Submission guide

In the complex realm of patient-derived cancer models (PDCMs), including PDX, organoids, and cell lines, finding the right model and associated data has been a formidable challenge. Researchers, clinicians, and bioinformaticians have struggled to navigate this vast landscape, hindered by a lack of shared data standards.

CancerModels.Org is here to simplify this process. We harmonise and integrate critical model attributes, offering a unified platform for efficient searching across diverse resources. Building on the success of the PDX Finder resource PMID:30535239 and the PDX Minimal Information standard (PDX-MI, PMID:29092942), we're dedicated to enabling seamless data exchange and accelerating cancer research.

Why Submit Your Models and Data to CancerModels.Org:

Increased Visibility: Your models and associated data becomes more discoverable to researchers and other users.
Standardisation: Your models adhere to published standards, making it easier for researchers to search and compare them.
Adherence to FAIR principles: Your data is structured to adhere to the FAIR data principles, which means it's Findable, Accessible, Interoperable, and Reusable.
Attribution: Clear links to production centres are provided, so users can inquire about obtaining your models for their studies.
Free Access: CancerModels.Org is a community-driven platform that's free for both model providers and users.

Eligible models and associated data

CancerModels.Org aggregates models from individual researchers, institutional biobanks, contract research organisations, external databases and consortia engaged in cancer research focusing on models from rare cancers and richly annotated models. All models and data should adhere to ethical and legal guidelines related to patient consent, data privacy, and data sharing. Since 1 January 2023 all model and data submissions are made available under CC0.

Data types and formats

Data type	Description	Format	Submission template
Metadata	Metadata related to the PDCMs, such as model information, and clinical information .	Excel	Metadata template
Molecular metadata	Metadata associated with the molecular data.	Excel	Molecular metadata template
Mutation	All sequencing data including WES, WGS & TGS used to generate mutation data for the PDCMs.	MAF, VCF	Mutation data template
Copy Number Alteration	Data related to copy number alterations in PDCMs, which can provide insights into genomic amplifications and deletions.	log2 ratio or discrete CNA data (GISTIC, PICNIC)	CNA data template
Gene expression	Information regarding gene expression patterns in PDCMs, which can shed light on gene activity and regulation.	Excel, TXT or CSV: TPM, FPKM,RPKM, Z-score	Expression data template
Biomarker	Information related to gene mutations, gene expression levels, protein markers, immune cell populations, chromosomal abnormalities, structural changes in the genome and other molecular characteristics of tumours. This data is derived from genomics, transcriptomics, proteomics, and immunohistochemistry.	Excel, TXT or CSV: Biomarker status, Immunohistochemistry results, TMB score	Biomarker data template
Immune markers	Information related to immune cell populations, chromosomal abnormalities, and other molecular characteristics of tumours. This data is derived from genomics, and immunohistochemistry.	Excel, TXT or CSV: MSI status, HLA type, TMB score	Immune marker template
Drug dosing	Information about drug dosing studies conducted on PDCMs, including drug names, responses and dosage information.	Excel, TXT or CSV	Drug dosing template
Patient treatment	Information related to the treatment patient received from whom PDCMs were derived. Include details of therapies administered, drug and regimen names, doses and their outcomes.	Excel, TXT or CSV	Patient treatment template
Image data	Histology Image data of the PDCMs	Excel file with URLs to model images per row	Via BioImage Archive Model image sheet part of Metadata template