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jhpoelen / msw-plazi

Mammal Species of the World treatments transcribed by Plazi
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Abrocoma bennetti is mentioned in MSW1/2 but Abrocoma bennettii was mentioned in original publication #2

Open jhpoelen opened 1 year ago

jhpoelen commented 1 year ago

via @myrmoteras -

[...] For example, Abrocoma bennetti does not match COL because it is spelled with out a ..ii in MSW2 (and also in MSW1, and 3). The original in has a ...ii though. https://doi.org/10.5281/zenodo.7457193 or https://github.com/plazi/treatments-xml/blob/main/data/03/FA/64/03FA64167865FF8AFF34F96C4ECCA3D4.xml and with access to the original publication. now also in BLR. [...]

jhpoelen commented 1 year ago

also via @myrmoteras

image

jhpoelen commented 1 year ago

@myrmoteras in running

preston ls | preston grep -o --no-line "(Abrocoma bennetti)([^i])"

after cloning

Plazi Community. (2022). Plazi Treatments XML Archive hash://sha256/3cfd60b8b19e76d208377537835de92efdb5b945a6a71765b74ed2fe22298b42 hash://md/594923284e3eb9965b8cbad149c76cd0f (hash://sha256/3cfd60b8b19e76d208377537835de92efdb5b945a6a71765b74ed2fe22298b42) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7443343

I was able to cite all locations of Abrocoma bennetti without the ...ii suffix in a recent plazi/treatments-xml corpus and appended them to annotations.csv via https://github.com/jhpoelen/msw-plazi/commit/ea24ff964ea1373302ac01d406a0ac9226f65c68 .

jhpoelen commented 1 year ago

The associated treatment metadata headers in which the name (without ii suffix) occurs are:

<document ID-DOI="http://doi.org/10.5281/zenodo.6228755" ID-GBIF-Dataset="aa7a2f2b-ea55-4ae2-863a-93bf3bdde535" ID-GBIF-Taxon="119379023" ID-ISSN="1175-5326" ID-Zenodo-Dep="6228755" checkinTime="1459984091607" checkinUser="plazi" docAuthor="Valim, Michel P. &amp; Linardi, Pedro Marcos" docDate="2008" docId="03948456FFB1FFED26E95090DEA41A59" docLanguage="en" docName="zt01899p024.pdf" docOrigin="Zootaxa 1899" docStyle="DocumentStylede.uka.ipd.idaho.easyIO.settings.Settings@1effd53c" docStyleName="zootaxa.2007.monograph" docTitle="Gyropus scalaris Werneck 1942" docType="treatment" docVersion="6" lastPageId="16" lastPageNumber="17" masterDocId="FFADFC2EFFBFFFFD267E5649DD2D1865" masterDocTitle="A taxonomic catalog, including host and geographic distribution, of the species of the genus Gyropus Nitzsch (Phthiraptera: Amblycera: Gyropidae)" masterLastPageNumber="24" masterPageNumber="1" pageId="14" pageNumber="15" updateTime="1645556127074" updateUser="ExternalLinkService">
<document ID-DOI="http://doi.org/10.5281/zenodo.4592306" ID-GBIF-Dataset="e61aa52f-2e17-4afc-b30a-6cd468eea36b" ID-GBIF-Taxon="180302034" ID-ISSN="1545-1410" ID-Zenodo-Dep="4592306" ID-ZooBank="B8876E05-78A8-45FA-A34A-9FFB56741A20" checkinTime="1614695199489" checkinUser="felipe" docAuthor="Pérez, M. Julieta &amp; Díaz, M. Mónica" docDate="2018" docId="03970124E858FFE6FF5BB08A2EBC056C" docLanguage="en" docName="MammalSpecies.50.963.74-83.pdf" docOrigin="Mammalian Species 50 (963)" docSource="http://dx.doi.org/10.1093/mspecies/sey010" docStyle="DocumentStyle:E260F2FEBB038053A7447521347BED36.2:MammalSpecies.2016-.journal_article" docStyleId="E260F2FEBB038053A7447521347BED36" docStyleName="MammalSpecies.2016-.journal_article" docStyleVersion="2" docTitle="Octodontomys gliroides" docType="treatment" docVersion="4" lastPageId="6" lastPageNumber="80" masterDocId="FFAE795CE859FFE0FF8AB0412A6B0312" masterDocTitle="Octodontomys gliroides (Rodentia: Octodontidae)" masterLastPageNumber="83" masterPageNumber="74" pageId="1" pageNumber="75" updateTime="1643466530690" updateUser="ExternalLinkService" zenodo-license-document="CLOSED">
<document ID-DOI="http://doi.org/10.5281/zenodo.6228735" ID-GBIF-Dataset="aa7a2f2b-ea55-4ae2-863a-93bf3bdde535" ID-GBIF-Taxon="119379012" ID-ISSN="1175-5326" ID-Zenodo-Dep="6228735" checkinTime="1459984091607" checkinUser="plazi" docAuthor="Valim, Michel P. &amp; Linardi, Pedro Marcos" docDate="2008" docId="03948456FFB8FFFA26E952E1DE221F7B" docLanguage="en" docName="zt01899p024.pdf" docOrigin="Zootaxa 1899" docStyle="DocumentStylede.uka.ipd.idaho.easyIO.settings.Settings@1effd53c" docStyleName="zootaxa.2007.monograph" docTitle="Gyropus longus Neumann 1912" docType="treatment" docVersion="6" lastPageNumber="8" masterDocId="FFADFC2EFFBFFFFD267E5649DD2D1865" masterDocTitle="A taxonomic catalog, including host and geographic distribution, of the species of the genus Gyropus Nitzsch (Phthiraptera: Amblycera: Gyropidae)" masterLastPageNumber="24" masterPageNumber="1" pageId="7" pageNumber="8" updateTime="1645556127074" updateUser="ExternalLinkService">
<document ID-DOI="http://doi.org/10.5281/zenodo.7353039" ID-ISBN="0-89327-235-3" ID-Zenodo-Dep="7353039" approvalRequired="41" approvalRequired_for_document="2" approvalRequired_for_matCits="35" approvalRequired_for_originalDoi="1" approvalRequired_for_treatments="3" checkinTime="1665792792562" checkinUser="GgServerImporter" docAuthor="James H. Honacki, Kenneth E. Kinman &amp; James W. Koeppl" docDate="1982" docId="03BC87A94624FFB823F2F6CB530FF624" docLanguage="en" docName="MammalSpeciesofTheWorld.1982.Rodentia.560-594.pdf.imd" docOrigin="Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA: Alien Press, Inc. &amp; The Association of Systematics Collections" docTitle="Abrocoma bennetti Waterhouse 1837" docType="treatment" docVersion="3" lastPageNumber="585" masterDocId="FF85FFD1463DFFA12306FFF55074FFFA" masterDocTitle="Order Rodentia (Part 6)" masterLastPageNumber="594" masterPageNumber="560" pageNumber="585" updateTime="1669255589438" updateUser="ExternalLinkService">
<document ID-DOI="http://doi.org/10.5281/zenodo.7353083" ID-ISBN="1-56098-217-9" ID-Zenodo-Dep="7353083" approvalRequired="3" approvalRequired_for_document="2" approvalRequired_for_originalDoi="1" checkinTime="1667534037376" checkinUser="GgServerImporter" docAuthor="Charles A. Woods" docDate="1993" docId="E11F878EFFCAFFC5FF3DF9DBFC54D984" docLanguage="en" docName="MammalSpeciesofTheWorld.1993.Hystricognathi.771-806.pdf.imd" docOrigin="Mammal Species of the World (2 nd Edition), Washington and London: Smithsonian Institution Press" docTitle="Abrocoma bennetti Waterhouse 1837" docType="treatment" docVersion="3" lastPageNumber="789" masterDocId="1D26FFF6FFD8FFD7FFE1FC69FFB0DF05" masterDocTitle="Order Rodentia - Suborder Hystricognathi" masterLastPageNumber="806" masterPageNumber="771" pageNumber="789" updateTime="1669256602727" updateUser="ExternalLinkService">
<document ID-DOI="http://doi.org/10.5281/zenodo.7353083" ID-ISBN="1-56098-217-9" ID-Zenodo-Dep="7353083" approvalRequired="3" approvalRequired_for_document="2" approvalRequired_for_originalDoi="1" checkinTime="1667534037376" checkinUser="GgServerImporter" docAuthor="Charles A. Woods" docDate="1993" docId="E11F878EFFCAFFC5FF50F949FDC9DA9C" docLanguage="en" docName="MammalSpeciesofTheWorld.1993.Hystricognathi.771-806.pdf.imd" docOrigin="Mammal Species of the World (2 nd Edition), Washington and London: Smithsonian Institution Press" docTitle="Abrocoma Waterhouse 1837" docType="treatment" docVersion="3" lastPageNumber="789" masterDocId="1D26FFF6FFD8FFD7FFE1FC69FFB0DF05" masterDocTitle="Order Rodentia - Suborder Hystricognathi" masterLastPageNumber="806" masterPageNumber="771" pageNumber="789" updateTime="1669256602727" updateUser="ExternalLinkService">

generated via 

cat ../msw-plazi2/annotations.csv\
 | grep Donat\
 | cut -d ',' -f6\
 | sed 's/cut://g'\
 | sed 's+!/b.*$++g'\
 | sort\
 | uniq\
 | grep hash\
 | parallel "preston cat {1} | head -n1"
jhpoelen commented 1 year ago

So,according to Plazi's recent treatments-xml corpus, the assumed invalid name (i.e., Abrocoma bennetti without ii prefix) appears in:

Valim, Michel P., & Linardi, Pedro Marcos. (2008). Gyropus scalaris Werneck 1942. In A taxonomic catalog, including host and geographic distribution, of the species of the genus Gyropus Nitzsch (Phthiraptera: Amblycera: Gyropidae), pp. 1-24 in Zootaxa (Vol. 1899, pp. 15–17). Zenodo. https://doi.org/10.5281/zenodo.6228755

Pérez, M. Julieta, & Díaz, M. Mónica. (2018). Octodontomys gliroides. In Octodontomys gliroides (Rodentia: Octodontidae), pp. 74-83 in Mammalian Species (Vol. 50, Number 963, pp. 75–80). Zenodo. https://doi.org/10.5281/zenodo.4592306

Valim, Michel P., & Linardi, Pedro Marcos. (2008). Gyropus longus Neumann 1912. In A taxonomic catalog, including host and geographic distribution, of the species of the genus Gyropus Nitzsch (Phthiraptera: Amblycera: Gyropidae), pp. 1-24 in Zootaxa (Vol. 1899, p. 8). Zenodo. https://doi.org/10.5281/zenodo.6228735

James H. Honacki, Kenneth E. Kinman, & James W. Koeppl. (1982). Order Rodentia (Part 6). In Mammal Species of the World (1st Edition) (pp. 560–594). Alien Press, Inc. & The Association of Systematics Collections. https://doi.org/10.5281/zenodo.7353039

Charles A. Woods. (1993). Order Rodentia - Suborder Hystricognathi. In Mammal Species of the World (2nd Edition) (pp. 771–806). Smithsonian Institution Press. https://doi.org/10.5281/zenodo.7353083

and . . . annotations now exist to point to exactly which position of the texts they occur. You should actually be able to generate a little web widget that places the annotation exact on top of the location the suspected text occurs. . .