Wiki source code of Methodology

Version 18.1 by manuelmenendez on 2025/02/13 12:52
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1 == **Overview** ==
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3 Neurodiagnoses develops a tridimensional diagnostic framework for CNS diseases, incorporating AI-powered annotation tools to improve interpretability, standardization, and clinical utility. The methodology integrates multi-modal data, including genetic, neuroimaging, neurophysiological, and biomarker datasets, and applies machine learning models to generate structured, explainable diagnostic outputs.
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5 ----
6
7 == **How to Use External Databases in Neurodiagnoses** ==
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9 To enhance the accuracy of our diagnostic models, Neurodiagnoses integrates data from multiple biomedical and neurological research databases. If you are a researcher, follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.
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11 === **Potential Data Sources** ===
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13 Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
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15 * Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
16
17 === **1. Register for Access** ===
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19 Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
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21 * Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
22 * Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
23
24 === **2. Download & Prepare Data** ===
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26 Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
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28 ==== **Supported File Formats** ====
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30 * Tabular Data: .csv, .tsv
31 * Neuroimaging Data: .nii, .dcm
32 * Genomic Data: .fasta, .vcf
33 * Clinical Metadata: .json, .xml
34
35 ==== **Mandatory Fields for Integration** ====
36
37 |=Field Name|=Description
38 |Subject ID|Unique patient identifier
39 |Diagnosis|Standardized disease classification
40 |Biomarkers|CSF, plasma, or imaging biomarkers
41 |Genetic Data|Whole-genome or exome sequencing
42 |Neuroimaging Metadata|MRI/PET acquisition parameters
43
44 === **3. Upload Data to Neurodiagnoses** ===
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46 Once preprocessed, data can be uploaded to EBRAINS or GitHub.
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48 * (((
49 **Option 1: Upload to EBRAINS Bucket**
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51 * Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
52 * Ensure correct metadata tagging before submission.
53 )))
54 * (((
55 **Option 2: Contribute via GitHub Repository**
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57 * Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
58 * Create a new folder under /data/ and include dataset description.
59 )))
60
61 //Note: For large datasets, please contact the project administrators before uploading.//
62
63 === **4. Integrate Data into AI Models** ===
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65 Once uploaded, datasets must be harmonized and formatted before AI model training.
66
67 ==== **Steps for Data Integration** ====
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69 * Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
70 * Standardize neuroimaging and biomarker formats using harmonization tools.
71 * Use machine learning models to handle missing data and feature extraction.
72 * Train AI models with newly integrated patient cohorts.
73 * Reference: [[Detailed instructions can be found in docs/data_processing.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]].
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75 ----
76
77 == **Database Sources Table** ==
78
79 === **Where to Insert This** ===
80
81 * GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
82 * EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
83
84 === **Key Databases for Neurodiagnoses** ===
85
86 |=Database|=Focus Area|=Data Type|=Access Link
87 |ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
88 |PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
89 |GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
90 |Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
91 |GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
92 |UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
93 |DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
94 |PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
95 |DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
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97 If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
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99 ----
100
101 == **Collaboration & Partnerships** ==
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103 === **Where to Insert This** ===
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105 * GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
106 * EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
107
108 === **Partnering with Data Providers** ===
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110 Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
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112 * Enable direct API-based data integration for real-time processing.
113 * Co-develop harmonized AI-ready datasets with standardized annotations.
114 * Secure funding opportunities through joint grant applications.
115
116 === **Interested in Partnering?** ===
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118 If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
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120 * Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
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122 ----
123
124 == **Final Notes** ==
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126 Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
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128 For additional technical documentation:
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130 * [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
131 * [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
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133 If you experience issues integrating data, open a [[GitHub Issue>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]] or consult the EBRAINS Neurodiagnoses Forum.