There is a newer version of this record available.

Dataset Open Access

CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary

Poelen, Jorrit; Upham, Nathan; Agosti, Donat; Ruschel, Tatiana; Guidoti, Marcus; Reeder, DeeAnn; Simmons, Nancy; Penev, Lyubomir; Dimitrova, Mariya; Csorba, Gabor; Groom, Quentin; Willoughby, Anna


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/datasets_under_review.tsv"
      }, 
      "checksum": "md5:9173f5ee0ec76fa88b148bec6e6c166c", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "datasets_under_review.tsv", 
      "type": "tsv", 
      "size": 3656
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/datasets.zip"
      }, 
      "checksum": "md5:e7732ccb720b0bb8c4c72de00415c80f", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "datasets.zip", 
      "type": "zip", 
      "size": 87204284
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/elton.jar"
      }, 
      "checksum": "md5:060da42bff9dfb0f488b6490efe7f4ab", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "elton.jar", 
      "type": "jar", 
      "size": 30990840
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/generate-report.log"
      }, 
      "checksum": "md5:88ecdd59b1e74b7089214a1883b273f2", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "generate-report.log", 
      "type": "log", 
      "size": 102144
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/generate-report.sh"
      }, 
      "checksum": "md5:5b94a46394463d66c13c5770598299a5", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "generate-report.sh", 
      "type": "sh", 
      "size": 6934
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/indexed_interactions_by_collection.tsv"
      }, 
      "checksum": "md5:632521e6700b947a77b06b890b26786d", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "indexed_interactions_by_collection.tsv", 
      "type": "tsv", 
      "size": 6499
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/indexed_interactions_full.tsv.gz"
      }, 
      "checksum": "md5:df5045907e995fa426d7570dd9b62efe", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "indexed_interactions_full.tsv.gz", 
      "type": "gz", 
      "size": 2231413
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/indexed_interactions_simple.tsv.gz"
      }, 
      "checksum": "md5:c90ab7a696e4f89a0725b68843e4c3c0", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "indexed_interactions_simple.tsv.gz", 
      "type": "gz", 
      "size": 321509
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/README"
      }, 
      "checksum": "md5:60b99045e63d96bf89c8bd2de70b8058", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "README", 
      "type": "", 
      "size": 6272
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/review_comments.tsv.gz"
      }, 
      "checksum": "md5:30e3c2c631d243c3387fdd5c5ffd1ae7", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "review_comments.tsv.gz", 
      "type": "gz", 
      "size": 7161780
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/review_summary_by_collection.tsv"
      }, 
      "checksum": "md5:7190347bae22bc14107a703736093e99", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "review_summary_by_collection.tsv", 
      "type": "tsv", 
      "size": 41883
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b/review_summary.tsv"
      }, 
      "checksum": "md5:12fa39207897f49a67d6b3b63bb64fa8", 
      "bucket": "3d285a36-668e-4230-8d00-3c84ffe75d8b", 
      "key": "review_summary.tsv", 
      "type": "tsv", 
      "size": 31599
    }
  ], 
  "owners": [
    7292
  ], 
  "doi": "10.5281/zenodo.3839098", 
  "stats": {
    "version_unique_downloads": 70.0, 
    "unique_views": 338.0, 
    "views": 380.0, 
    "version_views": 1183.0, 
    "unique_downloads": 34.0, 
    "version_unique_views": 1076.0, 
    "volume": 3840080195.0, 
    "version_downloads": 465.0, 
    "downloads": 355.0, 
    "version_volume": 9221587450.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.3839098", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.3838240", 
    "bucket": "https://zenodo.org/api/files/3d285a36-668e-4230-8d00-3c84ffe75d8b", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.3838240.svg", 
    "html": "https://zenodo.org/record/3839098", 
    "latest_html": "https://zenodo.org/record/4068958", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.3839098.svg", 
    "latest": "https://zenodo.org/api/records/4068958"
  }, 
  "conceptdoi": "10.5281/zenodo.3838240", 
  "created": "2020-05-22T03:55:30.633025+00:00", 
  "updated": "2020-10-06T19:52:27.674842+00:00", 
  "conceptrecid": "3838240", 
  "revision": 17, 
  "id": 3839098, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.3839098", 
    "description": "<p>This data publication originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action (https://cetaf.org/covid19-taf-communities-taking-action), a community-rooted initiative raised jointly by the Consortium of European Taxonomic Facilitaties (CETAF, https://cetaf.org) and Distributed Systems of Scientific Collections (DiSSCo, https://www.dissco.eu/).</p>\n\n<p>This archive contains the biodiversity datasets of interest identified in period 14 April-21 May 2020 through COVID19-TAF activities and subsequently indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org).&nbsp; GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, virus-host, parasite-host) by combining existing open datasets using open source software.</p>\n\n<p>These identified datasets (see references and reviews below) add to a growing collection of open species interaction datasets already indexed by GloBI. So, this data publication only includes a small subset of indexed datasets and include only datasets that were added as a direct consequence of COVID19-TAF activities of the biodiversity-related knowledge hub working group.</p>\n\n<p>If you have questions or comments about this publication, please open an issue at https://github.com/ParasiteTracker/tpt-reporting or contact the authors by email.</p>\n\n<p>Funding:<br>\nThe creation of this archive was made possible in part by reporting software developed as part of the National Science Foundation award &quot;Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease,&quot; Award numbers DBI:1901932 and DBI:1901926 . Also, this material is based upon work supported by the National Science Foundation under Grant No. DGE-1545433 .</p>\n\n<p>References:<br>\nJorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p>\n\n<p>GloBI Data Review Report</p>\n\n<p>Datasets under review:<br>\n&nbsp;- Marcus Guidoti, Tatiana Ruschel, Donat Agosti. 2020. Corona virus related biotic associations manually extracted from literature. Plazi. accessed via https://github.com/globalbioticinteractions/plazi-covid19/archive/326578b0d9f974760dcd2e962d86636a6487a6c0.zip on 2020-05-21T17:02:04.918Z<br>\n&nbsp;- De Rojas M, Do&ntilde;a J, Dimov I (2020) A comprehensive survey of Rhinonyssid mites (Mesostigmata: Rhinonyssidae) in Northwest Russia: New mite-host associations and prevalence data. Biodiversity Data Journal 8: e49535. https://doi.org/10.3897/BDJ.8.e49535 accessed via https://github.com/globalbioticinteractions/pensoft-table/archive/3488e0397ca4e083d5eca6949951e426a75713e3.zip on 2020-05-21T17:02:09.381Z<br>\n&nbsp;- Pensoft Darwin Core Archives with associateTaxa columns accessed via https://github.com/globalbioticinteractions/pensoft-dwca/archive/a3e075e4d7a03ba3605af144e3f2a4e55e4bdb03.zip on 2020-05-21T17:02:17.674Z<br>\n&nbsp;- Pensoft Darwin Core Archives available via Integrated Publication Toolkit accessed via https://github.com/globalbioticinteractions/pensoft-ipt/archive/4ad4b47978324681289e36f8c2b247b1bcc97b1a.zip on 2020-05-21T17:02:45.806Z<br>\n&nbsp;- Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., &amp; Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646&ndash;650. doi:10.1038/nature22975 accessed via https://github.com/globalbioticinteractions/olival2017/archive/f61070a5339d0e6c6e76d7eb4e2102decb52317d.zip on 2020-05-21T17:02:48.553Z<br>\n&nbsp;- Chen L, Liu B, Yang J, Jin Q, 2014. DBatVir: the database of bat-associated viruses. Database (Oxford). 2014:bau021. doi:10.1093/database/bau021 accessed via https://github.com/globalbioticinteractions/dbatvir/archive/bcfe5b7ada567771aedf291474c896dc94550681.zip on 2020-05-21T17:02:52.034Z<br>\n&nbsp;- Geiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org accessed via https://github.com/globalbioticinteractions/batplant/archive/1fe61d1e90335cf3716365d1322c79abde5a4ca7.zip on 2020-05-21T17:11:53.998Z<br>\n&nbsp;- Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Sch&auml;ffer, J. Rodney Brister, Virus Variation Resource &ndash; improved response to emergent viral outbreaks, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D482&ndash;D490, https://doi.org/10.1093/nar/gkw1065 . Data downloaded via https://www.ncbi.nlm.nih.gov/labs/virus/vssi on 2020-03-14 accessed via https://github.com/globalbioticinteractions/ncbi-virus/archive/60769efcda06b4719e358e3bae7bad93ccebabe6.zip on 2020-05-21T17:13:26.182Z<br>\n&nbsp;- Quentin J. Groom. 2020. Bat interation data manually extracted from literature. accessed via https://zenodo.org/record/3816676/files/qgroom/batinterations-v1.0.1.zip on 2020-05-22T02:13:51.699Z</p>\n\n<p>Generated on:<br>\n2020-05-22</p>\n\n<p>by:<br>\nGloBI&#39;s Elton 0.9.8<br>\n(see https://github.com/globalbioticinteractions/elton).</p>\n\n<p>Note that all files ending with .tsv are files formatted<br>\nas UTF8 encoded tab-separated values files.</p>\n\n<p>https://www.iana.org/assignments/media-types/text/tab-separated-values</p>\n\n<p><br>\nIncluded in this review archive are:</p>\n\n<p>README:<br>\n&nbsp; This file (lightly edited after initial automated generation).</p>\n\n<p>review_summary.tsv:<br>\n&nbsp; Summary across all reviewed collections of total number of distinct review comments.</p>\n\n<p>review_summary_by_collection.tsv:<br>\n&nbsp; Summary by reviewed collection of total number of distinct review comments.</p>\n\n<p>indexed_interactions_by_collection.tsv:<br>\n&nbsp; Summary of number of indexed interaction records by institutionCode and collectionCode.</p>\n\n<p>review_comments.tsv.gz:<br>\n&nbsp; All review comments by collection.</p>\n\n<p>indexed_interactions_full.tsv.gz:<br>\n&nbsp; All indexed interactions for all reviewed collections.</p>\n\n<p>indexed_interactions_simple.tsv.gz:<br>\n&nbsp; All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.</p>\n\n<p>datasets_under_review.tsv:<br>\n&nbsp; Details on the datasets under review.</p>\n\n<p>elton.jar:<br>\n&nbsp; Program used to update datasets and generate the review reports and associated indexed interactions.</p>\n\n<p>datasets.zip:<br>\n&nbsp; source datasets collected by elton in process of executing the generate_report.sh script.</p>\n\n<p>generate_report.sh:<br>\n&nbsp; program used to generate the report</p>\n\n<p>generate_report.log:<br>\n&nbsp; log file generated as part of running the generate_report.sh script</p>", 
    "language": "eng", 
    "title": "CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "relations": {
      "version": [
        {
          "count": 3, 
          "index": 1, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "3838240"
          }, 
          "is_last": false, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "4068958"
          }
        }
      ]
    }, 
    "communities": [
      {
        "id": "covid-19"
      }, 
      {
        "id": "zenodo"
      }
    ], 
    "version": "0.2", 
    "keywords": [
      "biodiversity", 
      "species interactions", 
      "virus-host", 
      "bats"
    ], 
    "publication_date": "2020-05-22", 
    "creators": [
      {
        "orcid": "0000-0003-3138-4118", 
        "affiliation": "Ronin Institute", 
        "name": "Poelen, Jorrit"
      }, 
      {
        "orcid": "0000-0001-5412-9342", 
        "affiliation": "Arizona State University", 
        "name": "Upham, Nathan"
      }, 
      {
        "orcid": "0000-0001-9286-1200", 
        "affiliation": "Plazi", 
        "name": "Agosti, Donat"
      }, 
      {
        "orcid": "0000-0002-9052-1760", 
        "name": "Ruschel, Tatiana"
      }, 
      {
        "orcid": "0000-0003-1744-6191", 
        "name": "Guidoti, Marcus"
      }, 
      {
        "orcid": "0000-0001-8651-2012", 
        "affiliation": "Bucknell University", 
        "name": "Reeder, DeeAnn"
      }, 
      {
        "orcid": "0000-0001-8807-7499", 
        "affiliation": "American Museum of Natural History", 
        "name": "Simmons, Nancy"
      }, 
      {
        "orcid": "0000-0002-2186-5033", 
        "affiliation": "Pensoft Publishers", 
        "name": "Penev, Lyubomir"
      }, 
      {
        "orcid": "0000-0002-8083-6048", 
        "affiliation": "Pensoft Publishers", 
        "name": "Dimitrova, Mariya"
      }, 
      {
        "orcid": "0000-0001-5720-4600", 
        "affiliation": "Hungarian Natural History Museum", 
        "name": "Csorba, Gabor"
      }, 
      {
        "orcid": "0000-0002-0596-5376", 
        "affiliation": "Agentschap Plantentuin Meise", 
        "name": "Groom, Quentin"
      }, 
      {
        "orcid": "0000-0002-0504-0605", 
        "affiliation": "University of Georgia: Athens, GA, US", 
        "name": "Willoughby, Anna"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "url", 
        "identifier": "https://github.com/globalbioticinteractions/elton", 
        "relation": "isSupplementTo", 
        "resource_type": "software"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3838240", 
        "relation": "isVersionOf"
      }
    ]
  }
}
1,183
465
views
downloads
All versions This version
Views 1,183380
Downloads 465355
Data volume 9.2 GB3.8 GB
Unique views 1,076338
Unique downloads 7034

Share

Cite as