Title: The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network
In 2017 NSF funded “oVert (openVertebrate): Open Exploration of Vertebrate Diversity in 3D,” which is the first Thematic Collections Network devoted entirely to vertebrate morphological specimens. The primary goal of oVert is to generate and serve high-resolution digital three-dimensional data for internal anatomy across vertebrate diversity. oVert will CT-scan >20,000 fluid-preserved specimens representing >80% of the living genera of vertebrates, providing broad coverage for exploration and research on all major groups of vertebrates. Contrast-enhanced scans will be generated to reveal soft tissues and organs for a majority of the living vertebrate families. This collection of digital imagery and three-dimensional volumes will be open for exploration, download, and use. These new media will provide unprecedented global access to valuable morphological data of specimens in US collections.oVert is developing best practices and guidelines for high-throughput CT-scanning, including efficient workflows, preferred resolutions, and archival formats that optimize the variety of downstream applications. Using the Integrated Digitized Biocollections (iDigBio) API, we have developed a workflow where people uploading media files to MorphoSource can search for and import metadata for specimens directly from iDigBio. Via a Rich Site Summary (RSS) feed from MorphoSource, Audubon Core data describing media files for a given scientific collection can be retrieved and integrated into institutional IPT and databases. Such data migration of large files requires attention to detail and the development of data workflows that ensure correct specimen mapping at all steps. The RSS feed from MorphoSource will also consolidate usage information for media files from specimens in each scientific collection for reporting. Additional goals of the project are to provide information vital to the creation of collection best practices for imaging permissions/copyright. A status report and update on best practices will be presented. more »« less
Whitman, Karie; Riddle, Catherine; Mazza, Amanda; Heritage, Steven; Neely, Kate; Yapuncich, Gabriel; Borths, Matthew
(, Society of Vertebrate Paleontology 2024 Annual Meeting Program and Abstracts)
Interpretations of extinct vertebrate anatomy, behavior, and life history are built upon comparative anatomy data from neontological collections. Ideally, these interpretations are informed by metadata collected while the organism was alive such as diet, mass throughout life, social relationships, and reproductive history. Unfortunately, these data are not available for many specimens as natural history collections have focused on wild-caught individuals for which mass at collection, sex, and collection locality are typically the only associated data. In contrast, extensive life-history data are collected from organisms in sustained human care, but transferring these data from zoos to natural history collections is not standardized or prioritized. The Duke Lemur Center (DLC) has been designing a database that allows researchers access to morphological and life-history data derived from animals that were part of the living research colony. The DLC is home to over 200 lemurs representing 16 different species. The colony has access to open air, multi-acre habitats. For over 50 years the AZA-accredited DLC has been a platform for non-invasive research on strepsirrhine primates and the DLC Museum is the repository for DLC specimens and fossils related to the evolution of primates. The colony’s breeding records, veterinary care, husbandry data, locomotor behaviors, and diets are recorded by researchers and staff. However, these data are disaggregated, making it difficult to explore. The DLC Data Team started by generating microCT scans of the osteology and frozen cadaver collection to make morphological data available on MorphoSource. Preserved specimens were rehoused and inventoried. Now we are using DLC-developed REDCap database management tools to network scans with life-history records, building a database that researchers can use to explore questions such as individual variation in tooth wear, osteological signatures of different pathologies, and individual biomechanical performance. The REDCap database is also used to store fossil metadata like field notes and specimen preparation records. Our goal is to make these database tools available to other living colonies and natural history collections, so life-history data can be shared and standardized across institutions. This effort – in collaboration with the ZooMu network – will ultimately make life histories accessible to researchers – including paleontologists exploring the fossil record.
Hendricks, Jonathan R; Lieberman, Bruce S
(, Paleobiology)
Abstract Most species exhibit morphological stasis following speciation, and this is a key feature of the concept of punctuated equilibria. Stasis results in species often having long durations on geological timescales. Durational data are fundamental to many types of paleobiological analyses and are ideally based on occurrence data represented by specimens in museum collections. Often, however, durational data are presented without supporting information about voucher specimens that document stratigraphic ranges, including first and last appearances. We use the iconic Devonian trilobiteEldredgeops ranato demonstrate that durational data can be challenging to determine at multiple taxonomic levels. Further, we show that different datasets—including Sepkoski’s published databases, the Paleobiology Database, and iDigBio—give discordant results concerning first and last occurrences. We argue that paleontologists should adopt two general best practices to help address these problems. First, systematists should clearly identify voucher specimens that represent stratigraphic occurrences of species. Second, we recommend that high-quality photographs of occurrence vouchers be placed in open access websites and be assigned public domain licensing before being paywalled by journals. Such voucher images also have a role to play in training artificial intelligence (AI) systems that will be applied to future paleobiological questions.
{"Abstract":["A biodiversity dataset graph: GBIF, iDigBio, BioCASe<\/p>\n\nThe 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>\n\nThis 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". <\/p>\n\nThis 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>\n\nTo retrieve and verify the downloaded GBIF, iDigBio, BioCASe biodiversity dataset graph, use the preston[2] command-line tool to "clone" this dataset using:<\/p>\n\n$$ java -jar preston.jar ls --remote https://zenodo.org/record/3484205/files > /dev/null<\/p>\n\nOptionally, you can retrieve all associated data (~500GB) files using:<\/p>\n\n$$ java -jar preston.jar clone --remote https://zenodo.org/record/3484205/files,https://deeplinker.bio<\/p>\n\nPlease 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>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55> .\n<hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d> <http://purl.org/pav/previousVersion> <hash://sha256/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55> .\n<hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93> <http://purl.org/pav/previousVersion> <hash://sha256/b83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d> .\n<hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd> <http://purl.org/pav/previousVersion> <hash://sha256/7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93> .\n<hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4> <http://purl.org/pav/previousVersion> <hash://sha256/05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd> .\n<hash://sha256/1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e> <http://purl.org/pav/previousVersion> <hash://sha256/b5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4> .\n<hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43> <http://purl.org/pav/previousVersion> <hash://sha256/1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e> .\n<hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe> <http://purl.org/pav/previousVersion> <hash://sha256/24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43> .\n<hash://sha256/102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9> <http://purl.org/pav/previousVersion> <hash://sha256/ba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe> .\n<hash://sha256/fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc> <http://purl.org/pav/previousVersion> <hash://sha256/102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9> .\n<hash://sha256/20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17> <http://purl.org/pav/previousVersion> <hash://sha256/fd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc> .\n<hash://sha256/7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29> <http://purl.org/pav/previousVersion> <hash://sha256/20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17> .\n<hash://sha256/c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6> <http://purl.org/pav/previousVersion> <hash://sha256/7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29> .\n<hash://sha256/dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda> <http://purl.org/pav/previousVersion> <hash://sha256/c1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6> .\n<hash://sha256/f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36> <http://purl.org/pav/previousVersion> <hash://sha256/dc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda> .\n<hash://sha256/650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79> <http://purl.org/pav/previousVersion> <hash://sha256/f3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36> .\n<hash://sha256/e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df> <http://purl.org/pav/previousVersion> <hash://sha256/650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79> .\n<hash://sha256/e69d186ff3be11830c2da67d1bfeb896ec6398fc9d555fa26eaae1baa54450fb> <http://purl.org/pav/previousVersion> <hash://sha256/e4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df> 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<hash://sha256/3dd674b7ad16391629948981a9cb6f6f86937d016861c3e59cd6e6bf3589f3b7> .\n<hash://sha256/58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70> <http://purl.org/pav/previousVersion> <hash://sha256/480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6> .\n<hash://sha256/a0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208> <http://purl.org/pav/previousVersion> <hash://sha256/58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70> .\n<hash://sha256/a7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6> <http://purl.org/pav/previousVersion> <hash://sha256/a0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208> .\n<hash://sha256/0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781> <http://purl.org/pav/previousVersion> <hash://sha256/a7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6> .\n<hash://sha256/8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4> <http://purl.org/pav/previousVersion> <hash://sha256/0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781> .\n<hash://sha256/d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3> <http://purl.org/pav/previousVersion> <hash://sha256/8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4> .\n<hash://sha256/af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae> <http://purl.org/pav/previousVersion> <hash://sha256/d99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3> .\n<hash://sha256/261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12> <http://purl.org/pav/previousVersion> <hash://sha256/af0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae> .\n<hash://sha256/5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7> <http://purl.org/pav/previousVersion> <hash://sha256/261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12> .\n<hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63> <http://purl.org/pav/previousVersion> <hash://sha256/5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7> .\n<hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e> <http://purl.org/pav/previousVersion> <hash://sha256/af8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63> .\n<hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd> <http://purl.org/pav/previousVersion> <hash://sha256/9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e> .\n<hash://sha256/09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2> <http://purl.org/pav/previousVersion> <hash://sha256/b9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd> .\n<hash://sha256/668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103> <http://purl.org/pav/previousVersion> <hash://sha256/09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2> .\n<hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7> <http://purl.org/pav/previousVersion> <hash://sha256/668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103> .\n<hash://sha256/d79fb9207329a2813b60713cf0968fda10721d576dcb7a36038faf18027eebc1> <http://purl.org/pav/previousVersion> <hash://sha256/6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7> .<\/p>\n\nIf 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.<\/p>\n\n$$ java -jar preston.jar verify\nhash://sha256/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362 file:/home/preston/preston-archive/data/3e/ff/3eff98d4b66368fd8d1f8fa1af6a057774d8a407a4771490beeb9e7add76f362 OK CONTENT_PRESENT_VALID_HASH 89931\nhash://sha256/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b file:/home/preston/preston-archive/data/18/48/184886cc6ae4490a49a70b6fd9a3e1dfafce433fc8e3d022c89e0b75ea3cda0b OK CONTENT_PRESENT_VALID_HASH 210344\nhash://sha256/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02 file:/home/preston/preston-archive/data/18/46/1846abf2b9623697cf9b2212e019bc1f6dc4a20da51b3b5629bfb964dc808c02 OK CONTENT_PRESENT_VALID_HASH 210344\nhash://sha256/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38 file:/home/preston/preston-archive/data/55/4f/554fdab07f2372bf363a1d7ef30fcf4c32e1da98b95a6342780c5eb35e0e7b38 OK CONTENT_PRESENT_VALID_HASH 202701<\/p>\n\nNote 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". <\/p>\n\nFiles in this data publication:<\/p>\n\n--- start of file descriptions ---<\/p>\n\n-- description of archive and its contents (this file) --\nREADME <\/p>\n\n-- executable java jar containing preston[2] v0.1.8. --\npreston.jar<\/p>\n\n-- individual provenance index files --\n049b0eb995b484c1e64184f582f51b3c608dcade70c4aefc2d53f903bae45098\n073315c32d7fd19868449bef1b11b15a86981dee53a31f7f5c882f7e3be413c3\n1172c6927e58113db668409d36b6a2cd84cf1a93e85b50d65d0bd008a5d8aaa4\n1707cb11cd9f696f1a86fd06742c1e14fad856747be88791f79f6fc7c979d5a6\n272ff1f12a573c667634d934d06b8bab0dd9cc6558795287ea99fab87620d005\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a\n37b8b636e939072d0df7246bf077ead4279f9dd33929be322e631104b0641308\n3901b6af522d535fb164823704686e72f73b7798a2a64eaeb817134552c69e2c\n395ed0c95a624f8853116442690965acf69151acd6b33cc4fc710f567828f784\n460c14ed0129c1469c9149ed1030cdc133f110fb32048748323982cb88dd7eda\n477b6c4e9ecf5c8cd1b5502e0245c8622fa4b358f6710f97db39b473ed3d8235\n52b7274f5d795e4987964bb1a327dd6d6e4f65870e6a7aac172481d0ba3013d4\n54786bde04751bc31bf38c9e89c010cfee7de91760e1f5f31218ff11acff8a70\n6135b237a49b37b857801836494f2c36bcb1526bdacf001a9d11727fff6bf1f1\n69b4d5ca9643c14501a48a2b1eb24971a6da68da5033c304f7f00b94e16a11d9\n70066ea7c6a9dd6c2193cdc90b3b1ff7664af235ab245f6c03d1dd497b376570\n7084702f8025c99a6608a3355ccad5ff5e644ad544121f5d524961f7fe29ceb6\n7ebb008412baaac3afcc8af68b796bf4ca98f367cfd61a815eee82cdffeab196\n886edb8d22973bb04fe3b42d12106029a00b9deab3fb77d8787123327b77ae3b\n8a6d7e2ab026ff56380235fd9696f5e538e5e426b9374f2ddf3a705e186a7788\n95f88f27ed3448534206406738dfb5c5030fe3d6883c6dda261649357600883f\n9d12cae409e8ea0a546f7945cc629d622400000c3338e4710d9c6084fca9274d\n9fa9ea50db419c75251026708183add8973d9e68a79062f7808b110bef21006e\na24abbe089556f51fe9c2a51febdcaf893b419556312bcc63515713fc4a52922\na3b0477fe46f09b0f51c0f651691665c149bc341f5c19996675d849252e86453\na486474333f05884580dd10c54c95999063c7d1bc22e2cbe3bead604aca0a183\na524b9af3f172793998e1f9c5c0e9c949cc935624a17ed3364d32bc0391c9382\naa0e508aeb96f240b551fe92ff4224325ddcdf66f97eef95ac78aec62e53a169\nab34300942ec02cca7adf2744f6fbc1ab7587060bea09ef92b65b66f89d1ddcd\nb05d4a17d9a02180669d7eb017102dd1a739fb4615759cba94baf944b2aee29c\nb37c79f95c22fc4d657cc89dedd7a870923285da690ad4f5121962492484a142\nbe6d8cd5f1405a5e3e8aa492fb8dab41f6521608834d746e6cbc58d2f550f918\nc06f4413a97a5540fbdd40bdbfb194435c154533df7fe388dfdd378084e19c3d\nc585b8addfb7f7991ad74c0bae158aecefc6be5b11c28b020135e0f13040e187\nc66587e9730a6f68e961240038892df656ea99a1a25f4ff8ce556c07b09a4878\ncea1aab236de5de8da8954797d846c225bf2ad4f8fe3cd413e60ab029f9e1b3e\nda05cc27a47e755ebe912fafae434df5bd31a5d92658fe1943acc0a2023fab32\nfcb2ee4d630a9a1440417b0c46da5bc1578a388d6aedd12189a23283b60dde7d\nff32a7cbc99eaf6b67695fd94284a9b1b47a76497ef4d10ffc4dae199cc0d7c3<\/p>\n\n--- individual provenance logs --\n05a877bdb8617144fe166a13bf51828d4ad1bc11631c360b9e648a9f7df2bbcd\n09574d9c1330c2b1bec9b7bf3a55ab9273bedbfed78affd70a058a1a25e052d2\n0e6b49850d96b4b58ea3759ecea45d273a48f074c4edaaec5e008791d7718781\n102cbfb1e800ef795ba1e1c51a34bff9b463b34c9443435069ddc76970c1e9c9\n1d3817d9cb9fc7de7a3b7a4181daba8de1e52b348280154e8a163c7dd7ee1a7e\n20d36a6f879ba1dd797d4288a4f2e32719d3c674156194c2765a3ec6b43f5e17\n24b3f981c88c747f44ad3372095767cd15dcf81bd6cd2e54328a90a21409df43\n261177a96185166f1c301beacf7350abff03d1b5710be6bfd8c4aff9caffef12\n3dd674b7ad16391629948981a9cb6f6f86937d016861c3e59cd6e6bf3589f3b7\n3e7f19a8a78b51437240f49c499e6e7f89b8d58d4e3ceb9480d4356721645cee\n480868b59e95f3ce2324a7308dba65795e857d34cfbdcea7440a6f2620c6fbf6\n58daa9a51e5dc0911163aa1b98d68c801106734cd29eab9980814057351aeb70\n5a39b7bbe9d1bc46ed2eb7bd76c490b5c85a09369a7cf7dc18fa04532679e9a7\n5c469224fa0b6159bf33a59ddaa0246634e81bddd1728e7bf3540745055eccfa\n6387c9ebed9507a0fbba2d161e83c2da73e0d6fa6dd51fb19ac4a4ca75b839c7\n650a28fff3e03dadba70dc05a34c580c04203380187953fa4a2fb778353fee79\n668d5d6e9c9e7ddb410073ff75eb7f2935c60cc62944ba1fd96ca60feec4a103\n7801a034fe3c7920e032d2338a690b700ca41a90a92d878fc3a67111cad16d29\n7efdea9263e57605d2d2d8b79ccd26a55743123d0c974140c72c8c1cfc679b93\n8c0752dc6425b9c716837c9713ce284158b4cff70a1e66be2beb0677018831f4\n9a41d2583f0b8169ffdd44fb2d3a5e057eba4a10e5d9193d0c6e9dcf07c3119e\na0a18b0e32f933112084b846863438038f66f63eeeb22fa9d8d734e8a25bb208\na7a5e7c6a4b21bdf67f48d6bea85f438b8133f674027b04625dfadec3ff985f6\naf0bb2c89571a30815d4488e72dede84a2ffc102bb87961f06884509fd5d1dae\naf8f9ed321d9c403617f54a96e3217adc918970fbbfe8b8715359669f4890b63\nb5a30bbd8d51e9faf08d4ddebbc5bda9bab1b12545172f1524ac5ebdb0038bd4\nb83cf099449dae3f633af618b19d05013953e7a1d7d97bc5ac01afd7bd9abe5d\nb9864a749112cad2fe19e62bf5d8bad580a7036d363d16d81d5c16be325fa0fd\nba02b235fd445904eae45b50bc637a195f25e9ca1637bcf26b2dc7f8698aa1fe\nc1b50502b1ca87046eeb7fe4863d0cf9319b6645ff2142db69f21b4cc23332b6\nc253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55\nd79fb9207329a2813b60713cf0968fda10721d576dcb7a36038faf18027eebc1\nd99fa37caa268f8061980001146ed2a566e814d0740bb1974b76847512be95d3\ndc293e26154b89273791b9674d81110029f987c686b386184d0b66a5b95f9cda\ne4e5736e8bfec6c686eedde4c6dfa62845930d04e12dfa6f8a7d70abc3d087df\ne69d186ff3be11830c2da67d1bfeb896ec6398fc9d555fa26eaae1baa54450fb\neb2c716ec85158a0785216de1b09965173fc368d12f213c1bf747bbc2e49c6a6\nf3ed6aa1bd15ee43d05e138b935040aaa745f6ca8c7e8f2dfbb0a3ae0df66f36\nfd27b0552c8a6800a8b3b1b822a2063a3215c1d9887badad09a62746b80846bc<\/p>\n\n--- end of file descriptions ---<\/p>\n\nReferences <\/p>\n\n[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.\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . <\/p>\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation<\/p>"]}
Patel, B.A.; Gilbert, C.C.; Sehgal, R.K.; Singh, N.P.; Di, A.; Choudhary, D.; Wazir, W.A.; Campisano, C.J.; Patnaik, R.
(, American journal of physical anthropology)
Vertebrate fossils have been known from Lower Siwalik Miocene deposits surrounding the town of Ramnagar (Udhampur District, Jammu & Kashmir) in northwest India since Barnum Brown’s American Museum of Natural History (AMNH) expedition in 1922. These fossils included dentognathic specimens of Sivapithecus and other Chinji Formation-aged mammals. Paleontological fieldwork has continued sporadically in the Ramnagar region ever since, and in that time, a large number of vertebrate fossils have been recovered by many different researchers and institutions, including the recently discovered primates Kapi and Ramadapis. Ramnagar fossils are currently housed in several institutions across India and the United States, thereby making it challenging to comprehensively study the entire collection. Consequently, a full understanding of important questions related to the taxonomy, paleobiology, paleoecology, and biochronology of the Ramnagar fauna cannot be readily obtained. Moreover, without answers to these questions, correlations and comparisons cannot be accurately made to other similar aged fossil localities in the Siwaliks (i.e., Potwar Plateau, Pakistan) and elsewhere in Eurasia. Therefore, the goal of this collaborative project is to establish and grow a 3D digital repository of all fossil specimens from the Ramnagar region for continued comprehensive study. We employ µCT, surface scanning, and photogrammetry to virtually bring together specimens from the AMNH, Panjab University, Wadia Institute of Himalayan Geology, and Yale Peabody Museum. Thus far, >100 specimens have been digitized and made openly accessible on the MorphoSource web platform. Here we highlight some of the best-preserved specimens, including recovered primates and micromammals, and discuss their scientific importance.
Biodiversity datasets, or descriptions of biodiversity datasets, are increasingly available through open digital data infrastructures such as Global Biodiversity Information Facility (GBIF, https://gbif.org), Integrated Digitized Biocollections (iDigBio, https://www.idigbio.org) and the Biological Collection Access Service (BioCASE, http://www.biocase.org). </p> However, little is known about how these networks, and the data accessed through them, change over time. This dataset provide snapshots of the biodiversity dataset graphs as tracked by Preston (https://github.com/bio-guoda/preston , https://doi.org/10.5281/zenodo.1410543 ).</p> The rdf/nquad and tsv snapshots were generated using the respective commands:</p> preston ls | bzip2 > preston-ls.nq.bz2</p> and</p> preston ls --log tsv | bzip2 > preston-ls.tsv.bz2</p> For convenience, the first 100 uncompressed entries of both files are included, as well as the sha256 hashes of the content of the files.</p>
Watkins-Colwell, Gregory, Love, Kevin, Randall, Zachary, Boyer, Doug, Winchester, Julie, Stanley, Edward, and Blackburn, David. The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network. Retrieved from https://par.nsf.gov/biblio/10066525. Biodiversity Information Science and Standards 2. Web. doi:10.3897/biss.2.26078.
Watkins-Colwell, Gregory, Love, Kevin, Randall, Zachary, Boyer, Doug, Winchester, Julie, Stanley, Edward, & Blackburn, David. The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network. Biodiversity Information Science and Standards, 2 (). Retrieved from https://par.nsf.gov/biblio/10066525. https://doi.org/10.3897/biss.2.26078
Watkins-Colwell, Gregory, Love, Kevin, Randall, Zachary, Boyer, Doug, Winchester, Julie, Stanley, Edward, and Blackburn, David.
"The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network". Biodiversity Information Science and Standards 2 (). Country unknown/Code not available. https://doi.org/10.3897/biss.2.26078.https://par.nsf.gov/biblio/10066525.
@article{osti_10066525,
place = {Country unknown/Code not available},
title = {The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network},
url = {https://par.nsf.gov/biblio/10066525},
DOI = {10.3897/biss.2.26078},
abstractNote = {In 2017 NSF funded “oVert (openVertebrate): Open Exploration of Vertebrate Diversity in 3D,” which is the first Thematic Collections Network devoted entirely to vertebrate morphological specimens. The primary goal of oVert is to generate and serve high-resolution digital three-dimensional data for internal anatomy across vertebrate diversity. oVert will CT-scan >20,000 fluid-preserved specimens representing >80% of the living genera of vertebrates, providing broad coverage for exploration and research on all major groups of vertebrates. Contrast-enhanced scans will be generated to reveal soft tissues and organs for a majority of the living vertebrate families. This collection of digital imagery and three-dimensional volumes will be open for exploration, download, and use. These new media will provide unprecedented global access to valuable morphological data of specimens in US collections.oVert is developing best practices and guidelines for high-throughput CT-scanning, including efficient workflows, preferred resolutions, and archival formats that optimize the variety of downstream applications. Using the Integrated Digitized Biocollections (iDigBio) API, we have developed a workflow where people uploading media files to MorphoSource can search for and import metadata for specimens directly from iDigBio. Via a Rich Site Summary (RSS) feed from MorphoSource, Audubon Core data describing media files for a given scientific collection can be retrieved and integrated into institutional IPT and databases. Such data migration of large files requires attention to detail and the development of data workflows that ensure correct specimen mapping at all steps. The RSS feed from MorphoSource will also consolidate usage information for media files from specimens in each scientific collection for reporting. Additional goals of the project are to provide information vital to the creation of collection best practices for imaging permissions/copyright. A status report and update on best practices will be presented.},
journal = {Biodiversity Information Science and Standards},
volume = {2},
author = {Watkins-Colwell, Gregory and Love, Kevin and Randall, Zachary and Boyer, Doug and Winchester, Julie and Stanley, Edward and Blackburn, David},
}
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