Global Biotic Interactions: Interpreted Data Products hash://md5/946f7666667d60657dc89d9af8ffb909 hash://sha256/4e83d2daee05a4fa91819d58259ee58ffc5a29ec37aa7e84fd5ffbb2f92aa5b8

Global Biotic Interactions: Interpreted Data Products

Global Biotic Interactions (GloBI, https://globalbioticinteractions.org, [1]) aims to facilitate access to existing species interaction records (e.g., predator-prey, plant-pollinator, virus-host). This data publication provides interpreted species interaction data products. These products are the result of a process in which versioned, existing species interaction datasets ([2]) are linked to the so-called GloBI Taxon Graph ([3]) and transformed into various aggregate formats (e.g., tsv, csv, neo4j, rdf/nquad, darwin core-ish archives). In addition, the applied name maps are included to make the applied taxonomic linking explicit. 

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 Also, mapping of verbatim names from datasets to known name concept may contains errors due to synonym mismatches, outdated names lists, typos or conflicting name authorities.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
--------

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

datasets.tsv.gz:
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. 

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.

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.

dwca-by-study.zip:
contains species interactions data as a Darwin Core Archive aggregated by study using a custom, occurrence level, association extension.

dwca.zip:
contains species interactions data as a Darwin Core Archive using a custom, occurrence level, association extension.

neo4j-graphdb.zip:
contains a neo4j v3.5.32 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. (2021). Global Biotic Interactions: Taxon Graph (Version 0.3.28) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451472

[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. (2023). Global Biotic Interactions: Interpreted Data Products hash://md5/89797a5a325ac5c50990581689718edf hash://sha256/946178b36c3ea2f2daa105ad244cf5d6cd236ec8c99956616557cf4e6666545b (0.6) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8284068

Content References
-----

hash://sha256/fb4e5f2d0288ab9936dc2298b0a7a22526f405e540e55c3de9c1cbd01afa9a00  citations.csv.gz
hash://sha256/12a154440230203b9d54f5233d4bda20c482d9d2a34a8363c6d7efdf4281ee47  citations.tsv.gz
hash://sha256/236882c394ff15eda4fe2e994a8f07cb9c0c42bd77d9a5339c9fac217b16a004  datasets.csv.gz
hash://sha256/236882c394ff15eda4fe2e994a8f07cb9c0c42bd77d9a5339c9fac217b16a004  datasets.tsv.gz
hash://sha256/42d50329eca99a6ded1b3fc63af5fa99b029b44ffeba79a02187311422c8710c  dwca-by-study.zip
hash://sha256/77f7e1db20e977287ed6983ce7ea1d8b35bd88fe148372b9886ce62989bc2c22  dwca.zip
hash://sha256/4fb8f91d5638ef94ddc0b301e891629802e8080f01e3040bf3d0e819e0bfbe9e  interactions.csv.gz
hash://sha256/c83ffa45ffc8e32f1933d23364c108fff92d8b9480401d54e2620a961ad9f0c5  interactions.nq.gz
hash://sha256/ce0d1ce3bebf94198996f471a03a15ad54a8c1aac5a5a6905e0f2fd4687427ac  interactions.tsv.gz
hash://sha256/e4adf8c0fe545410c08e497d3189075a262f086977556c0f0fd229f8a2f39ffe  neo4j-graphdb.zip
hash://sha256/8cbf6cd70ecbd724f1a4184aeeb0ba78b67747a627e5824d960fe98651871b34  refuted-interactions.csv.gz
hash://sha256/caa0f7bcf91531160fda7c4fc14020154ce6183215f77aacb8dbb0b823295022  refuted-interactions.tsv.gz
hash://sha256/29ed2703c0696d0d6ab1f1a00fcdce6da7c86d0a85ddd6e8bb00a3b1017daac9  refuted-verbatim-interactions.csv.gz
hash://sha256/5542136e32baa935ffa4834889f6af07989fab94db763ab01a3e135886a23556  refuted-verbatim-interactions.tsv.gz
hash://sha256/af742d945a1ecdb698926589fceb8147e99f491d7475b39e9b516ce1cfe2599b  taxonCache.tsv.gz
hash://sha256/1a85b81dc9312994695e63966dec06858bbcd3c084f5044c29371b1c14f15c3d  taxonMap.tsv.gz
hash://sha256/5f9ebc62be68f7ffb097c4ff168e6b7b45b1e835843c90a2af6b30d7e2a9eab1  verbatim-interactions.csv.gz
hash://sha256/d29704b6275a2f7aaffbd131d63009914bdbbf1d9bc2667ff4ce0713d586f4f6  verbatim-interactions.tsv.gz

hash://sha256/735599feaf18a416a375d985a27f51bb  citations.csv.gz
hash://sha256/328049ca46682b8aee2611fe3ef2e3c9  citations.tsv.gz
hash://sha256/8a645af66bf9cf8ddae0c3d6bc3ccb30  datasets.csv.gz
hash://sha256/8a645af66bf9cf8ddae0c3d6bc3ccb30  datasets.tsv.gz
hash://sha256/654eb9d9445ed382036f0e45398ec6bb  dwca-by-study.zip
hash://sha256/291e517d3ca72b727d85501a289d7d59  dwca.zip
hash://sha256/4dbfb8605adce1c0e2165d5bdb918f95  interactions.csv.gz
hash://sha256/4bc7f0d93f399b3fe8ee099032e8dc12  interactions.nq.gz
hash://sha256/2e79d1a5a20b57da97551cb18a3c0b8c  interactions.tsv.gz
hash://sha256/f072035dcc1f70b24ed40a9272f97a3d  neo4j-graphdb.zip
hash://sha256/e03f743d81be8e0119e50789f8d7afc0  refuted-interactions.csv.gz
hash://sha256/235f384c675b423616d06ab0b7c2b4e5  refuted-interactions.tsv.gz
hash://sha256/b50998b2ec875d7a99500e2da72159dd  refuted-verbatim-interactions.csv.gz
hash://sha256/ae6cdf71e2cafd9950303f3a0f514055  refuted-verbatim-interactions.tsv.gz
hash://sha256/6b8ac255112cecf59eb1c225b9ceb2e3  taxonCache.tsv.gz
hash://sha256/caa1298b5fe3489dd9a02a397fe075d1  taxonMap.tsv.gz
hash://sha256/ce10ff6ffcca235d77374a90392bee88  verbatim-interactions.csv.gz
hash://sha256/7e11573d83b2bac6425ee2482c4d73bc  verbatim-interactions.tsv.gz