Global Biotic Interactions: Interpreted Data Products

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<br> -------- 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<br> -------- 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 Also, mapping of verbatim names from datasets to known name concept may contains errors due to synonym mismatches, outdated names lists, typos or conflicting name authorities.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. Contents<br> -------- README:<br> this file citations.csv.gz:<br> contains data citations in a in a gzipped comma-separated values format. interactions.csv.gz:<br> contains species interactions tabulated as pair-wise interactions in a gzipped comma-separated values format. citations.tsv.gz:<br> contains data citations in a gzipped tab-separated values format. interactions.tsv.gz:<br> contains species interactions tabulated as pair-wise interactions in a gzipped tab-separated values format. interactions.nq.gz:<br> contains species interactions expressed in the resource description framework in a gzipped rdf/quads format. dwca-by-study.zip:<br> contains species interactions data as a Darwin Core Archive aggregated by study using a custom, occurrence level, association extension. dwca.zip:<br> contains species interactions data as a Darwin Core Archive using a custom, occurrence level, association extension. neo4j-graphdb.zip:<br> contains a neo4j v3.5.29 graph database snapshot containing a graph representation of the species interaction data. taxonCache.tsv.gz:<br> contains hierarchies and identifiers associated with names from naming schemes in a gzipped tab-separated values format. taxonMap.tsv.gz:<br> describes how names in existing datasets were mapped into existing naming schemes in a gzipped tab-separated values format. References<br> ----- [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. (2020) globalbioticinteractions/globalbioticinteractions v0.19.0. Zenodo. doi: 10.5281/ZENODO.3946991. Content References<br> ----- hash://sha256/602448aef7ce921dbce12424d710130dfd4e2168c8865c08f5d7bda93b71db40 citations.csv.gz<br> hash://sha256/602448aef7ce921dbce12424d710130dfd4e2168c8865c08f5d7bda93b71db40 citations.tsv.gz<br> hash://sha256/fbd954bd6baf4e0b2ae5929123a720466bfbca63a78ae2aa649b7793af43f54a dwca-by-study.zip<br> hash://sha256/ed312b03f5d06cedbba5128ff4bcda8dbf18bcb89331e4f3e549e36fc393d1d3 dwca.zip<br> hash://sha256/1944e095b2ced1c4ebe794bae9f509149da3bd4f1ae49041fd9d6320a8db4892 interactions.csv.gz<br> hash://sha256/1a0cfb23edde2a2521cbac2143179c16ad4e3f40cf14b050532768b0d1f79418 interactions.nq.gz<br> hash://sha256/c29262701a396623a9a8208ed14f9caf5e8aab3ec313146d6f7c069df992b365 interactions.tsv.gz<br> hash://sha256/1419974ff7ed79675bd2b41a39c03681490a93f4561df24d0ce5175444593ac3 neo4j-graphdb.zip<br> hash://sha256/d296a3b7c5577e06ec5b431203f5810523def180810c31ff9df65ea8ce7bb530 README<br> hash://sha256/daa148b6360506db0f207a00de27e91efb80021b81d3d4c4f6d0608e652ed4c6 refuted-interactions.csv.gz<br> hash://sha256/cd1121a27c26052c60543a9142e6c1d87db968201c5d7bba42670b12181dd036 refuted-interactions.tsv.gz<br> hash://sha256/66a14e68924a33029752a9230aa73d96c34dcd314c8b9c8c4eb8e829efc0d6e0 taxonCache.tsv.gz<br> hash://sha256/b48f18e48f0077dd655fc25bc2c6cd9c8a217364964d94ade159cf790d5c3a5b taxonMap.tsv.gz<br>