Find research datasets worth reusing

opencc-by-2.0Oct 2020View details →

Improving Methods to Measure Comparable Mortality by Cause - Gold Standard Verbal Autopsy Data 2011-2014

These data were collected and compiled as part of the Improving Methods to Measure Comparable Mortality by Cause (IMMCMC) project, funded by Australia's National Health and Medical Research Council (NHMRC). Verbal autopsies (VAs) were conducted between 2011 and 2014 in three sites: Bohol, Philippines; Chandpur and Comila Districts, Bangladesh; and Central and Eastern Highlands Provinces, Papua New Guinea. Diagnostic criteria and cause lists similar to those employed in the Population Health Metrics Research Consortium (PHMRC) study were used to identify gold standard (GS) deaths. This study added 3512 deaths (2491 adults, 320 children, and 701 neonates) to the GS VA database created from the PHMRC study. This dataset contains the combined PHMRC and IMMCMC data for an updated GS VA database.

opencc-by-4.0Dec 2017View details →

Gold seal of Viṣṇuvarman

Figure 52 in To engrave his virtues on the disc of the moon… Inscriptions of the Aulikaras and Their Associates Dániel Balogh, 2019 Gold seal of Viṣṇuvarman. Left: four faces of the object. Right: mirror image of inscribed face and hand tracing of inscription. Photograph courtesy of Devendra Handa, tracing by the author.

opencc-by-4.0Oct 2022View details →

DATASET: Predicting Protein Function and Orientation on a Gold Nanoparticle Surface Using a Residue-Based Affinity Scale

This upload contains data for the manuscript "Predicting Protein Function and Orientation on a Gold Nanoparticle Surface Using a Residue-Based Affinity Scale." It contains kinetics data, UV-vis data, surface calculations, and activity assays for the systems described in the manuscript.

opencc-by-4.0Nov 2022View details →

Translation Alignment: Ancient Greek to English. Annotation Style Guide and Gold Standard.

This dataset contains guidelines and a gold standard for the alignment of Ancient Greek texts with English translations. The guidelines were used to annotate a diverse dataset including Homeric epic, Attic prose, and Platonic dialogue, and were tested by measuring inter-annotator agreement of 80% or higher. The Ancient Greek texts used are almost entirely available through the Scaife viewer (<a href="https://scaife.perseus.org/">https://scaife.perseus.org/</a>). The datasets used to develop the gold standard were aligned using the Ugarit Translation Alignment Editor for Historical languages (<a href="http://ugarit.ialigner.com/">http://ugarit.ialigner.com/</a>). The materials available here can be used to perform and evaluate alignments of various texts in Ancient Greek, to create new gold standard corpora, and to train automated translation models. The guidelines can also be further adapted to address similar language pairs including an inflected and a synthetic language, such as Latin and English, or can provide a structure for the alignment of other historical texts against modern translations. However, the guidelines are not project-specific: they were specifically intended for the creation of a Gold Standard in the scenario of machine translation. Different scenarios, such as language research or pedagogy, may need further tweaking to these guidelines to make them more compatible with different underlying principles. For further information on Ugarit and translation alignment of historical languages, see <a href="http://ugarit.ialigner.com/bib.php">http://ugarit.ialigner.com/bib.php</a> and follow us on Twitter (@ugarit_ty).

opencc-by-4.0Nov 2022View details →

Raw Data: Gold Coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging

Two sets of raw data from gold coated ZnO microstructure (rod) investigated by Bragg coherent X-ray diffraction imaging used in publication: "Visualizing Intrinsic 3D-Strain Distribution in Gold Coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging and Transmission Electron Microscopy with Respect to Piezotronic Applications" (<a href="https://doi.org/10.1002/aelm.202100546">https://doi.org/10.1002/aelm.202100546</a>) Included is data from two different spatial positions along the c-axis of the ZnO rod. Futher on called position 1 (P1) and position 2 (P2). For each position there is a .nxs file of a rocking scan around the {10-10} Bragg reflection, collected by a 2D detector and other recorded values, e.g. motor positions, counter values.

Nos_Machine translation gold standard English-Galician 1

1777 carefully curated Galician-English parallel sentences for the evaluation of automatic machine translation. Sentence pairs are classified according to whether the translations are highly literal or not.

Nos_Machine translation gold standard Spanish-Galician 2

1998 carefully curated Galician-Spanish parallel sentences for the evaluation of automatic machine translation. Sentence pairs are classified according to whether the translations are highly literal or not.

Nos_Machine translation gold standard English-Galician 2

Nos_Machine translation gold standard Spanish-Galician 1

opencc-by-4.0Apr 2023View details →

PretoxTM Corpus: a gold standard corpus of preclinical treatment-related findings annotated from toxicology reports

The PretoxTM Corpus is a gold standard corpus of preclinical treatment-related findings annotated from toxicology reports. Example documents annotated by domain experts, also known as a gold standard corpus, are needed in order to develop, train, and validate text mining tools. To this aim we designed and performed an annotation activity for the development of the corpus of treatment-related findings: the PretoxTM corpus. A treatment-related finding expression enclose several named entities; the most relevant one is the abnormal effect detected; which depending on the study domain of the finding, can be given by a measurement, test, or examination named Study Test and an abnormal Manifestation result obtained for that study test; or by an abnormal Finding in study domains where there is no associated test or measurement (e.g., clinical, macroscopic and microscopic). Other related named entities that could be present to complete the treatment-related finding are; the Specimen of the abnormal observation, the Sex of the subject, the Group of subjects in which the observation was detected and the Dose level administration of the compound. Examples of sentences with treatment-related findings are: “The decrease in food consumption and body weight of the animals from the mid dose onwards is regarded as evidence of general toxicity.” and "At dose level 3, absolute and relative liver weights were increased in male rats.”. Contributions: The PretoxTM corpus was developed by BSC, with the contribution of IMIM and a team of experts from the eTRANSAFE EFPIA partners. License: Creative Commons Attribution-ShareAlike 4.0 International (cc by sa 4.0). The PretoxTM resources have been developed as part of the eTRANSAFE project. For more information about PretoxTM please visit: PretoxTM Corpus Gitlab: <a href="https://gitlab.bsc.es/inb/etransafe/preclinical-toxicological-corpus/">https://gitlab.bsc.es/inb/etransafe/preclinical-toxicological-corpus/</a> PretoxTM central documentation: <a href="https://pretoxtm.gitlab.io/documentation/">https://pretoxtm.gitlab.io/documentation/</a>

opencc-by-4.0Nov 2022View details →

Translation Alignment: Ancient Greek to Latin. Annotation Style Guide and Gold Standard

This dataset contains guidelines and a gold standard for the alignment of Ancient Greek texts with Latin scholarly translations.  The gold standard consists of 100 fragments randomly selected from the Digital Fragmenta Historicorum Graecorum (DFHG) (https://www.dfhg-project.org/), which were aligned manually by Chiara Palladino and David J. Wright using Ugarit (https://ugarit.ialigner.com/). The Annotation Style Guide was developed for this project. The resulting Inter-Annotator-Agreement (IAA) is 90.5%.   The materials available in this repository can be used to perform and evaluate alignments of various texts in Ancient Greek, to create gold standards, and to train automated translation alignment models.  The Guidelines can be further adapted to address similar language pairs including inflected languages, or can provide a structure for the alignment of other historical texts against modern translations. However, the guidelines are not project-specific: they were specifically intended for the scenario of machine translation. Different research questions, such as translation history or pedagogy, may need further tweaking of these guidelines.  For further information on Ugarit and translation alignment of historical languages, see http://ugarit.aligner.com/bib.php and follow us on Twitter (@ugarit_ty).

opencc-by-4.0Jun 2023View details →

Dataset supporting the paper "Large Orbital Moment of Two Coupled Spin‑Half Co Ions in a Complex on Gold. ACS Nano 17, 10608 (2023)"

Dataset corresponding to theoretical calculations in the paper "Large Orbital Moment of Two Coupled Spin‑Half Co Ions in a Complex on Gold" ACS Nano 17, 10608 (2023), https://pubs.acs.org/doi/10.1021/acsnano.3c01595 List of files: Several folders corresponding to the figures of the paper. They contain: .siesta files: STM images in WsXM format (http://www.wsxm.eu/) simulated using STMpw (https://doi.org/10.5281/zenodo.3581159). CONTCAR files: relaxed structures in VASP format. They can be visualized with VESTA (https://jp-minerals.org/vesta/en/). .agr: grace files (https://plasma-gate.weizmann.ac.il/Grace/).

opencc-by-4.0Aug 2023View details →

DATASET: Near-Infrared Photothermal Ablation of Biofilms using Protein-Functionalized Gold Nanospheres with a Tunable Temperature Response

This dataset contains the DLS, TEM, temperature data, and other experimental data to accompany the manuscript.

opencc-by-4.0Sep 2023View details →

Gold standard annotation of epilepsy clinic letters for the development of information extraction tools

This folder contains 200 synthetic letters, based on hospital outpatient epilepsy clinic consultations, written by neurology consultants, specialist trainees, and epilepsy specialist nurses. The letters were double annotated by trained researchers, according to annotation guidelines, uploaded separately (What and How of annotating with Markup). The 200 .ann annotation files are also included. We used Markup (https://getmarkup.com) for annotation (the configuration file is within the uploaded set of annotations) with an epilepsy concept list based on the Unified Medical Language System (UMLS) ontology. All annotations were compared, reviewed, and corrected to form a gold standard annotation set.

CAT 4.6 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: CAT SoftwareVersion: 4.6 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/dutilh/CAT ReferenceDatabase: prebuilt 2018-12-12 Taxonomy: NCBI 2018-12-12 ShortReadsUsed: False LongReadsUsed: False CommandUsed: CAT contigs -c anonymous_gsa_pooled.fasta -d CAT_prepare_20181212/2018-12-12_CAT_database/ -t CAT_prepare_20181212/2018-12-12_taxonomy/ --tmpdir tmp --nproc 16

PhyloPythiaS+ 1.4 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: PhyloPythiaS+ SoftwareVersion: 1.4 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/algbioi/ppsp DockerImage: cami/ppsp:1.4 IsBiobox: False ReferenceDatabase: RefSeq 93, SILVA 132 Taxonomy: NCBI 2018-02-26 ShortReadsUsed: False LongReadsUsed: False CommandUsed: run_ppsp.py --pipelineDir ppsp_pipepline --inputFastaFile anonymous_gsa_pooled.fasta --databaseFile ncbi_taxonomy --refSeq refseq93 --s16Database SILVA_132 --mgDatabase reference_NCBI201502/mg5

MetaBAT 2.12.1 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly Software: MetaBAT SoftwareVersion: 2.12.1 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://bitbucket.org/berkeleylab/metabat ShortReadsUsed: True LongReadsUsed: False CommandUsed: bowtie2-build anonymous_gsa_pooled.fasta anonymous_gsa_pooled.fasta for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done runMetaBat.sh -l anonymous_gsa_pooled.fasta anonymous_reads_sample_*.sorted.bam

Kraken 2.0.8 beta taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: Kraken SoftwareVersion: 2.0.8 beta DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://ccb.jhu.edu/software/kraken2/ ReferenceDatabase: built 2019-05-22 Taxonomy: NCBI 2019-05-22 ShortReadsUsed: False LongReadsUsed: False CommandUsed: kraken2-build --standard --db kraken2db_std --use-ftp kraken2 --db kraken2db_std --threads 16 --output 19122017_mousegut_scaffolds.kraken --report 19122017_mousegut_scaffolds.kreport anonymous_gsa_pooled.fasta cat 19122017_mousegut_scaffolds | awk '{print $2 "\t" $3}' > 19122017_mousegut_scaffolds.cami

opencc-by-4.0Aug 2020View details →

Fig. 21 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species

Fig. 21. Caridina poarae sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. Eggs. k. Cephalothorax. MNHN-IU-2018-2922 (a–k).