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

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/).

This archive contains the biodiversity datasets of interest identified in period 14 April-6 October 2020 through COVID19-TAF activities and subsequently indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org).  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 . Also, this material is based upon work supported by the National Science Foundation under Grant No. DGE-1545433 .

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:
 - Geiselman, Cullen K. & Sarah Younger. 2020. Bat Eco-Interactions Database. www.batbase.org accessed via https://github.com/globalbioticinteractions/batbase/archive/9c65cfeee1a054f9db8cd8bf6892017fd1b3c840.zip on 2020-10-04T22:53:45.576Z
 - Geiselman, Cullen K. and Tuli I. Defex. 2015. Bat Eco-Interactions Database. www.batplant.org accessed via https://github.com/globalbioticinteractions/batplant/archive/a2e1b57052244d5251d17e96ea61f58bea88975e.zip on 2020-10-04T22:54:28.727Z
 - Daniel Becker, Gregory F Albery, Anna R Sjodin, Timothee Poisot, Tad Dallas, Evan A. Eskew, Maxwell J. Farrell, Sarah Guth, Barbara A Han, Nancy B Simmons, Colin J Carlson. 2020. Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization. bioRxiv 2020.05.22.111344; doi: https://doi.org/10.1101/2020.05.22.111344 accessed via https://github.com/globalbioticinteractions/becker2020/archive/47c6ad28e1c5058f3c13ca69a59fdf21229e8d7f.zip on 2020-10-04T22:54:46.723Z
 - 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/a906d76e362484d3ca1edbe9683f672838ab70b0.zip on 2020-10-04T22:56:13.913Z
 - Chen L, Liu B, Wu Z, Jin Q, Yang J, 2017. DRodVir: A resource for exploring the virome diversity in rodents. J Genet Genomics. 44(5):259-264. accessed via https://github.com/globalbioticinteractions/drodvir/archive/0346c0e8d4d66c6400e9965bd6a6aeed24cd7586.zip on 2020-10-04T23:06:04.368Z
 - Agosti, Donat. 2020. Transcription of Linné, C. von, 1758. Systema naturae per regna tria naturae secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Available at: http://dx.doi.org/10.5962/bhl.title.542 . accessed via https://github.com/globalbioticinteractions/linnaeus1758/archive/a818060080fa04a88dac6df1ae5b897304ae8877.zip on 2020-10-05T00:46:04.852Z
 - Mollentze, Nardus, & Streicker, Daniel G. (2019). Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts (Version 1.0.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3516613 accessed via https://github.com/globalbioticinteractions/mollentze2019/archive/ad12dc74d03c3d992618f16c37cafb7f7ffd9d01.zip on 2020-10-05T00:50:55.878Z
 - 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 . accessed via https://github.com/globalbioticinteractions/ncbi-virus/archive/531a8d743d7adcf1153a19087e5d3c5b76750e3e.zip on 2020-10-05T00:53:53.646Z
 - 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 2020-10-05T00:56:43.356Z
 - Pensoft Darwin Core Archives with associateTaxa columns accessed via https://github.com/globalbioticinteractions/pensoft-dwca/archive/ee8831a2a391203f4fa8c05a0ddd927202b234bf.zip on 2020-10-05T00:56:51.868Z
 - Pensoft Darwin Core Archives available via Integrated Publication Toolkit accessed via https://github.com/globalbioticinteractions/pensoft-ipt/archive/4ad4b47978324681289e36f8c2b247b1bcc97b1a.zip on 2020-10-05T00:58:01.912Z
 - 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 2020-10-05T00:58:03.647Z
 - 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 2020-10-05T00:58:08.025Z
 - Shaw, LP, Wang, AD, Dylus, D, et al. The phylogenetic range of bacterial and viral pathogens of vertebrates. Mol Ecol. 2020; 29: 3361– 3379. https://doi.org/10.1111/mec.15463 accessed via https://github.com/globalbioticinteractions/shaw2020/archive/bb9ab857b7fdbb4e931752d01b43d37b3ada77cf.zip on 2020-10-05T01:05:23.554Z
 - OpenBiodiv. 2020. Annotated biotic interaction tables from Pensoft publications. accessed via https://github.com/pensoft/pensoft-interaction-tables/archive/bb7d1dc9f2eba220a61502e06e6114053fd30788.zip on 2020-10-05T03:03:23.372Z
 - Quentin J. Groom. 2020. Bat interation data manually extracted from literature. accessed via https://github.com/qgroom/batinterations/archive/70108945f9014aa0ac1db920191867f7e151c793.zip on 2020-10-05T03:04:11.533Z

Generated on:
2020-10-06

by:
GloBI's Elton 0.10.2
(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.

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

Files (708.2 MB)
Name Size
datasets.zip
md5:9a4edeb2ff35226159c192e1c6a2786c
658.6 MB Download
datasets_under_review.tsv
md5:985136f2da79948b29bcd43ca8c06ce3
6.6 kB Download
elton.jar
md5:4ee68fb9d33f15b7dcaf0cdcc2ec066d
31.0 MB Download
generate-report.log
md5:e7fc24b98ff862e3afaded62a6007c8c
112.6 kB Download
generate-report.sh
md5:271b153bf0276f40530801a6ca599c6f
6.9 kB Download
indexed_interactions_by_collection.tsv
md5:b86c5ae6ae2d1445420c658b33cd61d7
9.8 kB Download
indexed_interactions_full.tsv.gz
md5:6d1c9e1453cdac033a3fd437ceef53c6
4.1 MB Download
indexed_interactions_simple.tsv.gz
md5:356859f9659d55390508ffb1eafc3873
576.3 kB Download
README
md5:32cfbb52901434a7210ea76f55307530
8.8 kB Download
review_comments.tsv.gz
md5:1481893277be3b6c218ff47519b20efa
13.7 MB Download
review_summary.tsv
md5:f5349fcc90578573c88a6b2b37f08c26
32.7 kB Download
review_summary_by_collection.tsv
md5:994fa331cc98a5902c61a9ccf76c1bf6
46.2 kB Download
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