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1		-== **Overview** ==
	1	+**Neurodiagnoses AI** is an open-source, AI-driven framework designed to enhance the diagnosis and prognosis of central nervous system (CNS) disorders. Building upon the Florey Dementia Index (FDI) methodology, it now encompasses a broader spectrum of neurological conditions. The system integrates multimodal data sources—including EEG, neuroimaging, biomarkers, and genetics—and employs machine learning models to deliver explainable, real-time diagnostic insights. A key feature of this framework is the incorporation of the **Generalized Neuro Biomarker Ontology Categorization (Neuromarker)**, which standardizes biomarker classification across all neurodegenerative diseases, facilitating cross-disease AI training.
2	2
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.
	3	+**Neuromarker: Generalized Biomarker Ontology**
4	4
5		-----
	5	+Neuromarker extends the Common Alzheimer’s Disease Research Ontology (CADRO) into a comprehensive biomarker categorization framework applicable to all neurodegenerative diseases (NDDs). This ontology enables standardized classification, AI-based feature extraction, and seamless multimodal data integration.
6	6
7		-== **How to Use External Databases in Neurodiagnoses** ==
	7	+**Core Biomarker Categories**
8	8
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.
	9	+Within the Neurodiagnoses AI framework, biomarkers are categorized as follows:
10	10
11		-=== **Potential Data Sources** ===
	11	+|=**Category**|=**Description**
	12	+|**Molecular Biomarkers**|Omics-based markers (genomic, transcriptomic, proteomic, metabolomic, lipidomic)
	13	+|**Neuroimaging Biomarkers**|Structural (MRI, CT), Functional (fMRI, PET), Molecular Imaging (tau, amyloid, α-synuclein)
	14	+|**Fluid Biomarkers**|CSF, plasma, blood-based markers for tau, amyloid, α-synuclein, TDP-43, GFAP, NfL, autoantiboides
	15	+|**Neurophysiological Biomarkers**|EEG, MEG, evoked potentials (ERP), sleep-related markers
	16	+|**Digital Biomarkers**|Gait analysis, cognitive/speech biomarkers, wearables data, EHR-based markers
	17	+|**Clinical Phenotypic Markers**|Standardized clinical scores (MMSE, MoCA, CDR, UPDRS, ALSFRS, UHDRS)
	18	+|**Genetic Biomarkers**|Risk alleles (APOE, LRRK2, MAPT, C9orf72, PRNP) and polygenic risk scores
	19	+|**Environmental & Lifestyle Factors**|Toxins, infections, diet, microbiome, comorbidities
12	12
13		-Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
	21	+**Integrating External Databases into Neurodiagnoses**
14	14
15		-* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
	23	+To enhance diagnostic precision, Neurodiagnoses AI incorporates data from multiple biomedical and neurological research databases. Researchers can integrate external datasets by following these steps:
16	16
17		-=== **1. Register for Access** ===
	25	+1. (((
	26	+**Register for Access**
18	18
19		-Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
	28	+* Each external database requires individual registration and access approval.
	29	+* Ensure compliance with ethical approvals and data usage agreements before integrating datasets into Neurodiagnoses.
	30	+* Some repositories may require a Data Usage Agreement (DUA) for sensitive medical data.
	31	+)))
	32	+1. (((
	33	+**Download & Prepare Data**
20	20
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.
	35	+* Download datasets while adhering to database usage policies.
	36	+* (((
	37	+Ensure files meet Neurodiagnoses format requirements:
23	23
24		-=== **2. Download & Prepare Data** ===
	39	+|=**Data Type**|=**Accepted Formats**
	40	+|**Tabular Data**|.csv, .tsv
	41	+|**Neuroimaging**|.nii, .dcm
	42	+|**Genomic Data**|.fasta, .vcf
	43	+|**Clinical Metadata**|.json, .xml
	44	+)))
	45	+* (((
	46	+**Mandatory Fields for Integration**:
25	25
26		-Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
	48	+* Subject ID: Unique patient identifier
	49	+* Diagnosis: Standardized disease classification
	50	+* Biomarkers: CSF, plasma, or imaging biomarkers
	51	+* Genetic Data: Whole-genome or exome sequencing
	52	+* Neuroimaging Metadata: MRI/PET acquisition parameters
	53	+)))
	54	+)))
	55	+1. (((
	56	+**Upload Data to Neurodiagnoses**
27	27
28		-==== **Supported File Formats** ====
29		-
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** ===
45		-
46		-Once preprocessed, data can be uploaded to EBRAINS or GitHub.
47		-
48	48	* (((
49	49	**Option 1: Upload to EBRAINS Bucket**
50	50
51		-* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
	61	+* Location: EBRAINS Neurodiagnoses Bucket
52	52	* Ensure correct metadata tagging before submission.
53	53	)))
54	54	* (((
55	55	**Option 2: Contribute via GitHub Repository**
56	56
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.
	67	+* Location: GitHub Data Repository
	68	+* Create a new folder under /data/ and include a dataset description.
	69	+* For large datasets, contact project administrators before uploading.
59	59	)))
	71	+)))
	72	+1. (((
	73	+**Integrate Data into AI Models**
60	60
61		-//Note: For large datasets, please contact the project administrators before uploading.//
62		-
63		-=== **4. Integrate Data into AI Models** ===
64		-
65		-Once uploaded, datasets must be harmonized and formatted before AI model training.
66		-
67		-==== **Steps for Data Integration** ====
68		-
69	69	* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
70	70	* Standardize neuroimaging and biomarker formats using harmonization tools.
71		-* Use machine learning models to handle missing data and feature extraction.
	77	+* Utilize machine learning models to handle missing data and feature extraction.
72	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]].
74	74
75		-----
	80	+**Reference**: See docs/data_processing.md for detailed instructions.
	81	+)))
76	76
77		-== **Database Sources Table** ==
	83	+**AI-Driven Biomarker Categorization**
78	78
79		-=== **Where to Insert This** ===
	85	+Neurodiagnoses employs advanced AI models for biomarker classification:
80	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
	87	+|=**Model Type**|=**Application**
	88	+|**Graph Neural Networks (GNNs)**|Identify shared biomarker pathways across diseases
	89	+|**Contrastive Learning**|Distinguish overlapping vs. unique biomarkers
	90	+|**Multimodal Transformer Models**|Integrate imaging, omics, and clinical data
83	83
84		-=== **Key Databases for Neurodiagnoses** ===
	92	+**Collaboration & Partnerships**
85	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
	94	+Neurodiagnoses actively seeks partnerships with data providers to:
96	96
97		-If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
98		-
99		-----
100		-
101		-== **Collaboration & Partnerships** ==
102		-
103		-=== **Where to Insert This** ===
104		-
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** ===
109		-
110		-Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
111		-
112		-* Enable direct API-based data integration for real-time processing.
	96	+* Enable API-based data integration for real-time processing.
113	113	* Co-develop harmonized AI-ready datasets with standardized annotations.
114	114	* Secure funding opportunities through joint grant applications.
115	115
116		-=== **Interested in Partnering?** ===
	100	+**Interested in Partnering?**
117	117
118	118	If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
119	119
120		-* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
	104	+**Contact**: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
121	121
122		-----
123		-
124		-== **Final Notes** ==
125		-
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.
127		-
128		-For additional technical documentation:
129		-
130		-* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
131		-* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
132		-
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.
	106	+

workflow neurodiagnoses.png

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