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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.
	1	+== **Overview** ==
2	2
3		-**Neuromarker: Generalized Biomarker Ontology**
	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.
4	4
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.
	5	+----
6	6
7		-**Core Biomarker Categories**
	7	+== **How to Use External Databases in Neurodiagnoses** ==
8	8
9		-Within the Neurodiagnoses AI framework, biomarkers are categorized as follows:
	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.
10	10
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
	11	+=== **Potential Data Sources** ===
20	20
21		-**Integrating External Databases into Neurodiagnoses**
	13	+Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
22	22
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:
	15	+* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
24	24
25		-1. (((
26		-**Register for Access**
	17	+=== **1. Register for Access** ===
27	27
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**
	19	+Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
34	34
35		-* Download datasets while adhering to database usage policies.
36		-* (((
37		-Ensure files meet Neurodiagnoses format requirements:
	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.
38	38
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**:
	24	+=== **2. Download & Prepare Data** ===
47	47
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**
	26	+Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
57	57
	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	+
58	58	* (((
59	59	**Option 1: Upload to EBRAINS Bucket**
60	60
61		-* Location: EBRAINS Neurodiagnoses Bucket
	51	+* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
62	62	* Ensure correct metadata tagging before submission.
63	63	)))
64	64	* (((
65	65	**Option 2: Contribute via GitHub Repository**
66	66
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.
	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.
70	70	)))
71		-)))
72		-1. (((
73		-**Integrate Data into AI Models**
74	74
	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	+
75	75	* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
76	76	* Standardize neuroimaging and biomarker formats using harmonization tools.
77		-* Utilize machine learning models to handle missing data and feature extraction.
	71	+* Use machine learning models to handle missing data and feature extraction.
78	78	* 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]].
79	79
80		-**Reference**: See docs/data_processing.md for detailed instructions.
81		-)))
	75	+----
82	82
83		-**AI-Driven Biomarker Categorization**
	77	+== **Database Sources Table** ==
84	84
85		-Neurodiagnoses employs advanced AI models for biomarker classification:
	79	+=== **Where to Insert This** ===
86	86
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
	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
91	91
92		-**Collaboration & Partnerships**
	84	+=== **Key Databases for Neurodiagnoses** ===
93	93
94		-Neurodiagnoses actively seeks partnerships with data providers to:
	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
95	95
96		-* Enable API-based data integration for real-time processing.
	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.
97	97	* Co-develop harmonized AI-ready datasets with standardized annotations.
98	98	* Secure funding opportunities through joint grant applications.
99	99
100		-**Interested in Partnering?**
	116	+=== **Interested in Partnering?** ===
101	101
102	102	If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
103	103
104		-**Contact**: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
	120	+* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
105	105
106		-**Final Notes**
	122	+----
107	107
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.
	124	+== **Final Notes** ==
109	109
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.
	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.
111	111
112		-**For additional technical documentation and collaboration opportunities:**
	128	+For additional technical documentation:
113	113
114		-* **GitHub Repository:** [[Neurodiagnoses GitHub>>url:https://github.com/neurodiagnoses]]
115		-* **EBRAINS Collaboration Page:** [[EBRAINS Neurodiagnoses>>url:https://ebrains.eu/collabs/neurodiagnoses]]
	130	+* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
	131	+* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
116	116
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.
	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.

workflow neurodiagnoses.png

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