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README.md

PDX Finder

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Patient-derived tumor xenograft (PDX) models are a critical oncology platform for cancer research, drug development and personalized medicine. Because of the heterogeneous nature of PDXs repositories, finding models of interest is a challenge. The Jackson Laboratory and EMBL-EBI are developing PDX Finder, the world’s largest open PDX database containing more than 24M phenomic datapoints from over 4000 models (stats October 2020, www.pdxfinder.org). In support of this initiative, we developed the PDX Minimal Information standard (PDX-MI) which defines metadata necessary to describe models. Within PDX Finder, critical attributes like diagnosis, drug names or genes are harmonized into a cohesive ontological data model based on PDX-MI. An intuitive search and faceted search interface allow users to select models based on clinical/PDX attributes, tumor markers, dataset availability and/or drug dosing results. We are providing PDX, patient, drug and molecular data detail pages where all available information can be browsed and downloaded. To further facilitate users model selection, we are linking key external resources like publication platforms and cancer specific annotation tools enabling exploration and prioritisation of PDX variation data (COSMIC, CIViC, OpenCRAVAT, OncoMX). Links to originating resource protocols and contact information are provided facilitating data understanding and further collaboration.

Concomitant to its database development activities, PDX Finder has undertaken several specific activities to tackle areas of standards and tool development, data integration and outreach. PDX Finder is deeply embedded into the PDX community, collaborates and provides critical expertise and software components to support several worldwide consortia including PDXNet, PDMR and EurOPDX. We are driving and promoting models sharing, standard development and usage to ensure global data interoperability. Our PDX-MI standard has become the de facto community standard for data exchange and is adopted by PDX providers, consortia, and informatic tools integrating PDX data. It has been re-used by different initiatives in the context of data collection and data modelling allowing adherence to FAIR principles.

Through its various activities, PDX Finder is increasing model awareness, integration and triggering international collaboration to accelerate cancer research, drug discovery and maximising funding agencies investment and translational capabilities of PDX models.

PDX Finder is freely available under an Apache 2 license (https://github.com/PDXFinder). Work is supported by NCI U24 CA204781 01, U24 CA253539 01, R01 CA089713 and the European Molecular Biology Laboratory.

Publications:

Conte et al, 2019. PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery. NAR, 2019 Jan

Meehan, Conte et al, 2017. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov

About

PDX Finder performs integration, standardization, analysis and visualization of the complex and diverse data associated with PDX mouse models for the cancer community.

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