An informatics platform for translational disease research

Because each disease is different, there are significant challenges in obtaining enough information relevant to the patient’s condition to help inform diagnosis and treatment. The PXF standard will allow phenotypic data to be captured at the point of publication, to be transmitted in the context of diagnostic testing, to be used for exchange of data in clinical studies, and as a backbone for patient-contributed data registries and social media. Increasing the volume of computable phenotype data across a diversity of systems will support large-scale computational disease analysis using cross species genotype and phenotype data.

The initial version of the PXF standard is being implemented in the context of journals, but an editing tool to read and write PXF documents is needed to facilitate this exchange. This project can include one or more of the following tasks, depending on the status of the project at the start of the program and an agreement between the student and the mentor:

Add import and export of PXF files to the Monarch WebPhenote application. Create a lightweight web application that can be integrated into other research portals and platforms to ease the creation of PXF files and enable their distribution. Implement tools to convert variant descriptions in other formats to PXF format. This includes the parsing of plain text, HTML and more structured formats. The PXF output from this will then be reviewable and editable by a users prior to committing the PXF.

Candidates should have a good understanding of software tools such as Unix (MacOSX or Linux); Git; one or more high-level programming languages (NodeJS, Python, Go, Ruby); and a basic understanding of network usage (HTTP, SSH). Ability to write simple web applications (HTML, JavaScript, CSS) is important.

https://github.com/monarch-initiative/phenopacket-format/wiki/Overview-of-Phenotype-Exchange-Format

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Technologies

  • semantic web
  • javascript
  • text mining
  • named entity recognition
  • ontologies

Topics

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2016