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1. Mitigating RF Jamming Attacks at the Physical Layer with Machine Learning Dataset

   https://doi.org/10.5281/zenodo.6304194  

   Jacovic, Marko; Rivas, Xaime Rey (January 2022, Zenodo)

   {"Abstract":["Data files were used in support of the research paper titled \u201cMitigating RF Jamming Attacks at the Physical Layer with Machine Learning<\/em>" which has been submitted to the IET Communications journal.<\/p>\n\n---------------------------------------------------------------------------------------------<\/p>\n\nAll data was collected using the SDR implementation shown here: https://github.com/mainland/dragonradio/tree/iet-paper. Particularly for antenna state selection, the files developed for this paper are located in 'dragonradio/scripts/:'<\/p>\n\n'ModeSelect.py': class used to defined the antenna state selection algorithm<\/li>'standalone-radio.py': SDR implementation for normal radio operation with reconfigurable antenna<\/li>'standalone-radio-tuning.py': SDR implementation for hyperparameter tunning<\/li>'standalone-radio-onmi.py': SDR implementation for omnidirectional mode only<\/li><\/ul>\n\n---------------------------------------------------------------------------------------------<\/p>\n\nAuthors: Marko Jacovic, Xaime Rivas Rey, Geoffrey Mainland, Kapil R. Dandekar\nContact: krd26@drexel.edu<\/p>\n\n---------------------------------------------------------------------------------------------<\/p>\n\nTop-level directories and content will be described below. Detailed descriptions of experiments performed are provided in the paper.<\/p>\n\n---------------------------------------------------------------------------------------------<\/p>\n\nclassifier_training: files used for training classifiers that are integrated into SDR platform<\/p>\n\n'logs-8-18' directory contains OTA SDR collected log files for each jammer type and under normal operation (including congested and weaklink states)<\/li>'classTrain.py' is the main parser for training the classifiers<\/li>'trainedClassifiers' contains the output classifiers generated by 'classTrain.py'<\/li><\/ul>\n\npost_processing_classifier: contains logs of online classifier outputs and processing script<\/p>\n\n'class' directory contains .csv logs of each RTE and OTA experiment for each jamming and operation scenario<\/li>'classProcess.py' parses the log files and provides classification report and confusion matrix for each multi-class and binary classifiers for each observed scenario - found in 'results->classifier_performance'<\/li><\/ul>\n\npost_processing_mgen: contains MGEN receiver logs and parser<\/p>\n\n'configs' contains JSON files to be used with parser for each experiment<\/li>'mgenLogs' contains MGEN receiver logs for each OTA and RTE experiment described. Within each experiment logs are separated by 'mit' for mitigation used, 'nj' for no jammer, and 'noMit' for no mitigation technique used. File names take the form *_cj_* for constant jammer, *_pj_* for periodic jammer, *_rj_* for reactive jammer, and *_nj_* for no jammer. Performance figures are found in 'results->mitigation_performance'<\/li><\/ul>\n\nray_tracing_emulation: contains files related to Drexel area, Art Museum, and UAV Drexel area validation RTE studies.<\/p>\n\nDirectory contains detailed 'readme.txt' for understanding.<\/li>Please note: the processing files and data logs present in 'validation' folder were developed by Wolfe et al. and should be cited as such, unless explicitly stated differently. \n\tS. Wolfe, S. Begashaw, Y. Liu and K. R. Dandekar, "Adaptive Link Optimization for 802.11 UAV Uplink Using a Reconfigurable Antenna," MILCOM 2018 - 2018 IEEE Military Communications Conference (MILCOM), 2018, pp. 1-6, doi: 10.1109/MILCOM.2018.8599696.<\/li><\/ul>\n\t<\/li><\/ul>\n\nresults: contains results obtained from study<\/p>\n\n'classifier_performance' contains .txt files summarizing binary and multi-class performance of online SDR system. Files obtained using 'post_processing_classifier.'<\/li>'mitigation_performance' contains figures generated by 'post_processing_mgen.'<\/li>'validation' contains RTE and OTA performance comparison obtained by 'ray_tracing_emulation->validation->matlab->outdoor_hover_plots.m'<\/li><\/ul>\n\ntuning_parameter_study: contains the OTA log files for antenna state selection hyperparameter study<\/p>\n\n'dataCollect' contains a folder for each jammer considered in the study, and inside each folder there is a CSV file corresponding to a different configuration of the learning parameters of the reconfigurable antenna. The configuration selected was the one that performed the best across all these experiments and is described in the paper.<\/li>'data_summary.txt'this file contains the summaries from all the CSV files for convenience.<\/li><\/ul>"]} 

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2. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey; Thakkar, Ravindra; Velásquez-Silva, Astrid; Miranda-Carvajal, Ingrid (January 2022, Zenodo)

   {"Abstract":["This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.<\/p>\n\nVersion: 2.0<\/p>\n\nChanges versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.<\/p>\n\n\nConventions Used in These Files\n===============================<\/p>\n\nStructure Files\n----------------\n- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)<\/p>\n\n- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)\n- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)\n- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)\n- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)\n- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)<\/p>\n\nForce Field Parameters\n----------------------\nCHARMM format parameter files:\n- par_all36m_prot.prm (CHARMM36m FF for proteins)\n- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.\n- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)<\/p>\n\nTemplate NAMD Configuration Files\n---------------------------------\nThese contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):\n- template_min.namd (minimization)\n- template_eq.namd (NPT equilibration with lower graphene fixed)\n- template_abf.namd (for adaptive biasing force)<\/p>\n\nMinimization\n-------------\n- namd/min_*.0.namd<\/p>\n\nEquilibration\n-------------\n- namd/eq_*.0.namd<\/p>\n\nAdaptive biasing force calculations\n-----------------------------------\n- namd/eabfZRest7_graph_chp1404.0.namd\n- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)<\/p>\n\nLog Files\n---------\nFor each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.<\/p>\n\nSimulation Output\n-----------------\nThe simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.<\/p>\n\nScripts\n-------\nFiles with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.<\/p>\n\n\nCONTENTS\n========<\/p>\n\nThe directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.<\/p>\n\nSim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.<\/p>\n\nSim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 295 K.<\/p>\n\nSim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.<\/p>\n\nSim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).<\/p>\n\nSim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.<\/p>\n\nSim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene\u2013water interface in the initial configuration.<\/p>\n\nSim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.<\/p>\n\n <\/p>"],"Other":["This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030."]} 

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3. A biodiversity dataset graph: Biodiverity Heritage Library (BHL)

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

   Poelen, Jorrit (January 2020, Zenodo)

   {"Abstract":["A biodiversity dataset graph: BHL<\/p>\n\nThe 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>\n\nThis 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".<\/p>\n\nThe 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>\n\nTo 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:<\/p>\n\n$$ java -jar preston.jar clone --remote https://zenodo.org/record/3849560/files<\/p>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .\n<hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> <http://purl.org/pav/previousVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .\n<hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> <http://purl.org/pav/previousVersion> <hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> .\n<hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> <http://purl.org/pav/previousVersion> <hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> .\n<hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> <http://purl.org/pav/previousVersion> <hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> .\n<hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> <http://purl.org/pav/previousVersion> <hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> .\n<hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> <http://purl.org/pav/previousVersion> <hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> .\n<hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> <http://purl.org/pav/previousVersion> <hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> .\n<hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> <http://purl.org/pav/previousVersion> <hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> .\n<hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> <http://purl.org/pav/previousVersion> <hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> .\n<hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> <http://purl.org/pav/previousVersion> <hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> .\n<hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1> <http://purl.org/pav/previousVersion> <hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> .<\/p>\n\nTo 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.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    file:/home/preston/preston-bhl/data/e0/c1/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    OK    CONTENT_PRESENT_VALID_HASH    49458087    hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca\nhash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    file:/home/preston/preston-bhl/data/1a/57/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    OK    CONTENT_PRESENT_VALID_HASH    25745    hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99\nhash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    file:/home/preston/preston-bhl/data/85/ef/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    OK    CONTENT_PRESENT_VALID_HASH    519892    hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c\nhash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    file:/home/preston/preston-bhl/data/25/1e/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    OK    CONTENT_PRESENT_VALID_HASH    787414    hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743<\/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] v0.1.15. --\npreston.jar<\/p>\n\n-- preston archives containing BHL data files, associated provenance logs and a provenance index --\npreston-[00-ff].tar.gz<\/p>\n\n-- individual provenance index files --\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a\n2b1104cb7749e818c9afca78391b2d0099bbb0a32f2b348860a335cd2f8f6800\n4081bc59dff58d63f6a86c623cb770f01e9a355a42495b205bcb538cd526190f\n47a2816f8b5600b24487093adcddfea12434cc4f270f3ab09d9215fbdd546cd2\n6f99a1388823fca745c9e22ac21e2da909a219aa1ace55170fa9248c0276903c\n7ae46d7cd9b5a0f5889ba38bac53c82e591b0bdf8b605f5e48c0dce8fb7b717f\n82903464889fea7c53f53daedf4e41fa31092f82619edeb3415eb2b473f74af3\n9e8c86243df39dd4fe82a3f814710eccf73aa9291d050415408e346fa2b09e70\na8308fbf4530e287927c471d881ce0fc852f16543d46e1ee26f1caba48815f3a\nbcec6df2ea7f74e9a6e2830d0072e6b2fbe65323d9ddb022dd6e1349c23996e2\ncfe47c25ec0210ac73c06b407beb20d9c58355cb15bae427fdc7541870ca2e4e\nf73fc9e70bce8f21f0c96b8ef0903749d8f223f71343ab5a8910968f99c9b8b6<\/p>\n\n--- end of file descriptions ---<\/p>\n\n\nReferences<\/p>\n\n[1] Biodiversity Heritage Library (BHL, https://biodiversitylibrary.org) accessed from 2019-05-19 to 2020-05-09 with provenance hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1.\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .<\/p>\n\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.<\/p>"]} 

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4. A biodiversity dataset graph: DataONE

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

   Poelen, Jorrit H. (January 2019, Zenodo)

   {"Abstract":["A biodiversity dataset graph: DataONE<\/p>\n\nThe 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>\n\nThis 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". <\/p>\n\nThe 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>\n\nTo 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:<\/p>\n\n$$ java -jar preston.jar clone --remote https://zenodo.org/record/3483218/files<\/p>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .\n<hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .\n<hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .\n<hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .\n<hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .\n<hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .\n<hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .\n<hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .\n<hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .\n<hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .\n<hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> <http://purl.org/pav/previousVersion> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> .\n<hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> <http://purl.org/pav/previousVersion> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> .\n<hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> <http://purl.org/pav/previousVersion> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> .\n<hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> <http://purl.org/pav/previousVersion> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> .<\/p>\n\nTo 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.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580\nhash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035\nhash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935\nhash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553<\/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-- preston archives containing DataONE data files, associated provenance logs and a provenance index --\npreston-[00-ff].tar.gz <\/p>\n\n-- individual provenance index files --\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a\n2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf\n2f65ae542401d4c2daf1bca70de640211da6749188f67d28ea71acd7d8ba070b\n3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7\n66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba\n8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66\nc84dffef20fec958255e759db6445fc469d73695674a33ae6f7e567a088c9fe0\nd9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d\nda26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db\ne4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55\neb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94\nf13ab4bca04f894ae8eabb51fa01b4dfbc69f717eabc9896c728e2ba39c4db27\nf493baf276892a199a0b0d078359f64a38fe8ad3f807921f8d41ef73f7343b1f\nff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3<\/p>\n\n--- end of file descriptions ---<\/p>\n\n\nReferences <\/p>\n\n[1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-10-18 to 2019-10-03 with provenance hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650 .\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . <\/p>\n\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation\n <\/p>"]} 

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5. A biodiversity dataset graph: DataONE

   https://doi.org/10.5281/zenodo.1486279  

   Poelen, Jorrit H. (January 2018, Zenodo)

   {"Abstract":["The intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE, [1]). <\/p>\n\nDataONE is a distributed infrastructure that provides information about earth observation data. This dataset was derived from the DataONE network using Preston [2] between 17 October 2018 and 6 November 2018, resolving 335,213 urls at an average retrieval rate of about 5 seconds per url, or 720 files per hour, resulting in a data gzip compressed tar archive of 837.3 MB .  <\/p>\n\nThe archive associates 325,757 unique metadata urls [3] to 202,063 unique ecological metadata files [4]. Also, the DataONE search index was captured to establish provenance of how the dataset descriptors were found and acquired. During the creation of the snapshot (or crawl), 15,389 urls [5], or 4.7% of urls, did not successfully resolve. <\/p>\n\nTo facilitate discovery, the record of the Preston snapshot crawl is included in the preston-ls-* files . There files are derived from the rdf/nquad file with hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f . This file can also be found in the data.tar.gz at data/8c/67/e0/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f/data . For more information about concepts and format, please see [2]. <\/p>\n\nTo extract all EML files from the included Preston archive, first extract the hashes assocated with EML files using:<\/p>\n\ncat preston-ls.tsv.gz | gunzip | grep "Version" | grep -v "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep "hash://" | sort | uniq > eml-hashes.txt<\/p>\n\nextract data.tar.gz using:<\/p>\n\n~/preston-archive$$ tar xzf data.tar.gz <\/p>\n\nthen use Preston to extract each hash using something like:<\/p>\n\n~/preston-archive$$ preston get hash://sha256/00002d0fc9e35a9194da7dd3d8ce25eddee40740533f5af2397d6708542b9baa\n<eml:eml xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml_1.1" packageId="doi:10.18739/A24P9Q" system="https://arcticdata.io" scope="system" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 ~/development/eml/eml.xsd">\n  <dataset>\n    <alternateIdentifier>urn:x-wmo:md:org.aoncadis.www::d76bc3b5-7b19-11e4-8526-00c0f03d5b7c</alternateIdentifier>\n    <alternateIdentifier>d76bc3b5-7b19-11e4-8526-00c0f03d5b7c</alternateIdentifier>\n    <title>Airglow Image Data 2011 4 of 5</title>\n...<\/p>\n\nAlternatively, without using Preston, you can extract the data using the naming convention:<\/p>\n\ndata/[x]/[y]/[z]/[hash]/data<\/p>\n\nwhere x is the first 2 characters of the hash, y the second 2 characters, z the third 2 characters, and hash the full sha256 content hash of the EML file.<\/p>\n\nFor example, the hash hash://sha256/00002d0fc9e35a9194da7dd3d8ce25eddee40740533f5af2397d6708542b9baa can be found in the file: data/00/00/2d/00002d0fc9e35a9194da7dd3d8ce25eddee40740533f5af2397d6708542b9baa/data . For more information, see [2].<\/p>\n\nThe intended use of this archive is to facilitate meta-analysis of the DataONE dataset network. <\/p>\n\n[1] DataONE, https://www.dataone.org\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . DataONE was crawled via Preston with "preston update -u https://dataone.org".\n[3] cat preston-ls.tsv.gz | gunzip | grep "Version" | grep -v "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep -v "hash://" | sort | uniq | wc -l\n[4] cat preston-ls.tsv.gz | gunzip | grep "Version" | grep -v "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep "hash://" | sort | uniq | wc -l\n[5] cat preston-ls.tsv.gz | gunzip | grep "Version" | grep  "deeplinker" | grep -v "query/solr" | cut -f1,3 | tr '\\t' '\\n' | grep -v "hash://" | sort | uniq | wc -l<\/p>\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.<\/p>"]} 

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