Joyeuse Mujambere bio photo

Joyeuse Mujambere

Senior at Basis Tucson North

Email Github

Overview

Overview

Intern at the Critical Path Institute, a biomedical non-profit that is a public/private partnership that works to advance drug discovery for rare and underserved diseases. Served as an inern in the Data Science Team in the Data Collaboration Center from June 2023 - August 2024, under the supervision of Dr. Nicole Vasilevsky.

Github basic skills training

GitHub is a web-based platform for collaborative software development and project management. Gained basic knowledge about the software and its functions.

Did OBO Academy training to learn:

  • How to uses Markdown
  • How to create issues
  • Create a pull request
  • Create a website

Built personal website

Used skills learned about Github to contruct this personal website

Landscape of Data Science Team Competencies

Performed a landscape analysis of the skills in the C-Path Data Science team that assessed competencies amongst the team members.

These included:

  • Microsoft office
  • Programming
  • Python programming
  • GitLab Continuous Integration/Continous Development (CI/CD)
  • Git (including GitHub or GitLab)
  • SQL
  • SPARQL
  • Cyberinfracture/ High-Performance Computing (HPC)
  • Natural Language processing
  • Machine learning
  • Biocuration
  • Data curation and cleaning
  • Scientific writing
  • Public speaking
  • Proposal preparation/ writing
  • Communication
  • Data standards inclduing SDTM, OMOP, FHIR, OBO Ontologies
  • Data Management
  • Developing and presenting training material
  • Developing documentation
  • Project management
  • Community standards
  • Biomedical ontology development
  • Ontology management
  • Makefiles
  • Automated ontology pipelines
  • Ontology Development Kit (ODK)
  • Ontology mappings
  • Workflow design
  • Testing Apps/ Programs
  • Creating R Shiny Apps
  • Creating a statistical plan
  • Testing a statistical plan
  • Statistical consulting
  • Collaboration and teamwork
  • Outreach and community
  • Collaboration on coding projects
  • AWS Cloud Infra
  • Docker Containers
  • RESTful APIs
  • Jira

Scientific Publication

Vita, R., Aspromonte, M. C., Bello, S. M., Harris, N. L., Caufield, J. H., Haendel, M., Hoyt, C. T., Quaglia, F., Mujambere, J., Panossian, S. P., Reddy, T. B. K., Tuli, M. A., Khodiyar, V. K., & Vasilevsky, N. (2023). Careers in Biocuration: 2023 Workshop Report. 16th Annual International Biocuration Conference, Padova, Italy. Zenodo. https://doi.org/10.5281/zenodo.10246586

Description: Reported on a workshop held at the Biocuration Conferencein Padua, Italy in April 2023. The report describes the Careers Workshop which discussed relevant skill sets for biocurators, how to tailor a resume or curriculum vitae (CV) for finding a position or for career progression, as well as tips for recruitment.

Ontology Training

An ontology is a branch of metaphysics that studies the nature of being. Can also be refer to a formal description of knowledge as a set of consepts and relationships within a domain.

Did OBO Academy ontology training

Mapping of Rare Epilepsy Patient Data to Disease and Phenotype Ontologies

The Rare Epilepsy Network (REN) which connects over 125+ Rare Epilespy Organizations to promote awareness and advocacy.

Website: https://www.rareepilepsynetwork.org/

In order to make the data from the REN more discoverable and interoperable with other datasets, we mapped the survey questions to disease or phenotype terms from biomedical ontologies.

The Mondo Disease Ontology is a semi-automatically constructed ontology that merges in multiple disease resources to yeild a coherent merged ontology.

Website: https://mondo.monarchinitiative.org/

The Human Phenotype Ontology is a standardized vocabulary of phenotypic abnormalities encountered in human disease.

Website: https://hpo.jax.org/

The annotated data will be incorporated into the C-Path Knowledge Graph and made available via the Rare Disease Cures Accelerator and Data and Analytics Platform (RDCA-DAP) to researchers and clinicians to reuse the data to advance drug discovery.

Mapping of Clinical Outcome Assessments (COAs) to Phenotype Ontologies

A clinical outcome assessment (COA) is the patient assesment used in an endpoint and provides a rating that is intended to represent some aspect of a patient’s health status.

To enhance the findability of relevant COAs for clinical trials, we annotated COAs in the C-Path COA Resource to ontology terms.