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--**# Neurodiagnoses AI: Multimodal AI for Neurodiagnostic Predictions**
++Here is the updated **Methodology** section for the EBRAINS Wiki, incorporating the **Generalized Neuro Biomarker Ontology Categorization (Neuromarker)** for **biomarker classification across all neurodegenerative diseases**.
--## **Project Overview**
--Neurodiagnoses AI implements AI-driven diagnostic and prognostic models for central nervous system (CNS) disorders, adapting the Florey Dementia Index (FDI) methodology to a broader set of neurological conditions. The approach integrates **multimodal data sources** (EEG, neuroimaging, biomarkers, and genetics) and employs **machine learning models** to provide **explainable, real-time diagnostic insights**.##
++----
--## **How to Use External Databases in Neurodiagnoses**
--To enhance diagnostic accuracy, Neurodiagnoses integrates data from multiple biomedical and neurological research databases. Researchers can follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.##
++== **Neurodiagnoses AI: Multimodal AI for Neurodiagnostic Predictions** ==
--### **Potential Data Sources**
--Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases. ##
++=== **Project Overview** ===
--**Reference: List of Potential Databases**
--- **ADNI**: Alzheimer's Disease data ([ADNI](https://adni.loni.usc.edu))
--- **PPMI**: Parkinson’s Disease Imaging and biospecimens ([PPMI](https://www.ppmi-info.org))
--- **GP2**: Whole-genome sequencing for PD ([GP2](https://gp2.org))
--- **Enroll-HD**: Huntington’s Disease Clinical and genetic data ([Enroll-HD](https://www.enroll-hd.org))
--- **GAAIN**: Multi-source Alzheimer’s data aggregation ([GAAIN](https://gaain.org))
--- **UK Biobank**: Population-wide genetic, imaging, and health records ([UK Biobank](https://www.ukbiobank.ac.uk))
--- **DPUK**: Dementia and Aging data ([DPUK](https://www.dementiasplatform.uk))
--- **PRION Registry**: Prion Diseases clinical and genetic data ([PRION Registry](https://prionregistry.org))
--- **DECIPHER**: Rare genetic disorder genomic variants ([DECIPHER](https://decipher.sanger.ac.uk))
++Neurodiagnoses AI implements **AI-driven diagnostic and prognostic models** for central nervous system (CNS) disorders, expanding the **Florey Dementia Index (FDI) methodology** to a broader set of neurological conditions. The approach integrates **multimodal data sources** (EEG, neuroimaging, biomarkers, and genetics) and employs machine learning models to provide **explainable, real-time diagnostic insights**. This framework now incorporates **Neuromarker**, a **generalized biomarker ontology** that categorizes biomarkers across neurodegenerative diseases, enabling **standardized, cross-disease AI training**.
--### **1. Register for Access**
--- Each external database requires **individual registration** and access approval.
--- Ensure compliance with **ethical approvals** and **data usage agreements** before integrating datasets into Neurodiagnoses.
--- Some repositories may require a **Data Usage Agreement (DUA)** for sensitive medical data.##
++== **Neuromarker: Generalized Biomarker Ontology** ==
--### **2. Download & Prepare Data**
--- Download datasets while adhering to database usage policies.
--- Ensure files meet **Neurodiagnoses format requirements**:
--  - **Tabular Data**: `.csv`, `.tsv`
--  - **Neuroimaging Data**: `.nii`, `.dcm`
--  - **Genomic Data**: `.fasta`, `.vcf`
--  - **Clinical Metadata**: `.json`, `.xml`##
++Neuromarker extends the **Common Alzheimer’s Disease Research Ontology (CADRO)** into a **cross-disease biomarker categorization framework** applicable to all neurodegenerative diseases (NDDs). It allows for **standardized classification, AI-based feature extraction, and multimodal integration**.
--- **Mandatory Fields for Integration**:
--  - **Subject ID**: Unique patient identifier
--  - **Diagnosis**: Standardized disease classification
--  - **Biomarkers**: CSF, plasma, or imaging biomarkers
--  - **Genetic Data**: Whole-genome or exome sequencing
--  - **Neuroimaging Metadata**: MRI/PET acquisition parameters
++=== **Core Biomarker Categories** ===
--### **3. Upload Data to Neurodiagnoses**
--**Option 1: Upload to EBRAINS Bucket**
--- Location: **EBRAINS Neurodiagnoses Bucket**
--- Ensure correct **metadata tagging** before submission.##
++The following ontology is used within **Neurodiagnoses AI** for biomarker categorization:
-- **Option 2: Contribute via GitHub Repository**
--- Location: **GitHub Data Repository**
--- Create a new folder under `/data/` and include a **dataset description**.
--- For large datasets, contact project administrators before uploading.
++|=**Category**|=**Description**
++|**Molecular Biomarkers**|Omics-based markers (genomic, transcriptomic, proteomic, metabolomic, lipidomic)
++|**Neuroimaging Biomarkers**|Structural (MRI, CT), Functional (fMRI, PET), Molecular Imaging (tau, amyloid, α-synuclein)
++|**Fluid Biomarkers**|CSF, plasma, blood-based markers for tau, amyloid, α-synuclein, TDP-43, GFAP, NfL
++|**Neurophysiological Biomarkers**|EEG, MEG, evoked potentials (ERP), sleep-related markers
++|**Digital Biomarkers**|Gait analysis, cognitive/speech biomarkers, wearables data, EHR-based markers
++|**Clinical Phenotypic Markers**|Standardized clinical scores (MMSE, MoCA, CDR, UPDRS, ALSFRS, UHDRS)
++|**Genetic Biomarkers**|Risk alleles (APOE, LRRK2, MAPT, C9orf72, PRNP) and polygenic risk scores
++|**Environmental & Lifestyle Factors**|Toxins, infections, diet, microbiome, comorbidities
--### **4. Integrate Data into AI Models**
--- Open **Jupyter Notebooks** on EBRAINS to run **preprocessing scripts**.
--- Standardize **neuroimaging and biomarker formats** using harmonization tools.
--- Use **machine learning models** to handle missing data and feature extraction.
--- Train AI models with **newly integrated patient cohorts**.##
++----
--**Reference**: See `docs/data_processing.md` for detailed instructions.
--
--## **Collaboration & Partnerships**##
--# **Partnering with Data Providers**
--Neurodiagnoses seeks partnerships with data repositories to:
--- Enable **API-based data integration** for real-time processing.
--- Co-develop **harmonized AI-ready datasets** with standardized annotations.
--- Secure **funding opportunities** through joint grant applications.
--
--**Interested in Partnering?**
--- If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
--- **Contact**: info@neurodiagnoses.com
--
--## **Final Notes**
--Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute **new datasets and methodologies**.##
--
--For additional technical documentation:
--- **GitHub Repository**: [Neurodiagnoses GitHub](https://github.com/neurodiagnoses)
--- **EBRAINS Collaboration Page**: [EBRAINS Neurodiagnoses](https://ebrains.eu/collabs/neurodiagnoses)
--
--If you experience issues integrating data, **open a GitHub Issue** or consult the **EBRAINS Neurodiagnoses Forum**.
--
  == **How to Use External Databases in Neurodiagnoses** ==
--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.
++To enhance diagnostic accuracy, Neurodiagnoses AI integrates data from **multiple biomedical and neurological research databases**. Researchers can follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.
  === **Potential Data Sources** ===
--Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
++Neurodiagnoses maintains an **updated list** of biomedical datasets relevant to neurodegenerative diseases:
--* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
++* **ADNI**: Alzheimer's Disease Imaging & Biomarkers → [[ADNI>>url:https://adni.loni.usc.edu/]]
++* **PPMI**: Parkinson’s Disease Imaging & Biospecimens → [[PPMI>>url:https://www.ppmi-info.org/]]
++* **GP2**: Whole-Genome Sequencing for PD → [[GP2>>url:https://gp2.org/]]
++* **Enroll-HD**: Huntington’s Disease Clinical & Genetic Data → [[Enroll-HD>>url:https://www.enroll-hd.org/]]
++* **GAAIN**: Multi-Source Alzheimer’s Data Aggregation → [[GAAIN>>url:https://gaain.org/]]
++* **UK Biobank**: Population-Wide Genetic, Imaging & Health Records → [[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
++* **DPUK**: Dementia & Aging Data → [[DPUK>>url:https://www.dementiasplatform.uk/]]
++* **PRION Registry**: Prion Diseases Clinical & Genetic Data → [[PRION Registry>>url:https://prionregistry.org/]]
++* **DECIPHER**: Rare Genetic Disorder Genomic Variants → [[DECIPHER>>url:https://decipher.sanger.ac.uk/]]
--=== **1. Register for Access** ===
++----
--Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
++== **1. Register for Access** ==
--* Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
--* Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
++* Each external database requires **individual registration and access approval**.
++* Ensure compliance with **ethical approvals and data usage agreements** before integrating datasets into Neurodiagnoses.
++* Some repositories may require a **Data Usage Agreement (DUA)** for sensitive medical data.
--=== **2. Download & Prepare Data** ===
++----
--Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
++== **2. Download & Prepare Data** ==
--==== **Supported File Formats** ====
++* Download datasets while adhering to **database usage policies**.
++* Ensure files meet **Neurodiagnoses format requirements**:
--* Tabular Data: .csv, .tsv
--* Neuroimaging Data: .nii, .dcm
--* Genomic Data: .fasta, .vcf
--* Clinical Metadata: .json, .xml
++|=**Data Type**|=**Accepted Formats**
++|**Tabular Data**|.csv, .tsv
++|**Neuroimaging**|.nii, .dcm
++|**Genomic Data**|.fasta, .vcf
++|**Clinical Metadata**|.json, .xml
--==== **Mandatory Fields for Integration** ====
++* **Mandatory Fields for Integration**:
++** **Subject ID**: Unique patient identifier
++** **Diagnosis**: Standardized disease classification
++** **Biomarkers**: CSF, plasma, or imaging biomarkers
++** **Genetic Data**: Whole-genome or exome sequencing
++** **Neuroimaging Metadata**: MRI/PET acquisition parameters
--|=Field Name|=Description
--|Subject ID|Unique patient identifier
--|Diagnosis|Standardized disease classification
--|Biomarkers|CSF, plasma, or imaging biomarkers
--|Genetic Data|Whole-genome or exome sequencing
--|Neuroimaging Metadata|MRI/PET acquisition parameters
++----
--=== **3. Upload Data to Neurodiagnoses** ===
++== **3. Upload Data to Neurodiagnoses** ==
--Once preprocessed, data can be uploaded to EBRAINS or GitHub.
++=== **Option 1: Upload to EBRAINS Bucket** ===
--* (((
--**Option 1: Upload to EBRAINS Bucket**
++* Location: **EBRAINS Neurodiagnoses Bucket**
++* Ensure **correct metadata tagging** before submission.
--* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
--* Ensure correct metadata tagging before submission.
--)))
--* (((
--**Option 2: Contribute via GitHub Repository**
++=== **Option 2: Contribute via GitHub Repository** ===
--* Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
--* Create a new folder under /data/ and include dataset description.
--)))
++* Location: **GitHub Data Repository**
++* Create a **new folder under /data/** and include a **dataset description**.
++* **For large datasets**, contact project administrators before uploading.
--//Note: For large datasets, please contact the project administrators before uploading.//
++----
--=== **4. Integrate Data into AI Models** ===
++== **4. Integrate Data into AI Models** ==
--Once uploaded, datasets must be harmonized and formatted before AI model training.
++* Open **Jupyter Notebooks** on EBRAINS to run **preprocessing scripts**.
++* **Standardize neuroimaging and biomarker formats** using harmonization tools.
++* Use **machine learning models** to handle **missing data** and **feature extraction**.
++* Train AI models with **newly integrated patient cohorts**.
--==== **Steps for Data Integration** ====
++**Reference**: See docs/data_processing.md for detailed instructions.
--* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
--* Standardize neuroimaging and biomarker formats using harmonization tools.
--* Use machine learning models to handle missing data and feature extraction.
--* Train AI models with newly integrated patient cohorts.
--* 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]].
--
  ----
--== **Database Sources Table** ==
++== **AI-Driven Biomarker Categorization** ==
--=== **Where to Insert This** ===
++Neurodiagnoses employs **AI models** for biomarker classification:
--* GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
--* EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
++|=**Model Type**|=**Application**
++|**Graph Neural Networks (GNNs)**|Identify shared biomarker pathways across diseases
++|**Contrastive Learning**|Distinguish overlapping vs. unique biomarkers
++|**Multimodal Transformer Models**|Integrate imaging, omics, and clinical data
--=== **Key Databases for Neurodiagnoses** ===
--
--|=Database|=Focus Area|=Data Type|=Access Link
--|ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
--|PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
--|GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
--|Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
--|GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
--|UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
--|DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
--|PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
--|DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
--
--If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
--
  ----
++== [[image:workflow neurodiagnoses.png]] ==
++
  == **Collaboration & Partnerships** ==
--=== **Where to Insert This** ===
--
--* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
--* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
--
  === **Partnering with Data Providers** ===
--Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
++Neurodiagnoses seeks partnerships with data repositories to:
--* Enable direct API-based data integration for real-time processing.
--* Co-develop harmonized AI-ready datasets with standardized annotations.
--* Secure funding opportunities through joint grant applications.
++* Enable **API-based data integration** for real-time processing.
++* Co-develop **harmonized AI-ready datasets** with standardized annotations.
++* Secure **funding opportunities** through joint grant applications.
--=== **Interested in Partnering?** ===
++**Interested in Partnering?**
--If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
++* If you represent a **research consortium or database provider**, reach out to explore **data-sharing agreements**.
++* **Contact**: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
--* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
--
  ----
  == **Final Notes** ==
--Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
++Neurodiagnoses continuously expands its **data ecosystem** to support **AI-driven clinical decision-making**. Researchers and institutions are encouraged to **contribute new datasets and methodologies**.
--For additional technical documentation:
++**For additional technical documentation**:
--* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
--* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
++* **GitHub Repository**: [[Neurodiagnoses GitHub>>url:https://github.com/neurodiagnoses]]
++* **EBRAINS Collaboration Page**: [[EBRAINS Neurodiagnoses>>url:https://ebrains.eu/collabs/neurodiagnoses]]
--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.
++**If you experience issues integrating data**, open a **GitHub Issue** or consult the **EBRAINS Neurodiagnoses Forum**.
++
++----
++
++This **updated methodology** now incorporates [[https:~~/~~/github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/biomarker_ontology>>https://Neuromarker]] for standardized biomarker classification, enabling **cross-disease AI training** across neurodegenerative disorders.

workflow neurodiagnoses.png

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