Wiki source code of Methodology

Version 19.1 by manuelmenendez on 2025/02/14 13:57

version	line-number	content
19.1	1	# Neurodiagnoses AI: Multimodal AI for Neurodiagnostic Predictions
1.1	2
19.1	3	## Project Overview
	4	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.##
1.1	5
19.1	6	## How to Use External Databases in Neurodiagnoses
	7	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.##
1.1	8
19.1	9	### Potential Data Sources
	10	Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases. ##
	11
	12	Reference: List of Potential Databases
	13	- ADNI: Alzheimer's Disease data ([ADNI](https://adni.loni.usc.edu))
	14	- PPMI: Parkinson’s Disease Imaging and biospecimens ([PPMI](https://www.ppmi-info.org))
	15	- GP2: Whole-genome sequencing for PD ([GP2](https://gp2.org))
	16	- Enroll-HD: Huntington’s Disease Clinical and genetic data ([Enroll-HD](https://www.enroll-hd.org))
	17	- GAAIN: Multi-source Alzheimer’s data aggregation ([GAAIN](https://gaain.org))
	18	- UK Biobank: Population-wide genetic, imaging, and health records ([UK Biobank](https://www.ukbiobank.ac.uk))
	19	- DPUK: Dementia and Aging data ([DPUK](https://www.dementiasplatform.uk))
	20	- PRION Registry: Prion Diseases clinical and genetic data ([PRION Registry](https://prionregistry.org))
	21	- DECIPHER: Rare genetic disorder genomic variants ([DECIPHER](https://decipher.sanger.ac.uk))
	22
	23	### 1. Register for Access
	24	- Each external database requires individual registration and access approval.
	25	- Ensure compliance with ethical approvals and data usage agreements before integrating datasets into Neurodiagnoses.
	26	- Some repositories may require a Data Usage Agreement (DUA) for sensitive medical data.##
	27
	28	### 2. Download & Prepare Data
	29	- Download datasets while adhering to database usage policies.
	30	- Ensure files meet Neurodiagnoses format requirements:
	31	- Tabular Data: `.csv`, `.tsv`
	32	- Neuroimaging Data: `.nii`, `.dcm`
	33	- Genomic Data: `.fasta`, `.vcf`
	34	- Clinical Metadata: `.json`, `.xml`##
	35
	36	- Mandatory Fields for Integration:
	37	- Subject ID: Unique patient identifier
	38	- Diagnosis: Standardized disease classification
	39	- Biomarkers: CSF, plasma, or imaging biomarkers
	40	- Genetic Data: Whole-genome or exome sequencing
	41	- Neuroimaging Metadata: MRI/PET acquisition parameters
	42
	43	### 3. Upload Data to Neurodiagnoses
	44	Option 1: Upload to EBRAINS Bucket
	45	- Location: EBRAINS Neurodiagnoses Bucket
	46	- Ensure correct metadata tagging before submission.##
	47
	48	Option 2: Contribute via GitHub Repository
	49	- Location: GitHub Data Repository
	50	- Create a new folder under `/data/` and include a dataset description.
	51	- For large datasets, contact project administrators before uploading.
	52
	53	### 4. Integrate Data into AI Models
	54	- Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
	55	- Standardize neuroimaging and biomarker formats using harmonization tools.
	56	- Use machine learning models to handle missing data and feature extraction.
	57	- Train AI models with newly integrated patient cohorts.##
	58
	59	Reference: See `docs/data_processing.md` for detailed instructions.
	60
	61	## Collaboration & Partnerships##
	62	# Partnering with Data Providers
	63	Neurodiagnoses seeks partnerships with data repositories to:
	64	- Enable API-based data integration for real-time processing.
	65	- Co-develop harmonized AI-ready datasets with standardized annotations.
	66	- Secure funding opportunities through joint grant applications.
	67
	68	Interested in Partnering?
	69	- If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
	70	- Contact: info@neurodiagnoses.com
	71
	72	## Final Notes
	73	Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.##
	74
	75	For additional technical documentation:
	76	- GitHub Repository: [Neurodiagnoses GitHub](https://github.com/neurodiagnoses)
	77	- EBRAINS Collaboration Page: [EBRAINS Neurodiagnoses](https://ebrains.eu/collabs/neurodiagnoses)
	78
	79	If you experience issues integrating data, open a GitHub Issue or consult the EBRAINS Neurodiagnoses Forum.
	80
18.1	81	== How to Use External Databases in Neurodiagnoses ==
1.1	82
18.1	83	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.
12.2	84
18.1	85	=== Potential Data Sources ===
12.2	86
18.1	87	Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
12.2	88
18.1	89	* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
12.2	90
18.1	91	=== 1. Register for Access ===
12.2	92
18.1	93	Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
12.2	94
18.1	95	* Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
	96	* Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
12.2	97
18.1	98	=== 2. Download & Prepare Data ===
12.2	99
18.1	100	Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
12.2	101
18.1	102	==== Supported File Formats ====
12.2	103
18.1	104	* Tabular Data: .csv, .tsv
	105	* Neuroimaging Data: .nii, .dcm
	106	* Genomic Data: .fasta, .vcf
	107	* Clinical Metadata: .json, .xml
12.2	108
18.1	109	==== Mandatory Fields for Integration ====
12.2	110
18.1	111	\|=Field Name\|=Description
	112	\|Subject ID\|Unique patient identifier
	113	\|Diagnosis\|Standardized disease classification
	114	\|Biomarkers\|CSF, plasma, or imaging biomarkers
	115	\|Genetic Data\|Whole-genome or exome sequencing
	116	\|Neuroimaging Metadata\|MRI/PET acquisition parameters
12.2	117
18.1	118	=== 3. Upload Data to Neurodiagnoses ===
12.2	119
18.1	120	Once preprocessed, data can be uploaded to EBRAINS or GitHub.
12.2	121
18.1	122	* (((
	123	Option 1: Upload to EBRAINS Bucket
12.2	124
18.1	125	* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
	126	* Ensure correct metadata tagging before submission.
	127	)))
	128	* (((
	129	Option 2: Contribute via GitHub Repository
12.2	130
18.1	131	* Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
	132	* Create a new folder under /data/ and include dataset description.
	133	)))
12.2	134
18.1	135	//Note: For large datasets, please contact the project administrators before uploading.//
12.2	136
18.1	137	=== 4. Integrate Data into AI Models ===
12.2	138
18.1	139	Once uploaded, datasets must be harmonized and formatted before AI model training.
12.2	140
18.1	141	==== Steps for Data Integration ====
12.2	142
18.1	143	* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
	144	* Standardize neuroimaging and biomarker formats using harmonization tools.
	145	* Use machine learning models to handle missing data and feature extraction.
	146	* Train AI models with newly integrated patient cohorts.
	147	* 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]].
12.2	148
17.1	149	----
12.2	150
18.1	151	== Database Sources Table ==
12.2	152
18.1	153	=== Where to Insert This ===
12.2	154
18.1	155	* GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
	156	* EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
1.1	157
18.1	158	=== Key Databases for Neurodiagnoses ===
12.2	159
18.1	160	\|=Database\|=Focus Area\|=Data Type\|=Access Link
	161	\|ADNI\|Alzheimer's Disease\|MRI, PET, CSF, cognitive tests\|ADNI
	162	\|PPMI\|Parkinson’s Disease\|Imaging, biospecimens\|[[PPMI>>url:https://www.ppmi-info.org/]]
	163	\|GP2\|Genetic Data for PD\|Whole-genome sequencing\|[[GP2>>url:https://gp2.org/]]
	164	\|Enroll-HD\|Huntington’s Disease\|Clinical, genetic, imaging\|[[Enroll-HD>>url:https://enroll-hd.org/]]
	165	\|GAAIN\|Alzheimer's & Cognitive Decline\|Multi-source data aggregation\|[[GAAIN>>url:https://www.gaain.org/]]
	166	\|UK Biobank\|Population-wide studies\|Genetic, imaging, health records\|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
	167	\|DPUK\|Dementia & Aging\|Imaging, genetics, lifestyle factors\|[[DPUK>>url:https://www.dementiasplatform.uk/]]
	168	\|PRION Registry\|Prion Diseases\|Clinical and genetic data\|[[PRION Registry>>url:https://www.prionalliance.org/]]
	169	\|DECIPHER\|Rare Genetic Disorders\|Genomic variants\|DECIPHER
1.1	170
18.1	171	If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
	172
1.1	173	----
	174
18.1	175	== Collaboration & Partnerships ==
6.1	176
18.1	177	=== Where to Insert This ===
6.1	178
18.1	179	* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
	180	* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
6.1	181
18.1	182	=== Partnering with Data Providers ===
6.1	183
18.1	184	Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
1.1	185
18.1	186	* Enable direct API-based data integration for real-time processing.
	187	* Co-develop harmonized AI-ready datasets with standardized annotations.
	188	* Secure funding opportunities through joint grant applications.
1.1	189
18.1	190	=== Interested in Partnering? ===
1.1	191
18.1	192	If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
1.1	193
18.1	194	* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
1.1	195
	196	----
	197
18.1	198	== Final Notes ==
1.1	199
18.1	200	Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
1.1	201
18.1	202	For additional technical documentation:
1.1	203
18.1	204	* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
	205	* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
1.1	206
18.1	207	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.

Wiki source code of Methodology

Neurodiagnoses