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Title: Data in: Aging power spectrum of membrane protein transport and other subordinated random walks

Datasets generated in the report "Aging power spectrum of membrane protein transport and other subordinated random walks". Included data are:

Numerical simulations 
RWdata1.mat: 10,000 realizations, subordinated random walk with Hurst exponent, H=0.3 and \(\alpha\)=0.4.
RWdata3.mat: 10,000 realizations, subordinated random walk with Hurst exponent, H=0.7 and \(\alpha\)=0.4.
RWdata8.mat: 5,000 realizations, subordinated random walk with Hurst exponent, H=0.75 and \(\alpha\)=0.8.
RWdataCTRW.mat: 10,000 realizations, continuous time random walk (CTRW), \(\alpha\)=0.7.

Spectra of simulations
PSDdata1.mat: Power spectral density (PSD) of a subordinated random walk with Hurst exponent, H=0.3 and \(\alpha\)=0.4. Five different realization times are used to compute the PDS: 2^8, 2^10, 2^12, 2^14, and 2^16.
PSDdata3.mat: PSD of a subordinated random walk with Hurst exponent, H=0.7 and \(\alpha\)=0.4. Five different realization times are used to compute the PDS: 2^8, 2^10, 2^12, 2^14, and 2^16.
PSDdata8.mat: PSD of a subordinated random walk with Hurst exponent, H=0.75 and \(\alpha\)=0.8. Four different realization times are used to compute the PDS: 2^15, 2^16, 2^17, and 2^18.
PSDs_CTRW.mat: PSD of a continuous-time random walk (CTRW), \(\alpha\)=0.7. Five different realization times are used to compute the PDS: 2^8, 2^10, 2^12, 2^14, and 2^16.

Experimental data of Nav1.6 channels in the soma of hippocampal neurons
NavMSDtimes.csv: ensemble-averaged (EA) MSD and time-averaged (TA) MSD. The TA-MSD is measured for three observation times, 64, 128, and 256 frames (3.2, 6.4, and 12.8 s).
NavPSD.csv: Power spectral density (PSD) measured for three observation times, 64, 128, and 256 frames.

We acknowledge the support of the National Science Foundation grant 2102832 (to DK) and Israel Science Foundation grant 1898/17 (to EB). {"references": ["Fox, Z.R., Barkai, E. & Krapf, D. Aging power spectrum of membrane protein transport and other subordinated random walks. Nat Commun 12, 6162 (2021). https://doi.org/10.1038/s41467-021-26465-8"]} 
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Award ID(s):
2102832
NSF-PAR ID:
10341514
Author(s) / Creator(s):
; ;
Publisher / Repository:
Zenodo
Date Published:
Edition / Version:
1
Subject(s) / Keyword(s):
["subordinated random walks, fractional Brownian motion, power soectrum"]
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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  1. A biodiversity dataset graph: DataONE

    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.

    This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-11-06 and 2020-05-07 using "preston update -u https://dataone.org".

    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 .  

    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 > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:

    $ java -jar preston.jar clone --remote https://zenodo.org/record/3849494/files

    After that, verify the index of the archive by reproducing the following provenance log history:

    $ java -jar preston.jar history
    <0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
    <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
    <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .
    <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .
    <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .
    <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .
    <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .
    <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .
    <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .
    <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .
    <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> <http://purl.org/pav/previousVersion> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> .
    <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> <http://purl.org/pav/previousVersion> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> .
    <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> <http://purl.org/pav/previousVersion> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> .
    <hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> <http://purl.org/pav/previousVersion> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> .
    <hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77> <http://purl.org/pav/previousVersion> <hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> .
    <hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12> <http://purl.org/pav/previousVersion> <hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77> .
    <hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f> <http://purl.org/pav/previousVersion> <hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12> .
    <hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87> <http://purl.org/pav/previousVersion> <hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f> .
    <hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef> <http://purl.org/pav/previousVersion> <hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87> .
    <hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3> <http://purl.org/pav/previousVersion> <hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef> .

    To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.

    $ java -jar preston.jar verify
    hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580    hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945
    hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035    hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f
    hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935    hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53
    hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553    hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687


    Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".

    Files in this data publication:

    --- start of file descriptions ---

    -- description of archive and its contents (this file) --
    README

    -- executable java jar containing preston[2] v0.1.15. --
    preston.jar

    -- preston archives containing DataONE data files, associated provenance logs and a provenance index --
    preston-[00-ff].tar.gz

    -- individual provenance index files --
    2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a
    2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf
    2f65ae542401d4c2daf1bca70de640211da6749188f67d28ea71acd7d8ba070b
    35eb1e17e2bf3e71212cde35bdb03e8a6545a57483ea3c1633929257b70cf637
    3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7
    66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba
    7466a35e42dea7e2be068060ec0c926f9a8686388ed504ef5c6c990c1ba4e8d0
    81161d9746c2a5823641c436e773fb4508516b055da85f4494b38c545349da39
    8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66
    a90eed8d70c54c8e554f2dfde4fceb434eda162d9615d62de96ded2344f88a78
    c33ef5e29100b323412f1f3bc66908c8e01e4f0d1db4ea3685d2fffc47981dd6
    c84dffef20fec958255e759db6445fc469d73695674a33ae6f7e567a088c9fe0
    d362d599d72000c4feb464db5a669b12e15fc3ca1a49b1e7d4d6f7d6d5d15411
    d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d
    da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db
    e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55
    eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94
    f13ab4bca04f894ae8eabb51fa01b4dfbc69f717eabc9896c728e2ba39c4db27
    f493baf276892a199a0b0d078359f64a38fe8ad3f807921f8d41ef73f7343b1f
    ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3

    --- end of file descriptions ---


    References

    [1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-11-06 to 2020-05-07 with provenance hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3.
    [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.

     
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  2. A biodiversity dataset graph: DataONE

    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. 

    This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-10-18 and 2019-10-03 using "preston update -u https://dataone.org". 

    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).  

    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 > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:

    $ java -jar preston.jar clone --remote https://zenodo.org/record/3483218/files

    After that, verify the index of the archive by reproducing the following provenance log history:

    $ java -jar preston.jar history
    <0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
    <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
    <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .
    <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .
    <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .
    <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .
    <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .
    <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .
    <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .
    <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .
    <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> <http://purl.org/pav/previousVersion> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> .
    <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> <http://purl.org/pav/previousVersion> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> .
    <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> <http://purl.org/pav/previousVersion> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> .
    <hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> <http://purl.org/pav/previousVersion> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> .

    To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.

    $ java -jar preston.jar verify
    hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580
    hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035
    hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935
    hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553

    Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston". 

    Files in this data publication:

    --- start of file descriptions ---

    -- description of archive and its contents (this file) --
    README 

    -- executable java jar containing preston[2] v0.1.8. --
    preston.jar

    -- preston archives containing DataONE data files, associated provenance logs and a provenance index --
    preston-[00-ff].tar.gz 

    -- individual provenance index files --
    2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a
    2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf
    2f65ae542401d4c2daf1bca70de640211da6749188f67d28ea71acd7d8ba070b
    3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7
    66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba
    8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66
    c84dffef20fec958255e759db6445fc469d73695674a33ae6f7e567a088c9fe0
    d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d
    da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db
    e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55
    eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94
    f13ab4bca04f894ae8eabb51fa01b4dfbc69f717eabc9896c728e2ba39c4db27
    f493baf276892a199a0b0d078359f64a38fe8ad3f807921f8d41ef73f7343b1f
    ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3

    --- end of file descriptions ---


    References 

    [1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-10-18 to 2019-10-03 with provenance hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650 .
    [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
     

     
    more » « less
  3. A biodiversity dataset graph: BHL

    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.

    This dataset provides versioned snapshots of the BHL network as tracked by Preston [2] between 2019-05-19 and 2020-05-09 using "preston update -u https://biodiversitylibrary.org".

    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 .  

    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 > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:

    $ java -jar preston.jar clone --remote https://zenodo.org/record/3849560/files

    After that, verify the index of the archive by reproducing the following provenance log history:

    $ java -jar preston.jar history
    <0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .
    <hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> <http://purl.org/pav/previousVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .
    <hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> <http://purl.org/pav/previousVersion> <hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> .
    <hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> <http://purl.org/pav/previousVersion> <hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> .
    <hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> <http://purl.org/pav/previousVersion> <hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> .
    <hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> <http://purl.org/pav/previousVersion> <hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> .
    <hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> <http://purl.org/pav/previousVersion> <hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> .
    <hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> <http://purl.org/pav/previousVersion> <hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> .
    <hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> <http://purl.org/pav/previousVersion> <hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> .
    <hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> <http://purl.org/pav/previousVersion> <hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> .
    <hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> <http://purl.org/pav/previousVersion> <hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> .
    <hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1> <http://purl.org/pav/previousVersion> <hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> .

    To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.

    $ java -jar preston.jar verify
    hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    file:/home/preston/preston-bhl/data/e0/c1/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    OK    CONTENT_PRESENT_VALID_HASH    49458087    hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca
    hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    file:/home/preston/preston-bhl/data/1a/57/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    OK    CONTENT_PRESENT_VALID_HASH    25745    hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99
    hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    file:/home/preston/preston-bhl/data/85/ef/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    OK    CONTENT_PRESENT_VALID_HASH    519892    hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c
    hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    file:/home/preston/preston-bhl/data/25/1e/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    OK    CONTENT_PRESENT_VALID_HASH    787414    hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743

    Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".

    Files in this data publication:

    --- start of file descriptions ---

    -- description of archive and its contents (this file) --
    README

    -- executable java jar containing preston[2] v0.1.15. --
    preston.jar

    -- preston archives containing BHL data files, associated provenance logs and a provenance index --
    preston-[00-ff].tar.gz

    -- individual provenance index files --
    2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a
    2b1104cb7749e818c9afca78391b2d0099bbb0a32f2b348860a335cd2f8f6800
    4081bc59dff58d63f6a86c623cb770f01e9a355a42495b205bcb538cd526190f
    47a2816f8b5600b24487093adcddfea12434cc4f270f3ab09d9215fbdd546cd2
    6f99a1388823fca745c9e22ac21e2da909a219aa1ace55170fa9248c0276903c
    7ae46d7cd9b5a0f5889ba38bac53c82e591b0bdf8b605f5e48c0dce8fb7b717f
    82903464889fea7c53f53daedf4e41fa31092f82619edeb3415eb2b473f74af3
    9e8c86243df39dd4fe82a3f814710eccf73aa9291d050415408e346fa2b09e70
    a8308fbf4530e287927c471d881ce0fc852f16543d46e1ee26f1caba48815f3a
    bcec6df2ea7f74e9a6e2830d0072e6b2fbe65323d9ddb022dd6e1349c23996e2
    cfe47c25ec0210ac73c06b407beb20d9c58355cb15bae427fdc7541870ca2e4e
    f73fc9e70bce8f21f0c96b8ef0903749d8f223f71343ab5a8910968f99c9b8b6

    --- end of file descriptions ---


    References

    [1] Biodiversity Heritage Library (BHL, https://biodiversitylibrary.org) accessed from 2019-05-19 to 2020-05-09 with provenance hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1.
    [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.

     
    more » « less
  4. A biodiversity dataset graph: DataONE

    The intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE, [1]). DataONE is a distributed infrastructure that provides information about earth observation data. 

    This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 17 October 2018 and 7 July 2019.  

    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 eestablish a versioning mechanism. Provenance files describe how, when and where the DataONE meta-data files were retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543).  

    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 > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:

    $ java -jar preston.jar clone --remote https://zenodo.org/record/3277312/files

    After that, verify the index of the archive by reproducing the following result:

    $ java -jar preston.jar history
    <0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
    <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .
    <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .
    <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .
    <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .
    <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .
    <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .
    <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .
    <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .
    <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .

    To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.

    $ java -jar preston.jar verify
    hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580
    hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035
    hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935
    hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553

    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:

    README - this file

    preston.jar - executable java jar containing preston[2] v0.1.1.

    preston-[00-ff].tar.gz - preston archives containing DataONE meta-data files, their provenance and a provenance index.

    2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a - preston index file
    2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf - preston index file
    3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7 - preston index file
    66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba - preston index file
    8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66 - preston index file
    d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d - preston index file
    da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db - preston index file
    e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55 - preston index file
    eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94 - preston index file
    ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3 - preston index file

    [1] DataONE, https://www.dataone.org
    [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . DataONE was crawled via Preston with "preston update -u https://dataone.org".

    This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation

     
    more » « less
  5. A biodiversity dataset graph: UCSB-IZC

    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.

    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 "https://api.gbif.org/v1/occurrence/search/?datasetKey=d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"].

    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].

    The images were counted using:

    $ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\
     | grep -o -P ".*depict"\
     | sort\
     | uniq\
     | wc -l

    And the occurrences were counted using:

    $ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\
     | grep -o -P "occurrence/([0-9])+"\
     | sort\
     | uniq\
     | wc -l

    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.

    To retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a "data" folder. Alternatively, you can use the Preston [2,3] command-line tool to "clone" this dataset using:

    $ 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

    After that, verify the index of the archive by reproducing the following provenance log history:

    $ java -jar preston.jar history
    <urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .
    <hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c> <http://purl.org/pav/previousVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .

    To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.

    $ java -jar preston.jar verify
    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    OK    CONTENT_PRESENT_VALID_HASH    66438    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c
    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    OK    CONTENT_PRESENT_VALID_HASH    4093    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844
    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    OK    CONTENT_PRESENT_VALID_HASH    5746    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef
    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    OK    CONTENT_PRESENT_VALID_HASH    6147    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b

    Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".

    Files in this data publication:

    --- start of file descriptions ---

    -- description of archive and its contents (this file) --
    README

    -- executable java jar containing preston [2,3] v0.3.1. --
    preston.jar

    -- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --
    preston-[00-ff].tar.gz

    -- individual provenance index files --
    2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a

    -- example image and meta-data --
    sample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)
    sample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)

    --- end of file descriptions ---


    References

    [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.
    [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .
    [3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132
    [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

    This work is funded in part by grant NSF OAC 1839201 and NSF DBI 2102006 from the National Science Foundation. 
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