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1. A biodiversity dataset graph: GBIF, iDigBio, BioCASe

   https://doi.org/10.5281/zenodo.3484205  

   Poelen, Jorrit H. ( January 2019 )

   Abstract

   <p>A biodiversity dataset graph: GBIF, iDigBio, BioCASe</p> <p>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. </p> <p>This dataset provides versioned provenance logs of snapshots of the GBIF, iDigBio, BioCASe network as tracked by Preston [2] between 2018-09-03 and 2019-10-02 using &#34;preston update -u https://gbif.org,https://idigbio.org,http://biocase.org&#34;. </p> <p>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 .  </p> <p>To retrieve and verify the downloaded GBIF, iDigBio, BioCASe biodiversity dataset graph, use the preston[2] command-line tool to &#34;clone&#34; this dataset using:</p> <p>$ java -jar preston.jar ls --remote https://zenodo.org/record/3484205/files &gt; /dev/null</p> <p>Optionally, you can retrieve all associated data (~500GB) files using:</p> <p>$ java -jar preston.jar clone --remote https://zenodo.org/record/3484205/files,https://deeplinker.bio</p> <p>Please note https://deeplinker.bio is a Preston remote that provided access to GBIF, iDigBio, BioCASe data files at time of writing (13 Oct 2019). This remote can replaced with any other Preston remote(s) if needed. This may take a while depending on network speed and hardware constraints.</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br /> &lt;0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55&gt; .<br /> &lt;hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55&gt; .<br /> &lt;hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d&gt; .<br /> &lt;hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93&gt; .<br /> &lt;hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd&gt; .<br /> &lt;hash://sha256/1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4&gt; .<br /> &lt;hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e&gt; .<br /> &lt;hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43&gt; .<br /> &lt;hash://sha256/102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe&gt; .<br /> &lt;hash://sha256/fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9&gt; .<br /> &lt;hash://sha256/20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc&gt; .<br /> &lt;hash://sha256/7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17&gt; .<br /> &lt;hash://sha256/c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29&gt; .<br /> &lt;hash://sha256/dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6&gt; .<br /> &lt;hash://sha256/f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda&gt; .<br /> &lt;hash://sha256/650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36&gt; .<br /> &lt;hash://sha256/e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79&gt; .<br /> &lt;hash://sha256/e69d186ff3be11830c2da67d1bfeb896ec6398fc9d555fa26eaae1baa54450fb&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df&gt; .<br /> &lt;hash://sha256/3e7f19a8a78b51437240f49c499e6e7f89b8d58d4e3ceb9480d4356721645cee&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/e69d186ff3be11830c2da67d1bfeb896ec6398fc9d555fa26eaae1baa54450fb&gt; .<br /> &lt;hash://sha256/5c469224fa0b6159bf33a59ddaa0246634e81bddd1728e7bf3540745055eccfa&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/3e7f19a8a78b51437240f49c499e6e7f89b8d58d4e3ceb9480d4356721645cee&gt; .<br /> &lt;hash://sha256/eb2c716ec85158a0785216de1b09965173fc368d12f213c1bf747bbc2e49c6a6&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/5c469224fa0b6159bf33a59ddaa0246634e81bddd1728e7bf3540745055eccfa&gt; .<br /> &lt;hash://sha256/3dd674b7ad16391629948981a9cb6f6f86937d016861c3e59cd6e6bf3589f3b7&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/eb2c716ec85158a0785216de1b09965173fc368d12f213c1bf747bbc2e49c6a6&gt; .<br /> &lt;hash://sha256/480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/3dd674b7ad16391629948981a9cb6f6f86937d016861c3e59cd6e6bf3589f3b7&gt; .<br /> &lt;hash://sha256/58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6&gt; .<br /> &lt;hash://sha256/a0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70&gt; .<br /> &lt;hash://sha256/a7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/a0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208&gt; .<br /> &lt;hash://sha256/0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/a7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6&gt; .<br /> &lt;hash://sha256/8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781&gt; .<br /> &lt;hash://sha256/d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4&gt; .<br /> &lt;hash://sha256/af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3&gt; .<br /> &lt;hash://sha256/261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae&gt; .<br /> &lt;hash://sha256/5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12&gt; .<br /> &lt;hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7&gt; .<br /> &lt;hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63&gt; .<br /> &lt;hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e&gt; .<br /> &lt;hash://sha256/09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd&gt; .<br /> &lt;hash://sha256/668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2&gt; .<br /> &lt;hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103&gt; .<br /> &lt;hash://sha256/d79fb9207329a2813b60713cf0968fda10721d576dcb7a36038faf18027eebc1&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7&gt; .</p> <p>If you retrieved data files, you can check the integrity of the extracted archive by confirming that each line produce by the command &#34;preston verify&#34; produces lines as shown below, with each line including &#34;CONTENT_PRESENT_VALID_HASH&#34;. Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br /> hash://sha256/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362    file:/home/preston/preston-archive/data/3e/ff/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362    OK    CONTENT_PRESENT_VALID_HASH    89931<br /> hash://sha256/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b    file:/home/preston/preston-archive/data/18/48/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b    OK    CONTENT_PRESENT_VALID_HASH    210344<br /> hash://sha256/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02    file:/home/preston/preston-archive/data/18/46/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02    OK    CONTENT_PRESENT_VALID_HASH    210344<br /> hash://sha256/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38    file:/home/preston/preston-archive/data/55/4f/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38    OK    CONTENT_PRESENT_VALID_HASH    202701</p> <p>Note that a copy of the java program &#34;preston&#34;, preston.jar, is included in this publication. The program runs on java 8&#43; virtual machine using &#34;java -jar preston.jar&#34;, or in short &#34;preston&#34;. </p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br /> README </p> <p>-- executable java jar containing preston[2] v0.1.8. --<br /> preston.jar</p> <p>-- individual provenance index files --<br /> 049b0eb995b484c1e64184f582f51b3c608dcade70c4aefc2d53f903bae45098<br /> 073315c32d7fd19868449bef1b11b15a86981dee53a31f7f5c882f7e3be413c3<br /> 1172c6927e58113db668409d36b6a2cd84cf1a93e85b50d65d0bd008a5d8aaa4<br /> 1707cb11cd9f696f1a86fd06742c1e14fad856747be88791f79f6fc7c979d5a6<br /> 272ff1f12a573c667634d934d06b8bab0dd9cc6558795287ea99fab87620d005<br /> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<br /> 37b8b636e939072d0df7246bf077ead4279f9dd33929be322e631104b0641308<br /> 3901b6af522d535fb164823704686e72f73b7798a2a64eaeb817134552c69e2c<br /> 395ed0c95a624f8853116442690965acf69151acd6b33cc4fc710f567828f784<br /> 460c14ed0129c1469c9149ed1030cdc133f110fb32048748323982cb88dd7eda<br /> 477b6c4e9ecf5c8cd1b5502e0245c8622fa4b358f6710f97db39b473ed3d8235<br /> 52b7274f5d795e4987964bb1a327dd6d6e4f65870e6a7aac172481d0ba3013d4<br /> 54786bde04751bc31bf38c9e89c010cfee7de91760e1f5f31218ff11acff8a70<br /> 6135b237a49b37b857801836494f2c36bcb1526bdacf001a9d11727fff6bf1f1<br /> 69b4d5ca9643c14501a48a2b1eb24971a6da68da5033c304f7f00b94e16a11d9<br /> 70066ea7c6a9dd6c2193cdc90b3b1ff7664af235ab245f6c03d1dd497b376570<br /> 7084702f8025c99a6608a3355ccad5ff5e644ad544121f5d524961f7fe29ceb6<br /> 7ebb008412baaac3afcc8af68b796bf4ca98f367cfd61a815eee82cdffeab196<br /> 886edb8d22973bb04fe3b42d12106029a00b9deab3fb77d8787123327b77ae3b<br /> 8a6d7e2ab026ff56380235fd9696f5e538e5e426b9374f2ddf3a705e186a7788<br /> 95f88f27ed3448534206406738dfb5c5030fe3d6883c6dda261649357600883f<br /> 9d12cae409e8ea0a546f7945cc629d622400000c3338e4710d9c6084fca9274d<br /> 9fa9ea50db419c75251026708183add8973d9e68a79062f7808b110bef21006e<br /> a24abbe089556f51fe9c2a51febdcaf893b419556312bcc63515713fc4a52922<br /> a3b0477fe46f09b0f51c0f651691665c149bc341f5c19996675d849252e86453<br /> a486474333f05884580dd10c54c95999063c7d1bc22e2cbe3bead604aca0a183<br /> a524b9af3f172793998e1f9c5c0e9c949cc935624a17ed3364d32bc0391c9382<br /> aa0e508aeb96f240b551fe92ff4224325ddcdf66f97eef95ac78aec62e53a169<br /> ab34300942ec02cca7adf2744f6fbc1ab7587060bea09ef92b65b66f89d1ddcd<br /> b05d4a17d9a02180669d7eb017102dd1a739fb4615759cba94baf944b2aee29c<br /> b37c79f95c22fc4d657cc89dedd7a870923285da690ad4f5121962492484a142<br /> be6d8cd5f1405a5e3e8aa492fb8dab41f6521608834d746e6cbc58d2f550f918<br /> c06f4413a97a5540fbdd40bdbfb194435c154533df7fe388dfdd378084e19c3d<br /> c585b8addfb7f7991ad74c0bae158aecefc6be5b11c28b020135e0f13040e187<br /> c66587e9730a6f68e961240038892df656ea99a1a25f4ff8ce556c07b09a4878<br /> cea1aab236de5de8da8954797d846c225bf2ad4f8fe3cd413e60ab029f9e1b3e<br /> da05cc27a47e755ebe912fafae434df5bd31a5d92658fe1943acc0a2023fab32<br /> fcb2ee4d630a9a1440417b0c46da5bc1578a388d6aedd12189a23283b60dde7d<br /> ff32a7cbc99eaf6b67695fd94284a9b1b47a76497ef4d10ffc4dae199cc0d7c3</p> <p>--- individual provenance logs --<br /> 05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd<br /> 09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2<br /> 0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781<br /> 102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9<br /> 1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e<br /> 20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17<br /> 24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43<br /> 261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12<br /> 3dd674b7ad16391629948981a9cb6f6f86937d016861c3e59cd6e6bf3589f3b7<br /> 3e7f19a8a78b51437240f49c499e6e7f89b8d58d4e3ceb9480d4356721645cee<br /> 480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6<br /> 58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70<br /> 5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7<br /> 5c469224fa0b6159bf33a59ddaa0246634e81bddd1728e7bf3540745055eccfa<br /> 6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7<br /> 650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79<br /> 668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103<br /> 7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29<br /> 7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93<br /> 8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4<br /> 9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e<br /> a0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208<br /> a7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6<br /> af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae<br /> af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63<br /> b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4<br /> b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d<br /> b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd<br /> ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe<br /> c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6<br /> c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55<br /> d79fb9207329a2813b60713cf0968fda10721d576dcb7a36038faf18027eebc1<br /> d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3<br /> dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda<br /> e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df<br /> e69d186ff3be11830c2da67d1bfeb896ec6398fc9d555fa26eaae1baa54450fb<br /> eb2c716ec85158a0785216de1b09965173fc368d12f213c1bf747bbc2e49c6a6<br /> f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36<br /> fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc</p> <p>--- end of file descriptions ---</p> <p>References </p> <p>[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 2019-10-02 with provenance hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7.<br /> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . </p> <p>This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation</p>
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2. UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph

   https://doi.org/10.5281/zenodo.5660088  

   Cheadle Center for Biodiversity and Ecological Restoration, University of ( January 2021 )

   Abstract

   <p>A biodiversity dataset graph: UCSB-IZC</p> <p>The intended use of this archive is to facilitate (meta-)analysis of the UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC). UCSB-IZC is a natural history collection of invertebrate zoology at Cheadle Center of Biodiversity and Ecological Restoration, University of California Santa Barbara.</p> <p>This dataset provides versioned snapshots of the UCSB-IZC network as tracked by Preston [2,3] between 2021-10-08 and 2021-11-04 using [preston track &#34;https://api.gbif.org/v1/occurrence/search/?datasetKey&#61;d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0&#34;].</p> <p>This archive contains 14349 images related to 32533 occurrence/specimen records. See included sample-image.jpg and their associated meta-data sample-image.json [4].</p> <p>The images were counted using:</p> <p>$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\<br />  | grep -o -P &#34;.*depict&#34;\<br />  | sort\<br />  | uniq\<br />  | wc -l</p> <p>And the occurrences were counted using:</p> <p>$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\<br />  | grep -o -P &#34;occurrence/([0-9])&#43;&#34;\<br />  | sort\<br />  | uniq\<br />  | wc -l</p> <p>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 files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to establish a versioning mechanism.</p> <p>To retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a &#34;data&#34; folder. Alternatively, you can use the Preston [2,3] command-line tool to &#34;clone&#34; this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://archive.org/download/preston-ucsb-izc/data.zip/,https://zenodo.org/record/5557670/files,https://zenodo.org/record/5557670/files/5660088</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br /> &lt;urn:uuid:0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36&gt; .<br /> &lt;hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36&gt; .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command &#34;preston verify&#34; produces lines as shown below, with each line including &#34;CONTENT_PRESENT_VALID_HASH&#34;. Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br /> hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    OK    CONTENT_PRESENT_VALID_HASH    66438    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c<br /> hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    OK    CONTENT_PRESENT_VALID_HASH    4093    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844<br /> hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    OK    CONTENT_PRESENT_VALID_HASH    5746    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef<br /> hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    OK    CONTENT_PRESENT_VALID_HASH    6147    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b</p> <p>Note that a copy of the java program &#34;preston&#34;, preston.jar, is included in this publication. The program runs on java 8&#43; virtual machine using &#34;java -jar preston.jar&#34;, or in short &#34;preston&#34;.</p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br /> README</p> <p>-- executable java jar containing preston [2,3] v0.3.1. --<br /> preston.jar</p> <p>-- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --<br /> preston-[00-ff].tar.gz</p> <p>-- individual provenance index files --<br /> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a</p> <p>-- example image and meta-data --<br /> sample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)<br /> sample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)</p> <p>--- end of file descriptions ---</p> <p><br /> References</p> <p>[1] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-11-04 as indexed by the Global Biodiversity Informatics Facility (GBIF) with provenance hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36 hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c.<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<br /> [4] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08. https://www.gbif.org/occurrence/3323647301 . hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c</p>
   

   Other

   This work is funded in part by grant NSF OAC 1839201 and NSF DBI 2102006 from the National Science Foundation.
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3. A biodiversity dataset graph: DataONE

   https://doi.org/10.5281/zenodo.3849494  

   Poelen, Jorrit H. ( January 2020 )

   Abstract

   <p>A biodiversity dataset graph: DataONE</p> <p>The intended use of this archive is to facilitate (meta-)analysis of the Data Observation Network for Earth (DataONE). DataONE is a distributed infrastructure that provides information about earth observation data.</p> <p>This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-11-06 and 2020-05-07 using &#34;preston update -u https://dataone.org&#34;.</p> <p>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 DataONE content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .  </p> <p>To retrieve and verify the downloaded DataONE 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 &#34;data&#34; folder. Alternatively, you can use the preston[2] command-line tool to &#34;clone&#34; this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://zenodo.org/record/3849494/files</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br /> &lt;0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f&gt; .<br /> &lt;hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f&gt; .<br /> &lt;hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685&gt; .<br /> &lt;hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f&gt; .<br /> &lt;hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88&gt; .<br /> &lt;hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90&gt; .<br /> &lt;hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372&gt; .<br /> &lt;hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42&gt; .<br /> &lt;hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb&gt; .<br /> &lt;hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb&gt; .<br /> &lt;hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de&gt; .<br /> &lt;hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807&gt; .<br /> &lt;hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7&gt; .<br /> &lt;hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650&gt; .<br /> &lt;hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814&gt; .<br /> &lt;hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77&gt; .<br /> &lt;hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12&gt; .<br /> &lt;hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f&gt; .<br /> &lt;hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87&gt; .<br /> &lt;hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef&gt; .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command &#34;preston verify&#34; produces lines as shown below, with each line including &#34;CONTENT_PRESENT_VALID_HASH&#34;. Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br /> hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580    hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945<br /> hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035    hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f<br /> hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935    hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53<br /> hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553    hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687</p> <p><br /> Note that a copy of the java program &#34;preston&#34;, preston.jar, is included in this publication. The program runs on java 8&#43; virtual machine using &#34;java -jar preston.jar&#34;, or in short &#34;preston&#34;.</p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br /> README</p> <p>-- executable java jar containing preston[2] v0.1.15. --<br /> preston.jar</p> <p>-- preston archives containing DataONE data files, associated provenance logs and a provenance index --<br /> preston-[00-ff].tar.gz</p> <p>-- individual provenance index files --<br /> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<br /> 2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf<br /> 2f65ae542401d4c2daf1bca70de640211da6749188f67d28ea71acd7d8ba070b<br /> 35eb1e17e2bf3e71212cde35bdb03e8a6545a57483ea3c1633929257b70cf637<br /> 3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7<br /> 66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba<br /> 7466a35e42dea7e2be068060ec0c926f9a8686388ed504ef5c6c990c1ba4e8d0<br /> 81161d9746c2a5823641c436e773fb4508516b055da85f4494b38c545349da39<br /> 8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66<br /> a90eed8d70c54c8e554f2dfde4fceb434eda162d9615d62de96ded2344f88a78<br /> c33ef5e29100b323412f1f3bc66908c8e01e4f0d1db4ea3685d2fffc47981dd6<br /> c84dffef20fec958255e759db6445fc469d73695674a33ae6f7e567a088c9fe0<br /> d362d599d72000c4feb464db5a669b12e15fc3ca1a49b1e7d4d6f7d6d5d15411<br /> d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d<br /> da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db<br /> e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55<br /> eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94<br /> f13ab4bca04f894ae8eabb51fa01b4dfbc69f717eabc9896c728e2ba39c4db27<br /> f493baf276892a199a0b0d078359f64a38fe8ad3f807921f8d41ef73f7343b1f<br /> ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3</p> <p>--- end of file descriptions ---</p> <p><br /> References</p> <p>[1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-11-06 to 2020-05-07 with provenance hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3.<br /> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .</p> <p><br /> This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.</p>
   More>>
4. A biodiversity dataset graph: DataONE

   https://doi.org/10.5281/zenodo.3483218  

   Poelen, Jorrit H. ( January 2019 )

   Abstract

   <p>A biodiversity dataset graph: DataONE</p> <p>The intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE). DataONE is a distributed infrastructure that provides information about earth observation data. </p> <p>This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-10-18 and 2019-10-03 using &#34;preston update -u https://dataone.org&#34;. </p> <p>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 and where the DataONE content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543).  </p> <p>To retrieve and verify the downloaded DataONE 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 &#34;data&#34; folder. Alternatively, you can use the preston[2] command-line tool to &#34;clone&#34; this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://zenodo.org/record/3483218/files</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br /> &lt;0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f&gt; .<br /> &lt;hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f&gt; .<br /> &lt;hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685&gt; .<br /> &lt;hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f&gt; .<br /> &lt;hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88&gt; .<br /> &lt;hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90&gt; .<br /> &lt;hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372&gt; .<br /> &lt;hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42&gt; .<br /> &lt;hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb&gt; .<br /> &lt;hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb&gt; .<br /> &lt;hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de&gt; .<br /> &lt;hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807&gt; .<br /> &lt;hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7&gt; .<br /> &lt;hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650&gt; .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command &#34;preston verify&#34; produces lines as shown below, with each line including &#34;CONTENT_PRESENT_VALID_HASH&#34;. Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br /> hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580<br /> hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035<br /> hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935<br /> hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553</p> <p>Note that a copy of the java program &#34;preston&#34;, preston.jar, is included in this publication. The program runs on java 8&#43; virtual machine using &#34;java -jar preston.jar&#34;, or in short &#34;preston&#34;. </p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br /> README </p> <p>-- executable java jar containing preston[2] v0.1.8. --<br /> preston.jar</p> <p>-- preston archives containing DataONE data files, associated provenance logs and a provenance index --<br /> preston-[00-ff].tar.gz </p> <p>-- individual provenance index files --<br /> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<br /> 2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf<br /> 2f65ae542401d4c2daf1bca70de640211da6749188f67d28ea71acd7d8ba070b<br /> 3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7<br /> 66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba<br /> 8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66<br /> c84dffef20fec958255e759db6445fc469d73695674a33ae6f7e567a088c9fe0<br /> d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d<br /> da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db<br /> e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55<br /> eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94<br /> f13ab4bca04f894ae8eabb51fa01b4dfbc69f717eabc9896c728e2ba39c4db27<br /> f493baf276892a199a0b0d078359f64a38fe8ad3f807921f8d41ef73f7343b1f<br /> ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3</p> <p>--- end of file descriptions ---</p> <p><br /> References </p> <p>[1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-10-18 to 2019-10-03 with provenance hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650 .<br /> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . </p> <p><br /> This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation<br />  </p>
   More>>
5. A biodiversity dataset graph: Biodiverity Heritage Library (BHL)

   https://doi.org/10.5281/zenodo.3849560  

   Poelen, Jorrit ( January 2020 )

   Abstract

   <p>A biodiversity dataset graph: BHL</p> <p>The intended use of this archive is to facilitate (meta-)analysis of the Biodiversity Heritage Library (BHL). The Biodiversity Heritage Library improves research methodology by collaboratively making biodiversity literature openly available to the world as part of a global biodiversity community.</p> <p>This dataset provides versioned snapshots of the BHL network as tracked by Preston [2] between 2019-05-19 and 2020-05-09 using &#34;preston update -u https://biodiversitylibrary.org&#34;.</p> <p>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 BHL content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .  </p> <p>To retrieve and verify the downloaded BHL 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 &#34;data&#34; folder. Alternatively, you can use the preston[2] command-line tool to &#34;clone&#34; this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://zenodo.org/record/3849560/files</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br /> &lt;0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a&gt; .<br /> &lt;hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a&gt; .<br /> &lt;hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4&gt; .<br /> &lt;hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525&gt; .<br /> &lt;hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687&gt; .<br /> &lt;hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a&gt; .<br /> &lt;hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1&gt; .<br /> &lt;hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482&gt; .<br /> &lt;hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f&gt; .<br /> &lt;hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a&gt; .<br /> &lt;hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d&gt; .<br /> &lt;hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1&gt; &lt;http://purl.org/pav/previousVersion&gt; &lt;hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27&gt; .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command &#34;preston verify&#34; produces lines as shown below, with each line including &#34;CONTENT_PRESENT_VALID_HASH&#34;. Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br /> hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    file:/home/preston/preston-bhl/data/e0/c1/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    OK    CONTENT_PRESENT_VALID_HASH    49458087    hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca<br /> hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    file:/home/preston/preston-bhl/data/1a/57/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    OK    CONTENT_PRESENT_VALID_HASH    25745    hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99<br /> hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    file:/home/preston/preston-bhl/data/85/ef/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    OK    CONTENT_PRESENT_VALID_HASH    519892    hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c<br /> hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    file:/home/preston/preston-bhl/data/25/1e/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    OK    CONTENT_PRESENT_VALID_HASH    787414    hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743</p> <p>Note that a copy of the java program &#34;preston&#34;, preston.jar, is included in this publication. The program runs on java 8&#43; virtual machine using &#34;java -jar preston.jar&#34;, or in short &#34;preston&#34;.</p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br /> README</p> <p>-- executable java jar containing preston[2] v0.1.15. --<br /> preston.jar</p> <p>-- preston archives containing BHL data files, associated provenance logs and a provenance index --<br /> preston-[00-ff].tar.gz</p> <p>-- individual provenance index files --<br /> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<br /> 2b1104cb7749e818c9afca78391b2d0099bbb0a32f2b348860a335cd2f8f6800<br /> 4081bc59dff58d63f6a86c623cb770f01e9a355a42495b205bcb538cd526190f<br /> 47a2816f8b5600b24487093adcddfea12434cc4f270f3ab09d9215fbdd546cd2<br /> 6f99a1388823fca745c9e22ac21e2da909a219aa1ace55170fa9248c0276903c<br /> 7ae46d7cd9b5a0f5889ba38bac53c82e591b0bdf8b605f5e48c0dce8fb7b717f<br /> 82903464889fea7c53f53daedf4e41fa31092f82619edeb3415eb2b473f74af3<br /> 9e8c86243df39dd4fe82a3f814710eccf73aa9291d050415408e346fa2b09e70<br /> a8308fbf4530e287927c471d881ce0fc852f16543d46e1ee26f1caba48815f3a<br /> bcec6df2ea7f74e9a6e2830d0072e6b2fbe65323d9ddb022dd6e1349c23996e2<br /> cfe47c25ec0210ac73c06b407beb20d9c58355cb15bae427fdc7541870ca2e4e<br /> f73fc9e70bce8f21f0c96b8ef0903749d8f223f71343ab5a8910968f99c9b8b6</p> <p>--- end of file descriptions ---</p> <p><br /> References</p> <p>[1] Biodiversity Heritage Library (BHL, https://biodiversitylibrary.org) accessed from 2019-05-19 to 2020-05-09 with provenance hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1.<br /> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .</p> <p><br /> This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.</p>
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