A biodiversity dataset graph: Biological Associations in TaxonWorks hash://sha256/e4a47c067d6c125da60c9a1b92b5eecdea539cb8666cd3aed99db347ae5b8ed0 hash://md5/686007de79cc2a49ab23fd3debe56e3f
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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] during 2024-05-07 using: preston track -u https://sfg.taxonworks.org . 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: #!/bin/bash # # Generates GloBI interaction JSON Lines from provided provenance log as generated by preston tw-stream. # /usr/local/bin/preston cat hash://sha256/c1b081afa6ea0f60570c24cca85c4d9acd91eeefe36b9cacd1fe53b6893ea154\ | /usr/local/bin/preston tw-stream The script itself was executed using: cat transform.sh | preston bash The execution of this transform.sh script (with content id hash://sha256/6dfe3c4ebf877bed73aebbe88c7d388bf894c569578ed7b28ca68e57a6afe43b), 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: preston cat hash://sha256/e4a47c067d6c125da60c9a1b92b5eecdea539cb8666cd3aed99db347ae5b8ed0 And, the resulting JSON Lines file has content id (or signature) hash://sha256/4c2b8642251ced5985660d63c565efa6e5a9bf3d12b3b0c0d9ac577905f5e897 and is also included as interactions.json to facilitate access. The first json record can be generated using: preston cat hash://sha256/4c2b8642251ced5985660d63c565efa6e5a9bf3d12b3b0c0d9ac577905f5e897\ | head -n1\ | jq . or, provided that the interactions.json has content id starting with hash://sha256/4c2b86... cat interactions.json\ | head -n1\ | jq . This produces the following (formatted) json object: { "http://www.w3.org/ns/prov#wasDerivedFrom": "hash://sha256/fdbf13dc5f3d9c5afbc03db62699e2ce2724c499b7d91d8b0bf31e39409b153a", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "application/vnd.taxonworks+json", "referenceId": "https://sfg.taxonworks.org/api/v1/sources/213218", "interactionId": "https://sfg.taxonworks.org/api/v1/biological_associations/227664", "taxonRootsResolved": 2, "referenceResolved": true, "referenceCitation": "@article{213218,\n author = {Monzen, Kota},\n journal = {Annual Report of the Gakugei Faculty of the Iwate University},\n pages = {24-38},\n title = {Revision of the Japanese gall wasps with the descriptions of new genus, subgenus, species and subspecies (II). Cynipidae (Cynipinae) Hymenoptera.},\n volume = {6},\n year = {1954}\n}\n", "interactionTypeId": "gid://taxon-works/BiologicalRelationship/69", "interactionTypeName": "gall", "sourceTaxonName": "Neuroterus hakonensis", "sourceTaxonId": "gid://taxon-works/TaxonName/1174121", "sourceTaxonRank": "species", "sourceTaxonAuthorship": "Ashmead, 1904", "sourceTaxonPath": "Root | Cynipidae | Neuroterus | Neuroterus hakonensis", "sourceTaxonPathIds": "gid://taxon-works/TaxonName/623170 | gid://taxon-works/TaxonName/1170060 | gid://taxon-works/TaxonName/1170097 | gid://taxon-works/TaxonName/1174121", "sourceTaxonPathNames": "nomenclatural rank | family | genus | species", "targetTaxonName": "Quercus", "targetTaxonId": "gid://taxon-works/TaxonName/1173543", "targetTaxonRank": "genus", "targetTaxonAuthorship": "", "targetTaxonPath": "Root | Fagaceae | Quercus", "targetTaxonPathIds": "gid://taxon-works/TaxonName/623170 | gid://taxon-works/TaxonName/1173542 | gid://taxon-works/TaxonName/1173543", "targetTaxonPathNames": "nomenclatural rank | family | genus"} In this example, a claim is made that, according to https://sfg.taxonworks.org/api/v1/sources/213218 [6] Neuroterus hakonensis (a gall wasp) has a primary host in the genus of Quercus (oak tree). In total, 237,068 such claims can be found in the generated resource with alias interactions.json and content id starting with hash://sha256/4c2b86... . In addition, the archive preston.tar.gz to allow for batch download. 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, download preston.tar.gz. Then, extract the archive into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using: java -jar preston.jar clone --remote https://zenodo.org/record/11151783/files After that, verify the index of the archive by reproducing the following provenance log history: java -jar preston.jar history --log tsv to be: hash://sha256/e4a47c067d6c125da60c9a1b92b5eecdea539cb8666cd3aed99db347ae5b8ed0 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/c1b081afa6ea0f60570c24cca85c4d9acd91eeefe36b9cacd1fe53b6893ea154 hash://sha256/c1b081afa6ea0f60570c24cca85c4d9acd91eeefe36b9cacd1fe53b6893ea154 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/ab7550368905e7c919e70a306efbb97719a1edbba2cfe4c4515f635ebc0be4bb hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/ab7550368905e7c919e70a306efbb97719a1edbba2cfe4c4515f635ebc0be4bbhash://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 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. java -jar preston.jar verify 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) --README -- biological associations indexed from TaxonWorks expressed in a GloBI [5] compatible JSON Lines file --interactions.json -- first 10 biological associations indexed from TaxonWorks expressed in a GloBI [5] compatible JSON Lines file --interactions-10.json -- executable java jar containing preston [2,3,4] v0.8.5-SNAPSHOT. --preston.jar -- preston archive containing TaxonWorks data files, associated provenance logs and a provenance index --preston.tar.gz -- individual provenance index files -- 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 --- end of file descriptions --- 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.
本数据集档案的用途为辅助开展针对TaxonWorks[1]中收录的生物关联的（元）分析。TaxonWorks是一款面向分类学家与生物多样性研究者的集成化网页工作台，支持数据的采集、整理、富集，可与合作者共享数据，并可将数据打包以供分析与发表。 本数据集提供了2024年5月7日通过Preston[2,3,4]追踪的TaxonWorks网络的版本化快照，追踪命令为： bash preston track -u https://sfg.taxonworks.org 此外，本数据集还提供了经`preston tw-stream`命令处理后的生物关联数据，该处理流程由以下Bash脚本生成： bash #!/bin/bash # # 从Preston tw-stream生成的溯源日志中生成GloBI交互JSON Lines格式数据。 # /usr/local/bin/preston cat hash://sha256/c1b081afa6ea0f60570c24cca85c4d9acd91eeefe36b9cacd1fe53b6893ea154 | /usr/local/bin/preston tw-stream 该脚本的执行方式为：`cat transform.sh | preston bash`。 本数据集同时收录了该transform.sh脚本的执行过程（其内容ID为`hash://sha256/6dfe3c4ebf877bed73aebbe88c7d388bf894c569578ed7b28ca68e57a6afe43b`）及其执行结果。可通过以下命令获取工作流执行描述的RDF四元组格式机器可读版本： bash preston cat hash://sha256/e4a47c067d6c125da60c9a1b92b5eecdea539cb8666cd3aed99db347ae5b8ed0 最终生成的JSON Lines文件的内容ID（或称哈希签名）为`hash://sha256/4c2b8642251ced5985660d63c565efa6e5a9bf3d12b3b0c0d9ac577905f5e897`，同时以`interactions.json`为名收录以方便访问。 可通过以下方式生成该数据集的第一条JSON记录： bash preston cat hash://sha256/4c2b8642251ced5985660d63c565efa6e5a9bf3d12b3b0c0d9ac577905f5e897 | head -n1 | jq . 或者，若已存在`interactions.json`文件且其内容ID以`hash://sha256/4c2b86...`开头，则可执行： bash cat interactions.json | head -n1 | jq . 执行后将得到如下格式化后的JSON对象： json {"http://www.w3.org/ns/prov#wasDerivedFrom":"hash://sha256/fdbf13dc5f3d9c5afbc03db62699e2ce2724c499b7d91d8b0bf31e39409b153a","http://www.w3.org/1999/02/22-rdf-syntax-ns#type":"application/vnd.taxonworks+json","referenceId":"https://sfg.taxonworks.org/api/v1/sources/213218","interactionId":"https://sfg.taxonworks.org/api/v1/biological_associations/227664","taxonRootsResolved":2,"referenceResolved":true,"referenceCitation":"@article{213218, author = {Monzen, Kota}, journal = {Annual Report of the Gakugei Faculty of the Iwate University}, pages = {24-38}, title = {Revision of the Japanese gall wasps with the descriptions of new genus, subgenus, species and subspecies (II). Cynipidae (Cynipinae) Hymenoptera.}, volume = {6}, year = {1954} }","interactionTypeId":"gid://taxon-works/BiologicalRelationship/69","interactionTypeName":"gall","sourceTaxonName":"Neuroterus hakonensis","sourceTaxonId":"gid://taxon-works/TaxonName/1174121","sourceTaxonRank":"species","sourceTaxonAuthorship":"Ashmead, 1904","sourceTaxonPath":"Root | Cynipidae | Neuroterus | Neuroterus hakonensis","sourceTaxonPathIds":"gid://taxon-works/TaxonName/623170 | gid://taxon-works/TaxonName/1170060 | gid://taxon-works/TaxonName/1170097 | gid://taxon-works/TaxonName/1174121","sourceTaxonPathNames":"nomenclatural rank | family | genus | species","targetTaxonName":"Quercus","targetTaxonId":"gid://taxon-works/TaxonName/1173543","targetTaxonRank":"genus","targetTaxonAuthorship":"","targetTaxonPath":"Root | Fagaceae | Quercus","targetTaxonPathIds":"gid://taxon-works/TaxonName/623170 | gid://taxon-works/TaxonName/1173542 | gid://taxon-works/TaxonName/1173543","targetTaxonPathNames":"nomenclatural rank | family | genus"} 本示例表明，根据`https://sfg.taxonworks.org/api/v1/sources/213218`[6]，*Neuroterus hakonensis*（一种瘿蜂）的主要宿主为栎属（*Quercus*，橡树）。本生成资源中共包含237068条此类关联声明，其别名为`interactions.json`，内容ID以`hash://sha256/4c2b86...`开头。 此外，本数据集提供了用于批量下载的`preston.tar.gz`档案，该档案包含三类文件：索引文件、溯源日志与数据文件。为便于远程访问，本数据集出版物中已单独收录所有索引文件。索引文件可用于关联不同时间点的溯源文件，以构建版本化机制。溯源文件用于描述TaxonWorks内容的获取方式、时间、内容与位置。如需了解更多信息，请访问https://preston.guoda.bio 或 https://doi.org/10.5281/zenodo.1410543。 如需获取并验证下载的TaxonWorks生物多样性数据集图谱，请先下载`preston.tar.gz`，再将其解压至名为`data`的文件夹中。或者，可通过Preston命令行工具克隆本数据集： bash java -jar preston.jar clone --remote https://zenodo.org/record/11151783/files 执行完成后，可通过复现以下溯源日志历史来验证档案索引： bash java -jar preston.jar history --log tsv 预期输出应如下所示： hash://sha256/e4a47c067d6c125da60c9a1b92b5eecdea539cb8666cd3aed99db347ae5b8ed0 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/c1b081afa6ea0f60570c24cca85c4d9acd91eeefe36b9cacd1fe53b6893ea154 hash://sha256/c1b081afa6ea0f60570c24cca85c4d9acd91eeefe36b9cacd1fe53b6893ea154 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 hash://sha256/a4d651aac5220487835e6178511886e98b845b2d98cb7c5447fb2b042e0654d2 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/ab7550368905e7c919e70a306efbb97719a1edbba2cfe4c4515f635ebc0be4bb 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 如需验证解压后档案的完整性，请执行`preston verify`命令，确认其输出的每一行均包含`CONTENT_PRESENT_VALID_HASH`。根据硬件配置不同，该过程可能耗时较长。 bash java -jar preston.jar verify 注意：本出版物中已包含Java程序Preston的可执行JAR文件`preston.jar`，该程序需在Java 8及以上版本的虚拟机中运行，执行命令为`java -jar preston.jar`，简称为`preston`。 本数据出版物包含以下文件： --- 开始文件描述 --- - 档案与内容说明（即本文件的另一种呈现形式）：README - 从TaxonWorks中索引得到的、采用GloBI[5]兼容格式的生物关联JSON Lines文件：interactions.json - 从TaxonWorks中索引得到的、采用GloBI[5]兼容格式的前10条生物关联JSON Lines文件：interactions-10.json - 包含Preston v0.8.5-SNAPSHOT的可执行Java JAR文件：preston.jar - 包含TaxonWorks数据文件、关联溯源日志与溯源索引的Preston档案：preston.tar.gz - 单个溯源索引文件：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 --- 结束文件描述 --- 本研究部分受到美国国家科学基金会（NSF）的NSF OAC 1839201、NSF DBI 1901932、NSF DBI 1901926以及NSF DBI 2102006项目资助。
