plazi or the challenge to free biodiversity data caught in hundreds of millions of pages of over 250...
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Donat Agosti, Plazi
Opportunities & Challenges of Citizen Science ETH Zentrum, Zurich
23.1.2015
Plazi or the challenge to free biodiversity data caught in hundreds
of millions of pages of over 250 years of scientific publications
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4 years after the Rio Earth Summit
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Image of ant book : not an easy social taskHarvard libraryOne book
1996: The Museum of Comparative
Zoology at Harvard University as the only
place on Earth with a complete collection of
ant taxonomic publications.
The ant community got together to create a
standard protocol to collect ants
1996
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14 years after the Rio Earth Summit
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Image of online catalogue and libraryAccess to everybody
2006: Antbase.org allowed as a first of its kind online open access to
all the literature with up to 10,000 visitors per month.
2006
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23 years after the Rio Earth Summit
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45,000,000 pages scanned by theBiodiversity Heritage Library; many more, but private digital repositories
Millions of specimens digitized
Better than before
2015
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23 years after the Rio Earth Summit
2015
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These are only scans of a fraction of theestimated 500,000,000 pages with poorOCR.
We still have no complete «phone book» of the species of the world, nor access tothe data provided when they have beendescribed or re-used.
2015
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because23 years after the Rio Earth Summit
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Taxonomic publications
PDFs are stupid –only we canunderstand them, lots of them arecopyrighted
despite…
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Text
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identifier="193329"/>
<tax:xmldata>
<dc:Genus>Mystrium</dc:Genus>
<dc:Species>leonie</dc:Species>
</tax:xmldata>
Mystrium leonie
</tax:name>
<tax:status>n. sp.</tax:status>
Fig 1 D - F
</tax:nomenclature>
<tax:div type="description">
<tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI 93, SL
1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin
to a sharp apical tooth, the apex parallel to the anterior
(Holotype with material in mandibles, so mandibles and
$ described below from paratypes.) Median clypeus
....
</treatment>
Semanticallyenhanced text
… alternatives: From human to machine readable text
RDF
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What does this mean?
The Linking Open Data cloud diagram
Linked Open Data Cloud
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zt03131p034lsid:zoobank.org:pub:8EDE33EB-3C43-4DFA-A1F4-5CC86DED76C8 http://treatment.plazi.org/id/BDA70EC9-F8AB-AED6-C2B7-628596A1714AJeremy Miller http://orcid.org/0000-0001-8918-9775Pardosa zyuzininew species
Developing persistent and openly accessible digital taxonomic literature
Pardosa zyuzini Kronestedt & Marusik, 2011
Torbjörn Kronestedt & Yuri M. Marusik, 2011, Studies on species of Holarctic Pardosa groups (Araneae, Lycosidae). VII. The Pardosa tesquorum group, Zootaxa 3131, pp. 1-34: 25-28. DOI: 10.5281/zenodo.10109
Pardosa zyuzini sp. nov.
Figs 7-8, 22-23, 28, 31, 94-106, 116
Pardosa paratesquorum (misidentification, in part): Schenkel 1963: 360, fig. 208b (♀, not ♂) Plazi.
Pardosa paratesquorum (misidentification): Logunov & Marusik 1995: 115 Plazi; Marusik et al. 1996: 35-36 Plazi; Logunov et al. 1998: 139 Plazi; Marusik & Logunov 1999: 247 Plazi.
Pardosa cf. paratesquorum . Marusik et al. 2000: 84 Plazi; Marusik & Buchar 2003: 157 Plazi; Logunov & Marusik 2004: 63 Plazi.
Pardosa sp. 2: Marusik & Logunov 2009: 151 Plazi.
Type material.Holotype♂ and GoogleMaps allotype ♀ from MONGOLIA, Oevoerkhangai Aimag, Zuunbayan-Ulaan Somon, ZamtynDavaa GoogleMaps (46°43'N102°51'E),2000 m,14-18 June 1997(Y.M. Marusik) in ZMMU. - GoogleMapsParatypes.MONGOLIA. OevoerkhangaiAimag GoogleMaps . same data as holotype (CAS, GoogleMaps ISEA, GoogleMapsIZAS, GoogleMaps NHRS, GoogleMaps ZMMU), GoogleMaps 110♂ 44 ♀. GoogleMaps Bayankhongor Aimag. Gurvanbulag Somon, Lake Khokh-Nuur GoogleMaps (47 ° 32'N98 ° 32'E),2600 m,7-10 June 1997(Y.M.,IBPN), 10♂. GoogleMapsAssonge, Tola (Tuul) River ,1909(du Chazaud,MNHN), 1♀ . Arkhangai Aimag. Uu-bulan, Saikhany saravi ,24 June 1976(TsugEnkhtuyaa,IBPN), 1♂ 1♀. - RUSSIA.Altai: 8 km S of Chagan-Uzun Village GoogleMaps (50°04’N,88°24’ E),1800m, grassy bank of Chuya River,13 June 2009(A.A. Fomichev,ISEA), 2♀ GoogleMaps ; 2 km SE of Kosh-Agach ,27 June 1996(A. & R. Dudko,ISEA), 1♂ ; 70-75 km W of Kosh-Agach,40-45 km W of Bel'tir , Taltura (Chagan-Uzun) River canyon ,2300-2500 m, mountain stony steppe,26-28 June 1999(V.V. Glupov,ISEA), 2♂ 1♀ ; Kosh-Agach VillageGoogleMaps (50°01'N,88°38'E),1800m, saline swamps,13 July 2009(A.A. Fomichev,ISEA), 1♂2♀ GoogleMaps . Tuva: MongunTaiga Distr.,12 km downstream from Mugur-Aksy by Kargy River ,1800 m, river bank,14 June 1989(D.L.,ISEA:SZM 001.1505), 2♂ 1♀ ; SE part of Kyzyl , steppe,22-24 July 1996(Y.M.,IBPN), 3♂ 2♀ ; Ovyur Distr, pass between Sagly and Onachy rivers ,2200 m, ca20-25 km W of Sagly Village , wet habitats,13 June 1989(D.L.,ISEA:SZM 001.1506), 2♂ ; Ulug-Khem Dist.,6-7 km E of Choduraa, Chulaanych site , near creek,10 May 1990(D.L.,ISEA:SZM 001.1514), 14♂ ; Tere-Khol' Lake, Sharlaa stand and around GoogleMaps (50 ° 1.47'N95° 3.45'E),1050 m,6- 14 July 1996(Y.M.,ISEA), 19♂ 6♀ GoogleMaps ; 30-35 km W of Erzin, Shara-NurLake GoogleMaps(50°12'N,94°32'E),900 m,8 June 1995(Y.M.,ISEA:SZM 001.1512), 5♂ 7♀ GoogleMaps ; Erzin Distr.,20 km NW of Erzin Village, Dus-Khol' Lake, Tes-Khem River ,800 m,31 May 1989(D.L.,ISEA:SZM 001.1515 & 001.1517), 39♂ 14♀ ; ~20 km WNW of Erzin, Dus-Khol' Lake
Treatment
about services projects communications Legal advocacy files
KingdomPhylumClassOrderFamilyGenus
Animalia [224130, 24756]Arthropoda [1869565, 15066]Arachnida [2959, 6934]Araneae [2785, 5430]Lycosidae [90, 850]Pardosa [35, 557]
2020
2000
1980
1960
Pardosa zyuziniKronestedt & Marusik 2011
Pardosa sp. 2Marusik & Logunov 2009
Pardosa cr. paratesquorumLogunov & Marusik 2004Marusik & Buchar 2003
Marusik et al. 2000 Pardosa paratesquorumMarusik & Logunov 1999
Logunov et al. 1998Marusik et al. 1996
Logunov & Marusik 1995
Expand all
Taxonomy [treatments, specimens]
Specimens
Pardosa paratesquorumSchenkel 1963
Verbatim Taxon Name
Taxonomic Status
Treatment
RDA of cited treatments
Count of treatments and specimens for and Taxon Kingdom, Taxon Phylum, Taxon Class, Taxon Order, Taxon Family, Taxon Genus for this species (e.g., Pardosa zyuzini)
Taxon Name Authority (1) Authority (2) Year
mods:identifier
Map of georeferenced points
publication IDpublication LSIDpersistent identifiertreatment provided byscientific namestatus
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FIGURES 29–31. Epigynes in dorsal view. 29, Pardosa eskovisp. nov. (from Yakutia: Suntar). 30, P. mulaiki Gertsch (from Saskatchewan: Hanley). 31, P. zyuzini sp. nov. (from type locality). cd, copulatory duct; sp, spermatheca. Scale line (applies
FIGURES 94–101. Pardosa zyuzini sp. nov. 94, left bulbus, ventral view. 95–96, left terminal part of bulbus in ventral (95) and retrolateral (96) view. 97, left male palp (patella, tibia and cymbium), dorsal view. 98, embolus of left palp,
FIGURES 102–106. Pardosa zyuzini sp. nov., male (from type locality). 99, terminal part of left bulbus in ventral (102), retrolateral (103) and ventro-frontal (104) view. 105, left tegulum with tegular apophysis in ventral view. 106, tarsus and
FIGURE 116. Distribution of Pardosa eskovi sp. nov. (■), P. mulaiki (), P. paratesquorum (), P. tesquorumoides () and
DownloadsDarwin Core materials citationsDarwin Core ArchivePlain XMLTaxonX
Shared with
Treatment reference graph
Pardosa zyuziniKronestedt & Marusik 2011
Schenkel 1963
2020
2000
1980
1960
Marusik & Logunov 2009
Logunov & Marusik 1995
Logunov & Marusik 2004
Logunov et al. 1998
Marusik & Buchar 2003
Marusik & Logunov 1999
Marusik et al. 1996
Marusik et al. 2000
view. 1, Pardosa eskovi sp. nov.♀ from Yakutia: Suntar. 2–3, P. mulaiki Gertsch ♂ (2) ♀ (3), both from Saskatchewan: Rosetown. 4, P. paratesquorum Schenkel ♂(paratype of P. daqingshanicaTang, Urita &
ventral view. 19, Pardosa eskovisp. nov. (from Yakutia: Suntar). 20, P. mulaiki Gertsch (from Saskatchewan). 21, P. tesquorumoides Song & Yu (from Sichuan: Hongyuan Co.). 22–23, P. zyuzini sp. nov. (from
ventral view. 25, Pardosa eskovisp. nov. (Yakutia: Suntar). 26, P. mulaiki Gertsch (from Saskatchewan: Hanley). 27, P. tesquorumoides Song & Yu (from Sichuan: Hongyuan Co.). 28, P. zyuzini sp. nov. (from type
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Journal of Hymenoptera Research
5170 specimens
4062 plottable specimens from
1138 unique locations
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Treatment
Plazi Search and Retrieval Server: Access to data
DwC-A
You
You
You
human
machine
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Treatment
Linking of treatments to external resources
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Pseudomyrmex ants and Vachellia ant-acaciasare a classic example of mutualism in biology.
allenii
melanoceras
ruddiae
chiapensis
collinsii
cookii
cornigera
globulifera
hindsii
janzenii
mayana
sphaerocephala
boopis
flavicornis
hesperius
ita
janzenikuenckeli
mixtecus
nigrocinctus
nigropilosus
opaciceps
particeps
peperi
reconditus
satanicus
simulansspinicola
subtilissimus
veneficus
ferrugineus
gentlei
gracilis
Transbiotic link networkAssociated species linked throughreferences in taxonomic treatments
Acacia-ant species: Pseudomyrmex gracili
Treatment: redescription
Associated ant-acacia: Acacia gentlei
Ants Plants
Photocredits: Alex Wild
Treatment
Treatments linked through citations
Treatment
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Solution: Biodiversity Literature Repository @ Zenodo/CERN
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• Swiss based international NGO andSME
• Founded in 2008• Mission to foster (Open Access) Linked
Open (scientific) Data• EU and volunteer support
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Build as start a TreatmentBank that
includes direct access to 1 million
citable treatments, related metadata
and digital copies of the source
publications
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Goal: Giant Global Species Graph
LegalSocialTechnicalOntologiesInfrastructure
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The paradox
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Citizen Scientists (red, probably gray) create discoveries:
Current descriptions of new species in Europe (10 years: 5881 species.)
http://127.0.0.1:8081/plosone/article?id=info:doi/10.1371/journal.pone.0036881
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Citizen scientists aka amateurs are majorcontributors to this knowledge.
They have at best a difficult access to itsdigital content. Even more so in the South, where most of the biodiversity is.
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In fact: citizen scientists have to discoverthe world’s biodiversity a second time - bymaking it digitally accessible this time.
The double work of citizen scientists
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The challenge
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Scientists and funding can only do so much.
digitizing collaboration, Open Access, sharing
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How can we mobilize citizen scientists tocomplement the scientists’ effort to buildan Open Biodiversity Knowledge Commons by creating semanticallyenhanced, linked data out of 500,000,000 million printed pages, 10s of millions of digitized specimens, gene sequences, etc?
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I want to be able to find out what speciesthis ant is and whether I can still see thisant in 20 years here in the mediterraneancity of Zurich.
I want to know how many species live on Earth.
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Links
LinksFurther reading: http://plazi.org/?q=plazi_publicationsCatapano, 2011 (http://www.ncbi.nlm.nih.gov/books/NBK47081/)Bouchout Declaration (http://bouchoutdeclaration.org)Blue List (http://plazi.org/?q=blue_list)Biodiversity Literature Repository (https://zenodo.org/collection/user-biosyslitZenodo (https://zenodo.org/about)Refindit (http://refindit.org)Refbank (http://refbank.org)Pro-iBiosphere (http://pro-ibiosphere.eu/)Introduction to persistent identifiers (http://wiki.pro-ibiosphere.eu/wiki/Best_practices_for_stable_URIs)
Twitter@plazi_treat; @bouchoutdec, @myrmoteras
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Additional resources on the impact of amateurs (By Frank Krell)
In Austria about fifteen years ago, four fifth of all entomologists were amateurs (Malicky 1978). In a recent compilation of the entomologists of Rhenania (Germany) of the last 250 years Evers (1992: 100) found out that only 23 % of the living entomologists are professionals, 77 % are amateurs (n = 78), 13 % of the deceased entomologists are professionals and 87 % amateurs (n = 111), altogether 17 % are professionals and 83 % amateurs (n = 189). At least in Central and Western Europe and Japan, the situation the same. Bello et al. (1992) imparted that 13 % of Spanish taxonomists were amateurs (56 % are professionals, 16 % have a temporary status, relying on grants, 13 % are "Other").I don’t know if there is anything newer. The references cited areBello, E. & Becerra, J.M. & G.-Valdecasas, A. 1992. Counting on taxonomy. Nature 357: 531.Evers, A.M.J. 1992. Entomologie und Entomologen des Rheinlandes, insbesondere des Niederrheins. Entomologische Blätter für Biologie und Systematik der Käfer 88: 93-102.Malicky, H. 1978. Am Beispiel der Entomologie. Amateurwissenschaftler und Amateurforschung. Österreichische Hochschulzeitung 30(4): 19-20.