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

2020-05-22T04:45:29Z (GMT) by Poelen, Jorrit

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This data publication originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action, a community-rooted initiative raised jointly by the Consortium of European Taxonomic Facilitaties (CETAF) and Distributed Systems of Scientific Collections (DiSSCo).

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).  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.

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.

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.

Funding:
The creation of this archive was made possible in part by reporting software developed as part of the National Science Foundation award "Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease," Award numbers DBI:1901932 and DBI:1901926 .

References:
Jorrit 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.

GloBI Data Review Report

Datasets under review:
 - 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
 - De Rojas M, Doña 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
 - 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
 - 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
 - Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., & Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646–650. doi:10.1038/nature22975 accessed via https://github.com/globalbioticinteractions/olival2017/archive/f61070a5339d0e6c6e76d7eb4e2102decb52317d.zip on 2020-05-21T17:02:48.553Z
 - 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
 - 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
 - Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister, Virus Variation Resource – improved response to emergent viral outbreaks, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D482–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
 - 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

Generated on:
2020-05-22

by:
GloBI's Elton 0.9.8
(see https://github.com/globalbioticinteractions/elton).

Note that all files ending with .tsv are files formatted
as UTF8 encoded tab-separated values files.

https://www.iana.org/assignments/media-types/text/tab-separated-values


Included in this review archive are:

README:
  This file (lightly edited after initial automated generation).

review_summary.tsv:
  Summary across all reviewed collections of total number of distinct review comments.

review_summary_by_collection.tsv:
  Summary by reviewed collection of total number of distinct review comments.

indexed_interactions_by_collection.tsv:
  Summary of number of indexed interaction records by institutionCode and collectionCode.

review_comments.tsv.gz:
  All review comments by collection.

indexed_interactions_full.tsv.gz:
  All indexed interactions for all reviewed collections.

indexed_interactions_simple.tsv.gz:
  All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.

datasets_under_review.tsv:
  Details on the datasets under review.

elton.jar:
  Program used to update datasets and generate the review reports and associated indexed interactions.

datasets.zip:
  source datasets collected by elton in process of executing the generate_report.sh script.

generate_report.sh:
  program used to generate the report

generate_report.log:
  log file generated as part of running the generate_report.sh script