Some priorities for September

[ypriverol]

Documents to be created

• Create a document outlining criteria for selecting datasets to be analyzed and sent to OpenTargets (OT). These criteria should be based on previous rules defined by @ypriverol and @Ananth-Prakash. Key factors could include instrument type, the number of raw files, technical/biological replicates, and more.
  MS Rules Template:

• Define a template based on the selection rules for OT datasets. This template should be discussed with the OT consortium (@Ananth-Prakash) to ensure alignment.

• Draft guidelines for selecting datasets for OT. The guidelines will use the MS Rules Template to evaluate each dataset, and the template will be circulated within the OT consortium for prioritization. Criteria such as experimental setup (e.g., knockout, drug exposure, treatment) will be considered.
  QC Rules and Metrics:

• Propose a set of QC rules and metrics to evaluate datasets before submission to OT.

Generate a List of Datasets by Disease

A list of diseases relevant to OT has been created. The next step is to map relevant datasets from PRIDE to these diseases and prioritize them based on the previously defined selection criteria.

Data Integration Discussion

@Ananth-Prakash and @ypriverol will prepare a presentation to discuss the challenges of integrating data from various datasets and analytical methods. This presentation will be shared with OT members to foster discussion and gather feedback on data integration strategies.

[ypriverol]

@Ananth-Prakash List of diseases with RNA expression datasets in OT and the number of datasets (more than 1 dataset), and the interest from companies:

Disease	# Datasets	Num. of interested OT partners
Alzheimer's Disease (AD)	7	4
Amyotrophic Lateral Sclerosis (ALS)	2	4
Atopic Dermatitis	-	4
Chronic Obstructive Pulmonary Disease (COPD)	4	4
Parkinson's Disease (PD)	5	4
Asthma	5	3
Breast Cancer	11	3
Colorectal Cancer	6	3
Multiple Sclerosis	2	3
Systemic Lupus Erythematosus (SLE)	3	3
Chronic Kidney Disease (CKD)	3	2
Chronic Spontaneous Urticaria	-	2
Crohn's Disease	13	2
Idiopathic Pulmonary Fibrosis	-	2
Lupus Nephritis	-	2
Metabolic dysfunction-Associated Steatohepatitis (MASH)	-	2
Non-Small Cell Lung Cancer (NSCLC)	8	2
Prurigo Nodularis	-	2
Psoriasis	12	2
Rheumatoid Arthritis	4	2
Ulcerative Colitis	13	2
Acute Lymphoblastic Leukaemia (ALL)	-	1
Acute Myeloid Leukemia (AML)	-	1
Age-related Macular Degeneration	-	1
Alcoholic Liver Disease (ALD)	-	1
All autoimmune/inflammatory	-	1
Bronchiectasis	-	1
Chronic Lymphocytic Leukemia (CLL)	2	1
Chronic Rhinosinusitis with Nasal Polyps	-	1
Clonal Hematopoiesis of Indeterminate Potential (CHIP)	-	1
Connective Tissue Diseases	-	1
Coronary Artery Disease	-	1
Diabetic Eye Disease	-	1
Diffuse Large B-Cell Lymphoma (DLBCL)	-	1
Endometrial Cancer	2	1
Glaucoma	-	1
Haematological cancers incl. Leukaemia, Lymphoma and Myeloma	-	1
Hepatitis B	-	1
Hidradenitis Suppurativa	-	1
Hypertension	-	1
Inflammatory Bowel Disease	-	1
Interstitial Lung Disease	-	1
Irritable Bowel Disease	-	1
Lung Adenocarcinoma (LUAD)	5	1
Lung Cancer	3	1
Lung Squamous Cell Carcinoma (LUSC)	-	1
Malaria	-	1
Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD)	-	1
Monoclonal Gammopathy Of Unknown Significance (MGUS)	-	1
Multiple Myeloma (MM)	-	1
Myelodysplastic Syndrome (MDS)	2	1
Nephropathy	-	1
Neuromuscular	-	1
Neuropathic Pain	0	1
Obesity	2	1
Osteoarthritis	3	1
Ovarian Cancer	-	1
Primary Biliary Cholangitis (PBC)	-	1
Primary Sclerosing Cholangitis (PSC)	-	1
Prostate Cancer	2	1
Respiratory syncytial virus (RSV)	-	1
Schizophrenia	0	1
Scleroderma - ILD	-	1
Small Cell Lung Cancer (SCLC)	-	1
Stroke	-	1
Systemic Sclerosis or Scleroderma	-	1
Tuberculosis	-	1
Type 1 Diabetes	2	1
Type 2 Diabetes Mellitus	4	-

[ypriverol]

@Ananth-Prakash I have updated the selection guidelines: https://github.com/PRIDE-Archive/opentargets/blob/main/guidelines/Dataset_Selection.md