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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		-----
	106	+**Final Notes**
123	123
124		-== **Final Notes** ==
	108	+Neurodiagnoses AI is committed to advancing the integration of artificial intelligence in neurodiagnostic processes. By continuously expanding our data ecosystem and incorporating standardized biomarker classifications through the Neuromarker ontology, we aim to enhance cross-disease AI training and improve diagnostic accuracy across neurodegenerative disorders.
125	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.
	110	+We encourage researchers and institutions to contribute new datasets and methodologies to further enrich this collaborative platform. Your participation is vital in driving innovation and fostering a deeper understanding of complex neurological conditions.
127	127
128		-For additional technical documentation:
	112	+**For additional technical documentation and collaboration opportunities:**
129	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/]]
	114	+* **GitHub Repository:** [[Neurodiagnoses GitHub>>url:https://github.com/neurodiagnoses]]
	115	+* **EBRAINS Collaboration Page:** [[EBRAINS Neurodiagnoses>>url:https://ebrains.eu/collabs/neurodiagnoses]]
132	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.
	117	+If you encounter any issues during data integration or have suggestions for improvement, please open a GitHub Issue or consult the EBRAINS Neurodiagnoses Forum. Together, we can advance the field of neurodiagnostics and contribute to better patient outcomes.

workflow neurodiagnoses.png

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