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It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. 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Refines predictions using rule-based heuristics for T2W, DWI and ADC.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-autoproseq", "biotoolsID": "auto-prostate-sequence-classifier", "biotoolsCURIE": "biotools:auto-prostate-sequence-classifier", "version": [ "v0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "The input can be provided as a DICOM dataset (which will require --dicom-recursion, details below or in the documentation) or as a single DICOM study. This command will print a CSV with 5 columns: i) patient_id, ii) study_uid, iii) series_uid, iv) classification from the XGBoost model, v) classification after heuristics-based corrections.\nThe sequence classification is performed between T2W, DWI, ADC, DCE or others. The provided <dicom-recursion> refers to the number of folders until a DICOM series is found. So if the provided input is a patient folder with nested studies with nested series, the level of DICOM recursion should be 2. If the provided input is a directory with patient folders, the level of DICOM recursion should be 3.", "cmd": "docker run -v <dir-with-dicom>:/data harbor.eucaim.cancerimage.eu/processing-tools/champ-autoproseq --dicom_recursion <dicom-recursion> --input_paths /data" } ], "toolType": [ "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CCIG-Champalimaud/metadata-classification", "type": [ "Repository" ], "note": "Repository containing code, README and additional usage information for this tool." } ], "download": [], "documentation": [ { "url": "https://github.com/CCIG-Champalimaud/metadata-classification", "type": [ "Other" ], "note": "Repository containing the code, README and additional information on how to run the tool. If used as an API (when integrated with Orthanc or DICOM-web), the documentation is available upon launching the API at <api-url>/docs." } ], "publication": [ { "doi": "10.1186/s13244-025-01938-2", "pmid": "40146375", "pmcid": "PMC12187622", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automatic sequence identification in multicentric prostate multiparametric MRI datasets for clinical machine-learning", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Insights into Imaging" } } ], "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", "Maintainer" ], "note": null }, { "name": "Nikolaos Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "josegcpa", "additionDate": "2025-12-02T17:37:57.215347Z", "lastUpdate": "2025-12-03T09:27:04.489071Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "gc-meox-tms", "description": "This package performs in-silico MeOX + TMS derivatization (as described e.g. in https://doi.org/10.1021/acs.analchem.7b01010):\n\nMethoximation: ketone R(C=O)R' and aldehyde (-HC=O) carbonyl groups are substituted with -C=NOCH3\nTrimethylsilylation: the acidic hydrogen in -OH, -SH, -COOH, -NH2, -NHR, =NH, the hydrogen is substituted with -Si(CH3)3 The substitution doesn't always have to happen; its probability is currently hardcoded in the package. Typically, multiple substitution attempts are run on each input molecule, and all distinct results are gathered.\nKnown limitation is methoximation on cycles which should be broken. This is not implemented yet.", "homepage": "https://github.com/RECETOX/gc-meox-tms", "biotoolsID": "gc-meox-tms", "biotoolsCURIE": "biotools:gc-meox-tms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0231", "term": "Sequence editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "note": "Produces MeOX/TMS derivatives of given compounds", "cmd": "add_derivatization_groups()" } ], "toolType": [ "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_3370", "term": "Analytical chemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://github.com/RECETOX/gc-meox-tms", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/RECETOX/gc-meox-tms/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/RECETOX/gc-meox-tms.git", "type": "Software package", "note": null, "version": "v1.0.1" } ], "documentation": [ { "url": "https://github.com/RECETOX/gc-meox-tms/blob/master/README.md", "type": [ "Installation instructions", "Command-line options" ], "note": null }, { "url": "https://github.com/RECETOX/gc-meox-tms/blob/master/example/derivatization.ipynb", "type": [ "Quick start guide", "Training material" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.analchem.7b01010", "pmid": "28520403", "pmcid": null, "type": [], "version": null, "note": "The package is based on this publication", "metadata": { "title": "Integrated Strategy for Unknown EI-MS Identification Using Quality Control Calibration Curve, Multivariate Analysis, EI-MS Spectral Database, and Retention Index Prediction", "abstract": "", "date": "2017-06-20T00:00:00Z", "citationCount": 44, "authors": [], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "RECETOX SpecDatRI", "email": null, "url": "https://www.recetox.muni.cz/en/services/data-services-2/spectrometric-data-processing-and-analysis", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Maintainer", "Provider", "Primary contact", "Developer" ], "note": null } ], "owner": "Ondrej_Bucek", "additionDate": "2025-11-28T17:29:53.564906Z", "lastUpdate": "2025-11-28T17:42:43.031944Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "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). 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This tool was trained on a cohort of patients from Sub-Saharan Africa.", "homepage": "https://github.com/BIT-UPM/EUCAIM/sub_saharan_africa_brain_glioma_segmenter", "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": [ "Web application", "Workflow", "Command-line tool" ], "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": "2025-11-28T13:57:16.132700Z", "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). 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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://github.com/BIT-UPM/EUCAIM/brain_glioma_segmenter", "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": [ "Workflow", "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "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": "2025-11-28T13:56:29.777759Z", "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://github.com/BIT-UPM/EUCAIM/pediatric_brain_tumor_segmenter", "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": [ "Web application", "Workflow", "Command-line tool" ], "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-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": "2025-11-28T13:55:19.273705Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "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://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-prostate-zone-segmentation", "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. This should also be used as documentation." }, { "url": "https://docs.google.com/spreadsheets/d/1bcdhs9Xg2MxAH0WDGz08SjEVMFr3e-TP/edit?usp=sharing&ouid=111102743696297094705&rtpof=true&sd=true", "type": [ "Other" ], "note": "The EUCAIM model card for this model, containing details on model training, data and libraries." } ], "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": "2025-11-28T12:18:55.232382Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "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: Deployed", "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", "2.1.1" ], "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_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "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_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Holders (ingestion-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n -v \"<config_path>:/config\" \\\n harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest" }, { "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" } ] } ], "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_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Users (processing-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest \\\n /app/entrypoint.sh --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": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "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": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Holders" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Users" } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": "Container file", "note": "EUCAIM user needed", "version": "2.1.0" } ], "documentation": [ { "url": "https://drive.google.com/file/d/1s8-nVAvSuAGTHWwun4AQcgHtRWclsFg2/view?usp=sharing", "type": [ "User manual" ], "note": null }, { "url": "https://drive.google.com/file/d/1pO_td7uvlsFWy6AZi8AOq3__hm4L2xSv/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "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": "2025-11-27T13:23:38.501118Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FTAG-Finder", "description": "Families and TAG Finder: a Snakemake workflow to identify gene families and detect Tandemly Arrayed Genes.", "homepage": "https://gitlab.com/sortion/FTAG-Finder", "biotoolsID": "ftag-finder", "biotoolsCURIE": "biotools:ftag-finder", "version": [ "0.1.0" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "mmseqs2", "type": "uses" }, { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "mcl", "type": "uses" } ], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "AWK", "C", "Bash", "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/sortion/FTAG-Finder", "type": [ "Repository" ], "note": null }, { "url": "https://gitlab.com/sortion/FTAG-Finder/-/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://gitlab.com/sortion/FTAG-Finder/-/releases", "type": "Downloads page", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "Carène Rizzon", "email": null, "url": "http://www.math-evry.cnrs.fr/members/crizzon/welcome", "orcidid": "https://orcid.org/0000-0003-1194-4130", "gridid": null, "rorid": "03jca6281", "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Samuel Ortion", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0001-0971-497X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "sortion", "additionDate": "2025-11-27T10:42:10.165590Z", "lastUpdate": "2025-11-27T10:42:10.168319Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "South Green Genome Hubs", "description": "The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).", "homepage": "https://banana-genome-hub.southgreen.fr/", "biotoolsID": "South_Green_Genome_Hubs", "biotoolsCURIE": "biotools:South_Green_Genome_Hubs", "version": [], "otherID": [], "relation": [ { "biotoolsID": "tripal", "type": "uses" }, { "biotoolsID": "banana_genome_hub", "type": "includes" }, { "biotoolsID": "coffee_genome_hub", "type": "includes" }, { "biotoolsID": "cocoa_genome_hub", "type": "includes" }, { "biotoolsID": "rice_genome_hub", "type": "includes" }, { "biotoolsID": "sugarcane_genome_hub", "type": "includes" }, { "biotoolsID": "southgreen", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [], "language": [ "JavaScript", "PHP" ], "license": "GPL-2.0", "collectionID": [ "Genome Hub" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data", "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/SouthGreenPlatform/genomehubs", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://banana-genome-hub.southgreen.fr/content/term-service", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/database/bat035", "pmid": "23707967", "pmcid": "PMC3662865", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The banana genome hub", "abstract": "", "date": "2013-12-01T00:00:00Z", "citationCount": 150, "authors": [], "journal": "Database" } }, { "doi": "10.1093/nar/gku1108", "pmid": "25392413", "pmcid": "PMC4383925", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The coffee genome hub: A resource for coffee genomes", "abstract": "", "date": "2015-01-28T00:00:00Z", "citationCount": 52, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/hr/uhac221", "pmid": "36479579", "pmcid": "PMC9720444", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The banana genome hub: a community database for genomics in the Musaceae", "abstract": "", "date": "2022-01-01T00:00:00Z", "citationCount": 29, "authors": [], "journal": "Horticulture Research" } }, { "doi": "10.1016/j.xplc.2022.100330", "pmid": "35617961", "pmcid": "PMC9482989", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly", "abstract": "", "date": "2022-09-12T00:00:00Z", "citationCount": 26, "authors": [], "journal": "Plant Communications" } } ], "credit": [ { "name": "Gaetan Droc", "email": "droc@cirad.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Provider", "Support" ], "note": null }, { "name": "Alexis Dereeper", "email": "alexis.dereeper@ird.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Mathieu Rouard", "email": "m.rouard@cgiar.org", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Maintainer", "Support" ], "note": null }, { "name": "Valentin Guignon", "email": "v.guignon@cgiar.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Chrisitine Tranchant", "email": "christine.tranchant@ird.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Stéphanie Bocs", "email": "stephanie.sidibe-bocs@cirad.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "mrouard", "additionDate": "2020-02-26T09:24:43Z", "lastUpdate": "2025-11-27T09:14:28.500250Z", "editPermission": { "type": "group", "authors": [ "gdroc", "Droc" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)", "description": "The tool is designed to perform radiomics harmonization on large and heterogeneous datasets, where the risk of over-harmonization is present. Instead of directly applying harmonization based on predefined batch labels, the tool first identifies groups of batches that share similar characteristics through clustering of the radiomics data. It then performs harmonization using these cluster-derived labels. The tool allows the harmonization of radiomics variables using two methods: (1) original ComBat (Rabinovic, 2007) method, where each original batch group is considered for the harmonization process and (2) cluster-based ComBat method, where batch groups with similar radiomics characteristics form clusters and the latter are being considered for the harmonization process.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab", "biotoolsID": "cluster_based_harmonization", "biotoolsCURIE": "biotools:cluster_based_harmonization", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3835", "term": "TIDE TXT" } ] } ], "note": null, "cmd": "docker run --rm --cpus CPUS -v input_path:/input -v output_path:/output -v config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0 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"note": null, "cmd": "docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0 --file_path /input/data.xlsx --identifier patient_id --start_col original_shape_Elongation --end_col lbp-3D-k_ngtdm_Strength --batch_col software_versions --output_dir /output/results --min_clusters 2 --max_clusters 100 --results full --approach soft --small_groups merge" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" } ], "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://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.google.com/file/d/1yWahAtCa5xUJesCqDws9X23coXpqKY5k/view?usp=drive_link", "type": [ "User manual" ], "note": null }, { "url": "https://drive.google.com/file/d/1UBOWOx6cNV2Ih2D8FZXMbfA-oF4rS0mz/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Aikaterini Vraka", "email": "aikaterini_vraka@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-5984-904X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martínez-Gironés", "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", "Support" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T10:41:57.535794Z", "lastUpdate": "2025-11-25T15:55:34.025556Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MADORA", "description": "A web application for processing and visualization of statistics for bone marrow donors registry - especially statistics of donors, executed searches for suitable donor, the typing and harvests before transplantation.", "homepage": "https://cds-madora.zcu.cz/", "biotoolsID": 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"orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "TA CR", "email": null, "url": "https://www.tacr.cz/index.php/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Daniel Georgiev", "email": "georgiev@ntis.zcu.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Daniel Georgiev", "email": "georgiev@ntis.zcu.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": 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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 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The database contains spectra from EI‐MS, fast atom bombardment MS, electrospray ionization (ESI)‐MSn data of thousands of authentic standards, EI‐MS and other‐MS data of thousands of volatile natural and synthetic compounds, and ESI‐MS2 data of synthetic drugs contributed by research groups worldwide. ESI‐MS2 data were analyzed under nonstandardized, independent experimental conditions. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS2 data. 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The database contains 605 electron-ionizationmass spectrometry(EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MSn data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10 286 volatile natural and synthetic compounds, and 3045 ESI-MS2 data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI-MS 2 data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass-to-charge ratio are optimized to the ESI-MS2 data. MassBank also provides a merged spectrum for each compound prepared bymerging the analyzed ESI-MS2 data on an identical compound under different collision-induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21-23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data. Copyright © 2010 John Wiley & Sons, Ltd.", "date": "2010-01-01T00:00:00Z", "citationCount": 1747, "authors": [ { "name": "Horai H." }, { "name": "Arita M." }, { "name": "Kanaya S." }, { "name": "Nihei Y." }, { "name": "Ikeda T." }, { "name": "Suwa K." }, { "name": "Ojima Y." }, { "name": "Tanaka K." }, { "name": "Tanaka S." }, { "name": "Aoshima K." }, { "name": "Oda Y." }, { "name": "Kakazu Y." }, { "name": "Kusano M." }, { "name": "Tohge T." }, { "name": "Matsuda F." }, { "name": "Sawada Y." }, { "name": "Hirai M.Y." }, { "name": "Nakanishi H." }, { "name": "Ikeda K." }, { "name": "Akimoto N." }, { "name": "Maoka T." }, { "name": "Takahashi H." }, { "name": "Ara T." }, { "name": "Sakurai N." }, { "name": "Suzuki H." }, { "name": "Shibata D." }, { "name": "Neumann S." }, { "name": "Iida T." }, { "name": "Tanaka K." }, { "name": "Funatsu K." }, { "name": "Matsuura F." }, { "name": "Soga T." }, { "name": "Taguchi R." }, { "name": "Saito K." }, { "name": "Nishioka T." } ], "journal": "Journal of Mass Spectrometry" } } ], "credit": [ { "name": "The MassBank Project", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Developer" ], "note": "Funded by JST-BIRD 2006-2010" }, { "name": "de.NBI MASH", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/501100002347", "typeEntity": "Project", "typeRole": [], "note": "Funding under FKZ 031L0107" }, { "name": "NORMAN Association", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "sneumann", "additionDate": "2020-09-23T13:04:28Z", "lastUpdate": "2025-11-03T16:47:10.013373Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TEtranscripts", "description": "TEtranscripts is a software package for including transposable elements in differential expression analysis of RNA-seq datasets. 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It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.", "homepage": "https://github.com/hgb-bin-proteomics/MSAnnika", "biotoolsID": "ms_annika", "biotoolsCURIE": "biotools:ms_annika", "version": [ "Proteome Discoverer 3.2: MS Annika 3.0 v3.0.7", "Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7", "Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fix", "Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3", "Proteome Discoverer 2.4: MS Annika v1.0.0", "Proteome Discoverer 2.3: MS Annika v1.0.0" ], "otherID": [], "relation": [ { "biotoolsID": "ms_amanda", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3755", "term": "PTM localisation" }, { "uri": "http://edamontology.org/operation_3645", "term": "PTM identification" }, { "uri": 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"Journal of Proteome Research" } }, { "doi": "10.1038/s42004-024-01386-x", "pmid": "39702463", "pmcid": "PMC11659399", "type": [ "Primary" ], "version": "3.0", "note": "MS Annika 3.0 for non-cleavable crosslink identification", "metadata": { "title": "Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex", "abstract": "", "date": "2024-12-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Communications Chemistry" } } ], "credit": [ { "name": "Viktoria Dorfer", "email": "viktoria.dorfer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0000-0002-5332-5701", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Micha Birklbauer", "email": "micha.birklbauer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0009-0005-1051-179X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "michabirklbauer", "additionDate": "2023-07-26T14:40:01.768324Z", "lastUpdate": "2025-10-26T02:38:48.643054Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SHAMAN", "description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].", "homepage": "http://shaman.c3bi.pasteur.fr/", "biotoolsID": "shaman", "biotoolsCURIE": "biotools:shaman", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" }, { "uri": "http://edamontology.org/operation_3221", "term": "Species frequency estimation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": "Quantitative metagenomics Count table & taxonomy Diversity, barplot, boxplot, scatterplot, rarefaction curves, heatmap", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/aghozlane/shaman", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://shaman.c3bi.pasteur.fr/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1073/pnas.1523899113", "pmid": "27140611", "pmcid": "PMC4878514", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection", "abstract": "Listeria monocytogenes is responsible for gastroenteritis in healthy individuals and for a severe invasive disease in immunocompromised patients. Among the three identified L. monocytogenes evolutionary lineages, lineage I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms underlying the higher virulence potential of strains of this lineage remain elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor only present in a subset of lineage I strains, is a bacteriocin highly expressed in the intestine of orally infected mice that alters the host intestinal microbiota and promotes intestinal colonization by L. monocytogenes, as well as deeper organ infection. To our knowledge, these results therefore identify LLS as the first bacteriocin described in L. monocytogenes and associate modulation of host microbiota by L. monocytogenes epidemic strains to increased virulence.", "date": "2016-05-17T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Quereda J.J." }, { "name": "Dussurget O." }, { "name": "Nahori M.-A." }, { "name": "Ghozlane A." }, { "name": "Volant S." }, { "name": "Dillies M.-A." }, { "name": "Regnault B." }, { "name": "Kennedy S." }, { "name": "Mondot S." }, { "name": "Villoing B." }, { "name": "Cossart P." }, { "name": "Pizarro-Cerda J." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } } ], "credit": [ { "name": "Stevenn Volant", "email": null, "url": "https://research.pasteur.fr/en/member/stevenn-volant/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hugo Varet", "email": null, "url": "https://research.pasteur.fr/en/member/hugo-varet/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pierre Lechat", "email": null, "url": "https://research.pasteur.fr/en/member/pierre-lechat/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Amine Ghozlane", "email": null, "url": "https://research.pasteur.fr/en/member/amine-ghozlane/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Institut Pasteur", "email": null, "url": "https://research.pasteur.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", 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Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).", "homepage": "http://bioconductor.org/packages/release/bioc/html/omicRexposome.html", "biotoolsID": "omicrexposome", "biotoolsCURIE": "biotools:omicrexposome", "version": [ "1.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "rexposome", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3809", "term": "Differentially-methylated region identification" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3659", "term": "Regression analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "MIT", "collectionID": [ "Proteomics", "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioconductor.org/packages/omicRexposome/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://bioconductor.org/packages/release/bioc/src/contrib/omicRexposome_1.2.0.tar.gz", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/manuals/omicRexposome/man/omicRexposome.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btz526", "pmid": "31243429", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages", "abstract": "Summary: Genomics has dramatically improved our understanding of the molecular origins of certain human diseases. Nonetheless, our health is also influenced by the cumulative impact of exposures experienced across the life course (termed 'exposome'). The study of the high-dimensional exposome offers a new paradigm for investigating environmental contributions to disease etiology. However, there is a lack of bioinformatics tools for managing, visualizing and analyzing the exposome. The analysis data should include both association with health outcomes and integration with omic layers. We provide a generic framework called rexposome project, developed in the R/Bioconductor architecture that includes object-oriented classes and methods to leverage high-dimensional exposome data in disease association studies including its integration with a variety of high-throughput data types. The usefulness of the package is illustrated by analyzing a real dataset including exposome data, three health outcomes related to respiratory diseases and its integration with the transcriptome and methylome.", "date": "2019-12-15T00:00:00Z", "citationCount": 18, "authors": [ { "name": "Hernandez-Ferrer C." }, { "name": "Wellenius G.A." }, { "name": "Tamayo I." }, { "name": "Basagana X." }, { "name": "Sunyer J." }, { "name": "Vrijheid M." }, { "name": "Gonzalez J.R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1038/s41467-022-34422-2", "pmid": "36411288", "pmcid": "PMC9678903", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Multi-omics signatures of the human early life exposome", "abstract": "Environmental exposures during early life play a critical role in life-course health, yet the molecular phenotypes underlying environmental effects on health are poorly understood. In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1301 mother-child pairs, we associate individual exposomes consisting of >100 chemical, outdoor, social and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, proteins and metabolites) in childhood. We identify 1170 associations, 249 in pregnancy and 921 in childhood, which reveal potential biological responses and sources of exposure. Pregnancy exposures, including maternal smoking, cadmium and molybdenum, are predominantly associated with child DNA methylation changes. In contrast, childhood exposures are associated with features across all omics layers, most frequently the serum metabolome, revealing signatures for diet, toxic chemical compounds, essential trace elements, and weather conditions, among others. Our comprehensive and unique resource of all associations (https://helixomics.isglobal.org/) will serve to guide future investigation into the biological imprints of the early life exposome.", "date": "2022-12-01T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Maitre L." }, { "name": "Bustamante M." }, { "name": "Hernandez-Ferrer C." }, { "name": "Thiel D." }, { "name": "Lau C.-H.E." }, { "name": "Siskos A.P." }, { "name": "Vives-Usano M." }, { "name": "Ruiz-Arenas C." }, { "name": "Pelegri-Siso D." }, { "name": "Robinson O." }, { "name": "Mason D." }, { "name": "Wright J." }, { "name": "Cadiou S." }, { "name": "Slama R." }, { "name": "Heude B." }, { "name": "Casas M." }, { "name": "Sunyer J." }, { "name": "Papadopoulou E.Z." }, { "name": "Gutzkow K.B." }, { "name": "Andrusaityte S." }, { "name": "Grazuleviciene R." }, { "name": "Vafeiadi M." }, { "name": "Chatzi L." }, { "name": "Sakhi A.K." }, { "name": "Thomsen C." }, { "name": "Tamayo I." }, { "name": "Nieuwenhuijsen M." }, { "name": "Urquiza J." }, { "name": "Borras E." }, { "name": "Sabido E." }, { "name": "Quintela I." }, { "name": "Carracedo A." }, { "name": "Estivill X." }, { "name": "Coen M." }, { "name": "Gonzalez J.R." }, { "name": "Keun H.C." }, { "name": "Vrijheid M." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@isglobal.org", "url": "http://www.carleshf.com", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Juan R Gonzalez", "email": "juanr.gonzalez@isglobal.org", "url": "https://brge.isglobal.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "chernan3", "additionDate": "2018-07-24T09:43:16Z", "lastUpdate": "2025-10-01T09:07:33.409402Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "chernan3", "rodney" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }