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Make fixSpecies() handle typical NCBI organism names #82

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LimaRAF opened this issue Nov 16, 2021 · 1 comment
Open

Make fixSpecies() handle typical NCBI organism names #82

LimaRAF opened this issue Nov 16, 2021 · 1 comment
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LimaRAF commented Nov 16, 2021 •
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Names in NCBI/GenBank commonly have a particularly notation that fixSpecies() currently does not handle well. Improvements are needed. Examples are:

  • "Syzygium sp. DIR045"
  • "Malaxis sp. TBG132709"
  • "Senecio lautus x Senecio repangae subsp. pokohinuensis"
  • "Arabidopsis thaliana x Arabidopsis arenosa"
  • "Juglans microcarpa x Juglans regia"
  • "Acacia aff. deltoidea x Acacia aff. stigmatophylla R5710"
  • "Metrosideros excelsa x Metrosideros kermadecensis"
  • "Metrosideros excelsa x Metrosideros robusta"
  • "Tetrastigma cf. magnum PBP-2017"
  • "Phyllanthus aff. sootepensis RWB059"
  • "Phyllanthus cf. gomphocarpus Yu 250"
  • "Phyllanthus cf. boehmii Friis 13159"
  • "Acacia aff. shirleyi Carroll s.n."
  • "Acacia aff. cowleana Carroll 18"
  • "Acacia aff. gracillima Barett 2931"
  • "Phyllanthus sp. RWB-2020a"
  • "Asarum sp. DT2604"
  • "Phyllanthus aff. vakinankaratrae Ravelonarivo 4264"
  • "Tragia sp. Philippines"
  • "Tragia sp. Merida"

E também:

  • "Syzygium spp."
  • "Paralychnophora harleyi (H.Rob.) D.J.N.Hind"
  • "Anemopaegma arvense (Vell.) Stellfeld ex de Souza"
  • "Maytenus boaria Molina"
  • "Sloanea fasciculata D. Sampaio & V.C. Souza"
  • "Conchocarpus albiflorus (Bruniera & Groppo) Bruniera & Groppo"
  • "Grabowskia boerhaaviifolia (L. f.) Schltdl."
@LimaRAF LimaRAF added the enhancement New feature or request label Nov 16, 2021
@LimaRAF LimaRAF self-assigned this Nov 16, 2021
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LimaRAF commented Jul 18, 2024 •
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There were improvements with the new version of ´fixSpecies()´ in version 0.1.8. but there is still work to do (those not checked below. Some cases, codes and hybrids go into author names and for case 3 there actually an error!

  • "Syzygium sp. DIR045"
  • "Malaxis sp. TBG132709"
  • "Senecio lautus x Senecio repangae subsp. pokohinuensis"
  • "Arabidopsis thaliana x Arabidopsis arenosa"
  • "Juglans microcarpa x Juglans regia"
  • "Acacia aff. deltoidea x Acacia aff. stigmatophylla R5710"
  • "Metrosideros excelsa x Metrosideros kermadecensis"
  • "Metrosideros excelsa x Metrosideros robusta"
  • "Tetrastigma cf. magnum PBP-2017"
  • "Phyllanthus aff. sootepensis RWB059"
  • "Phyllanthus cf. gomphocarpus Yu 250"
  • "Phyllanthus cf. boehmii Friis 13159"
  • "Acacia aff. shirleyi Carroll s.n."
  • "Acacia aff. cowleana Carroll 18"
  • "Acacia aff. gracillima Barett 2931"
  • "Phyllanthus sp. RWB-2020a"
  • "Asarum sp. DT2604"
  • "Phyllanthus aff. vakinankaratrae Ravelonarivo 4264"
  • "Tragia sp. Philippines"
  • "Tragia sp. Merida"
  • "Syzygium spp."
  • "Paralychnophora harleyi (H.Rob.) D.J.N.Hind"
  • "Anemopaegma arvense (Vell.) Stellfeld ex de Souza"
  • "Maytenus boaria Molina"
  • "Sloanea fasciculata D. Sampaio & V.C. Souza"
  • "Conchocarpus albiflorus (Bruniera & Groppo) Bruniera & Groppo"
  • "Grabowskia boerhaaviifolia (L. f.) Schltdl."

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