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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. It 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) **and** **Disease Knowledge Transfer (DKT), which standardizes disease and biomarker classification across all CNS 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		-**Recommended Software**
	7	+== **How to Use External Databases in Neurodiagnoses** ==
8	8
9		-There is a suite of software that can help implement the workflow needed in Neurodiagnoses. Find a list of recommendations [[here>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/recommended_software]].
	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		-**Core Biomarker Categories**
	11	+=== **Potential Data Sources** ===
12	12
13		-Within the Neurodiagnoses AI framework, biomarkers are categorized as follows:
	13	+Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
14	14
15		-|=**Category**|=**Description**
16		-|**Molecular Biomarkers**|Omics-based markers (genomic, transcriptomic, proteomic, metabolomic, lipidomic)
17		-|**Neuroimaging Biomarkers**|Structural (MRI, CT), Functional (fMRI, PET), Molecular Imaging (tau, amyloid, α-synuclein)
18		-|**Fluid Biomarkers**|CSF, plasma, blood-based markers for tau, amyloid, α-synuclein, TDP-43, GFAP, NfL, autoantiboides
19		-|**Neurophysiological Biomarkers**|EEG, MEG, evoked potentials (ERP), sleep-related markers
20		-|**Digital Biomarkers**|Gait analysis, cognitive/speech biomarkers, wearables data, EHR-based markers
21		-|**Clinical Phenotypic Markers**|Standardized clinical scores (MMSE, MoCA, CDR, UPDRS, ALSFRS, UHDRS)
22		-|**Genetic Biomarkers**|Risk alleles (APOE, LRRK2, MAPT, C9orf72, PRNP) and polygenic risk scores
23		-|**Environmental & Lifestyle Factors**|Toxins, infections, diet, microbiome, comorbidities
	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		-**Integrating External Databases into Neurodiagnoses**
	17	+=== **1. Register for Access** ===
26	26
27		-To enhance diagnostic precision, Neurodiagnoses AI incorporates data from multiple biomedical and neurological research databases. Researchers can integrate external datasets by following these steps:
	19	+Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
28	28
29		-1. (((
30		-**Register for Access**
	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.
31	31
32		-* Each external database requires individual registration and access approval.
33		-* Ensure compliance with ethical approvals and data usage agreements before integrating datasets into Neurodiagnoses.
34		-* Some repositories may require a Data Usage Agreement (DUA) for sensitive medical data.
35		-)))
36		-1. (((
37		-**Download & Prepare Data**
	24	+=== **2. Download & Prepare Data** ===
38	38
39		-* Download datasets while adhering to database usage policies.
40		-* (((
41		-Ensure files meet Neurodiagnoses format requirements:
	26	+Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
42	42
43		-|=**Data Type**|=**Accepted Formats**
44		-|**Tabular Data**|.csv, .tsv
45		-|**Neuroimaging**|.nii, .dcm
46		-|**Genomic Data**|.fasta, .vcf
47		-|**Clinical Metadata**|.json, .xml
48		-)))
49		-* (((
50		-**Mandatory Fields for Integration**:
	28	+==== **Supported File Formats** ====
51	51
52		-* Subject ID: Unique patient identifier
53		-* Diagnosis: Standardized disease classification
54		-* Biomarkers: CSF, plasma, or imaging biomarkers
55		-* Genetic Data: Whole-genome or exome sequencing
56		-* Neuroimaging Metadata: MRI/PET acquisition parameters
57		-)))
58		-)))
59		-1. (((
60		-**Upload Data to Neurodiagnoses**
	30	+* Tabular Data: .csv, .tsv
	31	+* Neuroimaging Data: .nii, .dcm
	32	+* Genomic Data: .fasta, .vcf
	33	+* Clinical Metadata: .json, .xml
61	61
	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	+
62	62	* (((
63	63	**Option 1: Upload to EBRAINS Bucket**
64	64
65		-* Location: EBRAINS Neurodiagnoses Bucket
	51	+* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
66	66	* Ensure correct metadata tagging before submission.
67	67	)))
68	68	* (((
69	69	**Option 2: Contribute via GitHub Repository**
70	70
71		-* Location: GitHub Data Repository
72		-* Create a new folder under /data/ and include a dataset description.
73		-* 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.
74	74	)))
75		-)))
76		-1. (((
77		-**Integrate Data into AI Models**
78	78
	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	+
79	79	* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
80	80	* Standardize neuroimaging and biomarker formats using harmonization tools.
81		-* Utilize machine learning models to handle missing data and feature extraction.
	71	+* Use machine learning models to handle missing data and feature extraction.
82	82	* 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]].
83	83
84		-**Reference**: See docs/data_processing.md for detailed instructions.
85		-)))
	75	+----
86	86
87		-**AI-Driven Biomarker Categorization**
	77	+== **Database Sources Table** ==
88	88
89		-Neurodiagnoses employs advanced AI models for biomarker classification:
	79	+=== **Where to Insert This** ===
90	90
91		-|=**Model Type**|=**Application**
92		-|**Graph Neural Networks (GNNs)**|Identify shared biomarker pathways across diseases
93		-|**Contrastive Learning**|Distinguish overlapping vs. unique biomarkers
94		-|**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
95	95
96		-**Collaboration & Partnerships**
	84	+=== **Key Databases for Neurodiagnoses** ===
97	97
98		-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
99	99
100		-* 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.
101	101	* Co-develop harmonized AI-ready datasets with standardized annotations.
102	102	* Secure funding opportunities through joint grant applications.
103	103
104		-**Interested in Partnering?**
	116	+=== **Interested in Partnering?** ===
105	105
106	106	If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
107	107
108		-**Contact**: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
	120	+* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
109	109
110		-**Final Notes**
	122	+----
111	111
112		-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** ==
113	113
114		-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.
115	115
116		-**For additional technical documentation and collaboration opportunities:**
	128	+For additional technical documentation:
117	117
118		-* **GitHub Repository:** [[Neurodiagnoses GitHub>>url:https://github.com/neurodiagnoses]]
119		-* **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/]]
120	120
121		-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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