A biodiversity dataset graph: GBIF, iDigBio, BioCASe hash://sha256/450deb8ed9092ac9b2f0f31d3dcf4e2b9be003c460df63dd6463d252bff37b55 hash://md5/898a9c02bedccaea5434ee4c6d64b7a2

DOI10.5281/zenodo.7651831Zenodo7651831MaRDI QIDQ6682796FDOQ6682796

Dataset published at Zenodo repository.

Jorrit Poelen

Publication date: 17 February 2023

Description

A biodiversity dataset graph: GBIF, iDigBio, BioCASe hash://sha256/450deb8ed9092ac9b2f0f31d3dcf4e2b9be003c460df63dd6463d252bff37b55 hash://md5/898a9c02bedccaea5434ee4c6d64b7a2 The intended use of this archive is to facilitate meta-analysis of the Global Biodiversity Information Facility, Integrated Digitized Biocollections, Biological Collection Access Service (GBIF, iDigBio, BioCASe). GBIF, iDigBio and BioCASe help provide access to biological data collections. This dataset provides versioned provenance logs of snapshots of the GBIF, iDigBio, BioCASe network as tracked by Preston [2] between 2018-09-03 and 2023-02-02 using preston update -u https://gbif.org,https://idigbio.org,http://biocase.org. This publication contains two types of files: index files and provenance logs. Associated data files are hosted elsewhere for pragmatic reasons. Index files provide a way to link provenance files in time to establish a versioning mechanism. Provenance logs describe how, when, what and where the GBIF, iDigBio, BioCASe 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 GBIF, iDigBio, BioCASe biodiversity dataset graph, use the preston[2] command-line tool to clone this dataset using: $ java -jar preston.jar ls --remote https://zenodo.org/record/7651831/files /dev/null Optionally, you can retrieve all associated data (500GB) files using: $ java -jar preston.jar clone https://zenodo.org/record/7651831/files --remote https://zenodo.org/record/7651831/files,https://linker.bio,https://archive.org/download/biodiversity-dataset-archives/data.zip/data/ Please note https://archive.org/download/biodiversity-dataset-archives/data.zip/data/ and https://linker.bio are Preston remotes that provided access to GBIF, iDigBio, BioCASe data files at time of writing (17Feb 2023). These remotes can replaced with any other Preston remote(s) if needed. This may take a while depending on network speed and hardware constraints. See also https://archive.org/details/biodiversity-dataset-archives . After that, verify the index of the archive by reproducing the following provenance log history: $ java -jar preston.jar history hash://sha256/450deb8ed9092ac9b2f0f31d3dcf4e2b9be003c460df63dd6463d252bff37b55 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/1621a777e4a7442e9864424820c5f825d9cf1c65599cbfbbda039384f1b74ada . hash://sha256/1621a777e4a7442e9864424820c5f825d9cf1c65599cbfbbda039384f1b74ada http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/b1c11d9231768def925b9d076c1c4b711a727326ad99e62982aa4ede288e5aa2 . hash://sha256/b1c11d9231768def925b9d076c1c4b711a727326ad99e62982aa4ede288e5aa2 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/125e67d7c5077af8fa958569644d61e44a39bbbbdaaf16af0430dcf441e05cec . hash://sha256/125e67d7c5077af8fa958569644d61e44a39bbbbdaaf16af0430dcf441e05cec http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/63fae82e8a3aacd11e4a06b5736242aabe40802c6259a38de066de14848e3718 . hash://sha256/63fae82e8a3aacd11e4a06b5736242aabe40802c6259a38de066de14848e3718 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/7cd305e9d275763c96e7685847460fcc381b5c97c1460c00441f663c1788800f . hash://sha256/7cd305e9d275763c96e7685847460fcc381b5c97c1460c00441f663c1788800f http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/38e8e17f6742d39379b96cec2d4e70a5a63a85a28aee49727031c9061f4b1e03 . hash://sha256/38e8e17f6742d39379b96cec2d4e70a5a63a85a28aee49727031c9061f4b1e03 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/da7450941e7179c973a2fe1127718541bca6ccafe0e4e2bfb7f7ca9dbb7adb86 . hash://sha256/da7450941e7179c973a2fe1127718541bca6ccafe0e4e2bfb7f7ca9dbb7adb86 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/aab08c5c87ce6a8f400972e2b09b7fa3421947b59407a8feb98388d7e42b49e8 . hash://sha256/aab08c5c87ce6a8f400972e2b09b7fa3421947b59407a8feb98388d7e42b49e8 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/f449a34dd80d4e33248a1a7cb0d0fa2b8dac49865a0a32ed5bbaacb22addb0d1 . hash://sha256/f449a34dd80d4e33248a1a7cb0d0fa2b8dac49865a0a32ed5bbaacb22addb0d1 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/b771ed09aea78055e39d5c955997e5d9b42dd9edc6b094d9b8a27df16bdc6b6c . hash://sha256/b771ed09aea78055e39d5c955997e5d9b42dd9edc6b094d9b8a27df16bdc6b6c http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/15edbac974fb77347e07cda76358f7f662dd800bfc5b3e476fc66ecdc6203d03 . hash://sha256/15edbac974fb77347e07cda76358f7f662dd800bfc5b3e476fc66ecdc6203d03 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/4000d2a1af6da5b46f374038d884f91768782a1905d4a75fff3c8c3bb6629913 . hash://sha256/4000d2a1af6da5b46f374038d884f91768782a1905d4a75fff3c8c3bb6629913 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/f6d133620a665569a13a3fb7ca31b163bf849864812d447238994226d35e3253 . hash://sha256/f6d133620a665569a13a3fb7ca31b163bf849864812d447238994226d35e3253 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hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd . hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93 . hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93 http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d . hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d http://www.w3.org/ns/prov#wasDerivedFrom hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55 . urn:uuid:0659a54f-b713-4f86-a917-5be166a14110 http://purl.org/pav/hasVersion hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55 . If you retrieved data files, you can check the integrity of the extracted archive by confirming 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 hash://sha256/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362file:/home/preston/preston-archive/data/3e/ff/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362OKCONTENT_PRESENT_VALID_HASH89931 hash://sha256/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0bfile:/home/preston/preston-archive/data/18/48/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0bOKCONTENT_PRESENT_VALID_HASH210344 hash://sha256/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02file:/home/preston/preston-archive/data/18/46/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02OKCONTENT_PRESENT_VALID_HASH210344 hash://sha256/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38file:/home/preston/preston-archive/data/55/4f/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38OKCONTENT_PRESENT_VALID_HASH202701 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 (this file) -- README -- executable java jar containing preston[2] v0.5.4-- preston.jar --- end of file descriptions --- References [1] Global Biodiversity Information Facility, Integrated Digitized Biocollections, Biological Collection Access Service (GBIF, iDigBio, BioCASe, https://gbif.org,https://idigbio.org,http://biocase.org) accessed from 2018-09-03 to 2023-02-02 with provenance hash://sha256/450deb8ed9092ac9b2f0f31d3dcf4e2b9be003c460df63dd6463d252bff37b55 hash://md5/898a9c02bedccaea5434ee4c6d64b7a2 . [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation

This page was built for dataset: A biodiversity dataset graph: GBIF, iDigBio, BioCASe hash://sha256/450deb8ed9092ac9b2f0f31d3dcf4e2b9be003c460df63dd6463d252bff37b55 hash://md5/898a9c02bedccaea5434ee4c6d64b7a2