Global Biotic Interactions: Interpreted Data Products hash://md5/77424dadd5b16a3e617643c8e2a4fbc4 hash://sha256/c277901ff9d1d8bf19f3bf3ced19c810f500f1542948291bfe755cbb348d6599

Description

Technical info

Citation
--------

GloBI is made possible by researchers, collections, projects and institutions openly sharing their datasets. When using this data, please make sure to attribute these *original data contributors*, including citing the specific datasets in derivative work. Each species interaction record indexed by GloBI contains a reference and dataset citation. Also, a full lists of all references can be found in citations.csv/citations.tsv files in this publication. If you have ideas on how to make it easier to cite original datasets, please open/join a discussion via https://globalbioticinteractions.org or related projects.

To credit GloBI for more easily finding interaction data, please use the following citation to reference GloBI:

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.

Bias and Errors
--------

As with any analysis and processing workflow, care should be taken to understand the bias and error propagation of data sources and related data transformation processes. The datasets indexed by GloBI are biased geospatially, temporally and taxonomically ([5], [6]). Also, mapping of verbatim names from datasets to known name concept may contains errors due to synonym mismatches, outdated names lists, typos or conflicting name authorities. Finally, bugs may introduce bias and errors in the resulting integrated data product.

To help better understand where bias and errors are introduced, only versioned data and code are used as an input: the datasets ([2]), name maps ([3]) and integration software ([6]) are versioned so that the integration processes can be reproduced if needed. This way, steps take to compile an integrated data record can be traced and the sources of bias and errors can be more easily found.

This version was preceded by [7]. 

Contents
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README:
this file

citations.csv.gz:
contains data citations in a in a gzipped comma-separated values format.

citations.tsv.gz:
contains data citations in a gzipped tab-separated values format.

datasets.csv:
contains list of indexed datasets in a gzipped comma-separated values format.

datasets.tsv:
contains list of indexed datasets in a gzipped tab-separated values format.

verbatim-interactions.csv.gz
contains species interactions tabulated as pair-wise interaction in a gzipped comma-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources.

verbatim-interactions.tsv.gz
contains species interactions tabulated as pair-wise interaction in a gzipped tab-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources. 

verbatim-interactions.parquet
contains species interactions tabulated as pair-wise interaction in parquet file format. Included taxonomic name are *not* interpreted, but included as documented in their sources. 

interactions.csv.gz:
contains species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.

interactions.tsv.gz:
contains species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.

interactions.parquet:
contains species interactions tabulated as pair-wise interactions in a parquet file format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.

refuted-interactions.csv.gz:
contains refuted species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.

refuted-interactions.tsv.gz:
contains refuted species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. Included taxonomic names are interpreted using taxonomic alignment workflows and may be different than those provided by the original sources.

refuted-verbatim-interactions.csv.gz:
contains refuted species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources. 

refuted-verbatim-interactions.tsv.gz:
contains refuted species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. Included taxonomic name are *not* interpreted, but included as documented in their sources. 

interactions.nq.gz:
contains species interactions expressed in the resource description framework in a gzipped rdf/quads format.

neo4j-graphdb.zip:
contains a neo4j v5.26 graph database snapshot containing a graph representation of the species interaction data.

taxonCache.tsv.gz:
contains hierarchies and identifiers associated with names from naming schemes in a gzipped tab-separated values format.

taxonMap.tsv.gz:
describes how names in existing datasets were mapped into existing naming schemes in a gzipped tab-separated values format.

References
-----

[1] 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. doi: 10.1016/j.ecoinf.2014.08.005.

[2] Poelen, J. H. (2020) Global Biotic Interactions: Elton Dataset Cache. Zenodo. doi: 10.5281/ZENODO.3950557.

[3] Poelen, J. H. (2026). Global Biotic Interactions: Taxon Graph hash://md5/93f3c48008d1ac849aac31a6f426585a hash://sha256/ae675dd4f77bb562810d2b748c665e51708d7049ba4ac3328c3106e48d9d7d9a (Version 0.7.0) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.21429614

[4] Hortal, J. et al. (2015) Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46(1), pp.523–549. doi: 10.1146/annurev-ecolsys-112414-054400.

[5] Cains, M. et al. (2017) Ivmooc 2017 - Gap Analysis Of Globi: Identifying Research And Data Sharing Opportunities For Species Interactions. Zenodo. Zenodo. doi: 10.5281/ZENODO.814978.

[6] Poelen, J. et al. (2022) globalbioticinteractions/globalbioticinteractions v0.24.6. Zenodo. doi: 10.5281/ZENODO.7327955.

[7] GloBI Community. (2026). Global Biotic Interactions: Interpreted Data Products hash://md5/726fac2c23e77efe0a95c7ebef1c9183 hash://sha256/5a8e0a5b6e19595f0e836d8ff60ba15c6bdcbf26fca382b6313ca3c55c854399 (Version 0.10) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.22309873

Content References
-----
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