DOI: 10.5281/zenodo.8253729
title: A biodiversity dataset graph: Biological Associations in TaxonWorks hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 hash://md5/849edbe55e31e54ea5cdaba0188c5655

description: The intended use of this archive is to facilitate (meta-)analysis of Biological Associations captured in TaxonWorks [1]. TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists. It allows you to capture, organize, and enrich your data; share it with collaborators; and package it for analysis and publication. This dataset provides versioned snapshots of the TaxonWorks network as tracked by Preston [2,3,4] between 2023-08-16 and 2023-08-16 using: <pre><code class="language-bash">preston track -u https://sfg.taxonworks.org</code></pre> . In addition, this dataset provides a processed version of the biological associations using the "preston tw-stream" command as generated by the following bash script: <pre><code class="language-bash">#!/bin/bash # # Generates GloBI interaction JSON Lines from provided provenance log as generated by preston tw-stream. # /usr/local/bin/preston cat hash://sha256/ff5e709305e593c87711e897b6341b94e775e2f312aa6d4ae5ed6120babd6f5e\ | /usr/local/bin/preston tw-stream </code></pre> <br> The script itself was executed using: <pre><code class="language-bash">cat transform.sh | preston bash </code></pre> The execution of this transform.sh script (with content id hash://sha256/ea6c131a7436c9080b9380c7712dd32654a564fbb6f0568ff97bd7a8f28337a4), as well as their results, is captured within this datasets also. A rdf/quads formatted machine readable version of the workflow execution description can be found via: <pre><code class="language-bash">preston cat hash://sha256/ab7550368905e7c919e70a306efbb97719a1edbba2cfe4c4515f635ebc0be4bb </code></pre> And, the resulting JSON Lines file has content id (or signature) hash://sha256/93c748c9e88a8c221f4d9cf4de37f0506d8427a4383cf1ee2078983cdeb31a14 and is also included as interactions.json to facilitate access. The first json record can be generated using: <pre><code class="language-bash">preston cat hash://sha256/93c748c9e88a8c221f4d9cf4de37f0506d8427a4383cf1ee2078983cdeb31a14\ | head -n1\ | jq . </code></pre> or, provided that the interactions.json has content id starting with hash://sha256/da34e70... <pre><code class="language-bash">cat interactions.json\ | head -n1\ | jq . </code></pre> This produces the following (formatted) json object: <pre><code class="language-json">{ "http://www.w3.org/ns/prov#wasDerivedFrom": "hash://sha256/f1c123b38bdfab129d8a393b06842eddae823bf08a2c91b1100399940b582a9a", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "application/vnd.taxonworks+json", "referenceId": "https://sfg.taxonworks.org/api/v1/sources/49013", "interactionId": "https://sfg.taxonworks.org/api/v1/biological_associations/84748", "taxonRootsResolved": 2, "referenceResolved": true, "referenceCitation": "@article{49013,\n author = {Abate, T.},\n booktitle = {Journal of Applied Entomology},\n journal = {Journal of Applied Entomology},\n month = {mar},\n day = {31},\n pages = {278-285},\n title = {The bean fly &lt;i&gt;Ophiomyia phaseoli&lt;/i&gt; Tryon (Diptera: Agromyzidae) and its parasitoids in Ethiopia.},\n volume = {111(3)},\n year = {1991},\n stated_year = {1991},\n year_suffix = {a},\n issn = {0044-2240}\n}\n", "interactionTypeId": "gid://taxon-works/BiologicalRelationship/14", "interactionTypeName": "Primary host", "sourceTaxonName": "Eupelmus", "sourceTaxonId": "gid://taxon-works/TaxonName/456381", "sourceTaxonRank": "genus", "sourceTaxonAuthorship": "Dalman, 1820", "sourceTaxonPath": "Root | Animalia | Arthropoda | Insecta | Hymenoptera | Chalcidoidea | Eupelmidae | Eupelminae | Eupelmus", "sourceTaxonPathIds": "gid://taxon-works/TaxonName/455455 | gid://taxon-works/TaxonName/703648 | gid://taxon-works/TaxonName/703653 | gid://taxon-works/TaxonName/703658 | gid://taxon-works/TaxonName/455456 | gid://taxon-works/TaxonName/455458 | gid://taxon-works/TaxonName/455504 | gid://taxon-works/TaxonName/455506 | gid://taxon-works/TaxonName/456381", "sourceTaxonPathNames": "nomenclatural rank | kingdom | phylum | class | order | superfamily | family | subfamily | genus", "targetTaxonName": "Agromyzidae", "targetTaxonId": "gid://taxon-works/TaxonName/513569", "targetTaxonRank": "family", "targetTaxonAuthorship": "", "targetTaxonPath": "Root | Animalia | Arthropoda | Insecta | Diptera | Agromyzidae", "targetTaxonPathIds": "gid://taxon-works/TaxonName/455455 | gid://taxon-works/TaxonName/703648 | gid://taxon-works/TaxonName/703653 | gid://taxon-works/TaxonName/703658 | gid://taxon-works/TaxonName/513567 | gid://taxon-works/TaxonName/513569", "targetTaxonPathNames": "nomenclatural rank | kingdom | phylum | class | order | family" }</code></pre> In this example, a claim is made that, according to https://sfg.taxonworks.org/api/v1/sources/49013 [6] Eupelmus (a parasitic wasp) has a primary host in the family of Agromyzidae (leaf-miner flies). In total, 138,246 such claims can be found in the generated resource with alias interactions.json and content id starting with hash://sha256/93c748c... . In addition, the archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance logs and data files. In addition, index files have been individually included in this dataset publication to facilitate remote access. Index files provide a way to links provenance files in time to establish a versioning mechanism. Provenance files describe how, when, what and where the TaxonWorks content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 . To retrieve and verify the downloaded TaxonWorks biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz &gt; preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using: <pre><code class="language-bash">java -jar preston.jar clone --remote https://zenodo.org/record/8253729/files </code></pre> After that, verify the index of the archive by reproducing the following provenance log history: <pre><code class="language-bash"> java -jar preston.jar history --log tsv</code></pre> to be: <pre><code>hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/ab7550368905e7c919e70a306efbb97719a1edbba2cfe4c4515f635ebc0be4bb hash://sha256/ab7550368905e7c919e70a306efbb97719a1edbba2cfe4c4515f635ebc0be4bb http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/ff5e709305e593c87711e897b6341b94e775e2f312aa6d4ae5ed6120babd6f5e urn:uuid:0659a54f-b713-4f86-a917-5be166a14110 http://purl.org/pav/hasVersion hash://sha256/ff5e709305e593c87711e897b6341b94e775e2f312aa6d4ae5ed6120babd6f5e </code></pre> <br> To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while. <pre><code class="language-bash">java -jar preston.jar verify</code></pre> Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston". Files in this data publication: --- start of file descriptions --- -- description of archive and its contents (a rendition of this file) --<br> README -- biological associations indexed from TaxonWorks expressed in a GloBI [5] compatible JSON Lines file --<br> interactions.json -- executable java jar containing preston [2,3,4] v0.7.4-SNAPSHOT. --<br> preston.jar -- preston archives containing TaxonWorks data files, associated provenance logs and a provenance index --<br> preston-[00-ff].tar.gz -- individual provenance index files -- 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<br> f98d36a9dc7bd833c93b3b61130865628f7bc2f7bb0920e95afcd16fba3dc6a8<br> 29306c5c144c3d7fd21be344d8b6b554b6f6efa3b8f8f5c0b27cdf0e88785652 --- end of file descriptions --- <br> References <br> [1] TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists. (TaxonWorks, https://sfg.taxonworks.org) accessed from 2023-08-16 to 2023-08-16 with provenance hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2.<br> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . <br> [3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132 hash://sha256/136c3c1808bcf463bb04b11622bb2e7b5fba28f5be1fc258c5ea55b3b84f482c<br> [4] MJ Elliott, JH Poelen, JAB Fortes (2023). Signing data citations enables data verification and citation persistence. Scientific Data. https://doi.org/10.1038/s41597-023-02230-y hash://sha256/f849c870565f608899f183ca261365dce9c9f1c5441b1c779e0db49df9c2a19d <br> [5] Poelen JH, Simons JD, Mungall CJ. (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.<br> [6] Abate, T. (1991) The bean fly Ophiomyia phaseoli Tryon (Diptera: Agromyzidae) and its parasitoids in Ethiopia. Journal of Applied Entomology 111(3), 278–285." <br> This work is funded in part by grant NSF OAC 1839201, NSF DBI 1901932, NSF DBI 1901926, and NSF DBI 2102006 from the National Science Foundation.<br>