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161 results for “AMR”
Filtered AMR Graphs Bank
<p>The filtered AMR graphs bank is the output of the <a href="http://github.com/polifonia-project/Polifonia-Knowledge-Extractor">Polifonia Knowledge Extractor</a> pipeline.</p> <p>The Polifonia Mini Textual Corpus is pre-processed through coreference resolution and minimal rule-based post-OCR correction, then it is given as input to <a href="https://github.com/SapienzaNLP/spring">SPRING</a> to obtain AMR graphs.</p> <p>The filtered AMR graphs bank encompasses the sentence-AMR graph pairs extrapolated from our initial AMR graphs bank corresponding to AMR2Text-generated sentences associated with a positive (>0) <a href="https://github.com/google-research/bleurt">BLEURT</a> score.</p> <p>Full description at: <a href="https://github.com/polifonia-project/Polifonia-Knowledge-Extractor">https://github.com/polifonia-project/Polifonia-Knowledge-Extractor</a></p>
Supplementary data files for manuscript titled "From spreadsheet lab data templates to knowledge graphs: A FAIR data journey in the domain of AMR research"
<div>This data repository contains all the necessary supplementary files for the manuscript titled "<strong>From spreadsheet lab data templates to knowledge graphs: A FAIR data journey in the domain of AMR research.</strong>"</div> <div> </div> <div>The repository is a copy of the <a href="https://github.com/IMI-COMBINE/template2graphs">GitHub page</a> with the source code used to generate the graph and additional files required for the Lab Data Template.</div> <div> </div> <div>Below we provide a brief overview of the data files in the `additional folder` and their underlying purpose:</div> <div> <ul> <li>The <strong>Data Survey</strong> collects relevant project and data set information to set up a Data Management Plan. It can serve as an input for Lab Data Template development.</li> <li>The <strong>Lab Data Templates</strong> facilitate the collection of AMR research data (in vivo and in vitro) in several sub-tables. The Excel format is compatible with upload procedures into the data repository 'grit' and serves as input for a knowledge graph workflow.</li> <li>The <strong>Data dictionary</strong> is connected to the Lab Data Templates and ensures harmonized data entries. In addition, the dictionaries collect metadata beyond the content of the Lab Data Template (e.g. bacterial strain information or compound information) and link to ontologies where possible.</li> <li>The <strong>FAIR assessments</strong> have been used as a primer for improving the template. This report is generated using the FAIR-DSM model.</li> </ul> </div> <div>The templates have been used during the IMI2 GNA NOW project to collect information and have been improved according to FAIR standards in collaboration with the IMI FAIRplus project ("post FAIRification").</div>
Pre-processed AMR data on S. aureus isolates from PATRIC database
<p>Pre-processed AMR data on S. aureus isolates from PATRIC database. The majority class size was decreased to reach the class ratio of 1:1 when the susceptible/resistant or resistant/susceptible class ratio exceeded 3.5.</p>
Dataset for "Bacterial genome annotation" and "AMR gene detection" workflows
<p>This dataset is associated with the workflows "Bacterial genome annotation" and "AMR gene detection in an assembled bacterial genome".</p>
Excel mapping tools for 2021 AMR data reporting
<p>The main objective of the mapping tools is to provide a simple and useable platform for Member States and other reporting countries to map their country-specific standard terminology to that used by EFSA and to enable the production of an XML file for the submission of antimicrobial resistance data via the Data Collection Framework (DCF).</p> <p>The tools can be used to report antimicrobial resistance data within the framework of Directive 2003/99/EC and Decision 2020/1729/EU.</p> <p>The catalogues and the specific hierarchy of each data model (AMR and ESBL) are already inserted into each of the specific mapping tool. Specific Excel mapping tools corresponding to each of the two data models are available.</p> <p>Dynamic or manual version of the tool can be chosen for each data models.</p>
RSYD-BASIC results for AMR benchmarking dataset subset (MiSeq data)
<p><strong>Input data:</strong></p> <ul> <li>20240905_test_config.yaml: original config file used to run the pipeline</li> <li>20241004_rsyd_largeset_reads.zip: renamed Illumina MiSeq reads</li> <li>20241011-sample-overview.xlsx: overview of SRR accession numbers to internal sample numbers</li> <li>ILM_Run0001_Y20240904_kts_new.xlsx: runsheet </li> <li>input_en.yaml: column name configuration for the run</li> <li>lis_data.zip: LIS report and bacteria list used for LIS-specific results</li> </ul> <p><strong>Expected results:</strong></p> <ul> <li>20240910_test_illumina_largeset.zip: Results of the RSYD-BASIC pipeline, version 1.15.1, with the reads used</li> </ul>
AMR datasets from diverse spp
<p>Public data-sets, composed of a variable number of assembly files belonging to different bacteria spp, are included from previously published AMR analysis.</p>
Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Ireland
<p>This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_IE_20200204: >> The Food Safety Authority of Ireland</p>
Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Sweden
<p>This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_SE_20200204: >> National Veterinary Institute, Swedish Zoonosis Centre</p>
Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Latvia
<p>This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_LV_20200204: >> Assessment and Registration Agency of Food and Veterinary Service of Latvia</p>
Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Spain
<p>This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_ES_20200204: >> Agencia Espaola de Consumo, Seguridad Alimentaria y Nutricin >> Ministerio de Agricultura, Pesca y Alimentacin</p>
Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Cyprus
<p>This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_CY_20200204: >> Ministry of Agriculture, Natural Resources and Evironment - Veterinary Services</p>
Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Iceland
<p>This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_IS_20200204: >> Icelandic Food and Veterinary Authority</p>
Ecosystem Map - SPEARHEAD - AMR stakeholders' mapping workshops
Open the record for dataset details and reuse information.
Webinar on "Fighting AMR in animals: experiences and progress from the field" - WAAW 2021
<p>During the WAAW campaign on 24 November, EU funded H2020 projects AVANT, DISARM, HealthyLivestock and ROADMAP joined forces to share experiences and progress from the field about the challenge of antimicrobial resistance in animals. Testimonials with hands-on experiences, actions and innovative solutions of livestock sector actors such as farmers, vets, pet owners and breeders on tackling AMR were demonstrated.</p> <p>The video is available on YouTube: <strong><a href="http://youtu.be/S5QIQ5Wff-Y">https://youtu.be/S5QIQ5Wff-Y</a></strong></p> <p>Disclaimer: The invited speakers and the attendees of the webinar have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679.</p> <p>The presentations and opinions disclosed in this video are only for general information purposes and do not constitute a joint declaration on behalf of the beneficiaries of the project AVANT, DISARM, Healthy Livestock and ROADMAP.</p> <p>For any further questions please contact us at:</p> <ul> <li><strong><a href="avant@rtds-group.com">avant@rtds-group.com</a></strong> (project AVANT),</li> <li><strong><a href="info@disarmproject.eu">info@disarmproject.eu</a></strong> (project DISARM),</li> <li><strong><a href="healthylivestockproject@yahoo.com">healthylivestockproject@yahoo.com</a></strong> (project Healthy Livestock) or</li> <li><strong><a href="mailto:roadmap.communication@gmail.com">roadmap.communication@gmail.com</a></strong> (project ROADMAP). </li> </ul> <p> </p> <p> </p>
AMR Benchmarking dataset - Metagenomics
<p>Metagenomic benchmarking dataset for AMR detection pipelines for assemblies focusing on ESKAPE pathogens in addition to Salmonella. This dataset consists of closed genomes from NCBI where paired-end Illumina data was available. These genomes were then randomly assigned a relative abundance, had additional AMR genes randomly inserted (to cover all AMR genes in CARD v3.1.4) and metagenomic Illumina reads simulated from them.<br> <br> Metagenomic simulation was performed using: https://github.com/fmaguire/AMR_Metagenome_Simulator and the entire process can be repeated using the <a href="https://zenodo.org/api/files/ba12e743-ae3d-43c0-98bd-2075d6f50340/metagenome_benchmark.sh">metagenome_benchmark.sh </a>script included above.<br> </p> <p><strong>Files</strong><br> `amr_benchmarking_metagenome.csv` contains the metadata the input genome accessions, paths, and simulated copy number used for creation of the AMR metagenome.</p> <p>`AMR_metagenome_labels.tsv` a two column csv containing names of all reads that are derived from an AMR gene and an identifier for the corresponding AMR gene. AMR genes are identified using CARD Antibiotic Resistance Ontology (ARO), with a suffix listing any SNVs for nmutation related resistance genes.<br> </p> <p>`simulated_metagenome.fna.gz` contains the full "assembled" true metagenomic contigs (derived directly from the input genome assemblies amplified to the correct copy number).</p> <p>`metagenome_unsorted.bed` contains the location of AMR genes in the full "assembled" true metagenomic contigs<br> <br> `simulated_metagenome_{1,2}.fq.gz` contain the simulated paired end metagenomics reads</p> <p>`simulated_metagenome_error_free.bam` contains the error-free mapping location from which simulated reads were derived</p> <table> <tbody> <tr> <td> </td> </tr> <tr> <td> </td> </tr> </tbody> </table>
MULTIPLIERS_WP5_Science learning project on AMR_UAB_Public data_v1
<p><span>The datasets contain the following data related to the science learning project on ARM: </span></p> <ul> <li><span>Summary of transcripts from interviews with OSC members, and student groups (Pseudo-/Anonymised).</span></li> </ul>
CFD dataset for AMR-Net
<p>This dataset contains the two dimensional fluid simulation data for AMR-Net.</p> <p>The inputs of simulations are signed distance functions (SDFs) and the outputs are 2D flow fields u and v. In each simulation, 1-5 objects are placed randomly at the center of the computational domain. The objects are randomly chosen from circles, ellipses, rectangles and rounded rectangles. Each hdf5 file includes the pair of input and output data. The details of the dataset is described in the <a href="https://github.com/yasahi-hpc/AMRNet">Github page</a>.</p>
Amr data challenge
<p>Graphs and plots </p>
An Long-term Follow-up Trial of Kidney Tx Patients Treated With Imlifidase or PE After an AMR
ClinicalTrials.gov study NCT04711850. IPD Sharing: NO. Countries: 3. Publications: 1.
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