }, 85 | "url": { 86 | "format": "uri", 87 | "type": "string" 88 | }, 89 | "feedbackUrl": { 90 | "format": "uri", 91 | "type": "string" 92 | }, 93 | "urlFormatter": { 94 | "type": "object", 95 | "properties": { 96 | "name": {"type": "string"}, 97 | "taxon": {"type": "string"}, 98 | "synonym": {"type": "string"}, 99 | "reference": {"type": "string"}, 100 | "author": {"type": "string"}, 101 | "typeMaterial": {"type": "string"} 102 | } 103 | }, 104 | "conversion": { 105 | "type": "object", 106 | "properties": { 107 | "description": {"type": "string"}, 108 | "url": {"type": "string", "format": "uri"} 109 | } 110 | }, 111 | "issn": { 112 | "type": "string" 113 | }, 114 | "license": { 115 | "type": "string" 116 | }, 117 | "logo": { 118 | "format": "uri", 119 | "type": "string" 120 | }, 121 | "source": { 122 | "items": { 123 | "$ref": "#/definitions/Citation" 124 | }, 125 | "type": "array" 126 | }, 127 | "notes": { 128 | "type": "string" 129 | } 130 | }, 131 | "required": [ 132 | "title", 133 | "creator", 134 | "issued", 135 | "license" 136 | ], 137 | "definitions": { 138 | "Agent": { 139 | "title": "Agent", 140 | "type": "object", 141 | "properties": { 142 | "orcid": { 143 | "type": "string" 144 | }, 145 | "family": { 146 | "type": "string" 147 | }, 148 | "given": { 149 | "type": "string" 150 | }, 151 | 152 | "rorid": { 153 | "type": "string" 154 | }, 155 | "department": { 156 | "type": "string" 157 | }, 158 | "organisation": { 159 | "type": "string" 160 | }, 161 | 162 | "city": { 163 | "type": "string" 164 | }, 165 | "state": { 166 | "type": "string" 167 | }, 168 | "country": { 169 | "type": "string", 170 | "minLength": 2, 171 | "maxLength": 2 172 | }, 173 | 174 | "email": { 175 | "format": "email", 176 | "type": "string" 177 | }, 178 | "url": { 179 | "format": "uri", 180 | "type": "string" 181 | }, 182 | "note": { 183 | "type": "string" 184 | } 185 | }, 186 | "additionalProperties": false, 187 | "anyOf": [ 188 | { "required":[ "family" ] }, 189 | { "required":[ "organisation" ] }, 190 | { "required":[ "email" ] } 191 | ] 192 | }, 193 | "Citation": { 194 | "additionalProperties": true, 195 | "properties": { 196 | "id": { 197 | "type": "string" 198 | }, 199 | "type": { 200 | "type": "string", 201 | "enum": ["article-journal", "book", "chapter", "thesis", "paper-conference", "manuscript", "dataset", "webpage", "personal_communication"] 202 | }, 203 | "title": { 204 | "type": "string" 205 | }, 206 | "version": { 207 | "type": "string" 208 | }, 209 | "author": { 210 | "items": { 211 | "$ref": "#/definitions/Person" 212 | }, 213 | "type": "array" 214 | }, 215 | "editor": { 216 | "items": { 217 | "$ref": "#/definitions/Person" 218 | }, 219 | "type": "array" 220 | }, 221 | "publisher": { 222 | "type": "string" 223 | }, 224 | "publisherPlace": { 225 | "type": "string" 226 | }, 227 | "issued": { 228 | "$ref": "#/definitions/isodate" 229 | }, 230 | "containerTitle": { 231 | "type": "string" 232 | }, 233 | "containerAuthor": { 234 | "items": { 235 | "$ref": "#/definitions/Person" 236 | }, 237 | "type": "array" 238 | }, 239 | "volume": { 240 | "type": "string" 241 | }, 242 | "issue": { 243 | "type": "string" 244 | }, 245 | "edition": { 246 | "type": "string" 247 | }, 248 | "page": { 249 | "type": "string" 250 | }, 251 | "collectionTitle": { 252 | "type": "string" 253 | }, 254 | "collectionEditor": { 255 | "items": { 256 | "$ref": "#/definitions/Person" 257 | }, 258 | "type": "array" 259 | }, 260 | "doi": { 261 | "$ref": "#/definitions/doi" 262 | }, 263 | "isbn": { 264 | "type": "string" 265 | }, 266 | "issn": { 267 | "type": "string" 268 | }, 269 | "url": { 270 | "format": "uri", 271 | "type": "string" 272 | }, 273 | "accessed": { 274 | "$ref": "#/definitions/doi" 275 | }, 276 | 277 | "note": { 278 | "type": "string" 279 | } 280 | }, 281 | "required": [ 282 | "id", 283 | "title" 284 | ], 285 | "title": "Source", 286 | "type": "object" 287 | }, 288 | "Person": { 289 | "title": "Person", 290 | "type": "object", 291 | "properties": { 292 | "family": { 293 | "type": "string" 294 | }, 295 | "given": { 296 | "type": "string" 297 | }, 298 | "literal": { 299 | "type": "string" 300 | } 301 | }, 302 | "additionalProperties": false 303 | }, 304 | "isodate": { 305 | "title": "ISO Date", 306 | "type": "string", 307 | "format": "regex", 308 | "pattern": "^[12][0-9][0-9][0-9](-[01][0-9](-[0123][0-9])?)?$" 309 | }, 310 | "doi": { 311 | "title": "DOI", 312 | "type": "string", 313 | "format": "regex", 314 | "pattern": "^(doi:|https://doi.org/)?10.[0-9]+/.+" 315 | } 316 | 317 | } 318 | } -------------------------------------------------------------------------------- /metadata.yaml: -------------------------------------------------------------------------------- 1 | # yaml-language-server: $schema=metadata.json 2 | 3 | # single, primary DOI for the dataset 4 | doi: 10.15468/2zjeva 5 | 6 | # List of alternative identifiers for the dataset with an ID and an optional type value 7 | # Supported ID types: DOI, GBIF, COL, PLAZI 8 | identifier: 9 | col: 1010 10 | gbif: b96ed603-b710-4b3a-b99b-9bf0de6ef85b 11 | plazi: 3378FFAB6B55FFE0B065C77BFF226429 12 | 13 | # Full dataset title 14 | title: ColDP Example. The full dataset title 15 | 16 | # Short, hopefully unique name for the dataset 17 | alias: ColDP Example 18 | 19 | # Multi parapgraph description / abstract of the dataset 20 | description: | 21 | An abstract about the content of this dataset. 22 | This can be as many paragraphs as you like in literal style YAML. 23 | 24 | # Keywords list. Added in v1.1 25 | keyword: 26 | - example 27 | - coldp 28 | - invasives 29 | - legal 30 | - fish 31 | # Official release date of this version in ISO YYYY-MM-DD. Will be part of the default citation! 32 | issued: 2018-06-01 33 | 34 | # Version name of this copy 35 | version: v.48 (06/2018) 36 | 37 | # ISSN number for a serial publication 38 | issn: 2405-8858 39 | 40 | 41 | # +++ AGENT +++ 42 | # 43 | # Agent entities are used for many fields below and can be either a person, an organisation or a combination of both. 44 | # The minimum requirement is either a persons family name, an organisation name or any of the identifiers for them. 45 | # 46 | # An agent combines the following fields for a person with fields for an organisation: 47 | # 48 | # PERSON fields 49 | # orcid: ORCID person ID, https://orcid.org example: 0000-0001-9745-636X 50 | # family: last name 51 | # given: first name 52 | # ORGANISATION fields 53 | # rorid: ROR organisation ID, https://ror.org example: https://ror.org/05fjyn938 54 | # organisation: name of the organisation / institution 55 | # department: subunit within the organisation, sometimes a project 56 | # city: city 57 | # state: state or province 58 | # country: ISO 2 letter country code 59 | # SHARED fields 60 | # email: email address 61 | # url: webpage 62 | # note: miscellaneous extra information, used for contributor roles 63 | # 64 | # In case no parsed agent can be provided it is permitted to supply a list of simple strings which will then be parsed. 65 | # For the parsing to given and family name to correctly work it is highly recommended to use one of the following formats: 66 | # GivenName FamilyName: Only use this in case the last name is a single token. There can be many first names e.g. John Paul Sartre 67 | # FamilyName, GivenName: Supports any conmplex last name. E.g. Brinch Hansen, Per 68 | 69 | 70 | # Single point of contact for questions 71 | contact: 72 | given: Rainer 73 | family: Froese 74 | email: rainer@mailinator.com 75 | 76 | # Creators of the dataset. Will be treated as authors in the default citation! 77 | # For available fields see Agent type at the top 78 | # Please provide an ORCID if you can so it can be included in DOI metadata 79 | creator: 80 | - given: Nicolas 81 | family: Bailly 82 | orcid: 0000-0003-4994-0653 83 | - given: Rainer 84 | family: Froese 85 | orcid: 0000-0001-9745-636X 86 | - given: Daniel 87 | family: Pauly 88 | orcid: 0000-0003-3756-4793 89 | 90 | # Editors of the dataset. Will be part of the default citation! 91 | editor: 92 | - given: Rainer 93 | family: Froese 94 | email: rainer@mailinator.com 95 | orcid: 0000-0001-9745-636X 96 | - given: Daniel 97 | family: Pauly 98 | orcid: 0000-0003-3756-4793 99 | 100 | # Single publishing organisation. Will be part of the default citation! 101 | publisher: 102 | rorid: 03rmrcq20 103 | organisation: University of British Columbia 104 | department: Global Fisheries Cluster 105 | city: Vancouver 106 | state: B.C. 107 | country: CA 108 | 109 | # Agent contributing to the dataset in any other way, but who is not considered an author of the dataset 110 | # Use the optional note field to specify the kind of contribution 111 | contributor: 112 | - given: Atheer 113 | family: Ali 114 | orcid: 0000-0002-2541-968X 115 | email: atheeralibu@gmail.com 116 | note: Provided references on fishes of Iraq 117 | 118 | - given: Richard Lawrence 119 | family: Pyle 120 | orcid: 0000-0003-0768-1286 121 | organisation: Bernice Pauahi Bishop Museum 122 | department: Natural Sciences 123 | city: Honolulu 124 | state: Hawaii 125 | country: US 126 | note: Review of Pacific species 127 | 128 | - given: Markus 129 | family: Döring 130 | orcid: 0000-0001-7757-1889 131 | note: IT support 132 | 133 | - organisation: The WorldFish Center 134 | city: Penang 135 | country: MY 136 | 137 | - rorid: 02h2x0161 138 | organisation: Helmholtz Centre for Ocean Research Kiel 139 | department: GEOMAR 140 | city: Kiel 141 | country: DE 142 | note: Hosting services 143 | 144 | - organisation: Food and Agriculture Organization of the United Nations 145 | rorid: 00pe0tf51 146 | city: Rome 147 | country: IT 148 | 149 | - organisation: Muséum National d'Histoire Naturelle 150 | rorid: 03wkt5x30 151 | city: Paris 152 | country: FR 153 | 154 | - organisation: Aristotle University of Thessaloniki 155 | rorid: 02j61yw88 156 | city: Thessaloniki 157 | country: GR 158 | 159 | # Description of the geographical scope of the dataset 160 | geographicScope: global 161 | 162 | # Taxonomic scope of the dataset, given in English vernacular names or as latin scientific names 163 | # concatenate lists with commas 164 | taxonomicScope: Fishes 165 | 166 | # Temporal scope of the dataset 167 | temporalScope: Extant taxa described until 1987 168 | 169 | # Integer between 1-5 with 5 expressing highest confidence in quality of the data 170 | confidence: 5 171 | 172 | # 0-100 to express the completeness of the dataset in regards to the defined scope 173 | completeness: 95 174 | 175 | # Any Open Definition license ID: https://licenses.opendefinition.org/licenses/groups/all.json 176 | # For ChecklistBank please use only CC0-1.0, CC-BY-4.0 or CC-BY-NC-4.0 177 | # Must be CC0-1.0 or CC-BY-4.0 to be used by COL !!! 178 | license: CC0-1.0 179 | 180 | # Link to a website for the dataset 181 | url: https://www.fishbase.org 182 | 183 | # Link to an website or issue tracker to provide feedback on data issues 184 | feedbackUrl: https://github.com/CatalogueOfLife/data/issues 185 | 186 | # URL to large logo image 187 | logo: https://www.fishbase.de/images/gifs/fblogo_new.gif 188 | 189 | # templates to build links to webpages for individual records of some kind using these variables: 190 | # {ID} individual record identifier 191 | # {TAXONID} individual record identifier for the taxon, i.e accepted name 192 | urlFormatter: 193 | name: https://fishbase.mnhn.fr/summary/{ID} 194 | taxon: https://fishbase.mnhn.fr/summary/{ID} 195 | synonym: https://fishbase.mnhn.fr/Nomenclature/SynonymSummary.php?GSID={TAXONID}&ID={ID} 196 | reference: https://fishbase.mnhn.fr/references/FBRefSummary.php?ID={ID} 197 | author: https://fishbase.mnhn.fr/collaborators/CollaboratorSummary.php?ID={ID} 198 | typeMaterial: 199 | 200 | # Documentation of the conversion process from the original source data 201 | # to the ColDP representation in this dataset 202 | conversion: 203 | # human description of what's being done 204 | description: The MySQL database is being exported on a monthly basis to ColDP CSV files with the help of a python script. 205 | # location of the conversion script code or more documentation of the process 206 | url: https://github.com/CatalogueOfLife/coldp-generator 207 | 208 | # List of Citations this dataset is derived from. 209 | # We use CSL-JSON fields to represent a structured citation, see below for the main fields used for bibliographies. 210 | # 211 | # NAME fields: 212 | # are lists of people represented either by a simple string or objects with family & given fields. 213 | # In case no parsed name can be provided, simple strings will be parsed. 214 | # For the parsing to given and family name to correctly work it is highly recommended to use one of the following formats: 215 | # 1) GivenName FamilyName: Only use this in case the last name is a single token. There can be many first names e.g. John Paul Sartre 216 | # 2) FamilyName, GivenName: Supports any conmplex last name. E.g. Brinch Hansen, Per 217 | # 218 | # DATE fields: 219 | # are ISO dates that can be truncated to represent a year, year & month or exact date: 1998, 1998-05 or 1998-05-21 220 | # 221 | source: 222 | # example record 223 | - id: ecf 224 | type: book 225 | title: Eschmeyer's Catalog of Fishes 226 | editor: 227 | - Ronald Fricke # simple format: GivenName FamilyName 228 | - Van der Laan, R. # simple format: FamilyName, GivenName 229 | - given: William N. # object format 230 | family: Eschmeyer 231 | issued: 2021-04 232 | version: 13 April 2021 233 | url: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp 234 | 235 | # Full list of supported CSL fields: 236 | - id: # identifier for the source, can be referenced from individual data records via sourceID to indicate the provenance on a record level. 237 | type: # CSL type, e.g. ARTICLE-JOURNAL, BOOK, CHAPTER, DATASET, WEBPAGE. See https://aurimasv.github.io/z2csl/typeMap.xml for a mapping of CSL types to field sets 238 | doi: # a DOI 239 | author: # author list. type=NAME[] 240 | editor: # editor list. type=NAME[] 241 | title: # primary title of the item 242 | containerAuthor: # author(s) of the container holding the item (e.g. the book author for a book chapter). type=NAME[] 243 | containerTitle: # title of the container holding the item (e.g. the book title for a book chapter, the journal title for a journal article) 244 | issued: # date the item was issued/published in possibly truncated ISO format, e.g. 1998, 1998-05 or 1998-05-21. type=DATE 245 | accessed: # date the item has been accessed. type=DATE 246 | collectionTitle: # title of the collection holding the item (e.g. the series title for a book) 247 | collectionEditor: # editor(s) of the collection holding the item (e.g. the series editor for a book). type=NAME[] 248 | volume: # (container) volume holding the item (e.g. “2” when citing a chapter from book volume 2). type=NUMBER 249 | issue: # (container) issue holding the item (e.g. “5” when citing a journal article from journal volume 2, issue 5). type=NUMBER 250 | edition: # (container) edition holding the item (e.g. “3” when citing a chapter in the third edition of a book). type=NUMBER 251 | page: # range of pages the item (e.g. a journal article) covers in a container (e.g. a journal issue) 252 | publisher: # publisher 253 | publisherPlace: # geographic location of the publisher 254 | version: # version of the dataset/source 255 | isbn: # International Standard Book Number 256 | issn: # International Standard Serial Number 257 | url: # link to webpage for electronic resources 258 | note: # (short) inline note giving additional item details (e.g. a concise summary or commentary) 259 | 260 | notes: Remarks, comments and usage notes about this dataset 261 | -------------------------------------------------------------------------------- /docs/publishing-guide.md: -------------------------------------------------------------------------------- 1 | # ColDP Publishing Guidelines 2 | This guide tries to provide help in publishing ColDP data by giving concrete examples for various cases. 3 | It should be seen as the intended way of using ColDP when there seemingly are several ways of expressing the same thing. 4 | 5 | 6 | * [Minimal information](#minimal-information) 7 | * [Names](#names) 8 | * [Name relations](#name-relations) 9 | * [Taxon concepts](#taxon-concepts) 10 | * [References](#references) 11 | 12 | 13 | ## Minimal information 14 | ColDP covers a range of entities and for names, references and usages also provides alternative representations, mostly parsed and unparsed, one can chose from. The information to be shared with ChecklistBank can be prioritized like the following, using only the simpler [NameUsage](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#nameusage) entity instead of Name, Taxon & Synonym. 15 | 16 | #### Minimal information 17 | - [NameUsage](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#nameusage) 18 | - ID 19 | - scientificName 20 | - authorship 21 | - rank 22 | - status 23 | - parentID (normalised) OR kingdom;phylum;class;order;family (denormalised) 24 | 25 | 26 | #### Highly recommended information 27 | - [NameUsage](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#nameusage) 28 | - basionymID 29 | - publishedInID 30 | - extinct 31 | - environment 32 | - link 33 | - [Reference](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#reference) 34 | - ID 35 | - citation 36 | - DOI 37 | - link 38 | 39 | 40 | #### Desired information 41 | - [NameUsage](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#nameusage) 42 | - code 43 | - publishedInPageLink 44 | - gender 45 | - genderAgreement 46 | - [NameRelation](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#namerelation) 47 | - nameID 48 | - relatedNameID 49 | - type 50 | - [TypeMaterial](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#typematerial) 51 | - nameID 52 | - citation 53 | - status 54 | - link 55 | - [VernacularName](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#vernacularname) 56 | - taxonID 57 | - name 58 | - language 59 | - [Media](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#media) 60 | - taxonID 61 | - url 62 | - type 63 | - license 64 | 65 | #### Optional information 66 | Anything else not mentioned above including [Distributions](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#media), [Treatments](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#treatment), [Author](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#author), [SpeciesInteraction](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#speciesinteraction) and [TaxonProperty](https://github.com/CatalogueOfLife/coldp/blob/master/README.md#taxonproperty) which can be used to share any other information about a taxon. 67 | 68 | 69 | 70 | ## Names 71 | Scientific names can be provided either as a simple pair of ```rank```, ```scientificName``` and ```authorship``` 72 | or as a more structured, parsed version supplying individual name parts in dedicated fields that often depend on the rank of the name. 73 | The simple version is always an option, but requires a consumer like ChecklistBank to parse the name into atoms. 74 | This works in 99.99% of names, but can lead to unexpected results in rare, special cases. 75 | The following example therefore focus on how to provide names as proper parsed names already, so there is no need to further interpret them. 76 | 77 | In addition to parsed names, the authorship can also be broken down into individual parts, i.e. authors 78 | including even identifiers for individual authors. See the [parsed authorship examples](#parsedAuthorships) below for more details. 79 | 80 | ### Binomials 81 | A regular species name like should be given as: 82 | 83 | ```Abies alba Mill.``` 84 | ``` 85 | rank: species 86 | genus: Abies 87 | specificEpithet: alba 88 | authorship: Mill. 89 | ``` 90 | 91 | ### Infraspecific names 92 | Infraspecific names like ```Abies alba subsp. apennina Brullo, Scelsi & Spamp.``` should be given as 93 | 94 | ``` 95 | rank: subspecies 96 | genus: Abies 97 | specificEpithet: alba 98 | infraspecificEpithet: apennina 99 | authorship: Brullo, Scelsi & Spamp. 100 | ``` 101 | 102 | There should be no rank marker given as part of the infraspecificEpithet, just the name part on its own. 103 | Note that botanical and zoological names prefer a different rendering of subspecies, but the atomised names look just the same. 104 | Consider the zoological subspecies ```Delphinus delphis ponticus Barabash, 1935```: 105 | ``` 106 | rank: subspecies 107 | genus: Delphinus 108 | specificEpithet: delphis 109 | infraspecificEpithet: ponticus 110 | authorship: Barabash, 1935 111 | ``` 112 | 113 | For consumers like ChecklistBank to render the name correctly it is recommended to supply also a [nomenclatoral code value](http://api.checklistbank.org/vocab/nomcode): 114 | ``` 115 | code: zoological 116 | ``` 117 | In many cases the code is the same for all names of an entire dataset. 118 | In Checklistbank this can be configured as [dataset options](https://www.checklistbank.org/dataset/2371/options) as a dataset wide default value. 119 | 120 | 121 | Different ranks like the form ```Abies alba f. compacta (Parsons) Rehder``` also follow the same scheme: 122 | ``` 123 | rank: forma 124 | genus: Abies 125 | specificEpithet: alba 126 | infraspecificEpithet: compacta 127 | authorship: (Parsons) Rehder 128 | ``` 129 | 130 | Some publications include infraspecific names with more than 3 name parts and various authorships, e.g. a variety that also includes the subspecies: 131 | ```Draba bruniifolia Steven subsp. heterocoma (Fenzl) Coode & Cullen var. nana (Stapf) O.E. Schulz ex Coode & Cullen``` 132 | 133 | These are not properly formed names according to the codes and only the terminal infraspecific epithet and authorship should in those cases be given: 134 | ``` 135 | rank: variety 136 | genus: Draba 137 | specificEpithet: bruniifolia 138 | infraspecificEpithet: nana 139 | authorship: (Stapf) O.E. Schulz ex Coode & Cullen 140 | ``` 141 | 142 | 143 | ### Infrageneric names 144 | Infrageneric names like a subgenus on the other hand are frequently classified into a genus and should *not* be using the uninomial field. 145 | Instead there is a dedicated ```infragenericEpithet``` that optionally can be accompanied by the genus field. 146 | ```Lasiurus (Aeorestes) (Geoffroy St.-Hilaire, 1806)```: 147 | ``` 148 | rank: subgenus 149 | genus: Lasiurus 150 | infragenericEpithet: Aeorestes 151 | authorship: (Geoffroy St.-Hilaire, 1806) 152 | code: zoological 153 | ``` 154 | Again infrageneric names are rendered differently between codes, so having an explicit code value given is recommended. 155 | If no genus is know, an unplaced subgenus should also be given using ```infragenericEpithet```: 156 | 157 | ``` 158 | rank: subgenus 159 | infragenericEpithet: Aeorestes 160 | authorship: (Geoffroy St.-Hilaire, 1806) 161 | ``` 162 | 163 | The species name for the bat ```Lasiurus (Aeorestes) villosissimus (Geoffroy St.-Hilaire, 1806)``` can also given given with an infrageneric name: 164 | ``` 165 | rank: species 166 | genus: Lasiurus 167 | infragenericEpithet: Aeorestes 168 | specificEpithet: villosissimus 169 | authorship: (Geoffroy St.-Hilaire, 1806) 170 | code: zoological 171 | ``` 172 | 173 | Similar botanical sections such as ```Lilium sect. Martagon Rchb.``` are given as: 174 | ``` 175 | rank: section 176 | genus: Lilium 177 | infragenericEpithet: Martagon 178 | authorship: Rchb. 179 | code: botanical 180 | ``` 181 | 182 | ### Genera 183 | Parsed genus names should be supplied using the ```uninomial``` field just as suprageneric names. 184 | The ```genus``` field is reserved only for classifying a species or infrageneric name, but not for standalone genera like ```Puma Jardine, 1834```: 185 | ``` 186 | rank: genus 187 | uninomial: Puma 188 | authorship: Jardine, 1834 189 | ``` 190 | 191 | ### Families and other suprageneric names 192 | Families and higher ranked names are given as uninomials just like a genus. E.g. the family ```Asteraceae Bercht. & J.Presl``` 193 | ``` 194 | rank: family 195 | uninomial: Asteraceae 196 | authorship: Bercht. & J.Presl 197 | ``` 198 | 199 | ### Cultivars 200 | Similar to infraspecific names cultivars according to the [International Code of Nomenclature for Cultivated Plants](https://www.ishs.org/sites/default/files/static/ScriptaHorticulturae_18.pdf) 201 | have their own field to capture the cultivar name: 202 | ```Chamaecyparis lawsoniana 'Golden Wonder'``` 203 | 204 | ``` 205 | rank: cultivar 206 | genus: Chamaecyparis 207 | specificEpithet: lawsoniana 208 | cultivarEpithet: Golden Wonder 209 | code: cultivars 210 | ``` 211 | 212 | Cultivar Groups are treated the same way just with a different rank. 213 | The rank marker "Group" is not mentioned again in the epithet field: 214 | ```Brassica oleracea Capitata Group``` 215 | 216 | ``` 217 | rank: cultivar group 218 | genus: Brassica 219 | specificEpithet: oleracea 220 | cultivarEpithet: Capitata 221 | code: cultivars 222 | ``` 223 | 224 | 225 | ### Hybrids 226 | There are two kind of hybrids that are syntactically very different. 227 | **Hybrid formulas** are combinations of several names and currently cannot be represented in a parsed way in ColDP. 228 | Names such as ```Festuca pratensis × Lolium perenne``` should be given as simple names only: 229 | ``` 230 | scientificName: Festuca pratensis × Lolium perenne 231 | ``` 232 | 233 | **Named hybrids** or notho taxa on the other hand are very much structured like regular Linnean names and can be represented as parsed ColDP names. 234 | For example the hybrid ```Lolium multiflorum × Schedonorus arundina``` 235 | has been described as the nothospecies ```×Schedolium krasanii H. Scholz```. 236 | The hybrid marker should be preserved as a prefix in the respective epithet field using the true multiplication sign: 237 | ``` 238 | rank: species 239 | genus: ×Schedolium 240 | specificEpithet: krasanii 241 | code: botanical 242 | ``` 243 | 244 | 245 | ### OTUs 246 | 247 | ### Informal names 248 | 249 | ### Placeholders 250 | 251 | 252 | ## Parsed authorships 253 | Instead of a single authorship string there are several individual properties that can be used to break down the string: 254 | 255 | - combinationAuthorship 256 | - combinationAuthorshipID 257 | - combinationExAuthorship 258 | - combinationExAuthorshipID 259 | - combinationAuthorshipYear 260 | - basionymAuthorship 261 | - basionymAuthorshipID 262 | - basionymExAuthorship 263 | - basionymExAuthorshipID 264 | - basionymAuthorshipYear 265 | 266 | Apart from the year all other fields can be a `|` concatenated list of values. 267 | For example ```Abies alba subsp. apennina Brullo, Scelsi & Spamp.``` could be given as 268 | 269 | ``` 270 | rank: subspecies 271 | genus: Abies 272 | specificEpithet: alba 273 | infraspecificEpithet: apennina 274 | combinationAuthorship: Brullo|Scelsi|Spamp. 275 | combinationAuthorshipID: 13165-1|36267-1|27048-1 276 | ``` 277 | 278 | with these entries in the Author table: 279 | ``` 280 | ID: 13165-1 281 | given: Brullo 282 | family: Brullo 283 | abbreviationBotany: Brullo 284 | sex: male 285 | birth: 1947 286 | country: Italy 287 | link: https://www.ipni.org/a/13165-1 288 | 289 | ID: 36267-1 290 | given: Fabrizio 291 | family: Scelsi 292 | abbreviationBotany: Scelsi 293 | sex: male 294 | country: Italy 295 | link: https://www.ipni.org/a/36267-1 296 | 297 | ID: 27048-1 298 | given: Giovanni 299 | family: Spampinato 300 | abbreviationBotany: Spamp. 301 | sex: male 302 | birth: 1958 303 | link: https://www.ipni.org/a/27048-1 304 | ``` 305 | 306 | 307 | ## Name relations 308 | tbd ... 309 | 310 | 311 | ### Basionyms or original names 312 | 313 | 314 | 315 | 316 | ## Taxon concepts 317 | tbd ... 318 | 319 | ### accordingTo 320 | 321 | 322 | 323 | 324 | ## References 325 | tbd ... 326 | 327 | -------------------------------------------------------------------------------- /templates/schema-pg-enum.sql: -------------------------------------------------------------------------------- 1 | -- Postgres ColDP schema 2 | 3 | -- enumeration types 4 | 5 | CREATE TYPE CONTINENT AS ENUM ( 6 | 'AFRICA', 7 | 'ANTARCTICA', 8 | 'ASIA', 9 | 'OCEANIA', 10 | 'EUROPE', 11 | 'NORTH_AMERICA', 12 | 'SOUTH_AMERICA' 13 | ); 14 | 15 | CREATE TYPE DISTRIBUTIONSTATUS AS ENUM ( 16 | 'NATIVE', 17 | 'DOMESTICATED', 18 | 'ALIEN', 19 | 'UNCERTAIN' 20 | ); 21 | 22 | CREATE TYPE ENVIRONMENT AS ENUM ( 23 | 'BRACKISH', 24 | 'FRESHWATER', 25 | 'MARINE', 26 | 'TERRESTRIAL' 27 | ); 28 | 29 | CREATE TYPE ESTIMATETYPE AS ENUM ( 30 | 'SPECIES_LIVING', 31 | 'SPECIES_EXTINCT', 32 | 'ESTIMATED_SPECIES' 33 | ); 34 | 35 | CREATE TYPE GAZETTEER AS ENUM ( 36 | 'TDWG', 37 | 'ISO', 38 | 'FAO', 39 | 'LONGHURST', 40 | 'TEOW', 41 | 'IHO', 42 | 'MRGID', 43 | 'TEXT' 44 | ); 45 | 46 | CREATE TYPE GENDER AS ENUM ( 47 | 'MASCULINE', 48 | 'FEMININE', 49 | 'NEUTER' 50 | ); 51 | 52 | CREATE TYPE MEDIATYPE AS ENUM ( 53 | 'IMAGE', 54 | 'VIDEO', 55 | 'AUDIO' 56 | ); 57 | 58 | CREATE TYPE NAMEPART AS ENUM ( 59 | 'GENERIC', 60 | 'INFRAGENERIC', 61 | 'SPECIFIC', 62 | 'INFRASPECIFIC' 63 | ); 64 | 65 | CREATE TYPE NOMCODE AS ENUM ( 66 | 'BACTERIAL', 67 | 'BOTANICAL', 68 | 'CULTIVARS', 69 | 'PHYTOSOCIOLOGICAL', 70 | 'VIRUS', 71 | 'ZOOLOGICAL' 72 | ); 73 | 74 | CREATE TYPE NOMRELTYPE AS ENUM ( 75 | 'SPELLING_CORRECTION', 76 | 'BASIONYM', 77 | 'BASED_ON', 78 | 'REPLACEMENT_NAME', 79 | 'CONSERVED', 80 | 'LATER_HOMONYM', 81 | 'SUPERFLUOUS', 82 | 'HOMOTYPIC', 83 | 'TYPE' 84 | ); 85 | 86 | CREATE TYPE NOMSTATUS AS ENUM ( 87 | 'ESTABLISHED', 88 | 'NOT_ESTABLISHED', 89 | 'ACCEPTABLE', 90 | 'UNACCEPTABLE', 91 | 'CONSERVED', 92 | 'REJECTED', 93 | 'DOUBTFUL', 94 | 'MANUSCRIPT', 95 | 'CHRESONYM' 96 | ); 97 | 98 | CREATE TYPE RANK AS ENUM ( 99 | 'SUPERDOMAIN', 100 | 'DOMAIN', 101 | 'REALM', 102 | 'SUBREALM', 103 | 'SUPERKINGDOM', 104 | 'KINGDOM', 105 | 'SUBKINGDOM', 106 | 'INFRAKINGDOM', 107 | 'SUPERPHYLUM', 108 | 'PHYLUM', 109 | 'SUBPHYLUM', 110 | 'INFRAPHYLUM', 111 | 'PARVPHYLUM', 112 | 'MICROPHYLUM', 113 | 'NANOPHYLUM', 114 | 'GIGACLASS', 115 | 'MEGACLASS', 116 | 'SUPERCLASS', 117 | 'CLASS', 118 | 'SUBCLASS', 119 | 'INFRACLASS', 120 | 'SUBTERCLASS', 121 | 'PARVCLASS', 122 | 'SUPERDIVISION', 123 | 'DIVISION', 124 | 'SUBDIVISION', 125 | 'INFRADIVISION', 126 | 'SUPERLEGION', 127 | 'LEGION', 128 | 'SUBLEGION', 129 | 'INFRALEGION', 130 | 'MEGACOHORT', 131 | 'SUPERCOHORT', 132 | 'COHORT', 133 | 'SUBCOHORT', 134 | 'INFRACOHORT', 135 | 'GIGAORDER', 136 | 'MAGNORDER', 137 | 'GRANDORDER', 138 | 'MIRORDER', 139 | 'SUPERORDER', 140 | 'ORDER', 141 | 'NANORDER', 142 | 'HYPOORDER', 143 | 'MINORDER', 144 | 'SUBORDER', 145 | 'INFRAORDER', 146 | 'PARVORDER', 147 | 'FALANX', 148 | 'MEGAFAMILY', 149 | 'GRANDFAMILY', 150 | 'SUPERFAMILY', 151 | 'EPIFAMILY', 152 | 'FAMILY', 153 | 'SUBFAMILY', 154 | 'INFRAFAMILY', 155 | 'SUPERTRIBE', 156 | 'TRIBE', 157 | 'SUBTRIBE', 158 | 'INFRATRIBE', 159 | 'SUPRAGENERIC_NAME', 160 | 'SUPERGENUS', 161 | 'GENUS', 162 | 'SUBGENUS', 163 | 'INFRAGENUS', 164 | 'SUPERSECTION', 165 | 'SECTION', 166 | 'SUBSECTION', 167 | 'SUPERSERIES', 168 | 'SERIES', 169 | 'SUBSERIES', 170 | 'INFRAGENERIC_NAME', 171 | 'SPECIES_AGGREGATE', 172 | 'SPECIES', 173 | 'INFRASPECIFIC_NAME', 174 | 'GREX', 175 | 'KLEPTON', 176 | 'SUBSPECIES', 177 | 'CULTIVAR_GROUP', 178 | 'CONVARIETY', 179 | 'INFRASUBSPECIFIC_NAME', 180 | 'PROLES', 181 | 'NATIO', 182 | 'ABERRATION', 183 | 'MORPH', 184 | 'SUPERVARIETY', 185 | 'VARIETY', 186 | 'SUBVARIETY', 187 | 'SUPERFORM', 188 | 'FORM', 189 | 'SUBFORM', 190 | 'PATHOVAR', 191 | 'BIOVAR', 192 | 'CHEMOVAR', 193 | 'MORPHOVAR', 194 | 'PHAGOVAR', 195 | 'SEROVAR', 196 | 'CHEMOFORM', 197 | 'FORMA_SPECIALIS', 198 | 'LUSUS', 199 | 'CULTIVAR', 200 | 'MUTATIO', 201 | 'STRAIN', 202 | 'OTHER', 203 | 'UNRANKED' 204 | ); 205 | 206 | CREATE TYPE SEX AS ENUM ( 207 | 'FEMALE', 208 | 'MALE', 209 | 'HERMAPHRODITE' 210 | ); 211 | 212 | CREATE TYPE SPECIESINTERACTIONTYPE AS ENUM ( 213 | 'RELATED_TO', 214 | 'CO_OCCURS_WITH', 215 | 'INTERACTS_WITH', 216 | 'ADJACENT_TO', 217 | 'SYMBIONT_OF', 218 | 'EATS', 219 | 'EATEN_BY', 220 | 'KILLS', 221 | 'KILLED_BY', 222 | 'PREYS_UPON', 223 | 'PREYED_UPON_BY', 224 | 'HOST_OF', 225 | 'HAS_HOST', 226 | 'PARASITE_OF', 227 | 'HAS_PARASITE', 228 | 'PATHOGEN_OF', 229 | 'HAS_PATHOGEN', 230 | 'VECTOR_OF', 231 | 'HAS_VECTOR', 232 | 'ENDOPARASITE_OF', 233 | 'HAS_ENDOPARASITE', 234 | 'ECTOPARASITE_OF', 235 | 'HAS_ECTOPARASITE', 236 | 'HYPERPARASITE_OF', 237 | 'HAS_HYPERPARASITE', 238 | 'KLEPTOPARASITE_OF', 239 | 'HAS_KLEPTOPARASITE', 240 | 'PARASITOID_OF', 241 | 'HAS_PARASITOID', 242 | 'HYPERPARASITOID_OF', 243 | 'HAS_HYPERPARASITOID', 244 | 'VISITS', 245 | 'VISITED_BY', 246 | 'VISITS_FLOWERS_OF', 247 | 'FLOWERS_VISITED_BY', 248 | 'POLLINATES', 249 | 'POLLINATED_BY', 250 | 'LAYS_EGGS_ON', 251 | 'HAS_EGGS_LAYED_ON_BY', 252 | 'EPIPHYTE_OF', 253 | 'HAS_EPIPHYTE', 254 | 'COMMENSALIST_OF', 255 | 'MUTUALIST_OF' 256 | ); 257 | 258 | CREATE TYPE TAXONCONCEPTRELTYPE AS ENUM ( 259 | 'EQUALS', 260 | 'INCLUDES', 261 | 'INCLUDED_IN', 262 | 'OVERLAPS', 263 | 'EXCLUDES' 264 | ); 265 | 266 | CREATE TYPE TAXONOMICSTATUS AS ENUM ( 267 | 'ACCEPTED', 268 | 'PROVISIONALLY_ACCEPTED', 269 | 'SYNONYM', 270 | 'AMBIGUOUS_SYNONYM', 271 | 'MISAPPLIED', 272 | 'BARE_NAME' 273 | ); 274 | 275 | CREATE TYPE TREATMENTFORMAT AS ENUM ( 276 | 'PLAIN_TEXT', 277 | 'MARKDOWN', 278 | 'XML', 279 | 'HTML', 280 | 'TAX_PUB', 281 | 'TAXON_X', 282 | 'RDF' 283 | ); 284 | 285 | CREATE TYPE TYPESTATUS AS ENUM ( 286 | 'EPITYPE', 287 | 'ERGATOTYPE', 288 | 'EX_TYPE', 289 | 'HAPANTOTYPE', 290 | 'HOLOTYPE', 291 | 'ICONOTYPE', 292 | 'LECTOTYPE', 293 | 'NEOTYPE', 294 | 'ORIGINAL_MATERIAL', 295 | 'PARATYPE', 296 | 'PATHOTYPE', 297 | 'SYNTYPE', 298 | 'TOPOTYPE', 299 | 'ISOTYPE', 300 | 'ISOEPITYPE', 301 | 'ISOLECTOTYPE', 302 | 'ISONEOTYPE', 303 | 'ISOPARATYPE', 304 | 'ISOSYNTYPE', 305 | 'PARALECTOTYPE', 306 | 'PARANEOTYPE', 307 | 'ALLOLECTOTYPE', 308 | 'ALLONEOTYPE', 309 | 'ALLOTYPE', 310 | 'PLASTOHOLOTYPE', 311 | 'PLASTOISOTYPE', 312 | 'PLASTOLECTOTYPE', 313 | 'PLASTONEOTYPE', 314 | 'PLASTOPARATYPE', 315 | 'PLASTOSYNTYPE', 316 | 'PLASTOTYPE', 317 | 'PLESIOTYPE', 318 | 'HOMOEOTYPE', 319 | 'OTHER' 320 | ); 321 | 322 | 323 | 324 | -- Postgres ColDP schema 325 | 326 | CREATE TABLE reference ( 327 | id TEXT PRIMARY KEY, 328 | alternative_id TEXT[], 329 | source_id TEXT, 330 | citation TEXT, 331 | type TEXT, 332 | author TEXT, 333 | editor TEXT, 334 | title TEXT, 335 | title_short TEXT, 336 | container_author TEXT, 337 | container_title TEXT, 338 | container_title_short TEXT, 339 | issued TEXT, 340 | accessed TEXT, 341 | collection_title TEXT, 342 | collection_editor TEXT, 343 | volume TEXT, 344 | issue TEXT, 345 | edition TEXT, 346 | page TEXT, 347 | publisher TEXT, 348 | publisher_place TEXT, 349 | version TEXT, 350 | isbn TEXT, 351 | issn TEXT, 352 | doi TEXT, 353 | link TEXT, 354 | remarks TEXT 355 | ); 356 | 357 | CREATE TABLE name_usage ( 358 | id TEXT PRIMARY KEY, 359 | alternative_id TEXT[], 360 | name_alternative_id TEXT[], 361 | source_id TEXT, 362 | parent_id TEXT REFERENCES name_usage, 363 | ordinal INTEGER, 364 | branch_length NUMERIC, 365 | basionym_id TEXT REFERENCES name_usage, 366 | status TEXT, 367 | scientific_name TEXT NOT NULL, 368 | authorship TEXT, 369 | rank RANK, 370 | uninomial TEXT, 371 | generic_name TEXT, 372 | infrageneric_epithet TEXT, 373 | specific_epithet TEXT, 374 | infraspecific_epithet TEXT, 375 | cultivar_epithet TEXT, 376 | notho NAMEPART, 377 | original_spelling BOOLEAN, 378 | combination_authorship TEXT, 379 | combination_ex_authorship TEXT, 380 | combination_authorship_year TEXT, 381 | basionym_authorship TEXT, 382 | basionym_ex_authorship TEXT, 383 | basionym_authorship_year TEXT, 384 | name_phrase TEXT, 385 | name_reference_id TEXT REFERENCES reference, 386 | name_published_id_year INTEGER, 387 | name_published_id_page TEXT, 388 | name_published_id_page_link TEXT, 389 | gender GENDER, 390 | gender_agreement BOOLEAN, 391 | code NOMCODE, 392 | name_status NOMSTATUS, 393 | according_to_id TEXT REFERENCES reference, 394 | scrutinizer TEXT, 395 | scrutinizer_id TEXT, 396 | scrutinizer_date TEXT, 397 | reference_id TEXT[], 398 | extinct BOOLEAN, 399 | temporal_range_start TEXT, 400 | temporal_range_end TEXT, 401 | environment ENVIRONMENT[], 402 | link TEXT, 403 | name_remarks TEXT, 404 | remarks TEXT 405 | ); 406 | 407 | CREATE TABLE name_relation ( 408 | name_id TEXT NOT NULL REFERENCES name_usage, 409 | related_name_id TEXT REFERENCES name_usage, 410 | source_id TEXT, 411 | type NOMRELTYPE NOT NULL, 412 | reference_id TEXT REFERENCES reference, 413 | remarks TEXT 414 | ); 415 | 416 | CREATE TABLE type_material ( 417 | id TEXT PRIMARY KEY, 418 | source_id TEXT, 419 | name_id TEXT NOT NULL REFERENCES name_usage, 420 | citation TEXT, 421 | status TYPESTATUS, 422 | institution_code TEXT, 423 | catalog_number TEXT, 424 | reference_id TEXT REFERENCES reference, 425 | locality TEXT, 426 | country CHARACTER(2), 427 | latitude DECIMAL, 428 | longitude DECIMAL, 429 | altitude INTEGER, 430 | host TEXT, 431 | sex SEX, 432 | "date" TEXT, 433 | collector TEXT, 434 | associated_sequences TEXT, 435 | link TEXT, 436 | remarks TEXT 437 | ); 438 | 439 | CREATE TABLE distribution ( 440 | taxon_id TEXT NOT NULL REFERENCES name_usage, 441 | source_id TEXT, 442 | area TEXT NOT NULL, 443 | area_id TEXT, 444 | gazetteer TEXT, 445 | status DISTRIBUTIONSTATUS, 446 | reference_id TEXT REFERENCES reference, 447 | remarks TEXT 448 | ); 449 | 450 | CREATE TABLE media ( 451 | taxon_id TEXT NOT NULL REFERENCES name_usage, 452 | source_id TEXT, 453 | url TEXT NOT NULL, 454 | type MEDIATYPE, 455 | format TEXT, 456 | title TEXT, 457 | created TEXT, 458 | creator TEXT, 459 | license TEXT, 460 | link TEXT, 461 | remarks TEXT 462 | ); 463 | 464 | CREATE TABLE treatment ( 465 | taxon_id TEXT NOT NULL REFERENCES name_usage, 466 | source_id TEXT, 467 | document TEXT NOT NULL, 468 | format TREATMENTFORMAT 469 | ); 470 | 471 | 472 | CREATE TABLE vernacular_name ( 473 | taxon_id TEXT NOT NULL REFERENCES name_usage, 474 | source_id TEXT, 475 | name TEXT NOT NULL, 476 | transliteration TEXT, 477 | language CHARACTER(3), 478 | preferred BOOLEAN, 479 | country CHARACTER(2), 480 | area TEXT, 481 | sex SEX, 482 | reference_id TEXT REFERENCES reference, 483 | remarks TEXT 484 | ); 485 | 486 | CREATE TABLE species_estimate ( 487 | taxon_id TEXT NOT NULL REFERENCES name_usage, 488 | source_id TEXT, 489 | estimate INTEGER NOT NULL, 490 | type ESTIMATETYPE NOT NULL, 491 | reference_id TEXT REFERENCES reference, 492 | remarks TEXT 493 | ); 494 | 495 | CREATE TABLE taxon_property ( 496 | taxon_id TEXT NOT NULL REFERENCES name_usage, 497 | source_id TEXT, 498 | property TEXT NOT NULL, 499 | value TEXT NOT NULL, 500 | reference_id TEXT REFERENCES reference, 501 | page TEXT, 502 | ordinal INTEGER, 503 | remarks TEXT 504 | ); 505 | 506 | CREATE TABLE species_interaction ( 507 | taxon_id TEXT NOT NULL REFERENCES name_usage, 508 | related_taxon_id TEXT REFERENCES name_usage, 509 | source_id TEXT, 510 | related_taxon_scientific_name TEXT, 511 | type SPECIESINTERACTIONTYPE NOT NULL, 512 | reference_id TEXT REFERENCES reference, 513 | remarks TEXT 514 | ); 515 | 516 | CREATE TABLE taxon_concept_relation ( 517 | taxon_id TEXT NOT NULL REFERENCES name_usage, 518 | related_taxon_id TEXT REFERENCES name_usage, 519 | source_id TEXT, 520 | type TAXONCONCEPTRELTYPE NOT NULL, 521 | reference_id TEXT REFERENCES reference, 522 | remarks TEXT 523 | ); 524 | -------------------------------------------------------------------------------- /data/treatments/Hind2013.txt: -------------------------------------------------------------------------------- 1 | 763. GUNDELIA TOURNEFORTII 2 | Compositae 3 | Nicholas Hind 4 | Summary. Gundelia tournefortii L. (Compositae: Gundelieae) is described and illustrated, and its strange inflorescence morphology highlighted. The history of the discovery of this fascinating plant is covered from one of the first natural history collections made in the late 16th century in the Levant. The problematic taxonomy of this genus is discussed, both supragenerically and infragenerically. The species has very rarely been cultivated throughout its recent history, making a commentary on its cultivation and propagation a little difficult. The wide range of uses cover a history dating back at least 10,000 years, from the Neolithic sites of Iraq and Turkey, to its present day usage in the region. The importance of herbarium specimen data, as well as literature, for the ethnobotany of taxa is emphasized. A possible biblical connection is commented on in relation to the Shroud of Turin. 5 | The subject of this plate is one of the more unusual plants to have appeared in Curtis's Botanical Magazine in that it has a demonstrable history of use of over 10,000 years, is still very rarely cultivated, and has potential links to the dawn of Christianity, via the Shroud of Turin; it also has one of the most complicated inflorescence structures in the family, and an interesting taxonomy. The plant is Gundelia tourneforti L. (Compositae: Gundelieae). 6 | 16TH CENTURY HISTORY Gundelia tournefortü, as we now know it, was first recorded in one of the earliest natural history collections made in the Near East by the German physician, botanist and traveller, Leonhard Rauwolf also as Leonhart Rauwolff] (1535–1596). His voyage, between 1573 and 1575, was principally made to search for supplies of herbal medicines, the botanical collections (which he glued upon paper very carefully ... with great and peculiar care' ... 'so that they are to be seen in their natural colours so exact, as if they were green.' - translations from Ray, 1738) preserved in bound quarto-sized, and one folio, herbaria (now in Leiden). A description of these volumes is provided by Legré (1900), covering the French collections, based in part upon Saint-Lager's account (Saint-Lager, 1885: 69–85), who also detailed the 338 specimens in the folio volume (the 'Vierte Kreutterbuch...), 7 | 114 8 | 9 | most collected during Rauwolf's Levant voyage - page number 251 is the specimen of Gundelia, from 'Alep. Baibout en Anatolie'. Rauwolf's views on the countries and cities, peoples and religion, and plants were recorded in the German Aigentliche beschreibung der Raiß, so er vor diser zeit gegen Auffgang inn die Morgenländer (Rauwolf, 1583) – 'A true account of the voyage to the Levant ... The Morgenländ (literally the *land of the morning") of the title is the Levant in English (from the French levant = ‘rising' i.e. where the sun rises), and Bilād ash-Shām 10 | in Arabic (دال بدم اشلام 11 | The Levant is an archaic English word, according to the New Oxford Dictionary of English, dating from the late 15th century, and is defined as the 'eastern part of the Mediterranean with its islands and neighbouring countries'. It is usually considered to include modern Lebanon, Syria, Jordan, Israel, Palestine, Cyprus, Hatay Province and parts of southern Turkey, northwestern Iraq and the Sinai Peninsula. The Levant portion of Rauwolf's expedition began in Tripoli, Lebanon, to the 'mighty city' (translated as the 'potent city' in Ray, 1738) of Aleppo, Baghdad and Mosul, returning to Tripoli and ending with a trip to Jerusalem. Rauwolf left Tripoli on November 9, 1573 bound for Aleppo (probably arriving later that month), spending several months in and around the city. Chapter VI of his book was 'Of the situation of the potent city of Aleppo; of the buildings therof, and also of the delicate fruits and fine plants, that grow there, within and without gardens'. [Translation from Staphorst in Ray, 1738]. 12 | 17TH CENTURY HISTORY Rauwolf's Aigentliche beschreibung der Rail was well illustrated with woodcut illustrations, including Gundelia, whose plate was effectively repeated in Bauhin et al.'s Historia plantarum universalis (1650–1651) under the name Hacub sive Silybum quibusdam. The plant was found in the area around Aleppo, in Syria. Bauhin et al.'s short description appears to have been taken straight from Rauwolf's account and suggested the plant was known to Dioscorides as Silybum, and to Serapio (Joannis Filii Serapionis or Yúhānnā Ibn Serapion; author of a 9th Century work called 'Practica ... an ancient materia medica as Hacub Alcardeg; the Arabic KA'UB or A'KUB is still in use today. It should, however, be noted that Rauwolf (1583), Bauhin et al. 13 | 14 | 15 | 117 16 | (1650-1651) and Ray (1738) were incorrect in declaring that this plant was Dioscorides' Silybum - that plant is now considered to be Silybum marianum (L.) Gaertn. (the MILK THISTLE). 17 | Based on Rauwolf's description Morison (1699: 167 - albeit in a work published long after he was dead), although admitting he had not seen the plant, provided a new name - Eryngium Syriacum foliis Chamaeleontis longis spinosis – based on the apparent similarity of the synflorescence to the inflorescences in several species of Eryngium L. [Umbelliferae). 18 | 18TH CENTURY HISTORY A little while after the publication of his seminal work, Eléments de botanique, ou méthode pour reconnaitre les plantes (1694), Joseph Pitton de Tournefort (1656-1708) travelled together with the German physician and botanist Andreas von Gundelsheimer (1668-1715) (eventually a physician to the Prussian royalty) and the painter Claude Aubriet (1665-1742), who became the principle artist at the Jardin des Plantes, Paris (where Tournefort had earlier been appointed professor of botany in 1683). Their expedition, between 1700 and 1702, was to travel through Greece, Turkey, Armenia (which included parts of present day Turkey) and Persia. Tournefort's account of the expedition was published posthumously as Relation d'un voyage du Levant (de Tournefort, 1717), the second volume of which appeared in English (de Tournefort, 1718). Tournefort's prose in his 19 | Voyage into the Levant is worth repeating here: 20 | Lett. VI. p. 187: 'We were oblig'd then to leave Baibout the 11th of June. We were told the Bassa' had pardoned all the Prisoners. Many in our Caravan commended his Clemency; others blamed him for not making some Examples. The Rogues were made to pass in review; and if one may judge by their Looks, most of them seem'd at least to deserve the Wheel. This day we gave a name to one of the finest Plants in the whole Levant; and because M. Gundelscheimer discover'd it first, we agreed that in Justice it ought to bear his Name. By ill fortune we had nothing but Water to celebrate the feast, but this agreed the better with this Ceremony, for the Plant grows no where but in dry stony places. The Bassa's Musick struck up just at the instant, which 21 | T= Pasha 22 | 118 23 | 24 | 25 | we took for a good Omen: yet we were a long while before we could find a Latin Name equivalent to that gallant Man's. We concluded that the Plant should be call'd Gundelia'. 26 | Tournefort's copperplate engraving (de Tournefort, 1718: plate 103 - see fig. 1), is named as Gundelia Orientalis, Acanthi aculeati folio, Capite glabro Coroll. Inst. Rei herb. 15, a polynomial cited by Linnaeus (1753: 814). Linnaeus celebrated both of the botanists on the expedition when he created the binomial for the plant about which Tournefort had written so glowingly. 27 | MORPHOLOGICAL INTRIGUE 28 | That Gundelia toumefortii resembles a generic thistle is in little doubt; Rauwolf referred to it, as did de Tournefort (1718: 183), and all authors since. However, Tournefort's eye for detail determined aspects of the “Tops like those of the Fuller's Thistle' were strange. He noted that the 'Flowers are truly Fleurons' and the 'Embryos are divided into as many Boxes or Apartments as there are Fleurons. Most of these Embroy's (sic!) prove abortive except the middlemost, which pressing the others makes them perish'. The terminology may be somewhat strange, but Tournefort had noticed something that has confused botanists until the late 1980s! Tournefort's "Tops' are what we now call third-order syncephalia (a synflorescence in my terminology!), also found in Platycarpha Less. (Tribe Platycarpheae), Triplocephalum O. Hoffm. (Tribe Inuleae) and Lagascea Cav. (Tribe Heliantheae). His 'Fleurons are now called florets; 'Embryos' are what we would probably term disseminules, however the structure is more complicated as will be seen below. 29 | In his Encyclopédie méthodique Lamarck (1789) likened the thistle-like leaves to those of the 'Chardon' = Cynara cardunculus L.) or 'Carline (= Carlina vulgaris L.), the habit and latex to that of 'Scolyme' = Scolymus L., probably S. maculatus L.) and form of the synflorescence was likened to those found in 'Cardère' = Dipsacus L.) or "Panicaut' and 'Panicaut des Alpes' (= Eryngium L. and Eryngium alpinum L.). 30 | Cassini (1821), in his continuing treatment of the Composées for Cuvier's Dictionnaire, recognized the complexity of the flower heads linking it with analogous genera such as Corymbium L. [1 floret per capitulum; Tribe Corymbieae), Lagascea Cav. [1 floret per capitulum, rarely 2-3; Tribe Heliantheae), Rolandra Røttb. [1 31 | 32 | 33 | 119 34 | foret per capitulum; Tribe Vernonieae) and Elephantopus L. [2-4 florets per capitulum; Tribe Vernonieae), but regretted somewhat that he'd only been able to look at the genus based on very old material. However, Cassini also credited Gaertner (1791), and a quick examination of Gaertner's description showed that he was aware of 'Flosc. marginales in singulo lobulo masculi, steriles; centralis, unus aut geminus, androgynus, fertilis. Semina lobulis immersa, coronata pappo substipitato, ...' Gaertner's tab. 163 was an excellent, very accurate representation of the synflorescences (see Fig. 2). 35 | Unfortunately, the whole flowering structure has been contin uously misinterpreted (e.g. Kupicha, 1975; Burtt, 1977; Bremer, 1994; Vassilczenko, [1961] 2000 [in English]). Most authors interpreted the disseminule, from which the whole spherical, or Teasel-like, synflorescence appeared to be constructed, was the primary capitulum when in reality it is nothing of the sort. The disseminule is in fact a secondary capitulum derived from a group of single-flowered primary capitula, the outer four or six subsidiary capitula with functionally male florets (acting initially as "pollen donors, and then as 'protective structures' - Claßen-Bockhoff, 1996: 150) surrounding a central capitulum with a perfect fertile 36 | et). The secondary heads are released as the functional dispersal units, or disseminules, admirably illustrated by Vitek et al. (2010). Gundelia 'is probably without parallel in the whole family because of this structure (Claßen-Bockhoff, 1996: 150). 37 | TAXONOMY AND NOMENCLATURE 38 | INFRAFAMILIAL CLASSIFICATION. The earliest accepted infrafamil ial placement of Gundelia appears to be that of Cassini (1821) when it was placed in the tribe Vernonieae, along with similar genera (see above). However, he later specifically placed it in to the 'Ver noniées-Rolandrées (Vernonieae-Rolandreae)' (Cassini, 1828: 345), later formalized as the subtribe Rolandrinae by Lessing (1831: 105). Although Cassini had recognized the complex synflorescence, and described it under Gundelia, he later had a complete change of mind and simply overturned Linnaeus (Cassini, 1828: 344), creating Gundelsheimera in its stead! This generic name is illegitimate. 39 | Within half a century, the tribal position of Gundelia was cast into doubt when Bentham & Hooker (1873: 211) placed 40 | 41 | 42 | 121 43 | A useful summary of the ins and outs of the genus was provided by Karis et al. (2009) in a summary table of 'Different classifications of Arctotidae', noting that Bremer (1994), based on cladistic analyses, placed it in the Arctotideae subtribe Gorteriinae Benth. & Hook.f., although it was excluded by Karis [2006] (2007); Jeffrey [2006] (2007): 199) has since modified its position, placing it in the tribe Gundelieae DC. ex Lecoq & Juilllet. 44 | The most recent proposed position, which is one I do not accept, is alongside Scolymus L. (Karis et al., 2001), Catananche L. and Hymenonema Cass., in the 'Cichorieae subtribe Scolyminae Less.' (Kilian et al., 2009). Gundelia would stand out in this tribe in that it possesses an actinomorphic lobed corolla, unlike the remainder of the tribe Lactuceae (= Cichoricae), and although it possesses latex, several other genera, in a diversity of tribes also do. I am happy to accept Jeffrey's views on the position of Gundelia, in its own tribe. 45 | HOW MANY SPECIES ARE THERE? A PROBLEM OF COROLLA COLOUR? The earliest descriptions of 'gundelia' referred to the corollas as cream or flesh coloured (Rauwolf, 1583) and purplish (de Tournefort, 1718), and Linnaeus (1753) clearly recognized both but merely placed the purple corolla'd plants under his (unnamed) variety B, the genus being monospecific. However, there is a common problem with herbarium material in that the corollas close up so the inner face of the corolla lobes is not visible, and is often not apparent when opened – plus there are often no colour notes on the collecting labels of any merit. Distinguishing the colour/s of the corollas is often difficult in dry material. Bornmüller (1939) formally recognized plants with the purplish corollas as forma purpurascens; earlier descriptions of infraspecific taxa solely relied up leaf characters regardless of corolla colour. 46 | Kupicha (1975) and Rechinger (1989), in their flora accounts, and Bremer (1994) and Jeffrey [2006] (2007) in their generic treat ments, treated Gundelia as monospecific and the apparently wide variation in corolla colour unrelated to gross morphology. Al-Taey & Hossain (1984) studied material in some detail and recognized that Bornmüller's and Tournefort's variants were in fact a second species, G.rosea Hossain & Al-Taey. Vitek et al. (2010) studied much material, 47 | 124 48 | 49 | 50 | especially live, in nature, and came to the conclusion that there are perfectly recognisable units that can be treated as separate species; the genus now has at least three, possibly four species! The typification of the genus by Vitek & Jarvis (2007) anchored the cream/yellowish corolla'd plants as typical Gundelia tournefortii, a corolla colour that can be found throughout the species distribution - alongside that of the darker corollas. 51 | Whilst there is little doubt that there is a significant variation in corolla colour I have one observation, and that stems directly from the writing of this article. Işık Güner's colour plate is from material collected in Turkey (from near Ankara), a considerable distance from the nearest similar coloured corolla'd taxon provided with a name by Vitek et al. (2010) - Gundelia aragatsi Vitek et al., Işık Güner's plant is most certainly G. tourneforti. Clearly, much more detailed studies are still needed into this complex. 52 | THE SHROUD OF TURIN One of the most startling recent findings is that pollen of Gundelia tournefortii was found on the Shroud of Turin during investigations in 1998. Danin (1998) and Danin & Baruch (1998) reported the palynological analysis of pollen by Dr Uri Baruch, of 'sticky tape' samples taken from the Shroud by Dr Max Frei in 1973 and 1978. A total of 313 pollen grains had been examined, 91 pollen grains (29%) were of Gundelia, suggesting that with so much pollen (> 10 grains in an area of 5 cm?) flowering plants were probably placed on the Shroud. Natural pollen rain in Israel rarely produced more than one or two grains of Gundelia. Gundelia flowers from February in Israel (in the warm semi-desert areas) through to May (in Jerusalem) suggesting a timeframe during which they may have been placed on the Shroud. Denin even pinpointed the Shroud's locality as coming from an area 10-20 km east and west of Jerusalem as demonstrated by the pollen, and access to live plants shown in the images of plants captured from the Shroud (which included one of a synflorescence of Gundelia seen close to the right shoulder); the date probably in the spring between March and April. The presence of Zygophyllum dumosum Boiss. leaves made this hypothesis probable because of the limited distribution, seasonality of leaf growth, and overlapping distribution with Gundelia. 53 | 54 | 55 | 125 56 | Possible religious connections are not reserved to just the Shroud. Indeed some scholars think that the tumbleweed referred to in Psalms 83:14 is none other than Gundelia tournefortii (Zohary, 1982; Duke et al., 2008; Musselman, 2012). The possibility of Gundelia being a contender for the Crown of thorns' is somewhat more tenuous. 57 | CULTIVATION. As far as can be determined, Lamarck (1789: 60) cited both 'André Michaut' (sic!] [= André Michaux (1746-1803), French botanist and explorer of Iran (1782-1785), North America (1785-1796) and later to Madagascar (1800-1805), where he died] and de la Billardiere (sic!] [= Jacques Julien Houttou de Labil lardière (1775-1834), French explorer and botanist of the Near East (1786)] as both having sent seeds to the Jardin du Roi from their trav els in the Levant. Since the late 18th century, Gundelia tournefortii has been grown intermittently at the École de Botanique, in the Jardin du Roi, Paris, and was recorded in the mid-19th century (Verlot, 1864). Seed proved slow to germinate, young plants were planted out out side but required a light, well-drained soil, and frost protection (using a cloche) during the winter. Introductions by the French botanical explorer Balansa (1825-1891) in the late 1850s, from 'Asia Minor, took some 3 years to establish and begin flowering, putting on little growth during the first year – having taken 2 years to germinate. 58 | Plants are best grown in the rock garden, or on raised beds, and given good drainage in a stony or gritty soil in full sun and the species is probably hardy to about -15°C/5°F (see Jeffrey, 1992). 59 | AVAILABILITY, Gundelia is not currently listed on the Royal Horticul tural Society Plant Finder web pages, and has only been listed from two sources since 1999 (Lord, 1999; 2004) in the printed version. It does not appear in the RHS Encyclopaedia (RHS, 1996), but was mentioned by Jeffrey (1992). 60 | PROPAGATION. Natural propagation of Gundelia is hinted at in one of the vernacular names, TUMBLEWEED. A note by Harris on a herbarium specimen in Kew (R. W. Harris W1451) indicates how the old inflorescences become tumbleweeds, and how the achenes are distributed 61 | The whole inflorescence loosens first below ground level, at a discoloured section, included in the specimens, and blows away. Several inflorescences were found at a distance from the plants; others, still on the plants, broke off at a touch'. 62 | 126 63 | The Board of Trustees of the Royal Botanic Gardens, Kew 2019. 64 | Gillet provided a startling account (see USES) of seeing them distributed by whirlwinds and carried hundreds of feet into the air! In this way long-distance dispersal of the disseminules is guaranteed! 65 | In cultivation a little more purpose is required, but regrettably information is somewhat lacking. When available, Gundelia is best propagated from seed sown in the spring in a cold frame. When large enough seedlings should be pricked out into individual pots. Verlot's comments, dating from the mid-19th century (Verlot, 1864), suggest growth is very slow at first – after a very protracted germination! The results of Shibli et al. (2009), albeit under laboratory conditions, suggest that the highest germination percentages (nearly 90%) are obtained by soaking the disseminules in a solution of 250 ppm GA3 for 6 hours, and placing them in an seed tray containing a 1:1 mix of peat: Perlite, under intermittent mist at 24 +2°C. The germination percentages were obtained after 4 weeks. 66 | Jeffrey (1992), in referring propagation to that under Carduncellus spp., also suggests division, but I have not been able to find any references – anywhere - to the success rate or methodology. 67 | Gundelia tournefortii L., Sp. Pl.: 814(1753). Types: 'Habitat in Armenia, Syria'. Lectotype (Vitek & Jarvis in Ann. Nat. Hist. Mus. Wien, 108B: 269, 2007): [icon) "Aleppo) Rauwolf (1583): t. 74.'[ 'Silybum dioscoridis s. Hacub alcardeg scrapionis' in Rauwolf, Aigent. Beschr. Morgenl.: 74, t. 74 (1583)'.] Epitype (selected by Vitek & Jarvis, 2007: 269): "(Aleppo), Rauwolf, hort, sicc. 81', L. 68 | Gundelia glabra Mill., Gard. Dict., ed. 8, n. 2 (1 768). Type: 'This plant was discovered by Dr. Gundelscheimer (sic!), in company with Tournefort, near Baibout in Armenia, but has since been found growing naturally in several places in the Levant, where it is generally found in dry strong land'. Holotype: ?BM. Note: There is material in P(00670374) that is most probably an isotype (bearing the Latin polynomial provided by Miller, and came via Vaillant's herbarium); it is a Tournefort collection from Armenia, and the material is named G. toumefortii L. 69 | Gundelia toumefortii L. var, glabra (Mill.) DC., Prodr. 5: 88 (1836). 70 | Gundelia tournefortii L. var. araneosas DC., Prodr. 5: 88 (1836), nom. illegit. effectively based on G. toumefortri L. 71 | Gundelia tournefortü L. [unranked/var.] B tenuisecta Boiss., Fl. Orient. 3: 421 (1875). Types: "[Turkey:] Hab. in monte Berytdagh Cataoniae 8000 (Haussknecht!), Syria: ] ad Gebel Antar prope Damascum (Gaillardor!)'. Syntype: Haussknecht s.n., JE(00015292). Syntype: Gaillardot 336, JE(00015293) 72 | delia tourneforti L. var. asperrima Trautv.. Acta Horti Petrop. 4/1): 146 (1876). Type: 'In Turciae districtu Erzerum, in montibus Palänteken, altit. 6300' (Radde)'. Holotype: LE. 73 | The Board of Trustees of the Royal Bolank Gardens, Kew 2013, 74 | 127 75 | Gundelia toumefortu L. var, armata Freyn & Sint., Oesterr. Bot. Zeit. 42(5): 168 (1892). Type: Turkey:) 'Armenia turcica. Egin in monte Hodschadur-Dagh die 3. junii 1890 leg. Sintenis (Exsicc. no. 2577)'. Holotype: ?LD(1045813, 1051142); isotypes: BR(5317943, 5318056), JE (00015289 - a single leaf, 00015290), W(0024856, 1891-0000229). 76 | Gundelia tenuisecta Freyn & Sint., Oestert. Bot. Zeit. 42(5): 168 (1892). Type: Armenia turcic, Egin: prope Szanduk die 26. majo 1890 leg. Sintenis (Exsicc. no. 2429Y. Holotype: ?LD(1064262, 1065798): isotypes: JE(00015291). Note: (1) This appeared without any indication that it was based on Boissier's variety, a position also apparently held by Bornmüller (1939: 197), although bemusingly he added 'übergehend'. (= temporarily) at the end of his comment; (2) In the protologue Freyn clearly stated Dimensiones (ex unico specimine) ...' which is odd considering there are two sheets in LD (both of a flowering specimen including the apex of the rootstock, and both ex herb. Sintenis) and a duplicate in JE. 77 | ILLUSTRATIONS. Selected examples include: Pre-Linnacan - Rauwolf (1583: t. 74); de Tournefort (1718: plate 103) [fig. 1]. Post Linnaean – Gaertner (1791: Tab. 163) [fig. 2]; Verlot (1864: 330); Rechinger (1989: tab. 75, 76); Blamey & Grey-Wilson (1993: 146-1919); Boulos & Hind (2002: Plate 32, p. 144); Burtt (2002: 141-143); Tohmé & Tohmé (2007: 83); Vitek et al. (2010: Figs 2-5). 78 | DESCRIPTION. Stout perennial herb, 20-100 cm tall, old stems becoming a tumbleweed when dry; roots, stems and leaves with milky latex; root stock woody, vertical, to 4cm diam., neck usually clothed in remains of old leaf bases. Stems erect, sometimes branched, glabrous or hairy to densely hairy. Leaves alternate, sessile or base decurrent with spiny wings, lower most leaves 7-302-42) x 4-16(-21) cm, decrescent above, lamina lanceolate to lanceolate-elliptic, pinnatifid to two-pinnatisect, strongly spiny-dentate, uppermost bracteate/involucrate, venation prominent, primary and secondary venation whitish, midrib sometimes purplish, lamina glabrous or thin arachnoid pubescent and usually glabrescent. Inflorescence a solitary dense globular to ovoid third-order synflorescence, 2-5 x 2-4cm, of few-headed aggregations of single flowered capitula (subtended by a single spiny bract and two subsidiary bracts) on a spherical secondary receptacle, synflorescence bracts spiny, ovate-acuminate scarcely exceeding or markedly exceeding synflorescence, arachnoid pubescent throughout, often glabrescent, apices glabrescent or glabrous, prolonged into hard, flattened spine to 5-7 cm long, spine often brownish-purple towards base. Primary aggregated capitula (forming a secondary capitulum or disseminule) 7-17 mm long, containing 5-7 (possibly more) primary capitula, central and subsidiary capitula single-flowered, homogamous and discoid, floret of central capitulum hermaphrodite and functionally female, subsidiary capitula with functionally male florets. Corollas 7-10 (-13) mm long, rusty brown, brownish purple or yellow outside, cream to bright or pale yellow, sometimes almost greenish, inside, very rarely white (Coode & Jones 546A); corolla lobes spreading, narrowly lanceolate, 3-4 mm long x 1 mm, glabrous inside; anther cylinder 4-6 mm long, yellow (usually darker than corolla lobes) or brownish; style arms brownish, Fruit complex or disseminule appearing as a turbinate cupule, obovoid to 79 | 128 80 | The Board of Trustees of the Royal Botanic Gardens, Kew 2019. 81 | GALGAL (literally a wheel or whirlwind, but can refer to quite a number of other plants!), TUMBLEWEED, TUMBLE THISTLE, SILIFA (Greek; Della et al., 2006). 82 | CONSERVATION STATUS. If considered in the broadest concept Gundelia toumeforti is Not Threatened. Locally, however, the plant has been recorded as Endangered - Cyprus (Tsintides et al., 2007), where it was recorded as EN: Blabi-v) + 2ab(i-v), because of few known localities, relatively few individuals, land clearance, herbicide use, and especially over-collection of edible parts. It was declared as possibly extinct in at least three locations where it had been recorded in the past. In Israel only collection for private consumption is now permitted. Clearly, continued pressures (predominantly exploitation for food) on natural populations may well threaten the species in some arcas and a reassessment is certainly needed in many countries. 83 | USES – FOOD, DRINK AND FODDER, ETC. 84 | The varied uses to which A'KUB (Gundelia tournefortii, and most probably the other species) have been put has been documented in summary by Lev-Yadum & Abbo (1999). However, notes of first hand observation are always useful to supplement literature records and its worthwhile covering the varied uses of these remarkable plants here. A direct comparison, spanning nearly three centuries, is worth making. 85 | Ray (1738: 49) provided a translation of Rauwolf's account (from his visit to the ancient city of Aleppo, in northern Syria), saying 86 | 'The other sort is also very plentiful, and is found in dry and rough places, which the inhabitants to this day, with Serapio, call Hacub, whereof he maketh mention in his 295th chapter, under the name of Hacub Alcardeg, whereof they cut in the spring the young shoots or sprouts, that grow round about it, boil and eat it as we do Asparagus, corruptly call'd Sparrowgrass; the whole plant is very like our Carlina, only this hath bigger, higher and more prickly heads, whereon appear flesh-coulour'd flowers. It being that it is every way like it, and that also the root hath the same virtue, for if you steep it in water, and drink of it, it maketh you vomit and fling up: therefore I am of opinion, that without doubt it must be the true 87 | Silybum Diofcorides; ... Herbarium specimen labels, and other associated notes attached to the sheets are frequently an excellent source of information, often direct from locals when the plant was collected, or direct observation/s 88 | The Bard of Trustees of the Royal Botanic Gardens, Kew 2013. 89 | 131 90 | by the collector. Collections of Gundelia in the Herbarium at Kew are no different. The labels of Rawi & Gillett 7571 (sheet 1), and Rawi & Gillett 10577, have been profusely annotated by Jan Gillett (1911-1995) in his inimitable style covering many of the uses, and peculiarities of Gundelia tournefortii. Gillet's note on the former reads: 91 | HULLE 92 | FLE 93 | “This plant is characteristic of moist type steppe and Quercus degilops where coppiced. The young shoots are eaten as a delicacy like asparagus and are brought to Baghdad market from the north. The fruits are also eaten as nuts, the spines being first singed off. They are also brought to Baghdad market. The mature foliage is gathered together as fodder in spite of the spines'. Of the latter, which duplicates part of Rawi & Gillett 7571 some additional details are provided: '... The hard inflorescences each contain a single fruit, like a nut and these form an article of commerce reaching the bazaars in Baghdad. The old dry foliage, in spite of the spines is collected as winter fodder. The fruiting inflorescences are distributed by wind devils (whirlwinds). I have seen them carried hundreds of feet into the air'. 94 | FLIELU 95 | Jan Gillet's notes summarize, from his first hand experiences, many of the uses of Gundelia, but it is worth covering some in a little more details. 96 | The young shoots are clearly a delicate vegetable throughout much of gundelia's range. The clipping season for G. tourneforti is during the spring (January to February in Israel and Palestine) but previous commercial exploitation (mentioned by Gillet for Iraq) has now led to legal restrictions in Israel so that only collection for personal use is allowed. - See CONSERVATION STATUS above 97 | Clearly, rural communities are still using Gundelia as a vegetable in other parts of its range. Ruckšāns (2007: 318 & plate 265) shows a 'Kurdish farmer' demonstrating how to find food in the mountains - an interesting diversion in a book on bulbous plants, and Gundelia isn't even in the index! The farmer demonstrated how to strip the leaves off and opened up the core of the stem' providing a source of refreshment - but not to eat every day. 98 | The young synflorescences have a rich flavour apparently some what similar to artichoke hearts (Cynara cardunculus). It is considered a high quality wild vegetable upgrading salads and warm vegetarian side dishes and Davis 3456 indicates that the synflorescences are eaten 99 | 132 100 | 101 | 102 | like globe artichokes in Cyprus. The simplest of recipes comes from several sources and indicates trimmed inflorescence initials are cov ered with mincemeat, fried in olive oil and then simmered in a lemon juice based sauce (see Lev-Yadum & Abbo, 1999; Wright, 2001). 103 | Kupicha (1975: 326) noted that a chewing gum (KENGER SAKIZI) is made from the latex, and a coffee substitute (KENGER KAHVESI) is made from the achenes (probably the disseminules) after torrefaction. The reference to chewing gum is inferred from the comments by de Tournefort (1718) referring to the fact that 'All the Plants yields a very sweet Milk, which clots into Grains of Mastick like that of the Carline of Columna'. Adil Güner (pers. comm.) has also indicated that the roots are similarly treated to provide a coffee substitute as well. 104 | The oldest demonstrable use was indicated by Prance & Nesbitt (2005) noting that 'In the recent past mature fruits have also been used as a source of oil. Charred fruits at Neolithic sites in Iraq and Turkey are evidence that oil extraction dates back at least 10,000 years. The potential of Gundelia has been well-demonstrated by Khanzadeh et al. (2012) where the seed oil content of the achenes has been shown to be 22.8%, with the oleic acid and linoleic acid of this oil to be 28 and 54.6% respectively, which puts the oil from Gundelia on a par with other vegetable oils such as soybean, corn, sunflower and sesame oils. This suggests that it would be a potential source of edible oil; the aim is obviously to get a spineless plant! 105 | ACKNOWLEDGEMENTS. The author would like to thank Işık Güner for preparing the colour plate from wild sourced material in Turkey (from near Ankara, at Polatlı), her father Prof. Dr Adil Güner, currently Director of the Nezahat Gökyiğ[g]it Botanik Bahcesi, İstanbul, Turkey, for providing a copy of issue of The Karaca Arboretum Magazine, and to Christine Grey-Wilson in preparing the relevant line drawings from herbarium material many years ago for the Flora of Iraq treatment of the genus. The author would also like to thank Christopher Ryan, Living Collections Department, RBG, Kew, for his colour photographs of more typical G. tournefortzi taken in Iran, and to Martyn Rix for his photograph of Gundelia habitat in Turkey. 106 | REFERENCES Al-Taey, R.A. & Hossain, M. (1984). Studies in Gundelia 1. A new species from 107 | Iraq. 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The Gardeners Dictionary: Containing the Best and Newest Methods 189 | of Cultivating and improving the Kitchen, Fruit, Flower Garden, and Nursery; as Also for Performing the Practical Parts of Agriculture: Including the Management of Vineyards, with the Methods of Making and Preserving Wine, According to the Present Practice of the Most Skilful Vignerons in the Several Wine Countries in Europe, Together with Directions for Propagating and improving, from Real Practices and Experience, all Sorts of Timber 190 | Trees. Ed. 8. J. & F. Rivington, London. Morison, R. (1699). Plantarum Historiae Universalis Oxoniensis pars Tertia seu Herbarum 191 | Distributio nova, per Tabulas Cognitionis & Affinitatis ex Libro Naturae Observata & Delecta, Vol. 3. Published Post Mortem by J. Bobartius. E Theatro Sheldoniano, Oxonii. p. 167, sp. 23. 192 | 136 193 | 194 | 195 | Musselman, LJ. (2012). A Dictionary of Bible Plants. Cambridge University Press, 196 | Cambridge. Norlindh, T.(1977). Chapter 33. Arctoteae - systematic review. In: Heywood, 197 | V.H., Harborne, J.B. & Turner, B.L. (eds). The Biology and Chemistry of the Compositae, Vol. 2. Academic Press, London, New York & San Francisco, pp. 198 | 943-959. Pancro, J.L. & Funk, V.A. (2002). Towards a phylogenetic subfamilial classi 199 | fication for the Compositae (Asteraceae). Proceedings of the Biological Society of Washington 115(4): 909-922. Prance, G.T. & Nesbitt, M. (eds), (2005). The Cultural History of Plants. Routledge, 200 | New York & London. pp. i-vii, 1-452. Rauwolf, L. [also as Rauwolff] (1583). Aigentliche Beschreibung der Raif, so er vor 201 | Diser zeit Gegen Auffgang inn die Morgenländer, Fürnemlich Syriam, Judaeam, Arabiam, Mesopotamiam, Babyloniam, Assyriam, Armeniam u. Nicht Ohne Geringe Mühe und Grosse Gefahr Selbs Volbracht: Neben Vermeldung Etlicher Mehr Garschön Frembden und Außlandischen Gemachsen, Sant iren mit Angehenkten Lebendigen Contarscturen, unnd Auch Anderer Denkwürdiger Sachen, die Alle er Auff Solcher Erkundiget, Gesehen und Observiert Hat Alles in Vier Underschidliche Thail mit Sonderem fleiß Abgethailet, und ein Jeden Weiller in Seine Sondere Capitel, wie dero Innhalt in zü end Gesetztem Register 202 | Züfinden. Leonhart Reinmichel, Launingen. Ray, J. (1738). A Collection of Curious Travels and Voyages, Containing Dr. Leonhart 203 | Rauwolf's Journey into the Eastern Countries, viz. Syria, Palestine, or the Holy Land, Armenia, Mesopotamia, Assyria, Chaldea, &c. Translated from the Original High Dutch by Nicholas Staphorst. And also, Travels into Greece, Asia Minor, Egypt, Arabia Petraca, Ethiopia, the Red Sea, &c. Collected from the Observations of Mons. Belon, Proper Alpinus, Dr. Huntingdon, Mr. Vernon, Sir George Wheeler, Dr. Smith, Mr. Greaves, and Others. To Which are Added Three Catalogues of such Trees, Shrubs, and Herbs, as Grow in the Levant. Ed. 2. Corrected and improved', Vol. 2. Printed for J. Walthoe et al., London. [The title page states "Translated from the 204 | original High Dutch by Nicholas Staphorst."). Rechinger, K.H. (1989). Tribus Arctotideae "Arctoteae" Cass. Gundelia. 205 | In: Rechinger, K.H. (ed.). Flora Iranica. (Flora des Iranischen Hochlandes und der Umrahmenden Gebirge Persien, Afghanistan, teile zon West-Pakistan, Nord-Iraq, Azerbaidjan, Turkmenistan) Compositae VII, Vol. 164. Akademische Druck- u. 206 | Verlangsanstalt, Graz. pp. 107-109 & tab. 75, 76. Royal Horticultural Society (1996). The Royal Horticultural Society - Encyclopedia 207 | of Garden Plants, Vol. A-J. (Revised edition 2003). Dorling Kindersley Limited, 208 | London. Ruckšāns, J. (2007). Buried Treasures: Finding and Growing the World's Choicest Bulbs. 209 | Timber Press, Portland. Saint-Lager, J.B. (1885). Histoire des Herbiers. Baillière et fils, Paris. Shibli, RA, Oweis, D.S., Eriefej, K.I. & Shatnawi, M.A. (2009). In vivo 210 | propagation of Akub (Gundelia troumefortii L.) by seeds. Jordan Journal of 211 | Agricultural Sciences 5(3): 266-272. Tohmé, G. & Tohmé, H. (2007). Illustrated flora of Lebanon. National Council for 212 | Scientific Research, Beirut. 213 | 214 | 215 | 137 216 | de Tournefort, J.P. (1717). Relation d'un Voyage du Levant, Fait par Ordre du 217 | Roi, Contenant l'Hisotire Ancienne & Moderne de plusieurs Isles de l'Archipel, de Constantinople, des Côtes des la Mer Noire, de l'Armenie, de la Georgie, des Frontieres de Perse & l'Asie Mineure, Avec les Plans des Villes & des Lieux Considerables; le Genie, les Moeurs, le Commerce & la Religion des Differens Peuples qui les Habitent; et l'explication des Médailles & des Monumens Antiques. Enrichie de Descriptions & de Figures d'un Grand Nombre de Plantes Rares, de Divers Animaux; et de Plusieurs Observations Touchant l'Histoire Naturelle, Vol. 1. L'Imprimerie Royal, Paris. 218 | [Also reprinted in 1718, La Compagnie, Amsterdam)., Paris. de Tournefort, J.P. (1718). A Voyage into the Levant: Performed by Command of the late 219 | French King. Containing the Ancient and Modern State of the Islands of the Archipelago; as also of Constantinople, the Coasts of the Black Sea, Armenia, Georgia, the Frontiers of Persia, and Asia Minor: with Plans of the Principal Towns and Places of Note; an Account of the Genius, Manners, Trade, and Religion of the Respective People Inhabiting those Parts: and an Explanation of Variety of Medals and Antique Monuments : Illustrated with Full Descriptions and Curious Copper-Plates of Great Numbers of Uncommon Plants, Animals, &c. and Several Observations in Natural History, Vol. 2. Printed for D. 220 | Browne, et al., London. Trautvetter, E.R.A. (1876). Plantarum messes anno 1974 in Armenia a Dre. 221 | G. Radde et in Daghestania ab A. Becker factas. Acta Horti Petropolitani 4(1): 222 | 97-192. Tsintides, T., Christodoulou, C.S., Delipetrou, P. & Georgiou, K. (eds) (2007). 223 | The Red Data Book of the Flora of Cyprus. Cyprus Forestry Association, Lefkosia. Vassilczenko, I.T. (2000). Compositae. Tribes Anthemideae, Senecioneae, and 224 | Calenduleae. In: Schischkin, B.K. & Bobrov, E.G. (vol. eds). Flora of the USSR, Vol. 26. Smithsonian Institution Libraries, Washington. pp. 819-821 [English 225 | translation; original Russian ed. publ. 1961, pp. 861-862). Verlot, B. (1864). Gundelia toumeforti. Revue Horticole 13: 330-331 & fig. 31. Vitek, E., Fayvush, G., Tamanyan, K. & Gemeinholzer, B. (2010). New taxa 226 | of Gundelia (Compositae) from Armenia. Annalen des Naturhistorischen Museums 227 | in Wien, 2009 111B: 85-100. Vitek, E. & Jarvis, C.E. (2007). The typification of Gundelia tournefortii L. (Com 228 | positae). Annalen des Naturhistorischen Museums in Wim, 2006 108B: 267-272. Wright, C.A. (2001). Mediterranean Vegetables: A Cook's ABC of Vegetables and their 229 | Preparation in Spain, France, Italy, Greece, Turkey, the Middle East, and North Africa with more than 200 Authentic Recipes for the Home Cook. Harvard Common Press, 230 | Boston, Massachusetts. pp. 181-182. Zohary, M. (1982). Plants of the Bible: A Complete Handbook. Cambridge University 231 | Press, Cambridge. 232 | 138 -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | # COL Data Package (ColDP) Specification 3 | The recommended exchange format for data to and from COL ChecklistBank 4 | is a tabular text format with a fixed set of files and columns. 5 | 6 | * [Status & Versioning](status-versioning) 7 | * [Schema](#schema) 8 | * [Archive Files](#archive-files) 9 | * [Default Values](#default-values) 10 | * [Dataset Metadata](#metadata) 11 | * [Document Changes](#changes) 12 | * [Raw Source Data](#raw-source-data) 13 | * [Identifiers](#identifiers) 14 | * [Format Comparison](#format-comparison) 15 | * [Publishing Guidelines](/docs/publishing-guide.md) 16 | * [Best Practises](#best-practices) 17 | 18 | ## Status & Versioning 19 | 20 | ### Latest Stable Release 21 | **Version 1.2 of ColDP has been released on [October 30th 2025](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.2.0)**. 22 | 23 | 24 | ### Development Branch 25 | **Version 2.0 of ColDP is still under development** 26 | and new fields are marked as such in the documentation below. 27 | 28 | There is no guarantee that these fields might still change until the version is released. 29 | [ChecklistBank](https://www.checklistbank.org) tries it's best to support already all new features, so it can be used already. 30 | 31 | 32 | ### Versioning 33 | ColDP adheres to [semantic versioning](http://semver.org/): 34 | - **patch** changes (1.0.x) do not alter the exchange schema at all. No more fields or entities will be renamed, removed or added. The documentation and enumeration of values are allowed to change. 35 | - **minor** changes (1.x.0) preserve backwards compatibility. Fields or entities can be added, but not renamed or removed. 36 | - **major** changes (x.0.0) break backwards compatibility. Fields or entities can be renamed, removed, added or changed in semantics. 37 | 38 | ### History 39 | All [changes](CHANGES.md) are documented since the initial 1.0.0 release. 40 | 41 | - ColDP 1.2.0, [October 30, 2025](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.2.0). 42 | - ColDP 1.1.0, [September 26, 2024](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.1.0). 43 | - ColDP 1.0.1, [April 7, 2022](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.0.1). 44 | - ColDP 1.0.0, [October 25, 2021](https://github.com/CatalogueOfLife/coldp/releases/tag/v1.0.0). 45 | 46 | 47 | ## Schema 48 | 49 | The ColDP format is a single ZIP archive that bundles various delimited text files described below together with a metadata.yaml file 50 | providing basic metadata about the entire dataset. 51 | Each file holds records for the same class of things shown in this diagram with columns explained in more detail in the [Data File section](#data-file-columns). 52 | It aligns closely to the Frictionless Tabular Data Package for which we provide a [descriptor](http://api.catalogueoflife.org/datapackage). 53 | 54 | ![schema](docs/schema.png) 55 | 56 | For simpler sharing ColDP also offers a merged [NameUsage](#nameusage) entity, 57 | which combines fields from the [Taxon](#taxon), [Synonym](#synonym) and [Name](#name) entity: 58 | 59 | ![NameUsage schema](docs/schemaNU.png) 60 | 61 | ## Archive Files 62 | A ColDP archive consists of several files in a folder. 63 | These are either data files corresponding to the schema diagram above: 64 | 65 | - [Name](#name) 66 | - [Author](#author) 67 | - [NameRelation](#namerelation) 68 | - [Taxon](#taxon) 69 | - [Synonym](#synonym) 70 | - [NameUsage](#nameusage) 71 | - [TaxonProperty](#taxonproperty) 72 | - [TaxonConceptRelation](#taxonconceptrelation) 73 | - [SpeciesInteraction](#speciesinteraction) 74 | - [SpeciesEstimate](#speciesestimate) 75 | - [Reference](#reference) 76 | - [Reference JSON-CSL](#reference-json-csl) 77 | - [Reference BIBTEX](#reference-bibtex) 78 | - [TypeMaterial](#typematerial) 79 | - [Distribution](#distribution) 80 | - [Media](#media) 81 | - [VernacularName](#vernacularname) 82 | - [Treatment documents](#treatment) 83 | 84 | or the following: 85 | - [metadata.yaml](#metadatayaml) 86 | - [CHANGES.md](#changes) 87 | - `logo.png` a logo image for the dataset 88 | 89 | 90 | ### Data Files 91 | The filename for an entity in the above diagram is a case insensitive version of the class name, any number of ignored hyphens or underscores and a known tabular text suffix. The suffix specifies one of the two supported tabular flavours, comma separated or tab separated files: 92 | 93 | - `csv`: a comma separated, optionally quoted CSV file as per [RFC 4180](https://tools.ietf.org/html/rfc4180) 94 | - `tsv`, `tab` or `txt`: indicates a tab separated file without quoting 95 | 96 | Valid examples are `Taxon.tsv` or `vernacular-name.csv` 97 | `tsv` files are simpler to produce and handle, so if you have the option we recommend `tsv` over `csv`. 98 | 99 | ### Quoting and Escaping 100 | `tsv` files do not have any quoting of values, i.e. values are represented as they are. There are just 2 characters that are special and one needs to escape to not break the format: `\t` tabs and `\n` new lines. As they are hardly ever important in ColDP data (they most often are dirty data) the simplest solution is to just replace them with an ordinary space if they appear in any value. 101 | 102 | Otherwise `tsv` offers escaping `\t`, `\n`, `\r` and `\` itself using the backslash `\` if you really want to keep these characters in your values. 103 | 104 | 105 | `csv` files use a comma as the delimiter which often also appears in values. The optional quoting of values using double quotes `"` at the beginning and end of the value allows to safely use a comma without escaping it. E.g. `1234,"Miller, 1887"` are 2 columns. That pushes the problem to the double quote symbol which then has to be escaped inside quoted values by doubling it, e.g. `1234,"Frederic ""The Great"", 1887"`. Here are the important rules from the [RFC 4180 specification](https://tools.ietf.org/html/rfc4180) 106 | 107 | 108 | > 4. Within the header and each record, there may be one or more 109 | fields, separated by commas. Each line should contain the same 110 | number of fields throughout the file. Spaces are considered part 111 | of a field and should not be ignored. The last field in the 112 | record must not be followed by a comma. For example: 113 | 114 | ``` 115 | aaa,bbb,ccc 116 | ``` 117 | 118 | > 5. Each field may or may not be enclosed in double quotes (however 119 | some programs, such as Microsoft Excel, do not use double quotes 120 | at all). If fields are not enclosed with double quotes, then 121 | double quotes may not appear inside the fields. For example: 122 | 123 | ``` 124 | "aaa","bbb","ccc" CRLF 125 | zzz,yyy,xxx 126 | ``` 127 | 128 | > 6. Fields containing line breaks (CRLF), double quotes, and commas 129 | should be enclosed in double-quotes. For example: 130 | 131 | ``` 132 | "aaa","b CRLF 133 | bb","ccc" CRLF 134 | zzz,yyy,xxx 135 | ``` 136 | 137 | > 7. If double-quotes are used to enclose fields, then a double-quote 138 | appearing inside a field must be escaped by preceding it with 139 | another double quote. For example: 140 | 141 | ``` 142 | "aaa","b""bb","ccc" 143 | ``` 144 | 145 | ### Character Encoding 146 | All files **must be encoded in UTF-8**. 147 | 148 | 149 | 150 | ## Default Values 151 | *added in v1.1* 152 | 153 | In some cases it is useful to declare a fixed, global value that applies to every record in the dataset, 154 | for example if all taxa are animals it makes sense to declare `Name.code=zoological` only once. 155 | This can be done in a single file default.yaml that provides default values for all terms. 156 | Term are organised under their entity/class name in the file. 157 | 158 | Example of a `default.yaml` file: 159 | 160 | ```yaml 161 | Name: 162 | code: zoological 163 | Taxon: 164 | extinct: false 165 | environment: marine 166 | kingdom: Animalia 167 | ``` 168 | 169 | If the term is defined in the actual data, default values will only apply in case the value is null. 170 | E.g. it can be used to have a default *code* value, but override it for exceptional records. 171 | This is similar to the default feature in the meta.xml file of DwC archives. 172 | 173 | 174 | 175 | ## Metadata 176 | A [YAML file](metadata.yaml) called `metadata.yaml` with metadata about the entire data package should be included. 177 | The file consists mostly of key value pairs like title, see the comments in [metadata.yaml](metadata.yaml) for all available keys. 178 | There is also a [JSON schema](metadata.json) available for validation. 179 | 180 | An exception are the contact and authors and editors properties which takes a compound person object 181 | and the organisations list which takes a structured organisation object. 182 | See [yaml example](metadata.yaml) for all available fields. 183 | Additional entries to the YAML file are allowed to express non standard properties. 184 | 185 | Note that there is no single preformatted citation string, but instead the structured metadata itself is the citation 186 | which can be formatted according to [various styles](https://www.zotero.org/styles) like [APA](https://apastyle.apa.org/products/publication-manual-7th-edition) which is the default style in checklistbank.org. 187 | For citations please pay special attention to the core fields `title`, `creator`, `editor`, `publisher` & `issued`. 188 | 189 | ## Changes 190 | To document past versions and changes in data it is recommended 191 | to include a dedicated changelog markdown file named `CHANGES.md`. 192 | See https://keepachangelog.com/en/1.0.0/ for best practices. 193 | 194 | 195 | ## Raw Source Data 196 | In many cases it is desirable to also include the raw source data files like PDFs, Excel spreadsheets, database dumps, XML files 197 | or any other custom or binary files inside the archive. 198 | This allows users interested in details not captured by ColDP to access them, but also 199 | improves transparency and increases trust. 200 | 201 | ColDP recommends to use a special `raw` folder to hold all the original source files. 202 | Please always consider the resulting total archive size and consider the inclusion of very large raw files if the total archive size exceeds 1GB. 203 | 204 | 205 | 206 | 207 | # Data File Columns 208 | All data files should contain a header row that specifies the name of the columns as given below. 209 | In the absence of a header row it is expected that all columns exist in the exact order given below. 210 | With headers given it is allowed to share additional columns which are not part of the standard as listed below. 211 | 212 | 213 | 214 | ## Name 215 | Names can be shared in a structured way using various fields, 216 | but rank, scientificName and authorship alone are sufficient. 217 | See [](https://github.com/Sp2000/colplus/blob/master/docs/) for examples and rationales. 218 | 219 | A structured `scientificName` can be given using the following fields: 220 | - [uninomial](#uninomial) 221 | - [genus](#genus) 222 | - [infragenericEpithet](#infragenericEpithet) 223 | - [specificEpithet](#specificEpithet) 224 | - [infraspecificEpithet](#infraspecificEpithet) 225 | - [cultivarEpithet](#cultivarEpithet) 226 | - [notho](#notho) 227 | 228 | An `authorship` of a name can be structured with: 229 | - [combinationAuthorship](#combinationAuthorship) 230 | - [combinationExAuthorship](#combinationExAuthorship) 231 | - [combinationAuthorshipYear](#combinationAuthorshipYear) 232 | - [basionymAuthorship](#basionymAuthorship) 233 | - [basionymExAuthorship](#basionymExAuthorship) 234 | - [basionymAuthorshipYear](#basionymAuthorshipYear) 235 | 236 | or can make use of the [Author](#author) entity and define authorships purely by using identifiers: 237 | - [combinationAuthorshipID](#combinationAuthorshipID) 238 | - [combinationExAuthorshipID](#combinationExAuthorshipID) 239 | - [combinationAuthorshipYear](#combinationAuthorshipYear) 240 | - [basionymAuthorshipID](#basionymAuthorshipID) 241 | - [basionymExAuthorshipID](#basionymExAuthorshipID) 242 | - [basionymAuthorshipYear](#basionymAuthorshipYear) 243 | 244 | #### ID 245 | Unique name identifier that is referred to elsewhere via `nameID`. 246 | 247 | #### alternativeID 248 | A comma concatenated list of alternative identifiers for the name. 249 | Every alternative identifier must be a URI/URN/URL or given in the form of `scope:id`. 250 | See [identifiers](#Identifiers) for all details and common scopes. 251 | 252 | *added in v1.1* 253 | 254 | #### sourceID 255 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 256 | 257 | #### basionymID 258 | Identifier of the name which is the original combination of this name. Also known as the basionym. 259 | Contrary to the strict basionym definition it is acceptable to populate this field also for original names which should point to itself. 260 | A basionym is a terminal relationship which cannot be "chained". 261 | The original name itself should not have another basionym relation to another name. 262 | When the basionym was established as a nomen novum to replace another name, e.g. a homonym, 263 | it should not use basionymID to refer to the replaced name (which has an entirely different epithet), 264 | but use the [NameRelation](#namerelation) with `type=replacement name` instead. 265 | 266 | Note there is an alternative way to share the information about an original name by using a [NameRelation](#namerelation) with `type=basionym`. 267 | The field basionymID exists for simplicity and because it is an important information to be shared. 268 | 269 | #### scientificName 270 | Required scientific name excluding the authorship 271 | 272 | #### authorship 273 | Authorship of the scientificName 274 | 275 | #### rank 276 | type: [rank enum](http://api.checklistbank.org/vocab/rank) 277 | 278 | The rank of the name preferably given in case insensitive english. The recommended vocabulary is included in [rank_enum](http://api.checklistbank.org/vocab/rank). 279 | 280 | #### uninomial 281 | The single-word name of generic or higher rank names. 282 | 283 | #### genus 284 | The genus part of a bi/trinomial. 285 | Note that for generic names the uninomial field should be used, not genus! 286 | 287 | #### infragenericEpithet 288 | The infrageneric epithet. Used as the terminal epithet for names at infrageneric ranks and optionally also for bi/trinomials 289 | In zoological names often the subgenus. 290 | 291 | #### specificEpithet 292 | The specific epithet in case of bi/trinomials. 293 | 294 | #### infraspecificEpithet 295 | The infraspecific epithet in case of bi/trinomials. 296 | 297 | #### cultivarEpithet 298 | The name of the cultivar for name governed by the cultivar code. 299 | 300 | #### notho 301 | For named hybrids the part of the name which is considered a hybrid 302 | and which usually is prefixed with the hybrid marker `×`. One of: 303 | 304 | - generic 305 | - infrageneric 306 | - specific 307 | - infraspecific 308 | 309 | type: [namePart enum](https://api.checklistbank.org/vocab/namePart) 310 | 311 | *added in v1.1* 312 | 313 | #### combinationAuthorship 314 | The authorteam of the main authorship for the exact combination (not the original combination). 315 | Multiple authors should be concatenated with a pipe `|` symbol. 316 | 317 | *added in v1.1* 318 | 319 | #### combinationAuthorshipID 320 | A list of identifiers for authors of the exact combination (not the original combination). 321 | Multiple author identifiers should be concatenated with a pipe `|` symbol. 322 | If `combinationAuthorship` is given, the order and number of author names and identifiers must always match up. 323 | Author identifiers must refer to an existing Author.ID within this data package. 324 | 325 | *added in v1.1* 326 | 327 | #### combinationExAuthorship 328 | The ex-authors part of the main authorship for the very combination (not the original combination). 329 | The `ex` prefix as normally found in the authorship should not be included here. 330 | Multiple authors should be concatenated with a pipe `|` symbol. 331 | 332 | *added in v1.1* 333 | 334 | #### combinationExAuthorshipID 335 | A list of identifiers for ex-authors of the exact combination (not the original combination). 336 | Multiple author identifiers should be concatenated with a pipe `|` symbol. 337 | If `combinationExAuthorship` is given, the order and number of author names and identifiers must always match up. 338 | Author identifiers must refer to an existing Author.ID within this data package. 339 | 340 | *added in v1.1* 341 | 342 | #### combinationAuthorshipYear 343 | The year given in the authorship for the very combination (not the original combination), given without brackets. 344 | 345 | *added in v1.1* 346 | 347 | #### basionymAuthorship 348 | The authorteam of the original name normally found in brackets, but given here without brackets. 349 | Multiple authors should be concatenated with a pipe `|` symbol. 350 | 351 | *added in v1.1* 352 | 353 | #### basionymAuthorshipID 354 | A list of identifiers for authors of the original combination (basionym) normally found in brackets. 355 | Multiple author identifiers should be concatenated with a pipe `|` symbol. 356 | If `basionymAuthorship` is given, the order and number of author names and identifiers must always match up. 357 | Author identifiers must refer to an existing Author.ID within this data package. 358 | 359 | *added in v1.1* 360 | 361 | #### basionymExAuthorship 362 | The ex-authors of the original name normally found in brackets, but given here without brackets. 363 | The `ex` prefix as normally found in the authorship should not be included here. 364 | Multiple authors should be concatenated with a pipe `|` symbol. 365 | 366 | *added in v1.1* 367 | 368 | #### basionymExAuthorshipID 369 | A list of identifiers for ex-authors of the original combination (basionym) normally found in brackets. 370 | Multiple author identifiers should be concatenated with a pipe `|` symbol. 371 | If `basionymExAuthorship` is given, the order and number of author names and identifiers must always match up. 372 | Author identifiers must refer to an existing Author.ID within this data package. 373 | 374 | *added in v1.1* 375 | 376 | #### basionymAuthorshipYear 377 | The year given in the authorship for the original combination normally found in brackets, but given here without brackets. 378 | 379 | *added in v1.1* 380 | 381 | 382 | #### code 383 | type: [code enum](http://api.checklistbank.org/vocab/nomCode) 384 | 385 | The nomenclatural code the name falls under. 386 | 387 | #### status 388 | type: [nomStatus enum](http://api.checklistbank.org/vocab/nomStatus) 389 | 390 | The broad nomenclatural status of the name. 391 | For the exact status note, e.g. *nomen nudum*, the remarks field should additionally be used 392 | Alternatively a URI or simple name from a class of the [NOMEN ontology](https://github.com/SpeciesFileGroup/nomen/blob/master/src/ontology/nomen.owl) can be used. 393 | 394 | #### referenceID 395 | A pointer to a Reference that is the publication in which the scientificName was originally established 396 | under the rules of the associated nomenclatural code. 397 | 398 | #### publishedInYear 399 | The effective year the name was published, given as a 4 digit integer. 400 | It is the year that is nomenclaturally relevant for the given combination. 401 | In most cases this will be the same as the publication year given in the linked reference record via referenceID. 402 | But in some cases this might be different. 403 | 404 | #### publishedInPage 405 | The exact single page number where the name was published. 406 | If the description spans multiple pages, the first page should be given. 407 | 408 | #### publishedInPageLink 409 | A URL to the exact page where the name was published. 410 | If the description spans multiple pages, the link to the first page should be given. 411 | 412 | #### gender 413 | type: [gender enum](http://api.checklistbank.org/vocab/gender) 414 | 415 | Gender of the name, i.e. the genus in case of bi/trinomials. 416 | Values for the gender field should be one of `masculine`, `feminine` or `neuter`. 417 | 418 | *added in v1.1* 419 | 420 | #### genderAgreement 421 | type: [boolean](https://frictionlessdata.io/specs/table-schema/#boolean) 422 | 423 | Flag that indicates for bi/trinomials whether the (infra)species epithet must follow and agree with the gender of the genus. 424 | 425 | *added in v1.1* 426 | 427 | #### originalSpelling 428 | type: [boolean](https://frictionlessdata.io/specs/table-schema/#boolean) 429 | 430 | Flag indicating that the name is given in it's original spelling when an emendation exists. 431 | Only use the flag if there is a known correction existing. 432 | The originalSpelling is usually indicated by placing [sic] after the name. 433 | 434 | A `originalSpelling=false` flag instead is indicating that the name is a corrected spelling, 435 | usually indicated by placing `corrig.` after the name. 436 | 437 | In most cases when it is unknown or the original spelling was never revised leave this flag empty. 438 | 439 | *added in v1.1* 440 | 441 | #### etymology 442 | Etymology of the name, i.e. the origin or meaning of the words forming the scientific name. 443 | Should be a short human readable paragraph. 444 | 445 | *added in v1.1* 446 | 447 | #### link 448 | A link to a webpage provided by the source depicting the name. 449 | 450 | #### remarks 451 | Additional nomenclatural remarks about the name. Often indicating its status or relevant rules in the code. 452 | 453 | #### modified 454 | UTC timestamp in ISO format to represent the time the record was last modified. 455 | 456 | *added in v1.1* 457 | 458 | #### modifiedBy 459 | Author identifier indicating the person who has last modified the record. 460 | 461 | *added in v1.1* 462 | 463 | 464 | 465 | ## Author 466 | Normalised and structured authors that can be referred to by names, references and taxon scrutinizers. 467 | All entities also allow to specify a modifedBy field which must reference an Author identifier here. 468 | 469 | *added in v1.1* 470 | 471 | 472 | #### ID 473 | Unique identifier for the author / person. 474 | Can be referenced from any modifiedBy field. 475 | 476 | #### sourceID 477 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 478 | 479 | #### alternativeID 480 | A comma concatenated list of alternative identifiers for the author. 481 | Every alternative identifier must be in the form of `scope:id`. 482 | See [identifiers](#Identifiers) for all details and common scopes. 483 | Recommended identifier scopes for authors are orcid, ipni, wikidata & viaf. 484 | 485 | #### given 486 | List of given names, concatenated by a comma. 487 | 488 | #### family 489 | The family name including any leading particles if existing. 490 | 491 | #### suffix 492 | Optional suffix to distinguish persons with identical surnames. 493 | In well known cases of father and son, the son should be distinguished by ‘f.’ or ‘filius’ in the suffix. 494 | 495 | #### abbreviationBotany 496 | Standard form (official abbreviation) of the persons name for use in a botanical author citation. 497 | 498 | #### alternativeNames 499 | A `|` separated list of alternative names this person is known under. 500 | 501 | #### sex 502 | Biological sex of the person. 503 | 504 | #### country 505 | Country of citizenship. Preferably as ISO code. 506 | If multiple concatenated by a comma. 507 | 508 | #### birth 509 | Date of birth, given as an ISO date string. 510 | 511 | #### birthPlace 512 | Location the person was born at. 513 | 514 | #### death 515 | Date of death, given as an ISO date string. 516 | 517 | #### affiliation 518 | Institution(s) the author is affiliated with. 519 | 520 | #### interest 521 | List of taxonomic groups the person has worked on. 522 | 523 | #### referenceID 524 | List of sources where the information was taken from or further information can be found about the author. 525 | 526 | #### link 527 | A link to a webpage provided by the source depicting the author. 528 | 529 | #### remarks 530 | Remarks about the person. 531 | 532 | #### modified 533 | UTC timestamp in ISO format to represent the time the record was last modified. 534 | 535 | *added in v1.1* 536 | 537 | #### modifiedBy 538 | Author identifier indicating the person who has last modified the record. 539 | 540 | *added in v1.1* 541 | 542 | 543 | 544 | 545 | 546 | ## NameRelation 547 | A directed nomenclatural name relation. 548 | See [#name-relations](https://github.com/Sp2000/colplus/blob/master/docs/#name-relations) for examples and definitions. 549 | 550 | #### nameID 551 | The subject name this relation originates from. 552 | Refers to an existing Name.ID or NameUsage.ID within this data package. 553 | 554 | #### relatedNameID 555 | The object name this relation relates to. 556 | Refers to an existing Name.ID or NameUsage.ID within this data package. 557 | 558 | #### sourceID 559 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 560 | 561 | #### type 562 | type: [enum](http://api.checklistbank.org/vocab/nomreltype) 563 | 564 | The kind of directed nomenclatural relation. 565 | 566 | #### referenceID 567 | The reference or nomenclatural act where this nomenclatural relation was established. 568 | 569 | #### page 570 | The exact single page number where the nomenclatural relation was published in the linked reference. 571 | If the value spans multiple pages, the first page should be given. 572 | 573 | *added in v1.1* 574 | 575 | #### remarks 576 | Remarks about the relation. 577 | 578 | #### modified 579 | UTC timestamp in ISO format to represent the time the record was last modified. 580 | 581 | *added in v1.1* 582 | 583 | #### modifiedBy 584 | Author identifier indicating the person who has last modified the record. 585 | 586 | *added in v1.1* 587 | 588 | 589 | 590 | 591 | ## TypeMaterial 592 | Type material designated to names. 593 | Type material should only be associated with the original name, not with a recombination. 594 | 595 | #### ID 596 | Optional unique identifier for the specimen. 597 | If possible use the existing specimen identifier, e.g. the collection/institution code and catalogue number. 598 | If coming from a Darwin Core world dwc:occurrenceID is a great fit. 599 | 600 | #### sourceID 601 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 602 | 603 | #### nameID 604 | A comma concatenated list of name IDs pointing to the typified name of this specimen. 605 | Each ID must refer to an existing Name.ID within this data package. 606 | See [best practices](#best-practices) for details on how to concatenate multi values. 607 | 608 | #### citation 609 | Material citation of the type material, i.e. type specimen. 610 | The citation is ideally given in the verbatim form as it was used in the original publication of the name or the subsequent designation. Otherwise it is recommended to follow the [material citation guidelines published by European Journal of Taxonomy](docs/material_citations_formatting_guide.pdf). 611 | If atomized fields below are given a citation is not needed. Otherwise it is required. 612 | 613 | #### status 614 | type: [type status enum](http://api.checklistbank.org/vocab/typeStatus) 615 | The status of the type material, e.g. holotype 616 | 617 | In case multiple names have been linked to the specimen through concatenated values in nameID, 618 | a list of comma concatenated status values can be given in the same order as the name IDs. 619 | If a single value is given it will be used for all names. 620 | 621 | #### referenceID 622 | A referenceID pointing to the Reference table indicating the publication of the type designation. 623 | Most often this is equivalent to the original names referenceID, but for subsequent designations a later reference should be cited. 624 | 625 | #### page 626 | The exact single page number where the type designation was published in the linked reference. 627 | If the value spans multiple pages, the first page should be given. 628 | 629 | *added in v1.1* 630 | 631 | #### locality 632 | The type locality. Ideally from largest area to smallest. 633 | 634 | #### country 635 | The country of the type locality. Preferably as ISO codes. 636 | 637 | #### latitude 638 | Decimal latitude of the type locality given in WGS84 639 | 640 | #### longitude 641 | Decimal longitude of the type locality given in WGS84 642 | 643 | #### altitude 644 | Altitude of the type locality. Ideally given as meters above mean seal level. 645 | Depth should be given as negative altitudes. 646 | 647 | #### host 648 | Indicates the host organism from which the type specimen was obtained (symbiotype). 649 | 650 | #### date 651 | Date the type material was gathered. Recommended to be given as ISO 8601 dates. 652 | 653 | #### collector 654 | The collectors name 655 | 656 | #### institutionCode 657 | The name or acronym in use by the institution having custody of the material. 658 | 659 | *added in v1.1* 660 | 661 | #### catalogNumber 662 | The identifier for the specimen in a collection. 663 | 664 | *added in v1.1* 665 | 666 | #### associatedSequences 667 | *added in v1.1* 668 | 669 | #### sex 670 | *added in v1.1* 671 | 672 | #### link 673 | A link to further information about the specimen, e.g. as provided by the institute holding the collection. 674 | 675 | #### remarks 676 | Any further remarks on the type material. 677 | 678 | #### modified 679 | UTC timestamp in ISO format to represent the time the record was last modified. 680 | 681 | *added in v1.1* 682 | 683 | #### modifiedBy 684 | Author identifier indicating the person who has last modified the record. 685 | 686 | *added in v1.1* 687 | 688 | 689 | 690 | 691 | ## Taxon 692 | An accepted name with a taxonomic classification given either as a parent-child relation or as a flat, denormalized record. 693 | 694 | #### ID 695 | Unique taxon identifier that is referred to elsewhere via `taxonID`. 696 | 697 | #### alternativeID 698 | A comma concatenated list of alternative identifiers for the taxonomic concept. 699 | Every alternative identifier must be a URI/URN/URL or given in the form of `scope:id`. 700 | See [identifiers](#Identifiers) for all details and common scopes. 701 | 702 | *added in v1.1* 703 | 704 | #### sourceID 705 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 706 | 707 | #### parentID 708 | The direct parent taxon's ID in the classification. This is the preferred way of exchanging a hierarchy and takes precedence over any classification given in the denormalized fields. 709 | 710 | #### ordinal 711 | A integer to specify an optional custom sort order for sibling taxa sharing the same parentID in the datasets. 712 | This can be used to define a traditional ordering of orders and families for example and can be existing for parts of the dataset, e.g. higher ranks, only. The natural ordering of integers from small to large should be applied. 713 | Not that this does not have to be a unique, global index. 714 | 715 | #### branchLength 716 | type: [number] 717 | The optional length of the parent edge to represent phylogenetic trees. 718 | 719 | #### nameID 720 | Pointer to the accepted name referring to an existing Name.ID within this data package. 721 | 722 | #### namePhrase 723 | An optional, unrestricted, lose phrase appended to the name just for this taxon. 724 | E.g. the phrase "sensu lato" may be added to the name to describe this taxon more precisely. 725 | 726 | #### accordingToID 727 | A reference ID to the publication that established the taxonomic concept used by this taxon. 728 | The author & year of the reference will be used to qualify the name with `sensu AUTHOR, YEAR`. 729 | The ID must refer to an existing Reference.ID within this data package. 730 | 731 | #### accordingToPage 732 | The exact single page number where the taxonomic concept was treated. 733 | If the treatment spans multiple pages, the first page should be given. 734 | 735 | *added in v1.1* 736 | 737 | #### accordingToPageLink 738 | A URL to the exact page where the taxonomic concept was published. 739 | If the treatment spans multiple pages, the link to the first page should be given. 740 | 741 | *added in v1.1* 742 | 743 | #### scrutinizer 744 | Name of the person who is the latest scrutinizer who revised or reviewed the taxonomic concept. 745 | 746 | #### scrutinizerID 747 | Identifier for the scrutinizer. Highly recommended are [ORCID](https://orcid.org) ids. 748 | 749 | #### scrutinizerDate 750 | type: [ISO8601 date](https://frictionlessdata.io/specs/table-schema/#date) 751 | The date when the taxonomic concept was last revised or reviewed by the scrutinizer. 752 | 753 | #### provisional 754 | type: [boolean](https://frictionlessdata.io/specs/table-schema/#boolean) 755 | 756 | A flag indicating that the taxon is only provisionally accepted and should be handled with care. 757 | 758 | #### referenceID 759 | A comma concatenated list of reference IDs supporting the taxonomic concept that has been reviewed by the scrutinizer. 760 | Each ID must refer to an existing Reference.ID within this data package. 761 | See [best practices](#best-practices) for details on how to concatenate multi values. 762 | 763 | #### extinct 764 | type: [boolean](https://frictionlessdata.io/specs/table-schema/#boolean) 765 | 766 | Nullable flag indicating that the taxon is extinct (true) or extant (false). This includes species that died out recently. 767 | 768 | #### temporalRangeStart 769 | type: [enum](http://api.checklistbank.org/vocab/geotime) 770 | 771 | Earliest appearance of the taxon in the geological time scale. 772 | Recommended values are geochronological names from the official [International Commission on Stratigraphy (ICS)](https://stratigraphy.org/chart) 773 | or million years before present, given with the unit `Ma` after the number, e.g. `17.4 Ma`. 774 | 775 | #### temporalRangeEnd 776 | type: [enum](http://api.checklistbank.org/vocab/geotime) 777 | 778 | Latest appearance of the taxon in the geological time scale. 779 | Recommended values are geochronological names from the official [International Commission on Stratigraphy (ICS)](https://stratigraphy.org/chart) 780 | or million years before present, given with the unit `Ma` after the number, e.g. `17.4 Ma`. 781 | 782 | #### environment 783 | type: [enum[]](http://api.checklistbank.org/vocab/environment) 784 | A comma delimited list of environments this taxon is known to exist in. 785 | 786 | #### species 787 | The species binomial the taxon is classified in. 788 | If parentID is given this field is ignored. 789 | 790 | #### section 791 | The (botanical) section the taxon is classified in. Considered a botanical rank below subgenus, not a zoological above family. 792 | If parentID is given this field is ignored. 793 | 794 | #### subgenus 795 | The subgenus the taxon is classified in. 796 | If parentID is given this field is ignored. 797 | 798 | #### genus 799 | The genus the taxon is classified in. 800 | If parentID is given this field is ignored. 801 | 802 | #### subtribe 803 | The subtribe the taxon is classified in. 804 | If parentID is given this field is ignored. 805 | 806 | #### tribe 807 | The tribe the taxon is classified in. 808 | If parentID is given this field is ignored. 809 | 810 | #### subfamily 811 | The subfamily the taxon is classified in. 812 | If parentID is given this field is ignored. 813 | 814 | #### family 815 | The family the taxon is classified in. 816 | If parentID is given this field is ignored. 817 | 818 | #### superfamily 819 | The superfamily the taxon is classified in. 820 | If parentID is given this field is ignored. 821 | 822 | #### suborder 823 | The suborder the taxon is classified in. 824 | If parentID is given this field is ignored. 825 | 826 | #### order 827 | The order the taxon is classified in. 828 | If parentID is given this field is ignored. 829 | 830 | #### subclass 831 | The subclass the taxon is classified in. 832 | If parentID is given this field is ignored. 833 | 834 | #### class 835 | The class the taxon is classified in. 836 | If parentID is given this field is ignored. 837 | 838 | #### subphylum 839 | The subphylum the taxon is classified in. 840 | If parentID is given this field is ignored. 841 | 842 | #### phylum 843 | The phylum the taxon is classified in. 844 | If parentID is given this field is ignored. 845 | 846 | #### kingdom 847 | The kingdom the taxon is classified in. 848 | If parentID is given this field is ignored. 849 | 850 | #### link 851 | A link to a webpage provided by the source depicting the taxon. 852 | 853 | #### remarks 854 | Any further taxonomic remarks. 855 | 856 | #### modified 857 | UTC timestamp in ISO format to represent the time the record was last modified. 858 | 859 | *added in v1.1* 860 | 861 | #### modifiedBy 862 | Author identifier indicating the person who has last modified the record. 863 | 864 | *added in v1.1* 865 | 866 | 867 | 868 | 869 | ## Synonym 870 | A synonymous name for a taxon. 871 | Note that the same name can be linked to multiple taxa by having several Synonym records to model pro parte synonyms. 872 | 873 | #### ID 874 | Optional unique identifier for the synonym. 875 | If given it should not clash with the taxon ids. 876 | 877 | #### sourceID 878 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 879 | 880 | #### taxonID 881 | Pointer to the taxon that this synonym is used for. 882 | For pro parte synonyms with multiple accepted names several synonym records sharing the same name but having different taxonIDs should be created. 883 | Refers to an existing Taxon.ID within this data package. 884 | 885 | #### nameID 886 | Pointer to the synonymous name referring to an existing Name.ID within this data package. 887 | 888 | #### namePhrase 889 | An optional, unrestricted, lose phrase appended to the name just for this synonym. 890 | E.g. the phrase "sensu lato" may be added to the name to describe this synonym more precisely. 891 | Or "auct. mult." or "auct. amer." for misapplied names that cannot refer to a single publication. 892 | Misapplied names that refer to a single publication should use `accordingToID` instead. 893 | 894 | #### accordingToID 895 | A reference ID to the publication that established the taxonomic concept used by this taxon. 896 | The author & year of the reference will be used to qualify the name with `sensu AUTHOR, YEAR`. 897 | Strongly recommended in case of misapplied names. 898 | The ID must refer to an existing Reference.ID within this data package. 899 | 900 | #### status 901 | type: [enum](http://api.checklistbank.org/vocab/taxonomicstatus) 902 | 903 | The kind of synonym. One of *synonym*, *ambiguous synonym* or *misapplied*. 904 | Defaults to *synonym*. 905 | 906 | #### referenceID 907 | A comma concatenated list of reference IDs supporting the synonym status of the name. 908 | Each ID must refer to an existing Reference.ID within this data package. 909 | 910 | #### link 911 | A link to a webpage provided by the source depicting the synonym. 912 | 913 | #### remarks 914 | Any further taxonomic remarks. 915 | 916 | #### modified 917 | UTC timestamp in ISO format to represent the time the record was last modified. 918 | 919 | *added in v1.1* 920 | 921 | #### modifiedBy 922 | Author identifier indicating the person who has last modified the record. 923 | 924 | *added in v1.1* 925 | 926 | 927 | 928 | 929 | ## NameUsage 930 | As a simpler alternative to the 3 entities [Name](#name), [Taxon](#taxon) and [Synonym](#synonym) a single `NameUsage` entity can be supplied. 931 | A NameUsage record can either be an accepted Taxon or a Synonym and is easily distinguished by its status. 932 | A NameUsage.ID acts both as a taxonID and nameID if referred to from other table, e.g TypeMaterial or VernacularName. 933 | For synonyms the `parentID` field is used to link to the accepted taxon. 934 | 935 | All properties available in the individual entities can also be used for the single NameUsage: 936 | 937 | ![NameUsage schema](docs/schemaNU.png) 938 | 939 | There are two clashing properties that exist both on a Name and Taxon/Synonym, but which have a slightly different meaning. 940 | Therefore the following properties deviate slightly from their usage in their classic version: 941 | 942 | - **parentID**: for taxa it points to the next higher taxon's ID to form the classification, for synonyms it points at the accepted taxon. 943 | - **status**: is the taxonomic name usage status which includes Synonym.status and the Taxon.provisional flag. 944 | A provisional taxon should be listed as `provisionally accepted`. 945 | Unresolved names which are neither accepted nor synonyms can be listed with status=`bare name` in which case only the Name properties are relevant. This corresponds to a lone Name record without a Taxon or Synonym record. 946 | - **nameStatus**: corresponds to the nomenclatural name status. 947 | - **nameRemarks**: corresponds to the nomenclatural name remarks otherwise given in Name.remarks. 948 | - **genus**: is the taxonomic classification of a name usage and corresponds to Taxon.genus. For synonyms it often is not the same as the genus part of the name 949 | - **genericName**: corresponds to the genus field of a name and represents the atomized genus of a scientificName. 950 | - **referenceID**: corresponds to the taxonomic reference(s) otherwise given in Taxon/Synonym.referenceID. 951 | - **nameReferenceID**: corresponds to the nomenclatural reference otherwise given in Name.referenceID. 952 | - **namePublishedInYear**: corresponds to Name.publishedInYear. 953 | - **namePublishedInPage**: corresponds to Name.publishedInPage. 954 | - **namePublishedInPageLink**: corresponds to Name.publishedInPageLink. 955 | - **nameAlternativeID**: corresponds to Name.alternativeID. *added in v1.1* 956 | 957 | If a single NameUsage entity is given no further Name, Taxon or Synonym entity must exist. 958 | 959 | 960 | 961 | 962 | 963 | ## TaxonProperty 964 | *added in v1.1* 965 | 966 | A flexible, generic way to assign arbitrary property values to a taxon. 967 | It can be used to share species profiles, traits, descriptions and any other dynamic information about a taxon. 968 | Every property value can optionally be referenced and ordered. 969 | 970 | #### taxonID 971 | The subject taxon the property is about. 972 | 973 | #### sourceID 974 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 975 | 976 | #### property 977 | The required name of the property the value is assigned to. 978 | For example a text label like "Biology" or "Illustration", 979 | a [Plinian core term](https://www.tdwg.org/community/species/plinian-core/) or some Wikidata P value like [P2974](https://www.wikidata.org/wiki/Property:P2974). 980 | 981 | #### value 982 | A required free text value for the given property. 983 | If markup is needed [Markdown](https://de.wikipedia.org/wiki/Markdown) is preferred. 984 | 985 | #### referenceID 986 | An optional reference where this property value was documented or who asserted it. 987 | 988 | #### page 989 | The exact single page number where the property value was published in the linked reference. 990 | If the value spans multiple pages, the first page should be given. 991 | 992 | #### ordinal 993 | An integer to specify an optional custom sort order for property values sharing the same taxonID in the dataset. 994 | 995 | #### remarks 996 | Remarks about the property value. 997 | 998 | #### modified 999 | UTC timestamp in ISO format to represent the time the record was last modified. 1000 | 1001 | *added in v1.1* 1002 | 1003 | #### modifiedBy 1004 | Author identifier indicating the person who has last modified the record. 1005 | 1006 | *added in v1.1* 1007 | 1008 | 1009 | 1010 | 1011 | 1012 | ## TaxonConceptRelation 1013 | A directed taxon relation representing RCC5 taxon concept assertions. 1014 | 1015 | #### taxonID 1016 | The subject taxon this relation originates from. 1017 | 1018 | #### relatedTaxonID 1019 | The object this taxon relates to. 1020 | 1021 | #### type 1022 | type: [enum](http://api.checklistbank.org/vocab/TaxonConceptRelType) 1023 | The kind of directed RCC5 relation that specifies how the two taxon concepts are related. 1024 | 1025 | #### referenceID 1026 | A reference where this relation was documented or who asserted it. 1027 | 1028 | #### remarks 1029 | Remarks about the concept relation. 1030 | 1031 | #### modified 1032 | UTC timestamp in ISO format to represent the time the record was last modified. 1033 | 1034 | *added in v1.1* 1035 | 1036 | #### modifiedBy 1037 | Author identifier indicating the person who has last modified the record. 1038 | 1039 | *added in v1.1* 1040 | 1041 | 1042 | 1043 | 1044 | ## SpeciesInteraction 1045 | A directed taxon relation representing species interactions. 1046 | Different to a [TaxonConceptRelation](#taxonconceptrelation) a species interaction can also point to a species (name) outside of the local dataset. 1047 | 1048 | #### taxonID 1049 | The subject taxon the species interaction is about. Always required to point to an existing taxonID in the local dataset. 1050 | 1051 | #### relatedTaxonID 1052 | The related taxon this interaction is describing. If given it must refer to a local taxonID from the dataset. 1053 | If missing, the 'relatedTaxonScientificName' must be given instead. 1054 | 1055 | #### sourceID 1056 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 1057 | 1058 | #### relatedTaxonScientificName 1059 | The scientificName of the related taxon this interaction is describing. Includes the authorship if known. 1060 | It is mutually exclusive with relatedTaxonID and if given no relatedTaxonID should exist. 1061 | The relatedTaxonScientificName can be used to document species interactions without the need to have full blown name and taxon records. 1062 | 1063 | #### type 1064 | type: [enum](http://api.checklistbank.org/vocab/SpeciesInteractionType) 1065 | 1066 | The kind of directed species interaction. Each interaction exists also in reverse to allow the alternative relatedTaxonScientificName field to be used. 1067 | Species interaction types are heavily inspired by https://www.globalbioticinteractions.org and the OBO Relation Ontology http://www.ontobee.org/ontology/RO 1068 | to which all entries are mapped. 1069 | 1070 | #### referenceID 1071 | A reference where the interaction was documented. 1072 | 1073 | #### remarks 1074 | Remarks about the species interaction. 1075 | 1076 | #### modified 1077 | UTC timestamp in ISO format to represent the time the record was last modified. 1078 | 1079 | *added in v1.1* 1080 | 1081 | #### modifiedBy 1082 | Author identifier indicating the person who has last modified the record. 1083 | 1084 | *added in v1.1* 1085 | 1086 | 1087 | 1088 | 1089 | ## SpeciesEstimate 1090 | An estimation of the number of species for a given higher taxon, e.g. a family. 1091 | The estimation must be based on a reference and should give the number of species according to a certain "type" that is expected to exist. 1092 | 1093 | #### taxonID 1094 | The higher taxon's ID that is the estimate refers to. 1095 | 1096 | #### sourceID 1097 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 1098 | 1099 | #### estimate 1100 | type: [integer] 1101 | The estimated number of species. 1102 | 1103 | #### type 1104 | type: [enum](http://api.checklistbank.org/vocab/estimatetype) 1105 | The exact kind of estimation, e.g. number of described living species or total estimated species including yet to be described organisms. 1106 | If none is given the type defaults to 'described species living'. 1107 | 1108 | #### referenceID 1109 | A mandatory reference ID that supports the estimate and also provides a temporal context. 1110 | 1111 | #### remarks 1112 | Remarks about the species estimate. Often used to explain the method used when the estimate is not directly taken from a publication. 1113 | 1114 | #### modified 1115 | UTC timestamp in ISO format to represent the time the record was last modified. 1116 | 1117 | *added in v1.1* 1118 | 1119 | #### modifiedBy 1120 | Author identifier indicating the person who has last modified the record. 1121 | 1122 | *added in v1.1* 1123 | 1124 | 1125 | 1126 | 1127 | ## Reference 1128 | Structured bibliographic references with a unique id to refer to from other entities. 1129 | References can be given either as a simple, single citation string, or in a structured form. 1130 | 1131 | ColDP supports fully parsed references in CSV based on the CSL-JSON format. 1132 | Alternatively references can also be provided in the native file formats for the well established BibTex or CSL-JSON formats. 1133 | See the sections below with for how to share alternative formats that do not conform to tabular CSV/TSV files. 1134 | 1135 | 1136 | #### ID 1137 | The local identifier for the reference as used in referenceID in other entities. 1138 | 1139 | #### alternativeID 1140 | A comma concatenated list of alternative identifiers for the reference. 1141 | Every alternative identifier must be a URI/URN/URL or given in the form of `scope:id`. 1142 | See [identifiers](#Identifiers) for all details and common scopes. 1143 | 1144 | #### sourceID 1145 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 1146 | 1147 | #### citation 1148 | Full bibliographic citation as one single string as an alternative to the rest of the more structured fields. 1149 | If individual fields are given the full citation can be ignored. 1150 | 1151 | #### type 1152 | type: [enum](http://api.catalogueoflife.org/vocab/csltype) 1153 | CSL type that defines what kind of structured reference this is and which fields are applicable. 1154 | E.g. ARTICLE-JOURNAL, BOOK, CHAPTER, DATASET or WEBPAGE. 1155 | See also https://aurimasv.github.io/z2csl/typeMap.xml for mapping of CSL types from Zotero and to field sets. 1156 | 1157 | #### author 1158 | The author(s) of the work. If multiple authors use a style that can safely be parsed. 1159 | Recommended are 2 common forms: 1160 | 1161 | 1. family1, given1; family2, given2; ... 1162 | 2. given1 family1, given2 family2, ... 1163 | 1164 | The first form using commas and semicolons can safely be parsed also for family names which include whitespace. 1165 | In accordance with BibTeX it is also permissable to use the english word `and` as a delimiter instead of the semicolon. 1166 | 1167 | The second form requires the family name to be a single word, as all words before the last whitespace are considered given names. 1168 | If a comma is used to separate surname, firstname please use a semicolon to delimit individual authors. 1169 | 1170 | #### authorID 1171 | List of Author.ID identifiers separated by a comma that act as authors for this reference. 1172 | Authors must exist in the local data package. 1173 | 1174 | *added in v1.1* 1175 | 1176 | #### editor 1177 | The editor(s) of the work. 1178 | See author for recommendations how to supply person names. 1179 | 1180 | #### editorID 1181 | List of Author.ID identifiers separated by a comma that act as editors for this reference. 1182 | Authors must exist in the local data package. 1183 | 1184 | *added in v1.1* 1185 | 1186 | #### title 1187 | The title of the work. 1188 | In case of journal articles the article title, not the journal itself. 1189 | 1190 | #### titleShort 1191 | The abbreviated title of the work. 1192 | 1193 | *added in v1.1* 1194 | 1195 | #### containerAuthor 1196 | Author(s) of the container holding the item, e.g. the book author for a book chapter. 1197 | See author for recommendations how to supply person names. 1198 | 1199 | #### containerAuthorID 1200 | List of Author.ID identifiers separated by a comma that act as the container authors for this reference. 1201 | Authors must exist in the local data package. 1202 | 1203 | *added in v1.1* 1204 | 1205 | #### containerTitle 1206 | Title of the container holding the item, e.g. the book title for a book chapter, the journal title for a journal article. 1207 | The containerTitle should exclude volume, edition, pages and other specifics. 1208 | 1209 | #### containerTitleShort 1210 | The abbreviated container title. 1211 | 1212 | *added in v1.1* 1213 | 1214 | #### issued 1215 | type: [ISO8601 date](https://frictionlessdata.io/specs/table-schema/#date) 1216 | Date the work was issued/published. 1217 | Use ISO dates that can be truncated to represent a year, year & month or exact date, e.g. 1998, 1998-05 or 1998-05-21 1218 | 1219 | #### accessed 1220 | type: [ISO8601 date](https://frictionlessdata.io/specs/table-schema/#date) 1221 | Date the item has been accessed. 1222 | See issued for how to use ISO dates. 1223 | 1224 | #### collectionTitle 1225 | Title of the collection holding the item, e.g. the series title for a book. 1226 | 1227 | #### collectionEditor 1228 | Editor(s) of the collection holding the item, e.g. the series editor for a book. 1229 | 1230 | #### collectionEditorID 1231 | List of Author.ID identifiers separated by a comma that act as collection editors for this reference. 1232 | Authors must exist in the local data package. 1233 | 1234 | *added in v1.1* 1235 | 1236 | #### volume 1237 | type: [number](https://specs.frictionlessdata.io/table-schema/#number) 1238 | (container) volume number holding the item, e.g. `2` when citing a chapter from book volume 2. 1239 | 1240 | #### issue 1241 | type: [number](https://specs.frictionlessdata.io/table-schema/#number) 1242 | (container) issue holding the item, e.g. `5` when citing a journal article from journal volume 2, issue 5. 1243 | 1244 | #### edition 1245 | type: [number](https://specs.frictionlessdata.io/table-schema/#number) 1246 | (container) edition holding the item, e.g. `3` when citing a chapter in the third edition of a book. 1247 | 1248 | #### page 1249 | Range of pages the item (e.g. a journal article) covers in a container (e.g. a journal issue) 1250 | 1251 | #### publisher 1252 | Name of the publisher 1253 | 1254 | #### publisherPlace 1255 | Geographic location of the publisher 1256 | 1257 | #### version 1258 | Version of the item or dataset 1259 | 1260 | #### isbn 1261 | International Standard Book Number 1262 | 1263 | #### issn 1264 | International Standard Serial Number 1265 | 1266 | #### doi 1267 | The DOI of the reference 1268 | 1269 | #### link 1270 | A URL link to the reference. A link to a webpage for electronic resources. 1271 | `url` in CSL-JSON terminology, but we prefer link to be consistent with other ColDP entities. 1272 | 1273 | #### remarks 1274 | Additional comments about the reference. 1275 | `note` in CSL-JSON terminology, but we prefer remarks to be consistent with other ColDP entities. 1276 | 1277 | #### modified 1278 | UTC timestamp in ISO format to represent the time the record was last modified. 1279 | 1280 | *added in v1.1* 1281 | 1282 | #### modifiedBy 1283 | Author identifier indicating the person who has last modified the record. 1284 | 1285 | *added in v1.1* 1286 | 1287 | 1288 | 1289 | 1290 | ## Reference JSON-CSL 1291 | Instead of the main reference file a `reference.json` file can be added to provide a JSON array of highly structured references 1292 | in the [CSL-JSON](https://citeproc-js.readthedocs.io/en/latest/csl-json/markup.html) format, e.g. as provided by CrossRef: 1293 | ``` 1294 | curl --location --silent --header "Accept: application/vnd.citationstyles.csl+json" https://doi.org/10.1126/science.169.3946.635 1295 | ``` 1296 | 1297 | The `id` field in each record of the array is used as the primary key and referred to from `referenceID` fields elsewhere. 1298 | 1299 | For efficient handling of larger lists the CSL data can also be formatted as [JSON Lines](https://jsonlines.org/) with each reference on a single row 1300 | and no outer JSON array in a file called `reference.jsonl`. 1301 | 1302 | 1303 | #### CSL-JSON example 1304 | 1305 | ``` 1306 | [ 1307 | { 1308 | "id": "science.169.3946.635", 1309 | "publisher": "American Association for the Advancement of Science (AAAS)", 1310 | "issue": "3946", 1311 | "published-print": { 1312 | "date-parts": [ 1313 | [ 1314 | 1970, 1315 | 8, 1316 | 14 1317 | ] 1318 | ] 1319 | }, 1320 | "DOI": "10.1126/science.169.3946.635", 1321 | "type": "article-journal", 1322 | "created": { 1323 | "date-parts": [ 1324 | [ 1325 | 2006, 1326 | 10, 1327 | 5 1328 | ] 1329 | ], 1330 | "date-time": "2006-10-05T12:56:56Z", 1331 | "timestamp": 1160053016000 1332 | }, 1333 | "page": "635-641", 1334 | "source": "Crossref", 1335 | "title": "The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance", 1336 | "prefix": "10.1126", 1337 | "volume": "169", 1338 | "author": [ 1339 | { 1340 | "given": "H. S.", 1341 | "family": "Frank", 1342 | "sequence": "first", 1343 | "affiliation": [] 1344 | } 1345 | ], 1346 | "container-title": "Science", 1347 | "original-title": [], 1348 | "language": "en", 1349 | "link": [ 1350 | { 1351 | "URL": "https://syndication.highwire.org/content/doi/10.1126/science.169.3946.635", 1352 | "content-type": "unspecified", 1353 | "content-version": "vor", 1354 | "intended-application": "similarity-checking" 1355 | } 1356 | ], 1357 | "deposited": { 1358 | "date-parts": [ 1359 | [ 1360 | 2020, 1361 | 2, 1362 | 5 1363 | ] 1364 | ], 1365 | "date-time": "2020-02-05T16:15:06Z", 1366 | "timestamp": 1580919306000 1367 | }, 1368 | "subtitle": [], 1369 | "short-title": [], 1370 | "issued": { 1371 | "date-parts": [ 1372 | [ 1373 | 1970, 1374 | 8, 1375 | 14 1376 | ] 1377 | ] 1378 | }, 1379 | "journal-issue": { 1380 | "published-print": { 1381 | "date-parts": [ 1382 | [ 1383 | 1970, 1384 | 8, 1385 | 14 1386 | ] 1387 | ] 1388 | }, 1389 | "issue": "3946" 1390 | }, 1391 | "URL": "http://dx.doi.org/10.1126/science.169.3946.635", 1392 | "ISSN": [ 1393 | "0036-8075", 1394 | "1095-9203" 1395 | ], 1396 | "subject": [ 1397 | "Multidisciplinary" 1398 | ], 1399 | "container-title-short": "Science" 1400 | } 1401 | ] 1402 | ``` 1403 | 1404 | ## Reference BIBTEX 1405 | Alternatively to CSL-JSON a [BibTex](http://www.bibtex.org/Format/) file `reference.bib` can be given to provide highly structured citations. 1406 | 1407 | The `id` field following the curly opening bracket is used as the primary key and referred to from `referenceID` fields elsewhere. 1408 | You can also download BibTex records from CrossRef using curl: 1409 | ``` 1410 | curl --location --silent --header "Accept: application/x-bibtex" https://doi.org/10.1080/11035890601282097 1411 | ``` 1412 | 1413 | For converting existing bibliographies into BibTex the [AnyStyle parser](https://anystyle.io) is highly recommended. 1414 | It is free and quick to use online for a few hundred to thousand references. For much larger amounts it needs to be run locally. 1415 | 1416 | 1417 | #### Bibtex example 1418 | ``` 1419 | @article{Droege_2016, 1420 | title={The Global Genome Biodiversity Network (GGBN) Data Standard specification}, 1421 | volume={2016}, 1422 | ISSN={1758-0463}, 1423 | url={http://dx.doi.org/10.1093/database/baw125}, 1424 | DOI={10.1093/database/baw125}, 1425 | journal={Database}, 1426 | publisher={Oxford University Press (OUP)}, 1427 | author={Droege, G. and Barker, K. and Seberg, O. and Coddington, J. and Benson, E. and Berendsohn, W. G. and Bunk, B. and Butler, C. and Cawsey, E. M. and Deck, J. and et al.}, 1428 | year={2016}, 1429 | pages={baw125} 1430 | } 1431 | 1432 | @article{Frank_1970, 1433 | title = {The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance}, 1434 | volume = {169}, 1435 | ISSN = {1095-9203}, 1436 | url = {http://dx.doi.org/10.1126/science.169.3946.635}, 1437 | DOI = {10.1126/science.169.3946.635}, 1438 | number = {3946}, 1439 | journal = {Science}, 1440 | publisher = {American Association for the Advancement of Science (AAAS)}, 1441 | author = {Frank, H. S.}, 1442 | year = {1970}, 1443 | month = {Aug}, 1444 | pages = {635–641} 1445 | } 1446 | ``` 1447 | 1448 | 1449 | 1450 | ## Distribution 1451 | A structured distribution record for a taxon in a given area. 1452 | 1453 | #### taxonID 1454 | Pointer to the taxon referring to an existing Taxon.ID within this data package. 1455 | 1456 | #### sourceID 1457 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 1458 | 1459 | #### areaID 1460 | The identifier/code for the geographic area this distribution record is about. 1461 | The value must be taken from the gazetteer this record declares. 1462 | E.g. country codes, `TDWG` codes or `TEOW` identifiers. 1463 | If the `TEXT` gazetteer is used only the free text area should be given with no areaID. 1464 | 1465 | #### area 1466 | The geographic area this distribution record is about. 1467 | The value provides a human label for the area specified by areaID. 1468 | Free text values can be provided here when the gazetteer is set to `TEXT`. 1469 | 1470 | #### gazetteer 1471 | type: [enum](http://api.checklistbank.org/vocab/gazetteer) 1472 | 1473 | The geographic gazetteer the area is defined in. 1474 | If none is given defaults to free `TEXT`. 1475 | 1476 | #### establishmentMeans 1477 | type: [enum](http://api.checklistbank.org/vocab/establishmentmeans) 1478 | Statement about whether the taxon has been introduced to the given area and time through the direct or indirect activity of modern humans. 1479 | 1480 | *added in v1.2* 1481 | 1482 | #### degreeOfEstablishment 1483 | type: [enum](http://api.checklistbank.org/vocab/degreeofestablishment) 1484 | The degree to which the taxon survives, reproduces, and expands its range at the given area and time. 1485 | 1486 | *added in v1.2* 1487 | 1488 | #### pathway 1489 | The process by which the taxon came to be in the given area at the given time. 1490 | 1491 | *added in v1.2* 1492 | 1493 | #### threatStatus 1494 | type: [enum](http://api.checklistbank.org/vocab/threatstatus) 1495 | Threat status of a species as defined by IUCN. 1496 | 1497 | *added in v1.2* 1498 | 1499 | #### year 1500 | type: integer 1501 | Year in which the distribution was assessed. 1502 | Relevant temporal context for the distribution record including all properties. 1503 | Given as a single year on which the distribution record is valid. 1504 | For the same area and taxon there could therefore be several records with different temporal scopes, e.g. in 5 year intervals for invasive species. 1505 | 1506 | *added in v1.2* 1507 | 1508 | #### season 1509 | type: [enum](http://api.checklistbank.org/vocab/season) 1510 | Optional restriction of the distribution record to some season. 1511 | 1512 | *added in v1.2* 1513 | 1514 | #### lifeStage 1515 | Optional restriction of the distribution record to just a particular life stage of the species. 1516 | 1517 | *added in v1.2* 1518 | 1519 | 1520 | #### referenceID 1521 | Pointer to the reference that supports this distribution. Refers to an existing Reference.ID within this data package. 1522 | 1523 | #### remarks 1524 | Remarks about the distribution. 1525 | 1526 | #### modified 1527 | UTC timestamp in ISO format to represent the time the record was last modified. 1528 | 1529 | *added in v1.1* 1530 | 1531 | #### modifiedBy 1532 | Author identifier indicating the person who has last modified the record. 1533 | 1534 | *added in v1.1* 1535 | 1536 | 1537 | 1538 | 1539 | ## Media 1540 | Multimedia items for a taxon such as an image, audio or video. 1541 | 1542 | #### taxonID 1543 | Pointer to the taxon referring to an existing Taxon.ID within this data package. 1544 | 1545 | #### sourceID 1546 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 1547 | 1548 | #### url 1549 | The URL that resolves to the media item itself, not a webpage that depicts it. 1550 | 1551 | #### type 1552 | The MIME-type of the media item the url identifies. 1553 | Preferably the full type/subtype combination, e.g `image/jpeg`, but the primary type alone is sufficient (`image`, `video`, `audio`). 1554 | 1555 | #### title 1556 | Optional title for the item. 1557 | 1558 | #### created 1559 | type: [ISO8601 date](https://frictionlessdata.io/specs/table-schema/#date) 1560 | Date the media item was recorded. 1561 | 1562 | #### creator 1563 | Author of the media item. 1564 | 1565 | #### license 1566 | type: [license](http://api.checklistbank.org/vocab/license) 1567 | 1568 | #### link 1569 | Optional webpage from the source this media item is shown on. 1570 | 1571 | #### remarks 1572 | Remarks about the media item. 1573 | 1574 | *added in v1.1* 1575 | 1576 | #### modified 1577 | UTC timestamp in ISO format to represent the time the record was last modified. 1578 | 1579 | *added in v1.1* 1580 | 1581 | #### modifiedBy 1582 | Author identifier indicating the person who has last modified the record. 1583 | 1584 | *added in v1.1* 1585 | 1586 | 1587 | 1588 | 1589 | ## VernacularName 1590 | A vernacular or common name for a taxon. 1591 | 1592 | #### taxonID 1593 | Pointer to the taxon referring to an existing Taxon.ID within this data package. 1594 | 1595 | #### sourceID 1596 | Optional identifier for the source this record came from as listed in the [metadata.yaml](metadata.yaml) 1597 | 1598 | #### name 1599 | The vernacular name in the original script. 1600 | 1601 | #### transliteration 1602 | An optional transliteration of the vernacular name into the latin script. 1603 | 1604 | #### language 1605 | Language of the vernacular name given as an ISO 639-3 letter code. 1606 | 1607 | #### preferred 1608 | type: boolean 1609 | A flag to indicate if this vernacular name is the preferred name for the given language. 1610 | 1611 | *added in v1.1* 1612 | 1613 | #### country 1614 | Country this vernacular name is used in given as an ISO 3166-2 letter code. 1615 | 1616 | #### area 1617 | Optional area describing the geographic use of the vernacular name in free text within the given country. 1618 | 1619 | #### sex 1620 | type: [enum](http://api.checklistbank.org/vocab/sex) 1621 | 1622 | Optional sex of the organism this vernacular name is restricted to. 1623 | 1624 | #### referenceID 1625 | Pointer to the reference that supports this vernacular name. Refers to an existing Reference.ID within this data package. 1626 | 1627 | #### remarks 1628 | Remarks about the vernacular name. 1629 | 1630 | *added in v1.1* 1631 | 1632 | #### modified 1633 | UTC timestamp in ISO format to represent the time the record was last modified. 1634 | 1635 | *added in v1.1* 1636 | 1637 | #### modifiedBy 1638 | Author identifier indicating the person who has last modified the record. 1639 | 1640 | *added in v1.1* 1641 | 1642 | 1643 | 1644 | 1645 | ## Treatment 1646 | [Treatments](https://plazi.org/treatmentbank/what-treatment/) are parts of publications that "treat" a single taxon. 1647 | They can be an original description for a new species, but also subsequent taxonomic works and usually include several sections such as a diagnosis, description, material examined, distribution, etc. 1648 | ColDP captures an entire treatment either as a PDF, TXT, HTML or XML document that lives as an individual file in a subfolder `treatments` and is named by the corresponding taxonID of the name usage it describes. 1649 | The taxons `accordingToID` should always point to the reference the treatment is published in. 1650 | Example: `treatments/19854332.html` would be an html document which is the marked up treatment for the taxon with ID `19854332`. 1651 | 1652 | 1653 | 1654 | # Identifiers 1655 | Identifiers are important and often come embedded with some resolution URL to make them globally unique and actionable. 1656 | For sharing the true identifiers only, which often have a local scope, ColDP requires them to be prefixed with a known scope abbreviation. 1657 | For example COL identifiers should be shared not by their API or portal URL (http://www.catalogueoflife.org/data/taxon/NN), but instead as `col:NN`. 1658 | 1659 | These type of compact identifiers are also known [CURIE](https://en.wikipedia.org/wiki/CURIE)s. 1660 | Scopes that are also registered prefixes in [identifiers.org](https://registry.identifiers.org) are linked. 1661 | 1662 | ## Identifier Scopes 1663 | To avoid conflicts of naming scopes we strongly recommend to use the following scope names which are case insensitive: 1664 | 1665 | - algaebase: AlgaeBase algae species - [algaebase:90](https://www.algaebase.org/search/species/detail/?species_id=90) 1666 | - avibase: Avibase taxon concept - [avibase:D754DB8552A7AA42](https://avibase.ca/D754DB85) 1667 | - bhl: Biodiversity Heritage Library page number - [bhl:45607882](https://www.biodiversitylibrary.org/page/45607882) 1668 | - [bold](https://registry.identifiers.org/registry/bold.taxonomy): BOLD BIN numbers - [BOLD:AAJ2287](http://v3.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAJ2287) 1669 | - clb: ChecklistBank identifier with a regex pattern of `clb:(\d+)(\/([unr])\.(.+))?` $1=datasetKey, $2=entity (**u**sage, **n**ame, **r**eference), $3=entity identifier 1670 | - A dataset with just an integer key: [clb:2019](https://www.checklistbank.org/dataset/2019/about): Mammal Species of the World in ChecklistBank 1671 | - A name usage with a compound key: [clb:2019/u.14000204](https://www.checklistbank.org/dataset/2019/taxon/14000204): Puma concolor (id 14000204) in Mammal Species of the World 1672 | - A reference: [clb:2144/r.10040](https://www.checklistbank.org/dataset/2144/reference/10040): _The Cactus Family (2001)_ in ITIS 1673 | - [col](https://registry.identifiers.org/registry/col): Catalogue of Life Checklist- [col:6W3C4](http://www.catalogueoflife.org/data/taxon/6W3C4) 1674 | - [doi](https://registry.identifiers.org/registry/doi): any Digital Object Identifier - [doi:10.5281/zenodo.6407053](https://doi.org/10.5281/zenodo.6407053) 1675 | - eunis: European Nature Information System - [eunis:193060](https://eunis.eea.europa.eu/species/193060) 1676 | - gbif: GBIF Backbone Taxonomy - [gbif:2704179](https://www.gbif.org/species/2704179) 1677 | - genbank: GenBank accession number - [genbank:U49845](https://www.ncbi.nlm.nih.gov/nucleotide/U49845) 1678 | - hol: Hymenoptera Online ID - [hol:31685](https://hol.osu.edu/index.html?id=31685) 1679 | - if: Index Fungorum - [if:550000](http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=550000) 1680 | - ina: Index Nominum Algarum - [ina:101744](http://ucjeps.berkeley.edu/cgi-bin/porp_cgi.pl?101744) 1681 | - inat: iNaturalist taxon identifier - [inat:52808](https://www.inaturalist.org/observations?taxon_id=52808) 1682 | - ipni: International Plant Name Index - [ipni:320035-2](https://www.ipni.org/n/320035-2) 1683 | - [isbn](https://registry.identifiers.org/registry/isbn): International Standard Book Number, with 10 or 13 numbers - [isbn:9780393978674](https://isbndb.com/book/9780393978674) 1684 | - irmng: Interim Register of Marine and Nonmarine Genera - [irmng:1038927]([https://apiv3.iucnredlist.org/api/v3/taxonredirect/10335](https://www.irmng.org/aphia.php?p=taxdetails&id=1038927)) 1685 | - iucn: IUCN Redlist species - [iucn:10335](https://apiv3.iucnredlist.org/api/v3/taxonredirect/10335) 1686 | - mb: Mycobank Fungal Database - [mb:309626](https://www.mycobank.org/page/Name%20details%20page/field/Mycobank%20%23/309626) 1687 | - ncbi: NCBI taxonomy - [ncbi:93036](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=93036) 1688 | - orcid: Open Researcher and Contributor ID - [orcid:0000-0001-6492-4016](https://orcid.org/0000-0001-6492-4016) 1689 | - otl: Open Tree of Life - [otl:510850](https://tree.opentreeoflife.org/taxonomy/browse?id=510850) 1690 | - pesi: Pan-European Species directories Infrastructure - [pesi:93A25572-521E-4130-B8C5-9C7D332E5605](http://www.eu-nomen.eu/portal/taxon.php?GUID=93A25572-521E-4130-B8C5-9C7D332E5605) 1691 | - silva: SILVA taxonomy - https://www.arb-silva.de/documentation/silva-taxonomy/ 1692 | - taxonid: taxon concepts as Linked Data - [taxonid:D92326](http://taxonid.org/D92326) 1693 | - tpl: The Plant List - [tpl:kew-435194](http://www.theplantlist.org/tpl1.1/record/kew-435194) 1694 | - tropicos: Missource Botanical Gardens TROPICOS - [tropicos:25509881](https://www.tropicos.org/name/25509881) 1695 | - tsn: ITIS Taxonomic Serial Number - [tsn:41107](https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=41107#null) 1696 | - [ubio](https://registry.identifiers.org/registry/ubio.namebank): uBio - [ubio:5408026](http://www.ubio.org/browser/details.php?namebankID=5408026) 1697 | - unite: UNITE Species Hypotheses - [unite:SH1659817.08FU](https://unite.ut.ee/sh/SH1659817.08FU) 1698 | - usda: USDA Plants - [usda:POAN](https://plants.sc.egov.usda.gov/home/plantProfile?symbol=POAN) 1699 | - viaf: [Virtual International Authority File database](https://viaf.org/) - [viaf:76389959](https://viaf.org/viaf/76389959) 1700 | - wfo: World Flora Online - [wfo:wfo-0000891536](http://www.worldfloraonline.org/taxon/wfo-0000891536) 1701 | - [wikidata](https://registry.identifiers.org/registry/wikidata): Wikidata items - [wikidata:Q157571](https://www.wikidata.org/wiki/Q157571) 1702 | - [worms](https://registry.identifiers.org/registry/worms): World Register of Marine Species - [worms:212808](https://www.marinespecies.org/aphia.php?p=taxdetails&id=212808) 1703 | - zoobank: ZooBank record - [zoobank:EEDEA832-A8A9-44DF-8F2F-684FFEC9C19B](https://zoobank.org/NomenclaturalActs/eedea832-a8a9-44df-8f2f-684ffec9c19b) 1704 | 1705 | 1706 | We do recommend to share bare identifiers with their scope if possible. 1707 | But sharing globally unique URN, URI or URLs can be done without any further scope: 1708 | 1709 | 1710 | - https://species.wikimedia.org/wiki/Poa_annua 1711 | - https://www.biodiversitylibrary.org/page/45607882 1712 | - urn:lsid:zoobank.org:act:EEDEA832-A8A9-44DF-8F2F-684FFEC9C19B 1713 | - urn:lsid:ipni.org:names:320035-2 1714 | - urn:lsid:Blattodea.speciesfile.org:TaxonName:1287 1715 | 1716 | If you plan to share identifiers with other scopes we encourage users to tell us about them so we can "register" them to guarantee their uniqueness 1717 | and inform others about their semantics. 1718 | 1719 | 1720 | 1721 | # Format Comparison 1722 | 1723 | The ColDP format was developed to overcome limitations existing in currently used formats for sharing taxonomic information, namely [Darwin Core Archives](https://dwc.tdwg.org/text/) and the Catalogue of Life submission format also known as [ACEF](http://www.catalogueoflife.org/content/contributing-your-data#ACEF) (Annual Checklist Exchange Format). Darwin Core Archives and ACEF could still be used for exchanging data to and from Catalogue of Life ChecklistBank, but the ColDP format will support the most features. The following table provides an overview of different features supported in each of the 3 formats: 1724 | 1725 | Feature|ACEF|DwC-A|ColDP 1726 | --- |:---:| :---:| :---: 1727 | Linnean classification (KPCOFG)|x|x|x 1728 | Extended Linnean classification (subranks)|-|-|x 1729 | Flexible Parent-child classification|-|x|x 1730 | Custom taxon ordering|-|-|x 1731 | Phylo trees|-|-|x 1732 | Unrestricted ranks|-|x|x 1733 | Higher taxon details|-|x|x 1734 | Infraspecific taxa|x|x|x 1735 | Nested infraspecific taxa|-|x|x 1736 | Basionyms|-|x|x 1737 | Synonyms|x|x|x 1738 | Synonyms for higher taxa|-|x|x 1739 | Name identifier|-|x|x 1740 | Nomenclatural status|x|x|x 1741 | Fossils/extinction flags|x|x|x 1742 | Name & taxon separation|-|-|x 1743 | Species interactions|-|-|x 1744 | Species estimates|-|-|x 1745 | Structured references|x|-|x 1746 | Nomenclatural relations|-|-|x 1747 | Type species|-|x|x 1748 | Type specimen|-|x|x 1749 | Taxon concepts|-|x|x 1750 | Taxon concept relations|-|x|x 1751 | Vernacular names|x|x|x 1752 | Structured distributions|x|x|x 1753 | Treatments|-|x|x 1754 | Multimedia metadata|-|x|x 1755 | 1756 | - `x` = supported 1757 | - `-` = not supported 1758 | 1759 | 1760 | # Best Practices 1761 | Please see also the [ColDP Publishing Guidelines](/docs/publishing-guide.md) for concrete examples. 1762 | 1763 | ## multiple value concatenation 1764 | Some fields are allowed to contain multiple values. These must be concatenated by a simple comma. Any surrounding whitespace should be ignored. 1765 | If the value itself contains a comma, it should be escaped by a backslash, i.e. `foo,bar` should become `foo\,bar`. 1766 | Any other combinations of a backslash with some other characters will be take literally, i.e. `\n` will remain `\n`. 1767 | 1768 | ## parentID vs flat ranks 1769 | A taxonomic hierarchy can be established either as a parent child relationship using `Taxon.parentID` or by using the flat, higher rank terms on each record. 1770 | If possible the parent child approach using `parentID` is preferable and the flat higher ranks are not needed in that case. 1771 | 1772 | ## Species with an uncertain genus 1773 | Sometimes there a cases of a described species with a taxonomically unresolved placement. 1774 | It appears to be a valid species, but there has been no updated taxonomic placement yet (or can't be because of missing types/information) 1775 | and a current placement into some other genus is not possible and/or no new combination has yet been published. 1776 | Instead of listing the same "split" genus twice COL strongly recommends to flag the species taxon with `provisional=true` and place it directly under it's next higher taxon, e.g. the family. 1777 | 1778 | ## Misapplied names 1779 | A misapplied name is when the name of one taxon is erroneously applied to a different taxon. 1780 | When "misidentifications" are in widespread use in publications they are often included as part of the synonymy of a taxon. 1781 | A misapplied name may refer to a single misapplication, but frequently indicates all usages of a name are wrong in a specific, e.g. regional, context. 1782 | There are various conventions in use and phrases like ```auct. nec Zeller, 1877```, ```sensu Li & Zheng 1997``` or Ficus exasperata ```auct. non Vahl: De Wildeman & Durand``` 1783 | strictly do not belong to the Name instance, but to the name usage, i.e. the Synonym or NameUsage coldp record. 1784 | Separating usage notes from the names authorship can be done in 2 ways in ColDP: 1785 | 1786 | 1. ```accordingToID``` can be used to refer to a single publication or author that contains the misapplication. 1787 | 2. ```namePhrase``` is used for any additions to the names authorship and can also be used for misapplications like ```Leucospermum bolusii E.Phillips, 1910 auct. non Gandoger``` 1788 | with ```E.Phillips, 1910``` being the Name.authorship and ```auct. non Gandoger``` the Synonym.namePhrase 1789 | 1790 | --------------------------------------------------------------------------------