Resource List
List all resources, or create a new resource.
GET /api/t/?accessibility=%22Open+access%22
{ "count": 8958, "next": "?page=2", "previous": null, "list": [ { "name": "PolySTest", "description": "Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.", "homepage": "http://computproteomics.bmb.sdu.dk/app_direct/PolySTest", "biotoolsID": "PolySTest", "biotoolsCURIE": "biotools:PolySTest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3932", "term": "Q-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_3905", "term": "Histogram" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Denmark" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/computproteomics/PolySTest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/mcp.RA119.001777", "pmid": "32424025", "pmcid": "PMC8015005", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features", "abstract": "", "date": "2020-08-01T00:00:00Z", "citationCount": 26, "authors": [], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [], "owner": "veits@bmb.sdu.dk", "additionDate": "2019-11-14T19:27:27Z", "lastUpdate": "2025-11-08T12:32:48.900143Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VSClust", "description": "Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance .", "homepage": "http://computproteomics.bmb.sdu.dk/app_direct/VSClust/", "biotoolsID": "vsclust", "biotoolsCURIE": "biotools:vsclust", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" }, { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" }, { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "uri": "http://edamontology.org/operation_3960", "term": "Principal component analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3768", "term": "Clustered expression profiles" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3932", "term": "Q-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "Proteomics" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bitbucket.org/veitveit/vsclust/src/master/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bitbucket.org/veitveit/vsclust", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty224", "pmid": "29635359", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "VSClust: Feature-based variance-sensitive clustering of omics data", "abstract": "", "date": "2018-09-01T00:00:00Z", "citationCount": 27, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Veit Schwämmle", "email": "veits@bmb.sdu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "veits@bmb.sdu.dk", "additionDate": "2018-06-02T07:03:53Z", "lastUpdate": "2025-11-08T12:32:14.933981Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Prostate zone segmentation tool", "description": "This tool automatically segments the the prostate into two zones: the central and transition zones (TZ+CZ) and the peripheral zone (PZ). It takes as input a T2-weighted image and produces a segmentation in the same input format.\n\nThree datasets were used to train this model: ProstateX (n=152), Prostate158 (n=119) and ProstateNet (the ProCAncer-I dataset; n=532). We used the T2-weighted images available in each dataset and trained a standard three-class nnU-Net model with three classes: background, peripheral zone and the combination of the transition and central zones as annotated by radiologists. Using 149 cases from the three previously noted datasets, this model achieved DSC=0.81 (95% CI=[0.59, 0.92]) for PZ and 0.87 (95% CI=[0.60, 0.96]) for CZ+TZ. In a clinical validation using ProCAncer-I data, this model achieved, for PZ and TZ+CZ, DSC=0.65 and DSC=0.77, respectively, comparable to the observed between-radiologist DSC for a subset of cases (DSC=0.61 and DSC=0.73, respectively).", "homepage": "https://github.com/josegcpa/nnunet_serve", "biotoolsID": "prostate_zone_segmentation_tool", "biotoolsCURIE": "biotools:prostate_zone_segmentation_tool", "version": [], "otherID": [], "relation": [ { "biotoolsID": "nnunet", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Image annotation for individual DICOM and Nifti images: Please note that it is easier to mount the input and output paths path and keep `--study_path` always as `/data/input` and `--output_dir` always as `/data/output`. This way only `--series_folders` requires any change. `--series_folders` can refer both to a Nifti file (if the input is Nifti) or the a DICOM series folder.\n\nIf the input is DICOM, `--is_dicom` should be used.", "cmd": "docker run --shm-size=1gb -v $(pwd)/example:/data/input:ro -v $(pwd)/test_output:/data/output:rw --gpus=\"all\" test-eucaim:latest nnunet-predict --study_path /data/input --series_folders <series-folder> --output_dir /data/output" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Batch image annotation for DICOM and Nifti images using dataset JSON and data directory supports two methods: using a dataset JSON and using a data directory. \n\nThe dataset JSON-based method relies on having a dataset JSON which has a list of dictionaries that follow this structure: `{\"study_path\": str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous to the previous modes. Be mindful that paths should be specified accordingly for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\nThe data directory-based method relies on having a directory structured as patient/study/series, where each series follows an nnU-Net-like convention (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should be `<series-id>_0000`. The data directory should be specified using `--data_dir` and requires the specification of an `--output_dir`.\n\nIf the input is DICOM, `--is_dicom` should be specified.", "cmd": "docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw --gpus=\"all\" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir /data/input --output_dir /data/output}}" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/josegcpa/nnunet_serve", "type": [ "Repository" ], "note": "This is the nnunet_serve repository, containing the generic nnU-Net building and serving functionalities used by the Computational Clinical Imaging Group at Champalimaud Foundation." } ], "download": [], "documentation": [ { "url": "https://github.com/josegcpa/nnunet_serve", "type": [ "API documentation" ], "note": "This is the repository containing all of the code together with a comprehensive README for deployment and examplar files." } ], "publication": [ { "doi": "10.1016/j.compbiomed.2024.108216", "pmid": "38442555", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Analysis of domain shift in whole prostate gland, zonal and lesions segmentation and detection, using multicentric retrospective data", "abstract": "", "date": "2024-03-01T00:00:00Z", "citationCount": 9, "authors": [], "journal": "Computers in Biology and Medicine" } } ], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": "https://josegcpa.net", "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Nickolas Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Nuno Rodrigues", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "josegcpa", "additionDate": "2025-11-07T18:15:49.962044Z", "lastUpdate": "2025-11-07T18:17:59.196564Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "HCC segmentation tool for contrast-enhanced abdominal CT", "description": "Features an nnU-Net based segmentation tool capable of performing HCC segmentation for both arterial and portal venous phase in polyphasic contrast-enhanced abdominal CT.\n\nPlease be mindful that the usage instructions below are for the image in the EUCAIM Harbor.", "homepage": "https://github.com/josegcpa/nnunet_serve", "biotoolsID": "hcc_segmentation_tool_for_contrast-enhanced_abdominal_ct", "biotoolsCURIE": "biotools:hcc_segmentation_tool_for_contrast-enhanced_abdominal_ct", "version": [], "otherID": [], "relation": [ { "biotoolsID": "nnunet", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Image annotation for individual DICOM and Nifti images: Please note that it is easier to mount the input and output paths path and keep `--study_path` always as `/data/input` and `--output_dir` always as `/data/output`. This way only `--series_folders` requires any change. `--series_folders` can refer both to a Nifti file (if the input is Nifti) or the a DICOM series folder.\n\nIf the input is DICOM, `--is_dicom` should be used.", "cmd": "docker run --shm-size=1gb -v $(pwd)/example:/data/input:ro -v $(pwd)/test_output:/data/output:rw --gpus=\"all\" test-eucaim:latest nnunet-predict --study_path /data/input --series_folders <series-folder> --output_dir /data/output" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Batch image annotation for DICOM and Nifti images using dataset JSON and data directory supports two methods: using a dataset JSON and using a data directory. \n\nThe dataset JSON-based method relies on having a dataset JSON which has a list of dictionaries that follow this structure: `{\"study_path\": str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous to the previous modes. Be mindful that paths should be specified accordingly for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\nThe data directory-based method relies on having a directory structured as patient/study/series, where each series follows an nnU-Net-like convention (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should be `<series-id>_0000`. The data directory should be specified using `--data_dir` and requires the specification of an `--output_dir`.\n\nIf the input is DICOM, `--is_dicom` should be specified.", "cmd": "docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw --gpus=\"all\" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir /data/input --output_dir /data/output}}" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/josegcpa/nnunet_serve", "type": [ "Repository" ], "note": "This is the nnunet_serve repository, containing the generic nnU-Net building and serving functionalities used by the Computational Clinical Imaging Group at Champalimaud Foundation." } ], "download": [], "documentation": [ { "url": "https://github.com/josegcpa/nnunet_serve", "type": [ "API documentation" ], "note": "This is the repository containing all of the code together with a comprehensive README for deployment and examplar files." } ], "publication": [], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": "https://josegcpa.net", "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Nickolas Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Nuno Rodrigues", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Teresa Sotto-Mayor", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "josegcpa", "additionDate": "2025-11-04T10:22:47.687623Z", "lastUpdate": "2025-11-07T18:15:59.638977Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Spectra", "description": "The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.", "homepage": "https://github.com/RforMassSpectrometry/Spectra", "biotoolsID": "spectra", "biotoolsCURIE": "biotools:spectra", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3621", "term": "SQLite format" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor", "Bioconductor" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Rformassspectrometry/Spectra", "type": [ "Repository" ], "note": null }, { "url": "https://rformassspectrometry.github.io/Spectra/", "type": [ "Other" ], "note": "Main documentation" } ], "download": [], "documentation": [ { "url": "https://rformassspectrometry.github.io/Spectra/", "type": [ "API documentation" ], "note": null }, { "url": "https://jorainer.github.io/SpectraTutorials/", "type": [ "Training material" ], "note": null } ], "publication": [], "credit": [], "owner": "jorainer", "additionDate": "2025-11-05T14:50:14.996722Z", "lastUpdate": "2025-11-07T11:38:15.960655Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ComplexBrowser", "description": "ComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps.", "homepage": "http://computproteomics.bmb.sdu.dk/Apps/ComplexBrowser/", "biotoolsID": "ComplexBrowser", "biotoolsCURIE": "biotools:ComplexBrowser", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" }, { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" }, { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" }, { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_3282", "term": "ID mapping" }, { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0531", "term": "Heat map generation" }, { "uri": "http://edamontology.org/operation_3659", "term": "Regression analysis" }, { "uri": "http://edamontology.org/operation_3463", "term": "Expression correlation analysis" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_2938", "term": "Dendrogram visualisation" }, { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "R" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://computproteomics.bmb.sdu.dk/", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://bitbucket.org/michalakw/complexbrowser/", "type": "Source code", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://bitbucket.org/michalakw/complexbrowser/raw/dc9d8f0c8dff610e2f58e3cb5f5087d050df26f2/Manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/573774", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Veit Schwämmle", "email": "veits@bmb.sdu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "vtsiamis", "additionDate": "2019-06-18T19:35:41Z", "lastUpdate": "2025-11-07T08:52:31.717711Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "prolfquapp", "description": "A command-line tool for differential expression analysis in quantitative proteomics", "homepage": "https://github.com/prolfqua/prolfquapp", "biotoolsID": "prolfquapp", "biotoolsCURIE": "biotools:prolfquapp", "version": [ "0.1.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": "./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN\n# and again you run the version within the docker container with\n# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN" }, { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/prolfqua/prolfquapp", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/prolfqua/prolfquapp/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6", "type": "Downloads page", "note": null, "version": "0.1.6" } ], "documentation": [ { "url": "https://github.com/prolfqua/prolfquapp/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.4c00911", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "0.0.6", "note": null, "metadata": { "title": "prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics", "abstract": "", "date": "2025-02-07T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Journal of Proteome Research" } } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2025-02-28T15:04:33.594183Z", "lastUpdate": "2025-11-06T14:37:12.116175Z", "editPermission": { "type": "group", "authors": [ "thatmariia" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COBRAR", "description": "The R package cobrar provides structures and functions for constraint-based metabolic network analysis, e.g. the prediction of metabolic fluxes using fluxes using Flux Balance Analysis (FBA). cobrar is inspired by the former CRAN R package sybil.", "homepage": "https://waschina.github.io/cobrar/", "biotoolsID": "cobrar", "biotoolsCURIE": "biotools:cobrar", "version": [ "0.2.2" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Metabolic network modelling" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://waschina.github.io/cobrar/", "type": [ "Other" ], "note": "Link to the GitHub repo added" } ], "download": [ { "url": "https://waschina.github.io/cobrar/", "type": "Source code", "note": null, "version": "0.2.2" } ], "documentation": [], "publication": [], "credit": [ { "name": "Silvio Waschina", "email": "s.waschina@nutrinf.uni-kiel.de", "url": "https://www.uni-kiel.de/en/person/waschina-silvio-44493", "orcidid": "https://orcid.org/0000-0002-6290-3593", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "rsmsheriff", "additionDate": "2025-11-05T13:55:16.717008Z", "lastUpdate": "2025-11-05T17:06:45.041194Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "xcms", "description": "Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.", "homepage": "http://bioconductor.org/packages/release/bioc/html/xcms.html", "biotoolsID": "xcms", "biotoolsCURIE": "biotools:xcms", "version": [ "3.0.2" ], "otherID": [], "relation": [ { "biotoolsID": "ramclustr", "type": "usedBy" }, { "biotoolsID": "camera", "type": "usedBy" }, { "biotoolsID": "workflow4metabolomics", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" }, { "uri": "http://edamontology.org/operation_3628", "term": "Chromatographic alignment" }, { "uri": "http://edamontology.org/operation_3634", "term": "Label-free quantification" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] }, { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3248", "term": "mzQuantML" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3203", "term": "Chromatogram visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "Bioconda", "RforMassSpectrometry", "Galaxy Tools", "BioConductor" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany", "France", "Czech Republic" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "http://metlin.scripps.edu/download/", "type": [ "Mirror" ], "note": null }, { "url": "https://github.com/sneumann/xcms", "type": [ "Repository" ], "note": "Link to the repository hosting the R code." }, { "url": "https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy1", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/xcms_1.50.1.tar.gz", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/sneumann/xcms", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/xcms.html", "type": [ "User manual" ], "note": null }, { "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html", "type": [ "Training material" ], "note": "Galaxy training material for LC-MS data preprocessing with XCMS" }, { "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html", "type": [ "Training material" ], "note": "Galaxy training for GC-MS data preprocessing with XCMS" }, { "url": "https://jorainer.github.io/xcmsTutorials/", "type": [ "Training material" ], "note": "Tutorial on using the XCMS R library" } ], "publication": [ { "doi": "10.1093/bioinformatics/btq441", "pmid": "20671148", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data", "abstract": "", "date": "2010-07-29T00:00:00Z", "citationCount": 165, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Steffen Neumann", "email": "sneumann@ipb-halle.de", "url": null, "orcidid": "https://orcid.org/0000-0002-7899-7192", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:54Z", "lastUpdate": "2025-11-05T14:44:25.643842Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "n.m.palmblad@lumc.nl", "recetox-specdatri", "sneumann" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Alfred", "description": "BAM Statistics, Feature Counting and Annotation", "homepage": "https://github.com/tobiasrausch/alfred", "biotoolsID": "alfred", "biotoolsCURIE": "biotools:alfred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0258", "term": "Sequence alignment analysis" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "JavaScript", "C++" ], "license": "BSD-3-Clause", "collectionID": [ "Gear Genomics", "Rare Disease" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "EMBL" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/tobiasrausch/alfred", "type": [ "Repository" ], "note": null }, { "url": "https://www.gear-genomics.com/alfred/", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.gear-genomics.com/docs/alfred/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty1007", "pmid": "30520945", "pmcid": "PMC6612896", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Alfred: Interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing", "abstract": "© 2018 The Author(s) 2018. Published by Oxford University Press.Summary: Harmonizing quality control (QC) of large-scale second and third-generation sequencing datasets is key for enabling downstream computational and biological analyses. We present Alfred, an efficient and versatile command-line application that computes multi-sample QC metrics in a read-group aware manner, across a wide variety of sequencing assays and technologies. In addition to standard QC metrics such as GC bias, base composition, insert size and sequencing coverage distributions it supports haplotype-aware and allele-specific feature counting and feature annotation. The versatility of Alfred allows for easy pipeline integration in high-throughput settings, including DNA sequencing facilities and large-scale research initiatives, enabling continuous monitoring of sequence data quality and characteristics across samples. Alfred supports haplo-tagging of BAM/CRAM files to conduct haplotype-resolved analyses in conjunction with a variety of next-generation sequencing based assays. Alfred's companion web application enables interactive exploration of results and comparison to public datasets.", "date": "2019-07-15T00:00:00Z", "citationCount": 14, "authors": [ { "name": "Rausch T." }, { "name": "Hsi-Yang Fritz M." }, { "name": "Korbel J.O." }, { "name": "Benes V." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Tobias Rausch", "email": "tobias.rausch@embl.de", "url": null, "orcidid": "https://orcid.org/0000-0001-5773-5620", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "rausch", "additionDate": "2020-04-22T11:39:28Z", "lastUpdate": "2025-11-05T13:53:16.423152Z", "editPermission": { "type": "group", "authors": [ "alirh" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "NLmCED Filter", "description": "The NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination between two filters such as the Non-Local mean filter and the Anisotropic Diffusion tensor method with an estimator of Rician noise. The NLmCED filter can benefit from the noise reduction capabilities of the NLM filter while maintaining the edge-preserving characteristics of anisotropic diffusion.", "homepage": "https://github.com/Feriel87/Denoising-CEST-MRI/tree/main/NLmCED_Filter", "biotoolsID": "nlmced_filter", "biotoolsCURIE": "biotools:nlmced_filter", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" }, { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3579", "term": "JPG" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3626", "term": "MAT" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python", "MATLAB" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/Denoising-CEST-MRI/tree/main/NLmCED_Filter", "type": [ "Repository" ], "note": "Github Link" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1504/IJCVR.2018.090012", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A new method for three-dimensional magnetic resonance images denoising", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 3, "authors": [], "journal": "International Journal of Computational Vision and Robotics" } }, { "doi": "10.1002/mrm.28676", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Evaluation of a similarity anisotropic diffusion denoising approach for improving in vivo CEST-MRI tumor pH imaging", "abstract": "", "date": "2021-06-01T00:00:00Z", "citationCount": 20, "authors": [], "journal": "Magnetic Resonance in Medicine" } } ], "credit": [ { "name": "Feriel Romdhane", "email": "ferielromdhane@yahoo.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-5854-9341", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Feriel", "additionDate": "2023-07-13T08:14:40.190855Z", "lastUpdate": "2025-11-05T12:10:02.656053Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Sub-Saharan Africa Brain Glioma Segmenter", "description": "The Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of gliomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis. This tool was trained on a cohort of patients from Sub-Saharan Africa.", "homepage": "https://segmenter.hope4kids.io/", "biotoolsID": "sub-saharan_africa_brain_glioma_segmenter", "biotoolsCURIE": "biotools:sub-saharan_africa_brain_glioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T11:45:08.078589Z", "lastUpdate": "2025-11-05T11:45:08.081083Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Intercranial Meningioma Segmenter", "description": "The Intercranial Meningioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of intercranial meningiomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://segmenter.hope4kids.io/", "biotoolsID": "intercranial_meningioma_segmenter", "biotoolsCURIE": "biotools:intercranial_meningioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T10:35:32.782850Z", "lastUpdate": "2025-11-05T10:50:57.540837Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Brain Metastasis Segmenter", "description": "The Brain Metastasis Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain metastases in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain metastases in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://segmenter.hope4kids.io/", "biotoolsID": "brain_metastasis_segmenter", "biotoolsCURIE": "biotools:brain_metastasis_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-04T18:24:22.573039Z", "lastUpdate": "2025-11-05T10:50:14.005776Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Brain Glioma Segmenter", "description": "The Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain gliomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain gliomas in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://segmenter.hope4kids.io/", "biotoolsID": "brain_glioma_segmenter", "biotoolsCURIE": "biotools:brain_glioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor", "Developer", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T10:49:02.917891Z", "lastUpdate": "2025-11-05T10:49:02.920603Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pediatric Brain Tumor Segmenter", "description": "The Pediatric Brain Tumor Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of pediatric brain tumors in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric brain tumors in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://segmenter.hope4kids.io/", "biotoolsID": "pediatric_brain_tumor_segmenter", "biotoolsCURIE": "biotools:pediatric_brain_tumor_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-10-28T18:31:05.926498Z", "lastUpdate": "2025-11-05T10:48:42.096715Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIR EVA for EUCAIM", "description": "FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.", "homepage": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "biotoolsID": "fair_eva_4_eucaim", "biotoolsCURIE": "biotools:fair_eva_4_eucaim", "version": [ "EUCAIM_plugin_0.3", "EUCAIM_plugin_0.3.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1052", "term": "URL" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": "python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out" } ], "toolType": [ "Command-line tool", "Web service", "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "type": [ "Repository" ], "note": "Repository for FAIR EVA, without the EUCAIM specific plugin" } ], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "Quick start guide" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "FAIR EVA: Bringing institutional multidisciplinary repositories into the FAIR picture", "abstract": "", "date": "2023-12-01T00:00:00Z", "citationCount": 11, "authors": [], "journal": "Scientific Data" } } ], "credit": [ { "name": "Fernando Aguilar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9462-4831", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor" ], "note": "Creator and devloper of the main package FAIR EVA.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647." }, { "name": "David Rodríguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9160-5106", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": "Developer of the EUCAIM plugin." }, { "name": "Inés Victoria", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0003-7950-3937", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Developer of the EUCAIM plugin." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2025-11-05T10:00:02.994330Z", "editPermission": { "type": "group", "authors": [ "ines.ifca", "davrodgon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HMDB", "description": "Freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.", "homepage": "http://www.hmdb.ca/", "biotoolsID": "hmdb", "biotoolsCURIE": "biotools:hmdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3035", "term": "Structure identifier" }, "format": [ { "uri": "http://edamontology.org/format_1196", "term": "SMILES" } ] }, { "data": { "uri": "http://edamontology.org/data_0982", "term": "Molecule identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0982", "term": "Molecule identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2050", "term": "Molecular property (general)" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0982", "term": "Molecule identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3421", "term": "Surgery" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Perl", "Java" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://hmdb.ca/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://hmdb.ca/downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.hmdb.ca/help", "type": [ "General" ], "note": null }, { "url": "https://hmdb.ca/simple/api", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": null, "pmid": "16302993", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Metabolomics: The principles and potential applications to transplantation", "abstract": "", "date": "2005-01-01T00:00:00Z", "citationCount": 152, "authors": [], "journal": "American Journal of Transplantation" } }, { "doi": null, "pmid": "17202168", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "HMDB: The human metabolome database", "abstract": "", "date": "2007-01-01T00:00:00Z", "citationCount": 2718, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": null, "pmid": "18953024", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "HMDB: A knowledgebase for the human metabolome", "abstract": "", "date": "2009-01-09T00:00:00Z", "citationCount": 1681, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Contact Form", "email": null, "url": "http://feedback.wishartlab.com/?site=hmdb", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-30T22:04:55Z", "lastUpdate": "2025-11-05T08:36:29.657267Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ipaPy2", "description": "Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data.", "homepage": "https://github.com/francescodc87/ipaPy2", "biotoolsID": "ipapy2", "biotoolsCURIE": "biotools:ipapy2", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1086", "term": "Compound identifier" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3370", "term": "Analytical chemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/francescodc87/ipaPy2", "type": [ "Repository" ], "note": null }, { "url": "https://toolshed.g2.bx.psu.edu/view/recetox/suite_ipapy2/63bdc5aee3b7", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/ipaPy2/", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2", "type": "Tool wrapper (Galaxy)", "note": null, "version": null } ], "documentation": [ { "url": "https://bit.ly/ipaPy2README", "type": [ "General" ], "note": null }, { "url": "https://github.com/francescodc87/ipaPy2/blob/main/README.ipynb", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAD455", "pmid": "37490466", "pmcid": "PMC10382385", "type": [], "version": null, "note": null, "metadata": { "title": "IpaPy2: Integrated Probabilistic Annotation (IPA) 2.0-an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data", "abstract": "", "date": "2023-07-01T00:00:00Z", "citationCount": 4, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Rainer Breitling", "email": "rainer.breitling@manchester.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Francesco Del Carratore", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "William Eagles", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Juraj Borka", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2024-01-02T16:37:22.478902Z", "lastUpdate": "2025-11-05T07:17:07.162287Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MatrixQCvis", "description": "shiny-based interactive data quality exploration for omics data.", "homepage": "https://www.bioconductor.org/packages/release/bioc/html/MatrixQCvis.html", "biotoolsID": "matrixqcvis", "biotoolsCURIE": "biotools:matrixqcvis", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.bioconductor.org/packages/release/bioc/html/MatrixQCvis.html", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://bioconda.github.io/recipes/bioconductor-matrixqcvis/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/tnaake/MatrixQCvis/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/release/bioc/manuals/MatrixQCvis/man/MatrixQCvis.pdf", "type": [ "API documentation" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/vignettes/MatrixQCvis/inst/doc/MatrixQCvis.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2021.06.17.448827", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Wolfgang Huber", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Thomas Naake", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7917-5580", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2021-11-06T22:47:59.994136Z", "lastUpdate": "2025-11-05T07:03:25.084499Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "EUCAIM CDM Federated Unbalance Cheker", "description": "EUCAIM CDM Federated Unbalance Checker is a lightweight framework for federating data quality checks across distributed datasets. It enables local computation of key statistics (age, sex, ethnicity) and centralized aggregation to detect imbalances across nodes. Ideal for pre-testing federated analysis pipelines, it provides modular runner and aggregator scripts, with a command-line interface for seamless execution and logging, helping validate dataset representativeness before federated learning or clinical research workflows.", "homepage": "https://gitlab.bsc.es/fl/eucaim-cdm-federated-unbalance", "biotoolsID": "eucaim-cdm-federated-unbalance-cheker", "biotoolsCURIE": "biotools:eucaim-cdm-federated-unbalance-cheker", "version": [ "alfa01" ], "otherID": [], "relation": [ { "biotoolsID": "eetl_toolset", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": "python3 main.py runner -i datasets/ds-1 -o out/stats-d1.json" }, { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": "python3 main.py aggregator -i out/stats-d1.json out/stats-d2.json -o out/agg-12.json" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "eucaim" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.bsc.es/fl/eucaim-cdm-federated-unbalance", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://gitlab.bsc.es/fl/eucaim-cdm-federated-unbalance/-/blob/main/README.md", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez2@bsc.es", "url": "https://carleshf.com/", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null } ], "owner": "chernan3", "additionDate": "2025-11-03T19:58:30.197476Z", "lastUpdate": "2025-11-04T21:20:11.065471Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MsQuality", "description": "Interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.", "homepage": "https://bioconductor.org/packages/MsQuality", "biotoolsID": "msquality", "biotoolsCURIE": "biotools:msquality", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "EMBL" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://github.com/tnaake/MsQuality/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://anaconda.org/bioconda/bioconductor-msquality", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/tnaake/MsQuality/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.posit.co/packages/release/bioc/vignettes/MsQuality/inst/doc/MsQuality.html", "type": [ "User manual" ], "note": null }, { "url": "https://bioconductor.posit.co/packages/release/bioc/manuals/MsQuality/man/MsQuality.pdf", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad618", "pmid": "37812234", "pmcid": "PMC10580266", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data", "abstract": "", "date": "2023-10-01T00:00:00Z", "citationCount": 4, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Wolfgang Huber", "email": "wolfgang.huber@embl.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2024-01-03T22:44:08.911102Z", "lastUpdate": "2025-11-04T20:24:56.422648Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MetCirc", "description": "This tool comprises a workflow to interactively explore metabolomics data by creating MSP or calculating m/z values and the similarity between precursors.", "homepage": "http://bioconductor.org/packages/release/bioc/html/MetCirc.html", "biotoolsID": "metcirc", "biotoolsCURIE": "biotools:metcirc", "version": [ "1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" }, { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tnaake/MetCirc/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/MetCirc_1.0.1.tar.gz", "type": "Source code", "note": null, "version": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/MetCirc.html", "type": "Software package", "note": null, "version": null }, { "url": "https://bioconda.github.io/recipes/bioconductor-metcirc/README.html", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/MetCirc.html", "type": [ "User manual" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/manuals/MetCirc/man/MetCirc.pdf", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx159", "pmid": "28402393", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data", "abstract": "", "date": "2017-08-01T00:00:00Z", "citationCount": 20, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Thomas Naake", "email": "thomasnaake@googlemail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:48Z", "lastUpdate": "2025-11-04T20:10:38.376023Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UM - Automated detection and segmentation NSCLC", "description": "Automated detection and segmentation of non-small cell lung cancer computed tomography images", "homepage": "https://github.com/primakov/DuneAI-Automated-detection-and-segmentation-of-non-small-cell-lung-cancer-computed-tomography-images", "biotoolsID": "automated_detection_and_segmentation_nsclc", "biotoolsCURIE": "biotools:automated_detection_and_segmentation_nsclc", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/s41467-022-30841-3", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Automated detection and segmentation of non-small cell lung cancer computed tomography images", "abstract": "", "date": "2022-12-01T00:00:00Z", "citationCount": 110, "authors": [], "journal": "Nature Communications" } } ], "credit": [], "owner": "sinaamirrajab", "additionDate": "2025-10-31T10:28:34.411099Z", "lastUpdate": "2025-11-04T15:05:08.990137Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UM - RQS 2.0 with RRLs", "description": "Radiomics is a medical imaging analysis tool that supports precision oncology by providing quantitative insights for clinical decision-making. The updated Radiomics Quality Score 2.0 (RQS 2.0) enhances the original RQS framework by integrating concepts of fairness, explainability, quality control, and harmonization, ensuring more rigorous and transparent evaluation of radiomics studies. It also introduces Radiomics Readiness Levels (RRLs)—a nine-stage framework inspired by technology readiness levels—to track progress from research to clinical implementation. Together, RQS 2.0 and RRLs provide a structured path to accelerate the clinical translation of radiomics and advance precision oncology.", "homepage": "https://www.radiomics.world/home", "biotoolsID": "um_rqs_2.0_with_rrls", "biotoolsCURIE": "biotools:um_rqs_2.0_with_rrls", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service" ], "topic": [], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": "Freeware", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.radiomics.world/rqs2", "type": [ "User manual" ], "note": "Framework to establish a structured, step-by-step approach to radiomics research." }, { "url": "https://www.radiomics.world/faq", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/s41571-025-01067-1", "pmid": "40903523", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "Radiomics Quality Score 2.0: towards radiomics readiness levels and clinical translation for personalized medicine", "abstract": "", "date": "2025-11-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Nature Reviews Clinical Oncology" } } ], "credit": [], "owner": "sinaamirrajab", "additionDate": "2025-11-04T15:00:53.996964Z", "lastUpdate": "2025-11-04T15:04:40.394407Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)", "description": "The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files.\n\nStatus : Containerized", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "biotoolsID": "dicom_file_integrity_checker_by_gibi230", "biotoolsCURIE": "biotools:dicom_file_integrity_checker_by_gibi230", "version": [ "2.0.0", "2.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": "docker run -it --rm -v \"<input_path>:/input\" -v \"<output_path>:/output\" dicom_file_integrity_checker:2.1.0 \\\n --config-string '{'QA': {'sequence_selection': ['ALL'], 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}'" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Other" ], "note": "Link to EUCAIM's Harbor" } ], "download": [], "documentation": [ { "url": "https://drive.google.com/file/d/1s8-nVAvSuAGTHWwun4AQcgHtRWclsFg2/view?usp=sharing", "type": [ "General" ], "note": "Pedro-Miguel Martinez-Girones 1,*, Adrian Galiana-Bordera 1, Carina Soler-Pons 1, Ignacio Gomez-Rico-Junquero 1, Ignacio Blanquer-Espert 3, Leonor Cerda-Alberich 1 and Luis Marti-Bonmati 1,2\n1\tBiomedical Imaging Research Group (GIBI230), La Fe Health Research Institute (IIS La Fe), Avenida Fernando Abril Martorell, València, 46026, Spain.\n2\tLa Fe Medical Imaging Department, Avenida Fernando Abril Martorell, València, 46026, Spain.\n3\tComputing Science Department, Universitat Politècnica de València, Cami de Vera s/n, València, 46022, Spain." } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2025-11-04T13:08:53.549989Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaboLights", "description": "Database for Metabolomics experiments and derived information.", "homepage": "http://www.ebi.ac.uk/metabolights/", "biotoolsID": "metabolights", "biotoolsCURIE": "biotools:metabolights", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2091", "term": "Accession" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "EMBL" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://www.ebi.ac.uk/metabolights/index", "type": [ "Service" ], "note": null }, { "url": "https://www.ebi.ac.uk/about/contact/support/metabolights", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.ebi.ac.uk/metabolights/help", "type": [ "General" ], "note": null }, { "url": "https://ebi-metabolights.github.io/guides/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1004", "pmid": "23109552", "pmcid": "PMC3531110", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MetaboLights - An open-access general-purpose repository for metabolomics studies and associated meta-data", "abstract": "", "date": "2013-01-01T00:00:00Z", "citationCount": 544, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "EMBL-EBI Databases", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.ebi.ac.uk/metabolights/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI_Databases", "additionDate": "2015-06-11T13:36:38Z", "lastUpdate": "2025-11-04T10:53:53.142342Z", "editPermission": { "type": "group", "authors": [ "n.m.palmblad@lumc.nl", "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Retip", "description": "Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.\n\nRetip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.\n\nRetip - Retention Time prediction for Metabolomics.\n\nRetip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.", "homepage": "https://www.retip.app", "biotoolsID": "retip", "biotoolsCURIE": "biotools:retip", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3633", "term": "Retention time prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0982", "term": "Molecule identifier" }, "format": [ { "uri": "http://edamontology.org/format_1196", "term": "SMILES" } ] }, { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2087", "term": "Molecular property" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3108", "term": "Experimental measurement" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0982", "term": "Molecule identifier" }, "format": [ { "uri": "http://edamontology.org/format_1196", "term": "SMILES" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" } ], "operatingSystem": [], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://github.com/oloBion/Retip", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/oloBion/pyRetip/tree/master", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.retip.app/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/ACS.ANALCHEM.9B05765", "pmid": "32390414", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics", "abstract": "", "date": "2020-06-02T00:00:00Z", "citationCount": 177, "authors": [], "journal": "Analytical Chemistry" } } ], "credit": [], "owner": "zsmag19", "additionDate": "2021-01-18T09:01:58Z", "lastUpdate": "2025-11-04T10:46:26.117809Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "UM - Precision Medicine Toolbox", "description": "precision-medicine-toolbox is an open-source python package for medical imaging data preparation for data science tasks. This package is aimed to provide a tool to curate the imaging data and to perform exploratory feature analysis.", "homepage": "https://precision-medicine-toolbox.readthedocs.io/en/latest/", "biotoolsID": "precision-medicine-toolbox", "biotoolsCURIE": "biotools:precision-medicine-toolbox", "version": [ "0.2" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://precision-medicine-toolbox.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null }, { "url": "https://precision-medicine-toolbox.readthedocs.io/en/latest/tutorials/", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1016/j.simpa.2023.100508", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Precision-medicine-toolbox: An open-source python package for the quantitative medical image analysis[Formula presented]", "abstract": "", "date": "2023-05-01T00:00:00Z", "citationCount": 6, "authors": [], "journal": "Software Impacts" } } ], "credit": [], "owner": "sinaamirrajab", "additionDate": "2025-10-31T09:55:55.072521Z", "lastUpdate": "2025-11-04T10:44:23.186251Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "recetox-xMSannotator", "description": "Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.", "homepage": "https://github.com/RECETOX/recetox-xMSannotator", "biotoolsID": "recetox-xmsannotator", "biotoolsCURIE": "biotools:recetox-xmsannotator", "version": [ "0.10.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" }, { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3632", "term": "Isotopic distributions calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Metabolomics" ], "link": [], "download": [ { "url": "https://bioconda.github.io/recipes/r-recetox-xmsannotator/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator", "type": "Tool wrapper (Galaxy)", "note": null, "version": null }, { "url": "https://github.com/RECETOX/recetox-xMSannotator", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": null, "pmid": null, "pmcid": "PMC5447360", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "recetox-specdatri", "additionDate": "2023-06-22T14:58:42.302085Z", "lastUpdate": "2025-11-04T10:33:14.526964Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EUCAIM Wizard Tool", "description": "The EUCAIM Wizard Tool performs an analysis of data re-identification risks of imaging and clinical data that follow the EUCAIM CDM. It includes and uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx), by supporting a wide variety of privacy and risk models as well methods for analyzing the usefulness of output data.", "homepage": "https://github.com/cbml-forth/eucaim_wizard_tool", "biotoolsID": "eucaim_wizard_tool", "biotoolsCURIE": "biotools:eucaim_wizard_tool", "version": [ "beta1.0" ], "otherID": [], "relation": [ { "biotoolsID": "arx", "type": "includes" }, { "biotoolsID": "arx", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3283", "term": "Anonymisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_4044", "term": "Data protection" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Java" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cbml-forth/eucaim_wizard_tool", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Aikaterini Nikiforaki", "email": "nikiforakik@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "vkalokyri", "additionDate": "2025-04-30T10:28:37.002350Z", "lastUpdate": "2025-11-04T10:26:14.812762Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MFAssignR", "description": "Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.\n\nUltrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.", "homepage": "https://github.com/skschum/MFAssignR", "biotoolsID": "mfassignr", "biotoolsCURIE": "biotools:mfassignr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://toolshed.g2.bx.psu.edu/view/recetox/suite_mfassignr/114e55a434da", "type": [ "Galaxy service" ], "note": null }, { "url": "https://github.com/skschum/MFAssignR", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/RECETOX/MFAssignR", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://bioconda.github.io/recipes/r-mfassignr/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr", "type": "Tool wrapper (Galaxy)", "note": null, "version": null } ], "documentation": [ { "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/mfassignr/tutorial.html", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1016/J.ENVRES.2020.110114", "pmid": "32866496", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MFAssignR: Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures", "abstract": "", "date": "2020-12-01T00:00:00Z", "citationCount": 91, "authors": [], "journal": "Environmental Research" } } ], "credit": [], "owner": "Niclaskn", "additionDate": "2021-01-18T11:04:22Z", "lastUpdate": "2025-11-04T10:19:55.271318Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "recetox-aplcms", "description": "recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.", "homepage": "https://github.com/RECETOX/recetox-aplcms", "biotoolsID": "recetox-aplcms", "biotoolsCURIE": "biotools:recetox-aplcms", "version": [ "0.11.0" ], "otherID": [], "relation": [ { "biotoolsID": "aplcms", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_3628", "term": "Chromatographic alignment" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3937", "term": "Feature extraction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] }, { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://umsa.cerit-sc.cz/root?tool_id=toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/0.11.0+galaxy1", "type": [ "Galaxy service" ], "note": null }, { "url": "https://github.com/RECETOX/recetox-aplcms", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/RECETOX/recetox-aplcms", "type": "Source code", "note": null, "version": null }, { "url": "https://bioconda.github.io/recipes/r-recetox-aplcms/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms", "type": "Tool wrapper (Galaxy)", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "RECETOX SpecDatRI", "email": null, "url": "https://www.recetox.muni.cz/en/services/data-services-1/spectrometric-data-processing-and-analysis", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer", "Provider", "Primary contact", "Developer" ], "note": null } ], "owner": "recetox-specdatri", "additionDate": "2023-06-16T12:32:16.082467Z", "lastUpdate": "2025-11-04T10:13:54.961114Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Quality Assessment metrics (IQA) for XNAT platform", "description": "Docker images developped at the Euro-BioImaging MED-Hub and National Research Council (CNR) for the XNAT platform hosted by University of Turin. A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of clinical image datasets within the XNAT platform at the scan and subject levels. The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.", "homepage": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "biotoolsID": "image_quality_assessment_metrics_iqa_for_xnat_platform", "biotoolsCURIE": "biotools:image_quality_assessment_metrics_iqa_for_xnat_platform", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python", "MATLAB" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/17goRA76d9vViR93HbhIcjPPxsCdtGhS9/edit?usp=sharing&ouid=114076787312989347088&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Feriel Romdhane", "email": "ferielromdhane@yahoo.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-5854-9341", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Feriel", "additionDate": "2025-10-15T07:25:34.085350Z", "lastUpdate": "2025-11-04T09:45:43.511264Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EUCAIM ETL toolset", "description": "Modular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools.\nContainerized, currently supports input datasets in CSV, JSON, XLSX.", "homepage": "https://scm.cloud-bahiasoftware.es/rpalpal/Eucaim_ETL", "biotoolsID": "eetl_toolset", "biotoolsCURIE": "biotools:eetl_toolset", "version": [ "0.1.1", "0.1.2" ], "otherID": [], "relation": [ { "biotoolsID": "tabular_data_curator", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Windows", "Linux" ], "language": [ "Python", "Java" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [ { "url": "https://scm.cloud-bahiasoftware.es/rpalpal/Eucaim_ETL", "type": [ "Repository" ], "note": "AUTH is provided to EUCAIM members and other stakeholders. This release repository is being used temporarily during the current testing stage." } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "victorsp", "additionDate": "2025-04-24T13:00:12.867477Z", "lastUpdate": "2025-11-04T09:35:56.564173Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Workflow4Metabolomics", "description": "First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data.", "homepage": "https://workflow4metabolomics.org/", "biotoolsID": "workflow4metabolomics", "biotoolsCURIE": "biotools:workflow4metabolomics", "version": [], "otherID": [], "relation": [ { "biotoolsID": "galaxy", "type": "uses" }, { "biotoolsID": "xcms", "type": "uses" }, { "biotoolsID": "camera", "type": "uses" }, { "biotoolsID": "ipo", "type": "uses" }, { "biotoolsID": "profia", "type": "uses" }, { "biotoolsID": "msnbase", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3488", "term": "NMR spectrum" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3834", "term": "mzData" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0982", "term": "Molecule identifier" }, "format": [ { "uri": "http://edamontology.org/format_2035", "term": "Chemical formula format" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" }, { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_3203", "term": "Chromatogram visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": null, "collectionID": [ "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://workflow4metabolomics.usegalaxy.fr", "type": [ "Galaxy service" ], "note": null }, { "url": "https://github.com/workflow4metabolomics", "type": [ "Repository" ], "note": null }, { "url": "http://www.mybiosoftware.com/workflow4metabolomics-v3-metabolomics-data-processing-analysis-and-annotation.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://twitter.com/workflow4metabo", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://workflow4metabolomics.org/howto", "type": [ "General" ], "note": null }, { "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/", "type": [ "Training material" ], "note": null }, { "url": "https://workflow4metabolomics.org/privacy_policy", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btu813", "pmid": "25527831", "pmcid": "PMC4410648", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics", "abstract": "", "date": "2015-05-01T00:00:00Z", "citationCount": 361, "authors": [], "journal": "Bioinformatics" } }, { "doi": "10.1016/j.biocel.2017.07.002", "pmid": "28710041", "pmcid": null, "type": [ "Usage" ], "version": null, "note": "This paper is also available on the open archive HAL: 10.1016/j.biocel.2017.07.002", "metadata": { "title": "Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics", "abstract": "", "date": "2017-12-01T00:00:00Z", "citationCount": 114, "authors": [], "journal": "International Journal of Biochemistry and Cell Biology" } } ], "credit": [ { "name": "Workflow4Metabolomics Team", "email": "contact@workflow4metabolomics.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Maintainer" ], "note": null }, { "name": "IFB - Institut Français de Bioinformatique", "email": null, "url": "https://www.france-bioinformatique.fr/en", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "MetaboHUB - National infrastructure in metabolomics & fluxomics", "email": null, "url": "https://www.metabohub.fr/home.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Franck Giacomoni", "email": "franck.giacomoni@inrae.fr", "url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse", "orcidid": "https://orcid.org/0000-0001-6063-4214", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Gildas Le Corguillé", "email": "lecorguille@sb-roscoff.fr", "url": "http://abims.sb-roscoff.fr", "orcidid": "https://orcid.org/0000-0003-1742-9711", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Marie Tremblay-Franco", "email": null, "url": "https://www6.toulouse.inrae.fr/axiomm", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Yann Guitton", "email": null, "url": "https://www.laberca.org/plateforme-analytique/presentation/", "orcidid": "https://orcid.org/0000-0002-4479-0636", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Etienne A. Thévenot", "email": null, "url": "http://www-list.cea.fr/index.php/en/", "orcidid": "https://orcid.org/0000-0003-1019-4577", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Mélanie Pétéra", "email": null, "url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Christophe Caron", "email": null, "url": "http://abims.sb-roscoff.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Christophe Duperier", "email": null, "url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Jean-François Martin", "email": null, "url": "https://www6.toulouse.inrae.fr/axiomm", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pierrick Roger-Melee", "email": null, "url": "http://www-list.cea.fr/index.php/en/", "orcidid": "https://orcid.org/0000-0001-8177-4873", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Cécile Canlet", "email": null, "url": "https://www6.toulouse.inrae.fr/axiomm", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null }, { "name": "Misharl Monsoor", "email": null, "url": "http://abims.sb-roscoff.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Marion Landi", "email": null, "url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pierre Pericard", "email": null, "url": "http://abims.sb-roscoff.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Alexis Delabrière", "email": null, "url": "http://www-list.cea.fr/index.php/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Sophie Goulitquer", "email": null, "url": "http://www.sb-roscoff.fr/en/research-and-training-centre-marine-biology-and-oceanography/services/technological-core-facilities/mass-spectrometry-core-facility", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "lecorguille", "additionDate": "2017-08-03T19:04:33Z", "lastUpdate": "2025-11-04T09:07:00.548978Z", "editPermission": { "type": "group", "authors": [ "fgiacomoni", "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MS2DeepScore", "description": "MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.", "homepage": "https://github.com/matchms/ms2deepscore", "biotoolsID": "ms2deepscore", "biotoolsCURIE": "biotools:ms2deepscore", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_4039", "term": "MSP" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_4039", "term": "MSP" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3343", "term": "Compound libraries and screening" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/matchms/ms2deepscore", "type": [ "Repository" ], "note": null }, { "url": "https://toolshed.g2.bx.psu.edu/view/recetox/suite_ms2deepscore/2b7360b26610", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore", "type": "Tool wrapper (Galaxy)", "note": null, "version": null }, { "url": "https://github.com/matchms/ms2deepscore", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/ms2deepscore/", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/2021.04.18.440324", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Florian Huber", "email": "f.huber@esciencecenter.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-3535-9406", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-10-11T08:42:43.272159Z", "lastUpdate": "2025-11-04T08:54:50.531589Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CAMERA", "description": "Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.", "homepage": "http://bioconductor.org/packages/release/bioc/html/CAMERA.html", "biotoolsID": "camera", "biotoolsCURIE": "biotools:camera", "version": [ "1.30.0" ], "otherID": [], "relation": [ { "biotoolsID": "workflow4metabolomics", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Metabolomics", "Galaxy" ], "link": [ { "url": "http://msbi.ipb-halle.de/msbi/CAMERA/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/CAMERA_1.30.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/CAMERA.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1021/ac202450g", "pmid": "22111785", "pmcid": "PMC3658281", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets", "abstract": "", "date": "2012-01-03T00:00:00Z", "citationCount": 947, "authors": [], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "Steffen Neumann", "email": "sneumann@ipb-halle.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:44Z", "lastUpdate": "2025-11-04T08:34:26.581536Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "metaMS", "description": "MS-based metabolomics data processing and compound annotation pipeline.", "homepage": "http://bioconductor.org/packages/release/bioc/html/metaMS.html", "biotoolsID": "metams", "biotoolsCURIE": "biotools:metams", "version": [ "1.10.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Metabolomics" ], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/metaMS_1.10.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/metaMS.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jchromb.2014.02.051", "pmid": "24656939", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MetaMS: An open-source pipeline for GC-MS-based untargeted metabolomics", "abstract": "", "date": "2014-09-01T00:00:00Z", "citationCount": 87, "authors": [], "journal": "Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences" } } ], "credit": [ { "name": "Ron Wehrens", "email": "ron.wehrens@gmail.com", "url": null, "orcidid": "http://orcid.org/0000-0002-8798-5599", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:47Z", "lastUpdate": "2025-11-03T16:55:41.956107Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MAW", "description": "Metabolome Annotation Workflow for untargeted tandem mass spectrometry.", "homepage": "https://github.com/zmahnoor14/MAW", "biotoolsID": "maw", "biotoolsCURIE": "biotools:maw", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3643", "term": "Tag-based peptide identification" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/zmahnoor14/MAW-Benchmark", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13321-023-00695-y", "pmid": "36871033", "pmcid": "PMC9985203", "type": [], "version": null, "note": null, "metadata": { "title": "MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry", "abstract": "Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC–MS) to achieve a high-throughput profile of metabolites from complex biological resources, only a small fraction of these metabolites can be annotated with confidence. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds such as in silico generated spectra and molecular networking. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data to further facilitate and automate the complex annotation by combining tandem mass spectrometry (MS2) input data pre-processing, spectral and compound database matching with computational classification, and in silico annotation. MAW takes the LC-MS2 spectra as input and generates a list of putative candidates from spectral and compound databases. The databases are integrated via the R package Spectra and the metabolite annotation tool SIRIUS as part of the R segment of the workflow (MAW-R). The final candidate selection is performed using the cheminformatics tool RDKit in the Python segment (MAW-Py). Furthermore, each feature is assigned a chemical structure and can be imported to a chemical structure similarity network. MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub (https://github.com/zmahnoor14/MAW) The performance of MAW is evaluated on two case studies. MAW can improve candidate ranking by integrating spectral databases with annotation tools like SIRIUS which contributes to an efficient candidate selection procedure. The results from MAW are also reproducible and traceable, compliant with the FAIR guidelines. Taken together, MAW could greatly facilitate automated metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.", "date": "2023-12-01T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Zulfiqar M." }, { "name": "Gadelha L." }, { "name": "Steinbeck C." }, { "name": "Sorokina M." }, { "name": "Peters K." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "Mahnoor Zulfiqar", "email": "mahnoor.zulfiqar@uni-jena.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christoph Steinbeck", "email": "christoph.steinbeck@uni-jena.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Kristian Peters", "email": "kristian.peters@ipb-halle.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Luiz Gadelha", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Maria Sorokina", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2023-08-24T10:15:08.106111Z", "lastUpdate": "2025-11-03T16:47:22.668278Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "El-MAVEN", "description": "Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.", "homepage": "https://github.com/ElucidataInc/ElMaven", "biotoolsID": "El-MAVEN", "biotoolsCURIE": "biotools:El-MAVEN", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElucidataInc/ElMaven", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ElucidataInc/ElMaven/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://elucidatainc.github.io/ElMaven/Downloads/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/ElucidataInc/ElMaven/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://elucidatainc.github.io/ElMaven/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-9236-2_19", "pmid": "31119671", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 106, "authors": [], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": null, "email": "info@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "elmaven@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:14:25Z", "lastUpdate": "2025-11-03T16:47:19.388844Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MSNovelist", "description": "De novo structure generation from mass spectra.", "homepage": "https://github.com/meowcat/MSNovelist", "biotoolsID": "msnovelist", "biotoolsCURIE": "biotools:msnovelist", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_4009", "term": "Small molecule design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "Java" ], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41592-022-01486-3", "pmid": "35637304", "pmcid": "PMC9262714", "type": [], "version": null, "note": null, "metadata": { "title": "MSNovelist: de novo structure generation from mass spectra", "abstract": "© 2022, The Author(s).Current methods for structure elucidation of small molecules rely on finding similarity with spectra of known compounds, but do not predict structures de novo for unknown compound classes. We present MSNovelist, which combines fingerprint prediction with an encoder–decoder neural network to generate structures de novo solely from tandem mass spectrometry (MS2) spectra. In an evaluation with 3,863 MS2 spectra from the Global Natural Product Social Molecular Networking site, MSNovelist predicted 25% of structures correctly on first rank, retrieved 45% of structures overall and reproduced 61% of correct database annotations, without having ever seen the structure in the training phase. Similarly, for the CASMI 2016 challenge, MSNovelist correctly predicted 26% and retrieved 57% of structures, recovering 64% of correct database annotations. Finally, we illustrate the application of MSNovelist in a bryophyte MS2 dataset, in which de novo structure prediction substantially outscored the best database candidate for seven spectra. MSNovelist is ideally suited to complement library-based annotation in the case of poorly represented analyte classes and novel compounds.", "date": "2022-07-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Stravs M.A." }, { "name": "Duhrkop K." }, { "name": "Bocker S." }, { "name": "Zamboni N." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Nicola Zamboni", "email": "zamboni@imsb.biol.ethz.ch", "url": null, "orcidid": "https://orcid.org/0000-0003-1271-1021", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sebastian Böcker", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9304-8091", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Kai Dührkop", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9056-0540", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Michael A. Stravs", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1426-8572", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-05T21:19:03.847868Z", "lastUpdate": "2025-11-03T16:47:18.329938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "peakPantheR", "description": "R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets.", "homepage": "https://phenomecentre.github.io/peakPantheR.github.io/", "biotoolsID": "peakpanther", "biotoolsCURIE": "biotools:peakpanther", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3937", "term": "Feature extraction" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bioconductor.org/packages/peakPantheR/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/phenomecentre/metabotyping-dementia-urine", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/phenomecentre/peakPantheR/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://phenomecentre.github.io/peakPantheR.github.io/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btab433", "pmid": "34125879", "pmcid": "PMC8665750", "type": [], "version": null, "note": null, "metadata": { "title": "Extraction and integration of annotated metabolic features in LC-MS profiling datasets", "abstract": "Summary: Untargeted liquid chromatography-mass spectrometry (LC-MS) profiling assays are capable of measuring thousands of chemical compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC-MS profiling experiments. It takes advantage of chromatographic and spectral databases and prior information of sample matrix composition to generate annotated and interpretable metabolic phenotypic datasets and power workflows for real-time data quality assessment.", "date": "2021-12-15T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Wolfer A.M." }, { "name": "Correia G.D.S." }, { "name": "Sands C.J." }, { "name": "Camuzeaux S." }, { "name": "Yuen A.H.Y." }, { "name": "Chekmeneva E." }, { "name": "Takats Z." }, { "name": "Pearce J.T.M." }, { "name": "Lewis M.R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Arnaud M Wolfer", "email": "phenomecentre@imperial.ac.uk", "url": null, "orcidid": "https://orcid.org/0000-0001-5856-3218", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Goncalo Correia", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8271-9294", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jake Pearce", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Caroline Sands", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2021-10-28T20:02:19.622064Z", "lastUpdate": "2025-11-03T16:47:17.380949Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PeakForest", "description": "A multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.", "homepage": "https://peakforest.org", "biotoolsID": "peakforest", "biotoolsCURIE": "biotools:peakforest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java", "JavaScript" ], "license": "Other", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/peakforest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/S11306-022-01899-3", "pmid": "35699774", "pmcid": "PMC9197906", "type": [], "version": null, "note": null, "metadata": { "title": "PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management", "abstract": "© 2022, The Author(s).Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. Methods: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. Results: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. Conclusion: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest.", "date": "2022-06-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Paulhe N." }, { "name": "Canlet C." }, { "name": "Damont A." }, { "name": "Peyriga L." }, { "name": "Durand S." }, { "name": "Deborde C." }, { "name": "Alves S." }, { "name": "Bernillon S." }, { "name": "Berton T." }, { "name": "Bir R." }, { "name": "Bouville A." }, { "name": "Cahoreau E." }, { "name": "Centeno D." }, { "name": "Costantino R." }, { "name": "Debrauwer L." }, { "name": "Delabriere A." }, { "name": "Duperier C." }, { "name": "Emery S." }, { "name": "Flandin A." }, { "name": "Hohenester U." }, { "name": "Jacob D." }, { "name": "Joly C." }, { "name": "Jousse C." }, { "name": "Lagree M." }, { "name": "Lamari N." }, { "name": "Lefebvre M." }, { "name": "Lopez-Piffet C." }, { "name": "Lyan B." }, { "name": "Maucourt M." }, { "name": "Migne C." }, { "name": "Olivier M.-F." }, { "name": "Rathahao-Paris E." }, { "name": "Petriacq P." }, { "name": "Pinelli J." }, { "name": "Roch L." }, { "name": "Roger P." }, { "name": "Roques S." }, { "name": "Tabet J.-C." }, { "name": "Tremblay-Franco M." }, { "name": "Traikia M." }, { "name": "Warnet A." }, { "name": "Zhendre V." }, { "name": "Rolin D." }, { "name": "Jourdan F." }, { "name": "Thevenot E." }, { "name": "Moing A." }, { "name": "Jamin E." }, { "name": "Fenaille F." }, { "name": "Junot C." }, { "name": "Pujos-Guillot E." }, { "name": "Giacomoni F." } ], "journal": "Metabolomics" } } ], "credit": [ { "name": "Franck Giacomoni", "email": "Franck.Giacomoni@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-6063-4214", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Estelle Pujos-Guillot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christophe Junot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "François Fenaille", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-04T23:10:37.868759Z", "lastUpdate": "2025-11-03T16:47:12.424836Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BUDDY", "description": "Open-source cheminformatic software platform developed for MS-based metabolomics research.", "homepage": "https://github.com/HuanLab/BUDDY", "biotoolsID": "buddy", "biotoolsCURIE": "biotools:buddy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" }, { "uri": "http://edamontology.org/operation_2425", "term": "Optimisation and refinement" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C#" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://philipbear.github.io/BUDDY_Metabolomics", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41592-023-01850-x", "pmid": "37055660", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "BUDDY: molecular formula discovery via bottom-up MS/MS interrogation", "abstract": "A substantial fraction of metabolic features remains undetermined in mass spectrometry (MS)-based metabolomics, and molecular formula annotation is the starting point for unraveling their chemical identities. Here we present bottom-up tandem MS (MS/MS) interrogation, a method for de novo formula annotation. Our approach prioritizes MS/MS-explainable formula candidates, implements machine-learned ranking and offers false discovery rate estimation. Compared with the mathematically exhaustive formula enumeration, our approach shrinks the formula candidate space by 42.8% on average. Method benchmarking on annotation accuracy was systematically carried out on reference MS/MS libraries and real metabolomics datasets. Applied on 155,321 recurrent unidentified spectra, our approach confidently annotated >5,000 novel molecular formulae absent from chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global optimization to refine formula annotations while revealing peak interrelationships. This approach allowed the systematic annotation of 37 fatty acid amide molecules in human fecal data. All bioinformatics pipelines are available in a standalone software, BUDDY (https://github.com/HuanLab/BUDDY)", "date": "2023-06-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Xing S." }, { "name": "Shen S." }, { "name": "Xu B." }, { "name": "Li X." }, { "name": "Huan T." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Tao Huan", "email": "thuan@chem.ubc.ca", "url": null, "orcidid": "http://orcid.org/0000-0001-6295-2435", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2023-12-01T15:46:02.196263Z", "lastUpdate": "2025-11-03T16:45:48.375514Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "tidyMass", "description": "An Object-oriented Reproducible Analysis Framework for LC-MS Data.", "homepage": "https://www.tidymass.org/", "biotoolsID": "tidymass", "biotoolsCURIE": "biotools:tidymass", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tidymass", "type": [ "Repository" ], "note": null }, { "url": "https://tidymass.tidymass.org/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/jaspershen/tidymass-case-study", "type": "Container file", "note": null, "version": null }, { "url": "https://hub.docker.com/r/jaspershen/tidymass", "type": "Container file", "note": null, "version": null }, { "url": "https://www.tidymass.org/start/tidymass_docker/", "type": "Container file", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1038/s41467-022-32155-w", "pmid": "35902589", "pmcid": "PMC9334349", "type": [], "version": null, "note": null, "metadata": { "title": "TidyMass an object-oriented reproducible analysis framework for LC–MS data", "abstract": "Reproducibility, traceability, and transparency have been long-standing issues for metabolomics data analysis. Multiple tools have been developed, but limitations still exist. Here, we present the tidyMass project (https://www.tidymass.org/) a comprehensive R-based computational framework that can achieve the traceable, shareable, and reproducible workflow needs of data processing and analysis for LC-MS-based untargeted metabolomics. TidyMass is an ecosystem of R packages that share an underlying design philosophy, grammar, and data structure, which provides a comprehensive, reproducible, and object-oriented computational framework. The modular architecture makes tidyMass a highly flexible and extensible tool, which other users can improve and integrate with other tools to customize their own pipeline.", "date": "2022-12-01T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Shen X." }, { "name": "Yan H." }, { "name": "Wang C." }, { "name": "Gao P." }, { "name": "Johnson C.H." }, { "name": "Snyder M.P." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Caroline H. Johnson", "email": "caroline.johnson@yale.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Michael P. Snyder", "email": "mpsnyder@stanford.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiaotao Shen", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-9608-9964", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Hong Yan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-11-25T21:43:37.501728Z", "lastUpdate": "2025-11-03T16:45:44.856713Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "GNPS", "description": "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.", "homepage": "https://gnps.ucsd.edu/", "biotoolsID": "gnps", "biotoolsCURIE": "biotools:gnps", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3637", "term": "Spectral counting" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [], "language": [], "license": "Other", "collectionID": [], "maturity": null, "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://groups.google.com/forum/#!forum/molecular_networking_bug_reports", "type": [ "Discussion forum" ], "note": null } ], "download": [], "documentation": [ { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/", "type": [ "General" ], "note": null }, { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/quickstart/", "type": [ "Quick start guide" ], "note": null }, { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/api/", "type": [ "API documentation" ], "note": null }, { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/faq/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/NBT.3597", "pmid": "27504778", "pmcid": "PMC5321674", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking", "abstract": "© 2016 Nature America, Inc. All rights reserved.The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu) an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.", "date": "2016-09-08T00:00:00Z", "citationCount": 1024, "authors": [ { "name": "Wang M." }, { "name": "Carver J.J." }, { "name": "Phelan V.V." }, { "name": "Sanchez L.M." }, { "name": "Garg N." }, { "name": "Peng Y." }, { "name": "Nguyen D.D." }, { "name": "Watrous J." }, { "name": "Kapono C.A." }, { "name": "Luzzatto-Knaan T." }, { "name": "Porto C." }, { "name": "Bouslimani A." }, { "name": "Melnik A.V." }, { "name": "Meehan M.J." }, { "name": "Liu W.-T." }, { "name": "Crusemann M." }, { "name": "Boudreau P.D." }, { "name": "Esquenazi E." }, { "name": "Sandoval-Calderon M." }, { "name": "Kersten R.D." }, { "name": "Pace L.A." }, { "name": "Quinn R.A." }, { "name": "Duncan K.R." }, { "name": "Hsu C.-C." }, { "name": "Floros D.J." }, { "name": "Gavilan R.G." }, { "name": "Kleigrewe K." }, { "name": "Northen T." }, { "name": "Dutton R.J." }, { "name": "Parrot D." }, { "name": "Carlson E.E." }, { "name": "Aigle B." }, { "name": "Michelsen C.F." }, { "name": "Jelsbak L." }, { "name": "Sohlenkamp C." }, { "name": "Pevzner P." }, { "name": "Edlund A." }, { "name": "McLean J." }, { "name": "Piel J." }, { "name": "Murphy B.T." }, { "name": "Gerwick L." }, { "name": "Liaw C.-C." }, { "name": "Yang Y.-L." }, { "name": "Humpf H.-U." }, { "name": "Maansson M." }, { "name": "Keyzers R.A." }, { "name": "Sims A.C." }, { "name": "Johnson A.R." }, { "name": "Sidebottom A.M." }, { "name": "Sedio B.E." }, { "name": "Klitgaard A." }, { "name": "Larson C.B." }, { "name": "Boya C.A.P." }, { "name": "Torres-Mendoza D." }, { "name": "Gonzalez D.J." }, { "name": "Silva D.B." }, { "name": "Marques L.M." }, { "name": "Demarque D.P." }, { "name": "Pociute E." }, { "name": "O'Neill E.C." }, { "name": "Briand E." }, { "name": "Helfrich E.J.N." }, { "name": "Granatosky E.A." }, { "name": "Glukhov E." }, { "name": "Ryffel F." }, { "name": "Houson H." }, { "name": "Mohimani H." }, { "name": "Kharbush J.J." }, { "name": "Zeng Y." }, { "name": "Vorholt J.A." }, { "name": "Kurita K.L." }, { "name": "Charusanti P." }, { "name": "McPhail K.L." }, { "name": "Nielsen K.F." }, { "name": "Vuong L." }, { "name": "Elfeki M." }, { "name": "Traxler M.F." }, { "name": "Engene N." }, { "name": "Koyama N." }, { "name": "Vining O.B." }, { "name": "Baric R." }, { "name": "Silva R.R." }, { "name": "Mascuch S.J." }, { "name": "Tomasi S." }, { "name": "Jenkins S." }, { "name": "Macherla V." }, { "name": "Hoffman T." }, { "name": "Agarwal V." }, { "name": "Williams P.G." }, { "name": "Dai J." }, { "name": "Neupane R." }, { "name": "Gurr J." }, { "name": "Rodriguez A.M.C." }, { "name": "Lamsa A." }, { "name": "Zhang C." }, { "name": "Dorrestein K." }, { "name": "Duggan B.M." }, { "name": "Almaliti J." }, { "name": "Allard P.-M." }, { "name": "Phapale P." }, { "name": "Nothias L.-F." }, { "name": "Alexandrov T." }, { "name": "Litaudon M." }, { "name": "Wolfender J.-L." }, { "name": "Kyle J.E." }, { "name": "Metz T.O." }, { "name": "Peryea T." }, { "name": "Nguyen D.-T." }, { "name": "VanLeer D." }, { "name": "Shinn P." }, { "name": "Jadhav A." }, { "name": "Muller R." }, { "name": "Waters K.M." }, { "name": "Shi W." }, { "name": "Liu X." }, { "name": "Zhang L." }, { "name": "Knight R." }, { "name": "Jensen P.R." }, { "name": "Palsson B.O." }, { "name": "Pogliano K." }, { "name": "Linington R.G." }, { "name": "Gutierrez M." }, { "name": "Lopes N.P." }, { "name": "Gerwick W.H." }, { "name": "Moore B.S." }, { "name": "Dorrestein P.C." }, { "name": "Bandeira N." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Mingxun Wang", "email": "miw023@ucsd.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:04:08Z", "lastUpdate": "2025-11-03T16:45:43.961672Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CliqueMS", "description": "Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.", "homepage": "https://github.com/osenan/cliqueMS", "biotoolsID": "CliqueMS", "biotoolsCURIE": "biotools:CliqueMS", "version": [ "0.3.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R", "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/osenan/cliqueMS/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://cran.r-project.org/src/contrib/Archive/cliqueMS/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/osenan/cliqueMS/blob/master/vignettes/annotate_features.Rmd", "type": [ "Training material" ], "note": "Tutorial material" } ], "publication": [ { "doi": "10.1093/bioinformatics/btz207", "pmid": "30903689", "pmcid": "PMC6792096", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network", "abstract": "The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample.Results: Here, we introduce CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is based on the similarity between coelution profiles and therefore, as opposed to most methods, allows for the annotation of a single spectrum. Furthermore, CliqueMS improves upon the state of the art in several dimensions: (i) it uses a more discriminatory feature similarity metric; (ii) it treats the similarities between features in a transparent way by means of a simple generativemodel; (iii) it uses a well-grounded maximum likelihood inference approach to group features; (iv) it uses empirical adduct frequencies to identify the parental mass and (v) it deals more flexibly with the identification of the parental mass by proposing and ranking alternative annotations. We validate our approach with simple mixtures of standards and with real complex biological samples. CliqueMS reduces the thousands of features typically obtained in complex samples to hundreds of metabolites, and it is able to correctly annotate more metabolites and adducts from a single spectrum than available tools.", "date": "2019-10-15T00:00:00Z", "citationCount": 48, "authors": [ { "name": "Senan O." }, { "name": "Aguilar-Mogas A." }, { "name": "Navarro M." }, { "name": "Capellades J." }, { "name": "Noon L." }, { "name": "Burks D." }, { "name": "Yanes O." }, { "name": "Guimera R." }, { "name": "Sales-Pardo M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Oriol Senan", "email": "oriol.senan@urv.cat", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Ruta", "additionDate": "2019-07-04T14:05:39Z", "lastUpdate": "2025-11-03T16:44:03.166147Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NeatMS", "description": "NeatMS is an open source python package for untargeted LCMS signal labelling and filtering. NeatMS enables automated filtering of false positive MS peaks reported by commonly used LCMS data processing pipelines. NeatMS relies on neural network based classification.", "homepage": "https://anaconda.org/bioconda/neatms", "biotoolsID": "neatms", "biotoolsCURIE": "biotools:neatms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bihealth/NeatMS", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://neatms.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1021/ACS.ANALCHEM.1C02220", "pmid": "35290737", "pmcid": "PMC8969107", "type": [], "version": null, "note": null, "metadata": { "title": "Deep Learning-Assisted Peak Curation for Large-Scale LC-MS Metabolomics", "abstract": "© 2022 American Chemical Society. All rights reserved.Available automated methods for peak detection in untargeted metabolomics suffer from poor precision. We present NeatMS, which uses machine learning based on a convoluted neural network to reduce the number and fraction of false peaks. NeatMS comes with a pre-trained model representing expert knowledge in the differentiation of true chemical signal from noise. Furthermore, it provides all necessary functions to easily train new models or improve existing ones by transfer learning. Thus, the tool improves peak curation and contributes to the robust and scalable analysis of large-scale experiments. We show how to integrate it into different liquid chromatography-mass spectrometry (LC-MS) analysis workflows, quantify its performance, and compare it to various other approaches. NeatMS software is available as open source on github under permissive MIT license and is also provided as easy-to-install PyPi and Bioconda packages.", "date": "2022-03-29T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Gloaguen Y." }, { "name": "Kirwan J.A." }, { "name": "Beule D." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "Dieter Beule", "email": "dieter.beule@bih-charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Yoann Gloaguen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0493-8592", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jennifer A. Kirwan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-07-06T15:00:55.171504Z", "lastUpdate": "2025-11-03T16:32:44.163513Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "UmetaFlow", "description": "Untargeted metabolomics workflow for high-throughput data processing and analysis.", "homepage": "https://github.com/biosustain/snakemake_UmetaFlow", "biotoolsID": "umetaflow", "biotoolsCURIE": "biotools:umetaflow", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/biosustain/pyOpenMS_UmetaFlow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13321-023-00724-w", "pmid": "37173725", "pmcid": "PMC10176759", "type": [], "version": null, "note": null, "metadata": { "title": "UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis", "abstract": "Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC–MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. We anticipate that UmetaFlow will provide a useful platform for the interpretation of large metabolomics datasets. Graphical Abstract: [Figure not available: see fulltext.]", "date": "2023-12-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Kontou E.E." }, { "name": "Walter A." }, { "name": "Alka O." }, { "name": "Pfeuffer J." }, { "name": "Sachsenberg T." }, { "name": "Mohite O.S." }, { "name": "Nuhamunada M." }, { "name": "Kohlbacher O." }, { "name": "Weber T." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "Tilmann Weber", "email": "tiwe@biosustain.dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2024-01-02T02:11:50.145026Z", "lastUpdate": "2025-11-03T16:16:27.787938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }