MedAI #73: Empowering Biomedical Informatics with Open Resources | Houcemeddine Turki

Title: Empowering Biomedical Informatics with Open Resources: Unleashing the Potential of Data and Tools

Speaker: Houcemeddine Turki

Abstract:
Biomedical informatics is a highly interdisciplinary field that has gained increasing importance in recent years. Combining computer science, statistics, and information science with clinical and basic biomedical research, it seeks to leverage data-driven approaches to solve healthcare challenges and accelerate biomedical discovery. With the explosion of biomedical data generated from various sources such as genomic sequencing, medical imaging, electronic health records, and wearable devices, the field has witnessed significant growth in recent years. One of the key drivers of this growth is the increasing availability of open resources, such as open-access data repositories and software tools. These resources have democratized access to biomedical data and tools, making it easier for researchers to conduct biomedical informatics research and drive scientific discoveries.
PubMed, an open-access bibliographic database maintained by the National Center for Biotechnology Information (NCBI), offers researchers access to millions of citations for biomedical literature, including links to full-text articles and MeSH (Medical Subject Headings) terms for indexing and searching. These resources can be used to develop and validate computational models and algorithms, enabling researchers to study different aspects of diseases and therapies. Wikidata, a free and open knowledge graph maintained by the Wikimedia Foundation, is another critical open resource that is driving biomedical informatics. With Wikidata, researchers can access and contribute to a structured and linked database of biomedical information, including genes, diseases, and drugs. The Open Biomedical Ontologies Foundry (OBO Foundry) is an initiative to develop and maintain a library of interoperable, open-source ontologies for biomedical research. These ontologies provide a common framework for annotating and integrating biomedical data from different sources, enabling data sharing and collaboration.
In this presentation, I will share our way of reusing open resources, particularly NCBI Resources, Wikidata, and the Python Package Index. I will highlight the advantages and challenges of using open resources in biomedical informatics research, share success stories, and discuss the potential of these resources in accelerating scientific discovery. Finally, I will provide some insights into the future of open resources in biomedical informatics, emphasizing the need for greater collaboration and data sharing to tackle the pressing challenges in healthcare.

Speaker Bio:
Houcemeddine Turki is a medical student at the University of Sfax, Tunisia, and a research assistant at the Data Engineering and Semantics Research Unit, University of Sfax, Tunisia. His research spans several interdisciplinary fields, including Biomedical Informatics, Library and Information Science, Semantic Technologies, Open Science, and Applied Linguistics. With a passion for open science, he is a dedicated contributor to Wikimedia Projects, particularly Wikipedia and Wikidata, and has held leadership roles within the Wikimedia community, including Vice-Chair of the Wikimedia Tunisia User Group (2020-2022), Board member of the Wikimedia and Libraries User Group (2019-2021), and member and advisor to the Affiliations Committee of the Wikimedia Foundation (2021-2023). Houcemeddine has played an active role in organizing several Wikimedia community conferences, such as Wikimania (2022) and WikiIndaba Conference (2018, 2020, and 2021), and is committed to advancing the mission of open access and open knowledge sharing for all.

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We will be having weekly sessions where invited speakers will give a talk presenting their work followed by an interactive discussion and Q&A. Our sessions are held every Thursday from 1pm-2pm PST.