DOI: 10.5281/zenodo.3484205
title: A biodiversity dataset graph: GBIF, iDigBio, BioCASe

description: A biodiversity dataset graph: GBIF, iDigBio, BioCASe 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 2019-10-02 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/3484205/files &gt; /dev/null Optionally, you can retrieve all associated data (~500GB) files using: $ java -jar preston.jar clone --remote https://zenodo.org/record/3484205/files,https://deeplinker.bio 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. After that, verify the index of the archive by reproducing the following provenance log history: $ 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; . 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<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 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) --<br> README -- executable java jar containing preston[2] v0.1.8. --<br> preston.jar -- 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> 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ff32a7cbc99eaf6b67695fd94284a9b1b47a76497ef4d10ffc4dae199cc0d7c3 --- 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> 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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 . This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation