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pmid:31274982
Biodiversidata: An Open-Access Biodiversity Database for Uruguay.
Florencia Grattarola · Germán Botto · Inés da Rosa · Noelia Gobel · Enrique M González · Javier González · Daniel Hernández · Gabriel Laufer · Raúl Maneyro · Juan A Martínez-Lanfranco · Daniel E Naya · Ana L Rodales · Lucía Ziegler · Daniel Pincheira-Donoso
Biodiversity data journal · 2019 doi:10.3897/BDJ.7.e36226
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Experiment
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Complete file
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However, despite the biological significance of Uruguay for the South American subcontinent, the distribution of biodiversity patterns in this country remain poorly understood, given the severe gaps in available records of geographic species distributions. Currently, national biodiversity datasets are not openly available and, thus, a dominant proportion of the primary biodiversity data produced by researchers and institutions across Uruguay remains highly dispersed and difficult to access for the wider scientific and environmental community. In this paper, we aim to fill this gap by developing the first comprehensive, open-access database of biodiversity records for Uruguay (Biodiversidata), which is the result of a large-scale collaboration involving experts working across the entire range of taxonomic diversity found in the country.\nNEW INFORMATION: As part of the first phase of Biodiversidata, we here present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates. The database provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country. The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https://doi.org/10.5281/zenodo.2650169. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date and it represents the first open repository for the country.", "claims": [{"id": "claim-data-access", "statement": "The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https://doi.org/10.5281/zenodo.2650169.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31274982", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https://doi.org/10.5281/zenodo.2650169."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31274982"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31274982", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3897/BDJ.7.e36226", "sha256": "sha256:0b7cdeaca630841545c8045abb5714084956d0c4990ea576396dec8736ac9a94", "bytes": 40574, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3897/BDJ.7.e36226", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6597616", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:31274982:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dd0795bca7405df82c957e1c649bcd43f9396c6c38d50f837dc75f836b0fb670", "bytes": 790, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#T5184678", "version": null, "note": "Records collected per tetrapod class showing: number of occurrence records (non-duplicated records/location/year), total number of species, records without information of the date of collection and records collected in the last 30 years, with percentage in parentheses.", "structure": {"pmcid": "PMC6597616", "section_index": 2, "section_title": "First open biodiversity database of Uruguay", "row_count": 6, "column_count": 5}, "table": {"label": "Table 1.", "caption": "Records collected per tetrapod class showing: number of occurrence records (non-duplicated records/location/year), total number of species, records without information of the date of collection and records collected in the last 30 years, with percentage in parentheses.", "rows": [["", "Number of Occurrence Records", "Number of Species", "Records without Date (%)", "Records from the last 30 years (%)"], ["Amphibia", "2,530", "51", "1,780 (70.4)", "683 (27.0)"], ["Reptilia", "2,308", "68", "1,999 (86.6)", "224 (9.7)"], ["Aves", "60,627", "437", "131 (0.2)", "60,308 (99.5)"], ["Mammalia", "3,915", "117", "1,687 (43.1)", "1,122 (28.7)"], ["Total", "69,380", "673", "", ""]], "row_count": 6, "column_count": 5, "numeric_cells": 19, "header_rows": 0, "locator": "section[2]/table-wrap[1]#T5184678"}}, {"id": "asset:table:pmid:31274982:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b54c74e0de238329dab88d7cffea055c1dd6befd7acabdf801546970a715e2d8", "bytes": 3501, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T5199711", "version": null, "note": "List of sources used to build the dataset, including the source type and the number of records extracted from each of the sources.", "structure": {"pmcid": "PMC6597616", "section_index": 4, "section_title": "Sampling description", "row_count": 54, "column_count": 4}, "table": {"label": "Table 2.", "caption": "List of sources used to build the dataset, including the source type and the number of records extracted from each of the sources.", "rows": [["Source", "Source type", "Number of records", "Groups"], ["Abreu (2015)", "Journal Article", "8", "Aves"], ["Andrade-Núñez and Aide (2010)", "Journal Article", "13", "Mammalia"], ["Azpiroz et al. (2012)", "Journal Article", "54", "Aves"], ["Bardier and Maneyro (2015)", "Journal Article", "20", "Amphibia"], ["Borteiro et al. (2006)", "Journal Article", "70", "Reptilia"], ["Borteiro et al. (2009)", "Journal Article", "1", "Reptilia"], ["Borteiro et al. (2013)", "Journal Article", "4", "Reptilia"], ["Borteiro et al. (2015)", "Journal Article", "13", "Reptilia"], ["Bou (2013)", "Thesis", "86", "Mammalia"], ["Carreira and Achaval (2007)", "Journal Article", "2", "Reptilia"], ["Carreira and Lombardo (2006)", "Journal Article", "1", "Reptilia"], ["Carreira et al. (2005)", "Book", "1880", "Reptilia"], ["Carreira et al. (2012)", "Journal Article", "2", "Reptilia"], ["Colina et al. (2012)", "Journal Article", "1", "Reptilia"], ["da Rosa", "This study", "13", "Amphibia + Reptilia"], ["de Giorgi Peirano (2016)", "Thesis", "67", "Aves"], ["Elgue and Maneyro (2017)", "Journal Article", "1", "Amphibia"], ["GBIF.org", "Online Database", "58355", "Amphibia + Reptilia + Aves + Mammalia"], ["Gobel & Laufer", "This study", "285", "Amphibia + Reptilia"], ["González-Paredes et al. (2017)", "Journal Article", "3", "Reptilia"], ["González & González", "This study", "1848", "Mammalia"], ["Grattarola", "This study", "53", "Mammalia"], ["Grattarola (2015)", "Thesis", "36", "Mammalia"], ["Hernández", "This study", "944", "Aves"], ["Kolenc et al. (2009)", "Journal Article", "2", "Amphibia"], ["Kolenc et al. (2012)", "Journal Article", "2", "Amphibia"], ["Kwet et al. (2002)", "Journal Article", "1", "Amphibia"], ["Lareschi et al. (2006)", "Journal Article", "11", "Mammalia"], ["Laufer et al. (2009)", "Journal Article", "2", "Amphibia"], ["Maneyro et al. (2008)", "Journal Article", "2", "Amphibia"], ["Maneyro", "This study", "165", "Amphibia + Reptilia"], ["Martínez-Lanfranco et al. (2010)", "Journal Article", "6", "Mammalia"], ["Martínez-Lanfranco", "This study", "1712", "Aves + Mammalia"], ["Masciadri et al. (2007)", "Conference Paper", "48", "Amphibia + Reptilia + Aves"], ["Montero (2016)", "Journal Article", "85", "Reptilia"], ["Naya and Achaval (2006)", "Journal Article", "5", "Mammalia"], ["Naya", "This study", "220", "Aves"], ["Núñez et al. (2004)", "Book", "1764", "Amphibia"], ["Prigioni et al. (2011)", "Journal Article", "43", "Amphibia + Reptilia"], ["Prigioni et al. (2013)", "Journal Article", "18", "Reptilia"], ["Prigioni et al. (2018)", "Journal Article", "3", "Mammalia"], ["Queirolo (2016)", "Journal Article", "1041", "Mammalia"], ["Rodales, Botto & González", "This study", "91", "Mammalia"], ["Rodríguez-Cajarville et al. (2017)", "Journal Article", "4", "Aves"], ["Rodríguez-Mazzini et al. 2001", "Report", "151", "Amphibia + Reptilia + Mammalia"], ["Santana et al. (2013)", "Journal Article", "1", "Amphibia"], ["Sarroca et al. 2009", "Report", "189", "Amphibia + Reptilia + Aves + Mammalia"], ["Vaz-Canosa and Rodríguez-Cajarville (2015)", "Journal Article", "1", "Aves"], ["Velasco-Charpentier et al. (2016)", "Journal Article", "4", "Reptilia"], ["Verrastro et al. (2006)", "Journal Article", "3", "Reptilia"], ["Verrastro et al. 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