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21 results for “biogeographic databases”
Database of weeds in cultivation fields of France and UK, with ecological and biogeographical information
<p>The database includes a list of 1577 weed plant taxa found in cultivated fields of France and UK, along with basic ecological and biogeographical information.<br> The database is a CSV file in which the columns are separated with comma, and the decimal sign is ".".<br> It can be imported in R with the command "tax.discoweed <- read.csv("tax.discoweed_18Dec2017_zenodo.csv", header=T, sep=",", dec=".", stringsAsFactors = F)"</p> <p>Taxonomic information is based on TaxRef v10 (Gargominy et al. 2016),<br> - 'taxref10.CD_REF' = code of the accepted name of the taxon in TaxRef,<br> - 'binome.discoweed' = corresponding latine name,<br> - 'family' = family name (following APG III),<br> - 'taxo' = taxonomic rank of the taxon, either 'binome' (species level) or 'infra' (infraspecific level),<br> - 'binome.discoweed.noinfra' = latine name of the superior taxon at species level (different from 'binome.discoweed' for infrataxa),<br> - 'taxref10.CD_REF.noinfra' = code of the accepted name of the superior taxon at species level.</p> <p>The presence of each taxon in one or several of the following data sources is reported:<br> - Species list from a reference flora (observations in cultivated fields over the long term, without sampling protocol),<br> * 'jauzein' = national and comprehensive flora in France (Jauzein 1995),<br> - Species lists from plot-based inventories in cultivated fields,<br> * 'za' = regional survey in 'Zone Atelier Plaine & Val de Sèvre' in SW France (Gaba et al. 2010),<br> * 'biovigilance' = national survey of cultivated fields in France (Biovigilance, Fried et al. 2008),<br> * 'fse' = Farm Scale Evaluations in England and Scotland, UK (Perry, Rothery, Clark et al., 2003),<br> * 'farmbio' = Farm4Bio survey, farms in south east and south west of England, UK (Holland et al., 2013)<br> - Reference list of segetal species (species specialist of arable fields),<br> * 'cambacedes' = reference list in France (Cambacedes et al. 2002)</p> <p>Life form information is extracted from Julve (2014) and provided in the column 'lifeform'.<br> The classification follows a simplified Raunkiaer classification (therophyte, hemicryptophyte, geophyte, phanerophyte-chamaephyte and liana). Regularly biannual plants are included in hemicryptophytes, while plants that can be both annual and biannual are assigned to therophytes.</p> <p>Biogeographic zones are also extracted from Julve (2014) and provided in the column 'biogeo'.<br> The main categories are 'atlantic', 'circumboreal', 'cosmopolitan, 'Eurasian', 'European', 'holarctic', 'introduced', 'Mediterranean', 'orophyte' and 'subtropical'.<br> In some cases, a precision is included within brackets after the category name. For instance, 'introduced(North America)' indicates that the taxon is introduced from North America.<br> In addition, some taxa are local endemics ('Aquitanian', 'Catalan', 'Corsican', 'corso-sard', 'ligure', 'Provencal').<br> A single taxon is classified 'arctic-alpine'.</p> <p>Red list status of weed taxa is derived for France and UK:<br> - 'red.FR' is the status following the assessment of the French National Museum of Natural History (2012),<br> - 'red.UK' is based on the Red List of vascular plants of Cheffings and Farrell (2005), last updated in 2006.<br> The categories are coded following the IUCN nomenclature.</p> <p>A habitat index is provided in column 'module', derived from a network-based analysis of plant communities in open herbaceous vegetation in France (Divgrass database, Violle et al. 2015, Carboni et al. 2016).<br> The main habitat categories of weeds are coded following the Divgrass classification,<br> - 1 = Dry calcareous grasslands<br> - 3 = Mesic grasslands<br> - 5 = Ruderal and trampled grasslands<br> - 9 = Mesophilous and nitrophilous fringes (hedgerows, forest edges...)<br> Taxa belonging to other habitats in Divgrass are coded 99, while the taxa absent from Divgrass have a 'NA' value.</p> <p>Two indexes of ecological specialization are provided based on the frequency of weed taxa in different habitats of the Divgrass database.<br> The indexes are network-based metrics proposed by Guimera and Amaral (2005),<br> - c = coefficient of participation, i.e., the propensity of taxa to be present in diverse habitats, from 0 (specialist, present in a single habitat) to 1 (generalist equally represented in all habitats),<br> - z = within-module degree, i.e., a standardized measure of the frequency of a taxon in its habitat; it is negatve when the taxon is less frequent than average in this habitat, and positive otherwise; the index scales as a number of standard deviations from the mean.</p>
Figure 9 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 9 - Top: to retrieve a scanned BHL book document from BHL click on the "Download Contents" icon on the top-right and select to browse the corresponding web page on the Internet Archive ("View at Internet Archive"). Bottom: The link to the jpeg2000 (JP2) image is found on the bottom right. Sources: top: http://biodiversitylibrary.org/page/9663476; bottom: https://archive.org/details/mittheilungenaus17staz.
Figure 3 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 3 - Examples of stylistic and typographic elements in legacy publications that delay the structured extraction of data: a) ranges or more than one value in one field; b) non-metric units which have to be converted to the SI system; c and d) unclear meaning of symbols; e) font type may cause problems in reading and/or optical character recognition (e.g. misinterpreting an "e" as "c" or "o"; "ll" as "11" or "U", "C" as "C" or "O") (based on a slide by Aglaia Legaki, Gabriella Papastefanou and Marilena Tsompanou).
Figure 10 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 10 - Open Data: an emerging landscape of data and other academic publications (based on a slide by Dmitry Schigel).
Figure 8 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 8 - Plazi workflow: from the publication through different levels of data processing to final availability of structured data.
Figure 5 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 5 - Biodiversity related articles and instructions to the authors available on the Biodiversity Literature Repository home page.
Figure 2 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 2 - Stations without coordinates (red box) are commonly listed, as well as non-SI units, here: depth as fathoms (based on a slide by Aglaia Legaki, Gabriella Papastefanou and Marilena Tsompanou).
Figure 4 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 4 - Complex natural language features that can lead to incorrect species-occurrence extraction (based on a slide by Aglaia Legaki, Gabriella Papastefanou and Marilena Tsompanou).
Figure 6 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 6 - Calman (1906) is available in BLR as https://zenodo.org/record/14941. The taxonomic treatment of Leucon longirostris G.O. Sars (shown above) extracted from this expedition document is also avaible in BLR: https://zenodo.org/record/14942. Both links have unique DOIs assigned to them and thus are also retrievable as https://doi.org/10.5281/zenodo.14941, and https://doi.org/10.5281/zenodo.14942, accordingly.
Figure 1 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 1 - Workflow depicting the process of manually extracting data from legacy literature workflow, as currently performed in in EMODnet WP4. Abbreviations: OCR = Optical Character Recognition; OBIS = Ocean Biogeographic Information System; DwC = Darwin Core; IPT = Integrated Publishing Toolkit; medOBIS = Mediterranean Ocean Biogeographic Information System, GBIF = Global Biodiversity Information Facility
Figure 6 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 6 - Calman 1906 is available in BLR as https://zenodo.org/record/14941. The taxonomic treatment of Leucon longirostris G.O. Sars (shown above) extracted from this expedition document is also avaible in BLR: https://zenodo.org/record/14942. Both links have unique DOIs assigned to them and thus are also retrievable as https://doi.org/10.5281/zenodo.14941, and https://doi.org/10.5281/zenodo.14942, accordingly.
Figure 2 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 2 - Stations without coordinates (red box) are commonly listed, as well as non-SI units, here: depth as fathoms (based on a slide by Aglaia Legaki, Gabriella Papastefanou and Marilena Tsompanou).
Figure 9 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 9 - Top: to retrieve a scanned BHL book document from BHL click on the "Download Contents" icon on the top-right and select to browse the corresponding web page on the Internet Archive ("View at Internet Archive"). Bottom: The link to the jpeg2000 (JP2) image is found on the bottom right. Sources: top: http://biodiversitylibrary.org/page/9663476; bottom: https://archive.org/details/mittheilungenaus17staz.
Figure 8 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 8 - Plazi workflow: from the publication through different levels of data processing to final availability of structured data.
Figure 10 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 10 - Open Data: an emerging landscape of data and other academic publications (based on a slide by Dmitry Schigel).
Figure 1 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 1 - Workflow depicting the process of manually extracting data from legacy literature workflow, as currently performed in in EMODnet WP4. Abbreviations: OCR = Optical Character Recognition; OBIS = Ocean Biogeographic Information System; DwC = Darwin Core; IPT = Integrated Publishing Toolkit; medOBIS = Mediterranean Ocean Biogeographic Information System.
Figure 5 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 5 - Biodiversity related articles and instructions to the authors available on the Biodiversity Literature Repository home page.
Figure 4 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 4 - Complex natural language features that can lead to incorrect species-occurrence extraction (based on a slide by Aglaia Legaki, Gabriella Papastefanou and Marilena Tsompanou).
Figure 3 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. https://doi.org/10.3897/rio.2.e9774
Figure 3 - Examples of stylistic and typographic elements in legacy publications that delay the structured extraction of data: a) ranges or more than one value in one field; b) non-metric units which have to be converted to the SI system; c and d) unclear meaning of symbols; e) font type may cause problems in reading and/or optical character recognition (e.g. misinterpreting an "e" as "c" or "o"; "ll" as "11" or "U", "C" as "C" or "O") (based on a slide by Aglaia Legaki, Gabriella Papastefanou and Marilena Tsompanou).
Figure 7 from: Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e10445. https://doi.org/10.3897/rio.2.e10445
Figure 7 - Example of a parsed materials citation in the GoldenGATE-Imagine editor
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.