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677 results for “Inversion”
Tropical Pacific SST and wind anomalies generated by a Nonlinear Inverse Model
<p>Tropical Pacific (40S-40N; 120E-50W) sea surface temperature (SST), zonal wind (U) and meridional wind (V) anomalies generated by the Nonlinear Inverse Model described in Martinez-Villalobos et al., 2024 (https://doi.org/10.1038/s41612-024-00675-5). The data consists in 99 realizations (<a href="../api/records/10411023/draft/files/NLIM_output_085.nc/content" target="_blank" rel="noopener noreferrer">NLIM_output_XXX.nc</a>) of 1,000yrs each emulating SST, U, and V monthly anomalies conditions during 1980-2020 (<a href="../api/records/10411023/draft/files/Monthly_obs_1980_2020.nc/content" target="_blank" rel="noopener noreferrer">Monthly_obs_1980_2020.nc</a>) given in a 2.5deg-2.5deg grid. For observations, we used the NOAA Extended Reconstruction SST v5 reanalysis (SST; Huang et al., 2017) and NCEP-NCAR reanalysis (winds; Kalnay et al., 1996) The observed anomalies are calculated as described in Martinez-Villalobos et al., 2024 (https://doi.org/10.1038/s41612-024-00675-5).</p> <p>Given that the stochastic forcing considered is white in time and space (https://doi.org/10.1038/s41612-024-00675-5; Methods, section "Offline simulation of SSH_{12}, PC2, and spatial patterns fron nonlinear inverse model output"), the spatial patterns and lead-lag relationships are better identified using composites. A modification of the methodology that allows for spatially coherent stochastic forcing will be implemented in a future article.</p> <p>When using the data please cite https://doi.org/10.5281/zenodo.10411023 (the data) and Martinez-Villalobos et al., 2024 (https://doi.org/10.1038/s41612-024-00675-5; for the methodology). </p> <p>Any question, please contact Cristian Martinez-Villalobos at his email cristian.martinez.v@uai.cl</p> <p>References</p> <p>Martinez-Villalobos, C., Dewitte, B., Garreaud, R.D. <em>et al.</em> Extreme coastal El Niño events are tightly linked to the development of the Pacific Meridional Modes. <em>npj Clim Atmos Sci</em> <strong>7</strong>, 123 (2024). https://doi.org/10.1038/s41612-024-00675-5</p> <p>Huang, B. et al. Extended Reconstructed Sea Surface Temperature, Version 5 (ERSSTv5): Upgrades, Validations, and Intercomparisons. Journal of Climate 30, 8179–8205 (2017).</p> <p>Kalnay, E. et al. The NCEP/NCAR 40-Year Reanalysis Project. Bulletin of the American Meteorological Society 77, 437–471 (1996).</p> <p> </p>
CPD model and data for CPD inversion
<div>This file includes the Curie Point Depth (CPD) model and related data files for the manuscript 'A continental model of Curie Point Depth for China and surroundings based on Equivalent Source Method'</div> <div>This work is fulfilled by Lei, Y., Jiao, L., Huang, Q., and Tu, J.</div> <div>For any questions, please contact us by Email: lgjiao@cea-igp.ac.cn; leiyu@cea-igp.ac.cn</div> <div> </div> <div>The files *.mat are data complied in Matlab, and the codes and data files should be placed in the same directory.</div> <div> </div> <div>The file cpd_result.xyz is the result of the inverted CPD in mainland China, which is shown in Figure 3. </div> <div> </div> <div>The file d_obs.mat is the observed lithospheric magnetic data from EMM2017 model, and magnetic responses generated by global oceanic remanent magnetization have been removed due to the assumption of induced magnetization. The spherical harmonic coefficients of the EMM2017 model can be download from https://www.ngdc.noaa.gov/geomag/EMM/. The global ocean remanent magnetization model is proposed by Masterton et al. (2013), https://doi.org/ 10.1093/gji/ggs063</div> <div> </div> <div>The file ini_cpd.mat is the initial CPD model proposed by Sun et al., 2022, which can be found in https://doi.org/10.5381/zenodo.6459746</div> <div> </div> <div>Outside the study area, the magnetization is refered to the global vertical integral susceptibility model proposed by Hemant & Maus, (2005). The magnetic responses base on their model are saved as mag_out.mat. </div> <div> </div> <div>The core field used in this study for the inducing field calculation is from the IGRF13 model. The model provide the spherical harmonic coefficients to the degree of 13 (stored in IGRF13.txt), can be download from https://www.ngdc.noaa.gov/IAGA/vmod/igrf.html</div> <div> </div> <div>The global topography data are from ETOPO global relief model, which can be found at https://www.ncei.noaa.gov/products/etopo-global-relief-model. The topography data in the study areas is stored in etopo30_6_66_62_146.mat</div> <div> </div> <div>The Crust1.0 model (crust1.bnds) used for establishing the susceptibility model are from https://igppweb.ucsd.edu/~gabi/crust1.html. </div> <div> </div> <div>The geoid topography comes from EGM2008 gravity model, and can be obtained from http://icgem.gfz-potsdam.de/calcgrid</div> <div> </div> <div>The surface heat flow data (HF_China.xlsx) are download from Jiang et al., 2019.</div> <div>Reference:</div> <div>Alken, P., Thébault, E., Beggan, C.D. et al. (2021). International Geomagnetic Reference Field: the thirteenth generation. Earth Planets Space 73, 49 . https://doi.org/10.1186/s40623-020-01288-x</div> <div>Hemant, K., Maus, S. (2005). Geological modeling of the new CHAMP magnetic anomaly maps using a geographical information system technique. Journal Geophysical Research Solid Earth 110, B12103, https://doi.org/10.1029/2005JB003837</div> <div>Jiang, G., Hu, S., Shi, Y., Zhang, C., Wang, Z., Hu, D. (2019). Terrestrial heat flow of continent China: Updated dataset and tectonic implications. Tectonophysics, 753, 36-48. https://doi.org/ 10.1016/j.tecto.2019.01.006 </div> <div>Laske, G., Masters, G., Ma, Z., Pasyanos, M. (2013). Update on Crust1.0 - A 1-degree global model of earth’s crust. Geophysical Research Abstracts, 15, Abstract EGU2013-2658. http://igppweb. ucsd.edu/~gabi/rem.html </div> <div>Sun, Y., Dong, S., Wang, X., Liu, Mian., Zhang, H., Shi, Y., (2022). Three-dimensional thermal structure of East Asian continental lithosphere. Journal Geophysical Research: Solid Earth, 127, e2021JB023432. https://doi.org/10.1029/2021JB023432</div> <div> </div> <div> </div> <div> </div>
Atmospheric Halocarbon Observations at Beromünster, Switzerland, and Bayesian Inverse Modeling to assess Emissions
<p>Atmospheric halocarbon (CFCs, halons, HCFCs, HFCs, PFCs, SF<sub>6</sub>, NF<sub>3</sub>, HFOs) and carbon monoxide (CO) observations (mole fractions) from the tall tower site at Beromünster, Switzerland (47.2 °N, 8.2 °E, 797 m a.s.l., 212 m a.g.l.), covering the period September 2019 to September 2020. The halocarbon measurements were conducted using a Medusa pre-concentration unit, coupled to gas chromatography (Agilent 6890N) and mass spectrometry (Agilent 5975, GC-MS).</p> <p>For further details see: Miller, B. R., Weiss, R. F., Salameh, P. K., Tanhua, T., Greally, B. R., Mühle, J., and Simmonds, P. G.: Medusa: A Sample Preconcentration and GC/MS Detector System for in Situ Measurements of Atmospheric Trace Halocarbons, Hydrocarbons, and Sulfur Compounds, Anal. Chem., 80, 1536–1545, https://doi.org/10.1021/ac702084k, 2008).</p> <p>The data format follows that used within the AGAGE network (see AGAGE data archive: <a href="http://agage.mit.edu/data/agage-data">http://agage.mit.edu/data/agage-data</a>).</p> <p>Data results for the Bayesian inversion conducted based on the measurement data from Beromünster to assess Swiss halocarbon emissions. Files are provided in netCDF format for the 28 individual substances discussed in (Rust, D. et al., 2022, <em>Swiss halocarbon emissions for 2019 to 2020 assessed from regional atmospheric observations</em>, Atmospheric Chemistry and Physics). Each file contains the a priori and a posteriori emissions as used or calculated in the Bayesian inversion. Data are provided on the grid used in the inversion (irregular longitude/latitude). Metadata are included as netCDF attributes. The netCDF files follow the CF conventions and are readable with any netcdf interface/tool.</p>
Upper lithospheric structure of northeastern Venezuela from joint inversion of surface wave dispersion and receiver functions
<p>Dataset from the publication: <strong>Upper lithospheric structure of northeastern Venezuela from joint inversion of surface wave dispersion and receiver functions</strong>. DOI: <a href="https://doi.org/10.5194/egusphere-2022-230">10.5194/egusphere-2022-230</a></p> <p> </p> <p>Includes: <em><strong>EGFs, Dispersion Curves measurements, RFs, Vs3dmodel and Moho depths</strong></em></p> <p> </p>
NMR data for "Rapid and simple 13C-hyperpolarization by 1H dissolution dynamic nuclear polarization followed by an in-line magnetic field inversion"
<p>Liquid-state and solid-state NMR data for "Rapid and simple 13C-hyperpolarization by 1H dissolution dynamic nuclear polarization followed by an in-line magnetic field inversion".</p> <p>The data enclosed are NMR data generated by the software Topspin by Burker Biospin. The experiments are dDNP runs that come in two parts: a solid-state and a liquid-state part.</p> <ul> <li>Experiments from 1 to 9 are reference experiments used to quantify polarization in other experiments</li> <li>Experiments 11-19, 21-29, 31-39, ... 61-69 correspond to 6 dDNP runs performed a different samples from the same batch. The numbers correspond between solid and liquid-state datasets</li> </ul> <p>The codes used to analyze the data are available at in a next upload.</p> <p>Refer to the main text of the paper and its supplementary material at 10.26434/chemrxiv-2023-6gd0l for more information.</p>
Final models for "Global-Scale Full-Waveform Ambient Noise Inversion" by Sager et al. (2020)
<p>The exodus model contains the inverted structure model and the source distribution can be found in the HDF5 file. Both can be visualized in ParaView. For the source model, we recommend opening it with the correspoding XDMF file (select "XDMF Reader" in the dialogue box).</p>
Dataset: Mapping intrinsic and scattering attenuation in the southern Aegean crust using S-wave envelope inversion and sensitivity kernels derived from perturbation theory
<p><strong>Data Set S1: </strong>File “ds01.csv” contains the catalogue of relocated events used in this study. The columns in the file represent origin time (in year-month-day’H’hour’M’minute’S’seconds format), event longitude, event latitude, event depth in a sequential manner.</p> <p><strong>Data Set S2: </strong>File “ds02.zip” contains four ASCII data files (ray_prmtrs12.txt, ray_prmtrs24.txt, ray_prmtrs48.txt and ray_prmtrs816.txt). The data files contain scattering coefficient (<em>g<sup>*</sup></em>) and intrinsic coefficient (<em>b</em>) values in 1-2, 2-4 Hz, 4-8 Hz and 8-16 Hz bands respectively. The columns in the text files represent event latitude, event longitude, event depth, station latitude, station longitude, station velocity, envelope duration, <em>g<sup>*</sup></em>, <em>b</em>, early-S window length, percentage error in early-S window, percentage error for full envelope, and event origin time in a sequential manner.</p> <p><strong>Data Set S3: </strong>File “ds03.zip” contains four data files (envnodes15g_3_3_1-2.txt, envnodes15g_3_3_2-4.txt, envnodes15g_3_3_4-8.txt, and envnodes15g_3_3_8-16.txt), one BASH script containing GMT and Octave commands (Qs_envg.gmt), and a lat-long coordinate file (SAegean_poly_coord_extnd.txt) to mask the area outside the seismic network. The data files contain log<sub>10</sub>(<em>Q<sub>sc</sub></em><sup>-1</sup>) values in 1-2, 2-4, 4-8 and 8-16 Hz bands respectively. The columns in the text files represent node latitude, node longitude and log<sub>10</sub>(<em>Q<sub>sc</sub></em><sup>-1</sup>) value of the node sequentially. This GMT script also uses GSHHG coastline data whose path can be added to the script by changing the value of variable GDIR at the beginning of the script. The BASH script file can be run to see the spatial distribution of log<sub>10</sub>(<em>Q<sub>sc</sub></em><sup>-1</sup>) using GMT-6 (Wessel et al., 2019) and Octave version 5.1 and above.</p> <p><strong>Data Set S4: </strong>File “ds04.zip” contains four data files (envnodes15b_3_3_1-2.txt, envnodes15b_3_3_2-4.txt, envnodes15b_3_3_4-8.txt, and envnodes15b_3_3_8-16.txt), one BASH script containing GMT and Octave commands (Qi_env.gmt), and a lat-long coordinate file (SAegean_poly_coord_extnd.txt) to mask the area outside the seismic network. The data files contain log<sub>10</sub>(<em>Q<sub>i</sub></em><sup>-1</sup>) values in 1-2, 2-4, 4-8 and 8-16 Hz bands respectively. The columns in the text files represent node latitude, node longitude and log<sub>10</sub>(<em>Q<sub>i</sub></em><sup>-1</sup>) value of the node sequentially. This GMT script also uses GSHHG coastline data whose path can be added to the script by changing the value of variable GDIR at the beginning of the script. The BASH script file can be run to see the spatial distribution of log<sub>10</sub>(<em>Q<sub>i</sub></em><sup>-1</sup>) using GMT-6 (Wessel et al., 2019) and Octave version 5.1 and above.</p> <p><strong>Data Set S5: </strong>File “ds05.zip” contains four data files (envnodes15a_3_3_1-2.txt, envnodes15a_3_3_2-4.txt, envnodes15a_3_3_4-8.txt, and envnodes15a_3_3_8-16.txt), one BASH script containing GMT and Octave commands (albd_env.gmt), and a lat-long coordinate file (SAegean_poly_coord_extnd.txt) to mask the area outside the seismic network. The data files contain Albedo (<em>B<sub>o</sub></em>) as % values in 1-2, 2-4, 4-8 and 8-16 Hz bands respectively. The columns in the text files represent node latitude, node longitude and <em>B<sub>o</sub></em> value of the node sequentially. This GMT script also uses GSHHG coastline data whose path can be added to the script by changing the value of variable GDIR at the beginning of the script. The BASH script file can be run to see the spatial distribution of <em>B<sub>o</sub></em> using GMT-6 (Wessel et al., 2019) and Octave version 5.1 and above. </p>
Dataset for: "Incremental Semiparametric Inverse Dynamics Learning"
<p>Dataset used in the experimental section of the paper:</p> <blockquote> <p>R. Camoriano, S. Traversaro, L. Rosasco, G. Metta and F. Nori, "<strong>Incremental semiparametric inverse dynamics learning,</strong>" <em>2016 IEEE International Conference on Robotics and Automation (ICRA)</em>, Stockholm, 2016, pp. 544-550.<br> <br> doi: 10.1109/ICRA.2016.7487177<br> <br> Abstract: This paper presents a novel approach for incremental semiparametric inverse dynamics learning. In particular, we consider the mixture of two approaches: Parametric modeling based on rigid body dynamics equations and nonparametric modeling based on incremental kernel methods, with no prior information on the mechanical properties of the system. The result is an incremental semiparametric approach, leveraging the advantages of both the parametric and nonparametric models. We validate the proposed technique learning the dynamics of one arm of the iCub humanoid robot.<br> <br> URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7487177&isnumber=7487087<br> </p> </blockquote> <p> </p> <p><strong>Description</strong></p> <p>The file "iCubDyn_2.0.mat" contains data collected from the right arm of the iCub humanoid robot, considering as input the positions, velocities and accelerations of the 3 shoulder joints and of the elbow joint, and as outputs the 3 force and 3 torque components measured by the six-axis F/T sensor in-built in the upper arm.</p> <p>The dataset is collected at 10Hz at as the end-effector tracks circumferences with 10cm radius on the transverse (XY) and sagittal (XZ) planes (For more information on the iCub reference frames, see [4]) at approximately 0.6 m/s. The total number of points for each dataset is 10000, corresponding to approximately 17 minutes of continuous operation. Trajectories are generated by means of the Cartesian Controller presented in [5].</p> <p> Input (X)</p> <p> columns 1-4: Joint (3 shoulder joints + 1 elbow joint) positions<br> columns 5-8: Joint (3 shoulder joints + 1 elbow joint) velocities<br> columns 9-12: Joint (3 shoulder joints + 1 elbow joint) accelerations</p> <p> Output (Y)</p> <p> Columns 1-3: Measured forces (N) along the X, Y, Z axes by the force-torque (F/T) sensor placed in the upper arm<br> Columns 4-6: Measured torques (N*m) along the X, Y, Z axes by the force-torque (F/T) sensor placed in the upper arm</p> <p> </p> <p><strong>Preprocessing</strong><br> <br> - Velocities and accelerations are computed by an Adaptive Window Polynomial Fitting Estimator, implemented through a least-squares based algorithm on a adpative window (see [2], [3]). Velocity estimation max window size: 16. Acceleration estimation max window size: 25.<br> - Positions, velocities and accelerations are recorded at 9Hz and oversampled to 20 Hz via cubic spline interpolation.<br> - Forces and torques are directly recorded at 20Hz.</p> <p>This dataset was used in [1] for experimental purposes. See section IV therein for further details.</p> <p>For more information, please contact:<br> Raffaello Camoriano - raffaello.camoriano@iit.it<br> Silvio Traversaro - silvio.traversaro@iit.it</p> <p> </p> <p><strong>References</strong><br> <br> [1] Camoriano, Raffaello; Traversaro, Silvio; Rosasco, Lorenzo; Metta, Giorgio; Nori, Francesco, "Incremental Semiparametric Inverse Dynamics Learning", eprint arXiv:1601.04549, 01/2016<br> [2] F. Janabi-Sharifi ; Dept. of Mech. Eng., Ryerson Polytech. Univ., Toronto, Ont., Canada ; V. Hayward ; C. -S. J. Chen, "Discrete-time adaptive windowing for velocity estimation", IEEE Transactions on Control Systems Technology, 1003 - 1009, Vol. 8, Issue 6, Nov 2000<br> [3] https://github.com/robotology/icub-main/blob/master/src/libraries/ctrlLib/include/iCub/ctrl/adaptWinPolyEstimator.h<br> [4] http://wiki.icub.org/wiki/ICubForwardKinematics<br> [5] U. Pattacini; F. Nori; L. Natale; G. Metta; and G. Sandini; “An experimental evaluation of a novel minimum-jerk cartesian controller for humanoid robots,” in Intelligent Robots and Systems (IROS), 2010 IEEE/RSJ International Conference on, Oct 2010, pp. 1668–1674.</p>
A global gridded CO2 flux dataset inferred from OCO-2 retrievals using the GONGGA inversion system (v2025)
<p><strong>Data Description</strong></p> <p>Here we provide a global monthly CO2 flux dataset at 1° × 1° spatial resolution for the period 2014.9-2024.12. The dataset is generated using the GONGGA (Global ObservatioN-based system for monitoring Greenhouse GAs) inversion system by assimilating OCO-2 (Observing Carbon Observatory 2) v11.2r column CO2 retrievals that scaled to the WMO X2019 standard. The dataset contains fluxes from biosphere (Net Ecosystem Exchange, NEE) (both prior and posterior), ocean (both prior and posterior), biomass burning emissions and fossil fuel emissions.</p> <p>We also provide the posterior model simulated values corresponding to all measurements contained in the lastest release of NOAA’s ObsPack database (obspack_co2_1_GLOBALVIEWplus_v10.1_2024-11-13 and obspack_co2_1_NRT_v10.1_2025-02-07).</p> <p><strong>Change from v2024</strong></p> <ul> <li>Assimilation of OCO-2 v11.2r retrievals</li> <li>Update of prior fluxes</li> </ul> <p><strong>Data version specification</strong></p> <p>v202x.ori refers to original GONGGA flux data with 3-hourly time resolution and 2° latitude × 2.5° longitude spatial resolution, v202x refers to GONGGA flux data resampled to monthly time resolution and 1° latitude × 1° longitude spatial resolution for facilitating comparisons with other GCP inversion results.</p> <p><strong>Article citation</strong></p> <p>Jin, Z., Wang, T., Zhang, H., Wang, Y., Ding, J., Tian, X., Constraint of satellite CO2 retrieval on the global carbon cycle from a Chinese atmospheric inversion system. Science China Earth Sciences, 2023, 66: 609-618, doi: 10.1007/s11430-022-1036-7.</p> <p>Jin, Z., Tian, X., Wang, Y., Zhang, H., Zhao, M., Wang, T., Ding, J., and Piao, S.: A global surface CO2 flux dataset (2015–2022) inferred from OCO-2 retrievals using the GONGGA inversion system, Earth System Science Data, 2024, 16: 2857-2876, doi: 10.5194/essd-16-2857-2024.</p>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWLNETS (v2.0.0 - May 2020)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-InverseRelations-OWLNETS</i></p><p><strong>Build Date: </strong>May 10, 2020</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-10%2C-2020">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWLNETS (v2.0.0 - January 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Inverse Relations-OWLNETS</i></p><p><strong>Build Date: </strong>January 25, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/January-25%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWL (v2.0.0 - May 2020)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-InverseRelations-OWL</i></p><p><strong>Build Date: </strong>May 10, 2020</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-10%2C-2020">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWL (v2.0.0 - January 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-Inverse Relations-OWL</i></p><p><strong>Build Date: </strong>January 25, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/January-25%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWLNETS (v2.0.0 - May 2020)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-InverseRelations-OWLNETS</i></p><p><strong>Build Date: </strong>May 10, 2020</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-10%2C-2020">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWLNETS (v2.0.0 - January 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-Inverse Relations-OWLNETS</i></p><p><strong>Build Date: </strong>January 25, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/January-25%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWL (v2.0.0 - January 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Inverse Relations-OWL</i></p><p><strong>Build Date: </strong>January 25, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/January-25%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWL (v2.0.0 - May 2020)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-InverseRelations-OWL</i></p><p><strong>Build Date: </strong>May 10, 2020</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-10%2C-2020">here</a>.</li></ul>
Mutual Induced Fit Transition Structure Stabilization of Corannulene's Bowl-to-Bowl Inversion in a Perylene Bisimide Cyclophane
<p>Additional data to report <a href="https://doi.org/10.1039/D3SC05341E">https://doi.org/10.1039/D3SC05341E</a>:<br><br>Corannulene is known to undergo a fast bowl-to-bowl inversion at r.t. <em>via</em> a planar transition structure (TS). Herein we present the catalysis of this process within a perylene bisimide (PBI) cyclophane composed of chirally twisted, non-planar chromophores, linked by <em>para</em>-xylylene spacers. Variable temperature NMR studies reveal that the bowl-to-bowl inversion is significantly accelerated within the cyclophane template despite the structural non-complementarity between the binding site of the host and the TS of the guest. The observed acceleration corresponds to a decrease in the bowl-to-bowl inversion barrier of 11.6 kJ mol<sup>−1</sup> compared to the uncatalyzed process. Comparative binding studies for corannulene (20 π-electrons) and other planar polycyclic aromatic hydrocarbons (PAHs) with 14 to 24 π-electrons were applied to rationalize this barrier reduction. They revealed high binding constants that reach, in tetrachloromethane as a solvent, the picomolar range for the largest guest coronene. Computational models corroborate these experimental results and suggest that both TS stabilization and ground state destabilization contribute to the observed catalytic effect. Hereby, we find a “mutual induced fit” between host and guest in the TS complex, such that mutual geometric adaptation of the energetically favored planar TS and curved π-systems of the host results in an unprecedented non-planar TS of corannulene. Concomitant partial planarization of the PBI units optimizes noncovalent TS stabilization by π–π stacking interactions. This observation of a “mutual induced fit” in the TS of a host–guest complex was further validated experimentally by single crystal X-ray analysis of a host–guest complex with coronene as a qualitative transition state analogue.</p>
3D FEM-based inverse model of Nevado del Ruiz - St. Isabel volcanoes (Colombia)
<p><strong>Description of model and data</strong></p> <p>The files include a FEM-based inverse model for the optimization of parameters of a pressure source responsible for surface deformation. The investigated source parameters are the position of the source center, the three semi-axis, the source strike orientation, the source dip orientation, and the source overpressure. The observations used for the inversion are ascending and descending ground velocities. The optimization is based on Least-Squares objectives using the Monte Carlo method. The file of observations needed for the computation of the Least-Squares objectives (to be uploaded in the optimization node) requires four columns (x,y,z, velocities. All in meters, UTM coordinates-UTM zone 18N, and comma-separated).</p> <p>The model takes into consideration the heterogeneous distribution of material elastic properties. The model does not provide the files for the observations and material properties (at the link: https://zenodo.org/record/5575972), but the structure for the optimization model in which new files can be uploaded for a customized model.</p> <p>The model includes the compensation for the stresses induced by the topography (edifices’ load). The file for the construction of the topographic surface is included as a .txt file (the position x,y of the points is in UTM coordinates-UTM zone 18N, the altitude z is in meters). The far-field is modeled as a hemisphere and it is located at 35 km from the center of the model, which is between the Nevado del Ruiz volcano and Santa Isabel volcano.</p> <p>The model is built with Comsol Multiphysics v 5.6 using the modules Optimization and Structural Mechanics modules, and it is provided as a Comsol .mph file.</p> <p> </p> <p>Datasets and model are results of PICVOLC project. PICVOLC has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 79381</p>
WINTERC-G: a global upper mantle thermochemical model from coupled geophysical–petrological inversion of seismic waveforms, heat flow, surface elevation and gravity satellite data
<p>WINTERC-G: A global, temperature and compositional model of the lithosphere<br> and upper mantle.<br> Version: v5.4, December 2020, J. Fullea, S. Lebedev, Z. Martinec, N. Celli<br> <br> Contact: Javier Fullea (jfullea@ucm.es)<br> Facultad de Fisica,<br> Universidad Complutense de Madrid (UCM),<br> Spain<br> ////////<br> Geophysics Section,<br> Dublin Institute for Advanced Studies<br> Dublin, Ireland<br> </p> <p>TYPE:<br> This contains files with:<br> i) the model directly on the triangular grid solved for in the surface wave inversion.</p> <p> ii) an interpolated grid at 0.5 deg lateral resolution for the density and density discontinuities used in the gravity field data inversion<br> </p> <p>If you have any questions regarding the methodology or the construction<br> of the model, please contact the authors. If you use the model, we would<br> request that you cite the reference indicated below, and appreciate<br> your feedback regarding the model and its application.</p> <p>Citation:</p> <p>Fullea, J., Lebedev, S., Martinec, Z., & Celli, N. L. (2021). WINTERC-G: mapping the upper mantle thermochemical heterogeneity from coupled geophysical–petrological inversion of seismic waveforms, heat flow, surface elevation and gravity satellite data. Geophysical Journal International, 226(1), 146-191.</p> <p>*******************************<br> Summary: construction of the model.<br> WINTERC-G is a Waveform tomography and Gravity (geoid and gravity anomalies and gradiometric measurements<br> from ESA's GOCE mission) INversion model of the TEmpeRature and Composition of the lithosphere and upper mantle at<br> global scale. WINTERC-G is based on upon the integrated geophysical-petrological<br> approach LitMod (Afonso et al., 2008; Fullea et al. 2009) and, hence, all<br> relevant mantle rock physical properties modelled (seismic velocities and density) are<br> computed within a thermodynamically self-consistent framework allowing for a direct<br> parameterization in terms of the temperature and composition of the lithosphere-upper<br> mantle. The inversion is a two-step procedure. In a first step, we invert surface-wave, Rayleigh and Love<br> fundamental mode dispersion curves from a high resolution global dataset measured using waveform inversion,<br> along with surface heat flow and elevation (isostasy) for temperature and crustal structure<br> using a point-wise, non-linear, gradient-search inversion<br> over a triangular grid with an average 225 km lateral inter-knot spacing. In a second step we<br> use a fully parallelized spherical harmonic formalism to invert satellite gravity field data in<br> order to refine the initial crustal density and mantle composition distributions from the step 1<br> for a fixed temperature field.</p> <p>The parameter space in step 1 includes crust (densities and S-wave velocities for a three-layered crust)<br> and mantle variables (the depth of the thermal Lithosphere-Athenosphere-Boundary,<br> the thickness of the sublithospheric thermal buffer, the sublithospheric temperatures at 3 different<br> equispaced nodes down to 400 km, the lithospheric and sublithospheric mantle compositon, and<br> the the radial anisotropy at the 3 crustal layers and at 56, 80, 110, 150, 200, 260, 330,<br> and 400 km depths.</p> <p>The parameter space in step 2 is defined by the average crustal density, and the<br> mantle composition in the lithosphere and sublithosphere.<br> We use the output crustal density from step 1 as the<br> initial value in step 2 inversion. Mantle densities are derived based on the output temperature<br> field from step 1 (kept fixed) and the bulk mantle composition inversion variables.</p> <p> </p> <p> </p> <p>*******************************</p> <p>This archive contains the following files:<br> README (this file)<br> WINTERC-G_Vp-Vs.lis (triangular grid)<br> WINTERC-G_rad_anis_Vs.lis (triangular grid)<br> WINTERC-G_Temperature.lis (triangular grid)<br> WINTERC-G_Density.lis (triangular grid)<br> WINTERC-G_LAB.lis (triangular grid)<br> WINTERC_T_rho_1D.z (1D average model of temperature and density)<br> rho_*_out.xyz (0.5 deg egular grid for gravity field)<br> ETOPO2_km_continental.xyz (0.5 deg egular grid for gravity field)<br> ETOPO2_km_depth_Ice.xyz (0.5 deg egular grid for gravity field)<br> ETOPO2_km_depth_Bed.xyz (0.5 deg egular grid for gravity field)<br> Global_Moho_WINTERC-G.xyz (0.5 deg egular grid for gravity field)</p> <p><br> Files in the triangular grid with an average 225 km lateral inter-knot spacing (12232 grid points):</p> <p>* WINTERC-G_Vp-Vs.lis: Vp and Vs (in km/s) in all model columns with a vertical grid step of 2 km<br> Format for each column:<br> #Column number longitude latitude depth(km, <0 downwards) Vp (km/s) Vs(km/s)<br> 5640 93.72 4.135 -5.0 3.91 2.11</p> <p><br> * WINTERC-G_rad_anis_Vs.lis: radial anisotropy, (Vsh-Vsv)/Vs_iso (in %) in all model columns with a vertical grid step of 2 km<br> Format for each column:<br> #Column number longitude latitude depth(km, <0 downwards) anisotropy (%)</p> <p>* WINTERC-G_Temperature.lis: temperature (in ºC) in all model columns with a vertical grid step of 2 km<br> Format for each column:<br> #Column number longitude latitude depth (km, <0 downwards) T (ºC) dT (%) dT(K) <br> 6437 297.20 -2.524 -259.000 1431.9 -1.91 -27.9<br> The anomalies dT are in % and K with respect to the 1D model in WINTERC_T_rho_1D.z (column 2).</p> <p>* WINTERC-G_Density.lis: density (in kg/m3) in all model columns with a vertical grid step of 2 km<br> Format for each column:<br> #Column number longitude latitude depth(km, <0 downwards) rho (kg/m3) drho(%) drho(kg/m3)<br> The anomalies drho are in % and kg/m3 with respect to the 1D model in WINTERC_T_rho_1D.z (column 3).</p> <p>* WINTERC_T_rho_1D.z: 1D average model of temperature (column 2 in ºC) and density (column 3 in kg/m3) with a vertical grid step of 2 km <br> 5.00000000 0.0000000000000000 6.0259973839110526<br> 3.00000000 0.0000000000000000 38.960571309690394<br> 1.00000000 0.33634006819423840 174.42296045978722<br> -1.00000000 3.8888495253719624 1692.8437489147236<br> -3.00000000 23.974111923225379 1863.8834351235944<br> -5.00000000 47.727920701943034 2568.2414495590924<br> -7.00000000 89.633398074381162 2819.8386016341910<br> -9.00000000 137.01489361657013 2839.5325893195904<br> -11.0000000 182.35233447017222 2897.6600872935287<br> -13.0000000 224.46247069572485 2945.2036923862997<br> -15.0000000 260.63395547331390 3069.6809340323475<br> -17.0000000 292.28175449521456 3132.4574175461721<br> -19.0000000 322.29571965406632 3145.5747337463940<br> -21.0000000 351.58698283375054 3157.2401512748038<br> -23.0000000 380.30002225705056 3177.0000420059773<br> -25.0000000 408.50259805632055 3183.6651032398490<br> -27.0000000 436.22632217636487 3190.9586785996116<br> -29.0000000 463.48733903170023 3198.9369509456310<br> -31.0000000 490.29841705549831 3209.7229872383764<br> -33.0000000 516.71149258457456 3221.6329506091679<br> ...</p> <p>Files in the interpolated regular grid at 0.5 deg lateral resolution used for gravity field data inversion:</p> <p> * rho_c_out.xyz: average crustal density<br> * rho_submoho_out.xyz: mantle density below the Moho discontinuity<br> * rho_*_out.xyz: mantle density defined at different model depths: 20, 35, 56, 80, 110, 150, 200, 260, 330 and 400 km.</p> <p> Format for the density files:<br> # longitude latitude density (kg/m3)<br> <br> Files containing layer discontinuities:</p> <p> * ETOPO2_km_continental.xyz: surface elevation including ice sheet and 0 in marine areas (km, <0 upwards)</p> <p> * ETOPO2_km_depth_Ice.xyz: surface elevation including ice sheet (km, >0 downwards, <0 above sea level)</p> <p> * ETOPO2_km_depth_Bed.xyz: bedrock surface elevation without ice sheet (km, >0 downwards, <0 above sea level)</p> <p> * Global_Moho_WINTERC-G.xyz: crust-mantle discontinuity depth (km, >0 downwards)</p> <p> Format for the discontinuity files:<br> # longitude latitude depth (km)<br> <br> <br> The gravity field in WINTERC-G is computed using an spherical harmonic formalism and a model discretization<br> in 13 layers with laterally varying density. The first 7 layers are characterized by top and bottom boundaries with laterally varying radius whereas the last 6 layers are defined by top and bottom boundaries with constant radius:</p> <p>1/ Water: from ETOPO2_km_continental.xyz to ETOPO2_km_depth_Ice.xyz with rho=1030 kg/m3 (constant vertically)</p> <p>2/ Ice: from ETOPO2_km_depth_Ice.xyz to ETOPO2_km_depth_Bed.xyz with rho=910 kg/m3 (constant vertically)</p> <p>3/ Crust: from ETOPO2_km_depth_Bed to Global_Moho_WINTERC-G.xyz with rho=rho_c_out.xyz (constant vertically)</p> <p>4/ submoho-20km: from Global_Moho_WINTERC-G.xyz to z_20km (file with 20 km everywhere except where z_moho>20km) with rho=rho_submoho_out.xyz (top) and rho=rho_20km_out.xyz (bottom)</p> <p>5/ 20km-36km: from z_20km (file with 20 km everywhere except where z_moho>20km) to z_36km (file with 36 km everywhere except where z_moho>36km) with rho=rho_20km_out.xyz (top) and rho=rho_36km_out.xyz (bottom)</p> <p>6/ 36km-56km: from z_36km (file with 36 km everywhere except where z_moho>36km) to z_56km (file with 56 km everywhere except where z_moho>56km) with rho=rho_36km_out.xyz (top) and rho=rho_56km_out.xyz (bottom)</p> <p>7/ 56km-80km: from z_56km (file with 56 km everywhere except where z_moho>56km) to 80 km depth with rho=rho_56km_out.xyz (top) and rho=rho_80km_out.xyz (bottom)</p> <p>The next 6 layers are computed using the constant radius option:</p> <p>8/ 80km-110km: from z=80km to z=110 km with rho=rho_80km_out.xyz (top) and rho=rho_110km_out.xyz (bottom)</p> <p>9/ 110km-150km: from z=110km to z=150 km with rho=rho_110km_out.xyz (top) and rho=rho_150km_out.xyz (bottom)</p> <p>10/ 150km-200km: from z=150km to z=200 km with rho=rho_150km_out.xyz (top) and rho=rho_200km_out.xyz (bottom)</p> <p>11/ 200km-260km: from z=200km to z=260 km with rho=rho_200km_out.xyz (top) and rho=rho_260km_out.xyz (bottom)</p> <p>12/ 260km-330km: from z=260km to z=330 km with rho=rho_260km_out.xyz (top) and rho=rho_330km_out.xyz (bottom)</p> <p>13/ 330km-400km: from z=330km to z=400 km with rho=rho_330km_out.xyz (top) and rho=rho_400km_out.xyz (bottom)</p> <p> </p> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.