cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15667
title: Bioportal Snapshot 27.01.2015

description: This is a BioPortal snapshot from late January 2015. It contains the original files as downloaded by the BioPortal webservices, the OWL/XML serialised version with save repair, and a version where all axioms are annotated with axiom identifiers.
DOI: 10.5281/zenodo.15668
title: Empirical Investigation Of Subsumption Test Hardness In Description Logic Classification

description: This is the dataset supporting the analysis for the submission "Empirical Investigation of Subsumption Test Hardness in Description Logic Classification" to CADE, 2015. Data in its very raw form is not included, but the dataset containing non aggregated subsumption test data (labelled subsumptiontest_data) and the overall module data (labelled module_data) contain all the records corresponding to the raw data (albeit amended by some additional measurements and ontology metadata). 

The r_scripts directory contains all the<strong> r files needed to run the analysis</strong>. However, the code is written ad hoc and is very slow, and should only be considered as a reference. Running the code does not work out of the box, as a series of directory paths need to be set manually.

The r_data directory contains all the <strong>datasets used in the analysis.</strong>.

-- map_subsumptiontest_data_non_aggregated contains the non aggregated subsumption test data from which the first experiment, the subsumption test hardness survey, is conducted<br>
-- map_module_data_non_aggregated contains the non aggregated module data from which the first experiment, the subsumption test hardness survey, is conducted

-- module_data_non_aggregated.RData contains the non aggregated module data from which the intra-module analysis is conducted<br>
-- subsumptiontest_data_non_aggregated.RData contains the non aggregated subsumption test data from which the intra-module analysis is conducted

-- inter_module_data.RData contains the results of the inter-module analysis from the perspective of the modules<br>
-- intra_module_data.RData contains the results of the intra-module analysis from the perspective of the modules<br>
-- inter_subsumptiontest_data.RData contains the results of the inter-module analysis from the perspective of the subsumption tests<br>
-- intra_subsumptiontest_data.RData contains the results of the intra-module analysis from the perspective of the subsumption tests

The csv_data directory contains the same data as the r_data directory in CSV form.
DOI: 10.5281/zenodo.15682
title: Module Data For The Empirical Investigation Of Subsumption Test Hardness In Description Logic Classification

description: This dataset contains 224 modules of 14 distinct ontologies for the submission "Empirical Investigation of Subsumption Test Hardness in Description Logic Classification" to CADE, 2015. The submitted version with the dataset description can be found here:

http://owl.cs.manchester.ac.uk/publications/supporting-material/subtest-hardness-in-classification/

The ontologies in this set are BioPortal ontologies from the snapshot provided at http://dx.doi.org/10.5281/zenodo.15667. 

The following ontologies are in the set: 

MFOEM - Emotion Ontology<br>
BT - Biotop Ontology<br>
NEMO - Neural Electromagnetic Ontology<br>
NTDO - Neglected Tropical Disease Ontology<br>
OBI - Ontology for Biomedical Investigations<br>
OGSF - Ontology for Genetic Susceptibility Factor<br>
ONL-MSA - Mental State Assemssment<br>
VSO - Vital Sign Ontology<br>
CAO - Clusters of Orthologous Groups Cog Analysis Ontology <br>
ICO - Informed Consent Ontology<br>
OMRSE - Ontology of Medically Related Social Entities<br>
STATO - Statistics Ontology<br>
NPO - Nanoparticle Ontology<br>
OBCS - Ontology of Biological and Clinical Statistics
DOI: 10.5281/zenodo.17300
title: Observation Logs For Apogee-1

description: These files are the observation logs for the SDSS-III/APOGEE survey. The provide information on when different locations on the sky were observed and for how long. They are to be used with the code at https://github.com/jobovy/apogee for determining the APOGEE selection function (the fraction of potential targets observed as in different parts of the sky).
description: {"references": ["The Tenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Apache Point Observatory Galactic Evolution Experiment, SDSS-III collaboration: Christopher P. Ahn, et al., Astrophys. J. Supp. 211, 17 (2014)", "The Eleventh and Twelfth data releases of the Sloan Digital Sky Survey: Final data from SDSS-III, SDSS-III collaboration: Shadab Alam, et al., Astrophys. J. Supp., in press (2015)"]}
DOI: 10.5281/zenodo.10520
title: Datasets For Set Containment Join

description: flickr, photo id as tuple, tag as set.
	orkut, people id as tuple, community as set.
	twitter, partition id as tuple, signature as set.
	webbase, page id as tuple, outlinks as set.
DOI: 10.5281/zenodo.10567
title: Jfrc2 Template Brain

description: This single female brain was generated by Arnim Jenett (Janelia Farm Research Campus) and is stained with the neuropil marker nc82. <strong>If you make use of this data, please cite:</strong>

<strong>A GAL4-Driver Line Resource for Drosophila Neurobiology</strong><br>
Arnim Jenett, Gerald M. Rubinemail, Teri-T.B. Ngo, David Shepherd, Christine Murphy, Heather Dionne, Barret D. Pfeiffer, Amanda Cavallaro, Donald Hall, Jennifer Jeter, Nirmala Iyer, Dona Fetter, Joanna H. Hausenfluck, Hanchuan Peng, Eric T. Trautman, Robert R. Svirskas, Eugene W. Myers, Zbigniew R. Iwinski, Yoshinori Aso, Gina M. DePasquale, Adrianne Enos, Phuson Hulamm, Shing Chun Benny Lam, Hsing-Hsi Li, Todd R. Laverty, Fuhui Long, Lei Qu, Sean D. Murphy, Konrad Rokicki, Todd Safford, Kshiti Shaw, Julie H. Simpson, Allison Sowell, Susana Tae, Yang Yu, Christopher T. Zugates<br>
http://dx.doi.org/10.1016/j.celrep.2012.09.011

The original image had an XY resolution of 0.622088 microns × 0.622088 microns and a 1 micron slice spacing. It was then upsampled in Z to give isotropic voxels. When received from Janelia Farm the image had no spatial calibration and was in tif format. The image was opened in Fiji/ImageJ and the voxel size set to 0.622088 microns × 0.622088 microns × 0.622088 microns, based on a personal communication from Arnim Jenett and inspection of the image data associated with http://dx.doi.org/10.1016/j.celrep.2012.09.011 that is available at http://flweb.janelia.org/cgi-bin/flew.cgi. The image was then saved in gzip encoded nrrd format using the ImageJ Nrrd_Writer plugin.
DOI: 10.5281/zenodo.10568
title: Fcwb Template Brain

description: The template brain (FCWB) was constructed by screening for whole brains within the FlyCircuit dataset, and manually selecting a pool of brains that appeared of good quality when the stacks were inspected. Separate average female and average male template brains were constructed from 17 and 9 brains, respectively using the CMTK (http://www.nitrc.org/projects/cmtk) avg_adm function which takes a single brain as a seed. After five iterations the resultant average male and average female brains were placed in an affine symmetric position within their image stacks so that a simple horizontal (x -axis) flip of either template brain resulted in an almost perfect overlap of left and right hemispheres. Finally the two sex-specific template brains were then averaged (with equal weight) to make an intersex template brain using the same procedure. Since the purpose of this template was to provide an optimal registration target for the flycircuit.tw dataset, no attempt was made to correct for the obvious disparity between the XY and Z voxel dimensions common to all the images in the dataset. The scripts used for the construction of the template are available at https://github.com/jefferislab/MakeAverageBrain.

Images from FlyCircuit were obtained from the NCHC (National Center for High-performance Computing) and NTHU (National Tsing Hua University), Hsinchu, Taiwan. If you use this template brain, to acknowledge the original raw data, <strong>please ensure that you additionally cite</strong>:

Three-dimensional reconstruction of brain-wide wiring networks in <em>Drosophila</em> at single-cell resolution

Ann-Shyn Chiangemail, Chih-Yung Lin11, Chao-Chun Chuang11, Hsiu-Ming Chang11, Chang-Huain Hsieh11, Chang-Wei Yeh, Chi-Tin Shih, Jian-Jheng Wu, Guo-Tzau Wang, Yung-Chang Chen, Cheng-Chi Wu, Guan-Yu Chen, Yu-Tai Ching, Ping-Chang Lee, Chih-Yang Lin, Hui-Hao Lin, Chia-Chou Wu, Hao-Wei Hsu, Yun-Ann Huang, Jing-Yi Chen, Hsin-Jung Chiang, Chun-Fang Lu, Ru-Fen Ni, Chao-Yuan Yeh, Jenn-Kang Hwang

Current Biology 2011, 21:1-11. http://dx.doi.org/10.1016/j.cub.2010.11.056
DOI: 10.5281/zenodo.10570
title: Cell07 Template Brain

description: <strong>If you make use of this data, please cite:</strong>

<strong>Comprehensive Maps of Drosophila Higher Olfactory Centers: Spatially Segregated Fruit and Pheromone Representation</strong><br>
Gregory S.X.E. Jefferis, Christopher J. Potter, Alexander M. Chan, Elizabeth C. Marin, Torsten Rohlfing, Calvin R. Maurer Jr., Liqun Luo<br>
http://dx.doi.org/10.1016/j.cell.2007.01.040

 

This intersex, averaged template brain is an average of 16 co-registered, nc82-stained brains. The initial seed brain was female; 13 additional female and 2 male brains were registered to this seed and then all 16 were averaged. The reference includes the dorsal posterior quarter of the left brain hemisphere, a volume of approximately 168 × 168 × 87 microns cubed.
DOI: 10.5281/zenodo.10590
title: T1 Template Brain

description: <strong>If you make use of this data, please cite:</strong>

<strong>Cellular Organization of the Neural Circuit that Drives Drosophila Courtship Behavior</strong><br>
Jai Y. Yu, Makoto I. Kanai, Ebru Demir, Gregory S. X. E. Jefferis, Barry J. Dickson<br>
http://dx.doi.org/10.1016/j.cub.2010.08.025

A nrrd version of the original intersex template brain available from http://brainbase.imp.ac.at/bbweb, consisting of an average of 45 brains. Voxel size: (0.5488761, 0.5488761, 1) microns.
DOI: 10.5281/zenodo.10591
title: Drosophila Melanogaster Template Brains

description: Male and female symmetric averaged templates (18 and 14 brains, respectively) and intersex template brain for <em>Drosophila melanogaster</em>. Voxel size: (0.461, 0.461, 1) micron.
DOI: 10.5281/zenodo.10593
title: Drosophila Virilis Template Brains

description: Male and female symmetric averaged templates (10 and 11 brains, respectively) and intersex template brain for <em>Drosophila virilis</em>. Voxel size: (0.461, 0.461, 1) micron. Individual brains were imaged with a Zeiss 710 confocal microscope using an EC Plan-Neofluar 40 × / 1.30 NA oil objective and zoom factor 0.6, with the resulting images being stitched together using the 'Pairwise stitching' plugin of Fiji.
DOI: 10.5281/zenodo.10594
title: Drosophila Simulans Template Brains

description: Male and female symmetric averaged templates (11 and 10 brains, respectively) and intersex template brain for <em>Drosophila simulans</em>. Voxel size: (0.461, 0.461, 1) micron.
DOI: 10.5281/zenodo.10595
title: Is2 Template Brain

description: An intersex, nc82-stained averaged brain constructed from 18 male and 16 female brains. Voxel size: (0.41, 0.41, 1.07) microns. <strong>If you make use of this data, please cite:</strong>

Sexual Dimorphism in the Fly Brain<br>
Sebastian Cachero, Aaron D. Ostrovsky, Jai Y. Yu, Barry J. Dickson, Gregory S.X.E. Jefferis<br>
http://dx.doi.org/10.1016/j.cub.2010.07.045
DOI: 10.5281/zenodo.10752
title: Supplementary Data For A Study Of Open Access Article Processing Charges - 2014

description: Article Processing Charges levied by a set of Gold Open Access journals and hybrid journals in 2014, as collected from the publishers' web sites. Supplementary data to 10.2314/CERN/C26P.W9DT
DOI: 10.5281/zenodo.17361
title: Data Sets For Orthologous Target Pair Analysis

description: The set of all 803 originally identified orthologous target pairs (OTPs) and the subset of 222 OTPs with at least 10 shared compounds are provided herein. For each OTP both organisms, the target, the number of shared compounds,the OTP category, and the number of reference articles is reported. In addtion, the list of all 1149 candidate compounds and their human target assignments is provided.
DOI: 10.5281/zenodo.10498
title: Eeg_Data_Plose One

description: 12 subjects<br>
Picture naming task<br>
sampling frequency: 1000 Hz<br>
74 trials/picture per session<br>
Epoch: -200ms:620ms<br>
256 channels

Recommended preprocessing:<br>
 - Filtering 3:45Hz<br>
 - Artefact removal: Using EEGLAB
DOI: 10.5281/zenodo.10842
title: Bioportal Snapshot 30.06.2014

description: This is a curated snapshot of the BioPortal ontology repository (http://bioportal.bioontology.org/). The dataset contains the original serialisation (fileextension .orig) and a curated OWL/XML serialisation, with the imports closure merged. The dataset is meant for ontology related empirical work such as surveys of biomedical ontologies and reasoner benchmarking, and not for any kind of use/re-use.
DOI: 10.5281/zenodo.10851
title: The Manchester Owl Corpus (Mowlcorp), Original Serialisation

description: The Manchester OWL corpus is a corpus of ontologies as they are found on the Web through various forms of data gathering techniques such as web crawls and calls to the Google Custom Search API. This is the version of the corpus where the files are completely uncurated, and it is mainly suitable for language surveys and people interested in particular serialisations. Word of caution: Due to the fleeting nature of imports, there is no guarantee that all ontologies in the corpus will parse at all times (UnloadableImportException). More information about the creation and contents of the corpus can be found on http://mowlrepo.cs.manchester.ac.uk and in a paper related to an earlier version of the corpus: http://link.springer.com/chapter/10.1007%2F978-3-642-41335-3_21.
DOI: 10.5281/zenodo.15698
title: Input Dataset For Carbon Forest Edge Effects Analysis

description: Dataset that is used for the calculation of forest edge biomass effect from the following github project: [DOI forest_carbon_edge_effect] (http://dx.doi.org/10.5281/zenodo.15697)

Contains global biomass, landcover data, anthrome, soil, elevation, water capacity, fire, luminosityr, cattle, goat, sheep, human population, and anthrome data.
DOI: 10.5281/zenodo.15843
title: Dartmouth Stellar Evolution Grids

description: Dartmouth stellar model grids, used by the 'isochrones' python package (github.com/timothydmorton/isochrones).  Update from previous grids; these now include WISE bands, ages &lt; 1Gyr, and have coarser Fe/H sampling.
description: models come from http://stellar.dartmouth.edu/models/
DOI: 10.5281/zenodo.17394
title: Brams Radio Spectrograms And Spectrogram Samples For Automatic Detection Of Meteor Echoes

description: The files in this dataset are based of radio recordings taped by BRAMS (Belgian RAdio Meteor Stations), the Belgian meteor detection network.

Included in the dataset are the original BRAMS radio recordings (stored as .wav audio files), the spectrogram data for each radio recording (stored as .csv files) and the meteor and non-meteor samples extracted from the radio spectrograms (stored as .csv files).

It should be noted that the the spectrogram data was sampled using a sliding window of size 30x20 pixels and the samples extracted in this manner were further processed by calculating the vertical average of each column in the 30x20 matrixes. The result of this sampling procedure is a set of data vectors containing the average power of the signal found in the original 30x20 spectrogram sample.
DOI: 10.5281/zenodo.17399
title: Chemistry Of The Surface Of Mars

description: Concentration of 11 major elements at the surface of Mars (SiO2, TiO2, Al2O3, FeO,MnO,MgO, CaO, Na2O, K2O, P2O5 and Cr23O3) following the approach presented in  the following article :

Baratoux, D., H. Samuel, C. Michaut, M. J. Toplis, M. Monnereau,<br>
M. Wieczorek, R. Garcia, and<br>
K. Kurita (2014), Petrological constraints on the density of the Martian crust, <em>J. Geophys. Res. Planets, 119, </em>1707-1727, doi:10.1002/2014JE004642.
DOI: 10.5281/zenodo.17400
title: Srtm Topography Of East Senegal At 1"/Pixel

description: SRTM Topography of East Senegal at 1"/pixel
DOI: 10.5281/zenodo.17413
title: Bioactive Compound Classes From Chembl20 For Molecular Hierarchy

description: Compound structure, scaffold, and CSK of 78,150 (all) and 54,042 (only compounds with a scaffold shared by at least one another compound) compounds, respectively, are provided herein. In addition, each compound is annotated with target and potency information.
DOI: 10.5281/zenodo.17418
title: Currently Available 3D Activity Cliffs And 2D-Analogs Of 3D-Cliff Compounds

description: Three dimensional activity cliffs (3D-cliffs) were systematically determined based on currently available X-ray structures in PDB. The list of all 236, 292, 595 3D-cliffs that were identified from the K<sub>i</sub>, IC<sub>50</sub>, and K<sub>i</sub>/IC<sub>50</sub> sets, respectively, is provided. In addition, on the basis of matched molecular pairs, the 2D structural analogs of 3D-cliff compounds identified from ChEMBL database (release 19) are given.
DOI: 10.5281/zenodo.11022
title: Classification Of Binding Modes For Kinase-Inhibitor Complex Structures, 3D Activity Cliffs Formed By Kinase Inhibitors, And Structural Analogues Of 3D-Cliff Compounds

description: The classification of crystallographic binding modes is provided for 884 kinase-inhibitor complex structures that were assembled from PDB. In addition, a total of 105 three-dimensional activity cliffs formed by 3D kinase inhibitors are listed. Their corresponding potency information is also given. Furthermore, the 2D structural analogues of 3D cliff-forming inhibitors were identified from ChEMBL database, on the basis of matched molecular pairs. These analogs and their activity information are also provided.
DOI: 10.5281/zenodo.15871
title: Citations In The German Wikipedia

description: Using https://github.com/halfak/Extract-scholarly-article-citations-from-Wikipedia we extracted citations from the February 2015 dump of the German Wikipedia based on DOIs, PubMed IDs, and ISBNs.
DOI: 10.5281/zenodo.17436
title: Genome Alignments From "Split-Alignment Of Genomes Finds Orthologies More Accurately"

description: Here are the genome alignments resulting from "Split-alignment of genomes finds orthologies more accurately", Genome Biology 2015, 16:106.


	In the terminology of that paper, these are 2-split, post-masked alignments.
	They are in MAF format (http://genome.ucsc.edu/FAQ/FAQformat.html), with "p" lines (http://last.cbrc.jp/doc/last-split.html).
	Alignments with high ambiguity have not been removed, so if you want unambiguously 1-to-1 alignments, remove those annotated with mismap &gt; 0.00001 or so.
	The chimp and orangutan alignments were made using the 500/30 gap costs suggested at the end of the paper.
DOI: 10.5281/zenodo.32405
title: On Genomic Repeats And Reproducibility

description: Supplementary Data Sets for Firtina et al (submitted)
DOI: 10.5281/zenodo.32570
title: Md Simulation Trajectory And Related Files For Popc Bilayer With 670Mm Cacl_2 (Charmm36, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36, 120ns, T=303K, 72 POPC molecules, 2165 water molecules, 26 Ca molecules, 52 Cl molecules.

Note! This dataset is NOT used in the NMRLipids II project (nmrlipids.blospot.fi), but the dataset http://dx.doi.org/10.5281/zenodo.35160

See also discussion in: https://github.com/NMRLipids/lipid_ionINTERACTION/issues/16
DOI: 10.5281/zenodo.32583
title: Umfrageergebnisse "Bedarf Und Anforderungen An Ressourcen Für Text Und Data Mining"

description: Daten der Umfrage "Bedarf und Anforderungen an Ressourcen für Text und Data Mining" der Schwerpunktinitiative "Digitale Information" der Allianz der deutschen Wissenschaftsorganisationen, Arbeitsgruppe Text und Data Mining, vom Mai 2015
description: Zusammenfassung der Umfrageergebnisse und von Arbeitsgruppe Text und Data Mining der Schwerpunktinitiative "Digitale Information" der Allianz der Wissenschaftsorganisationen in diesem Kontext durchgeführter Workshop siehe: http://dx.doi.org/10.5281/zenodo.32584
description: {"references": ["Zusammenfassung der Umfrageergebnisse und von Arbeitsgruppe Text und Data Mining der Schwerpunktinitiative \"Digitale Information\" der Allianz der Wissenschaftsorganisationen in diesem Kontext durchgef\u00fchrter Workshop siehe: http://dx.doi.org/10.5281/zenodo.32584"]}
DOI: 10.5281/zenodo.11120
title: 16S Rrna Sequence Data, Brazilian Coffee Soils

description: 16S sequencing data for DNA extracted from soils from Brazillian coffee farms. Sequenced on Illumina MiSeq with primers from Caporaso (2011, 2012).
DOI: 10.5281/zenodo.11121
title: Cbrbench - Canberra Ontology Ranking Benchmark

description: This benchmark suite for ontology ranking includes a collection of ontologies that was retrieved by crawling a seed set of ontology URIs derived from prefix.cc and a set of queries derived based on their popularity from a real query log from the Linked Open Vocabularies search engine in the period between 06/01/2012 and 16/04/2014. Further, it includes the results for the ideal ranking of the concepts in the ontology collection for the identified set of query terms established based on the opinions of ten ontology engineering experts.<br>
The ideal ranking is compared with eight state-of-the-art ranking algorithms and the precision at k, the mean average precision and the discounted cumulative gain is calculated for these algorithms representing a baseline to compare an ontology ranking model to.
DOI: 10.5281/zenodo.32661
title: Evaporation And Permeameter Data Hydraulic Properties Stony Soil

description: We used the evaporation method to determine the hydraulic conductivity and the retention curve of a soil sample. The principle of this method is to simultaneously measure the matric head at different depths and the water content of an initially saturated soil sample submitted to evaporation.

The experiments were performed over cylindrical Plexiglas samples of 1 L (height: 65 mm), perforated at the bottom to allow saturation from below and open to atmosphere on the upper side to allow evaporation of the soil moisture. Four 6 mm-long ceramic tensiometers (SDEC230) were introduced at 10, 25, 40 and 55 mm in height, respectively denoted T1 to T4 (the reference level is located at the bottom of the sample). In order to avoid preferential flow due to the introduction of the tensiometers on a same vertical line, each hole of the sample was horizontally shifted of 12 degrees vis-à-vis the center of the tube. The tensiometers are connected through a tube to a pressure transducer (DPT-100, DELTRAN). The setup was filled with degased water. The variation in pressure of the drying soil was recorded every 15 min by a CR800 (CAMPBELL SCIENTIFIC). Tensions beyond the consolidation point were not taken into account. The consolidation point refers to the state from which the measured pressure head starts to decrease as bubbles appear and water vapour accumulates (typically 68 kPa cm in this case).

The total water loss as a function of time was monitored by a balance (OHAUS) with a sensitivity of 0.2 g with an accuracy of  1 g with a time resolution of 15 min. A 50 W infrared lamp was positioned 1 m above the sample surface to slightly speed up the evaporation process. The light was turned off for the first 24 hours of every experiment, as the evaporation rate is already high in a saturated sample. A measuring campaign lasted until 3 of the 4 tensiometers ran dry (the tension sharply drops down to approximately a null value). At the end of the experiment, the sample was oven dried for 24 hours at 105°C to estimate the .