Dr Samantha Pendleton
Wrangler of data, ontologies, and clusters.
Thrower of pots, controllers, and eggs.
The PhD
Becoming a Doctor in Clinical Informatics The information in this post is my personal PhD journey. I aim to inform and share my PhD (experience and research) with you – the reader. Year 1 You don’t have as much experience as I would have thought…
This was one of the first things said to me…during my first week. Imposter syndrome was planted and settling in for the long haul.
For the first month there was no desk for me and so I sat alone in the quiet working room.
Hello World
Version 3 has been released I started this website journey around 2015 for university assignments: writing blogs for modules. I decided to create my own CSS and index page to better structure my work. In 2021, midway through my PhD, I progressed onto GitHub pages with Bootstrap and a terrible repo structure. Now in 2023, I’ve decided to try Hugo.
A few months ago, with COVID, I decided to revamp the site and intended to go with the markdown-file route.
Patient Voice
Investigations into the patient voice: a multi-perspective analysis of inflammation This work is my PhD1, completed in 2023.
Background The patient is the expert of their medical journey and their experiences go largely unheard in clinical practice. Understanding the patient is important as bridging gaps in the medical domain enhances clinical knowledge: benefiting patient care in addition to improving quality of life.
My PhD presented challenges and solutions exploring quality of life pertaining to two inflammatory diseases, Uveitis and Inflammatory Bowel Disease (IBD), which are often undifferentiated.
Fashun
Fashun: an R Shiny app of fashion trends I want to start by saying fashion (or fashun) is whatever you want it to be - whether that is wearing double denim, or two completely different patterns. I enjoy fashion. By “fashion” I mean any outfit - I find clothing an outlet to expressing oneself.
» Fashun app
Introduction Setting the scene: I have just handed in my PhD thesis and found that there’s extra free time in my evenings.
PatientINF
PatientINF & COID Resources in this project are both are available open-source for secondary research use:
PatientINF is an embedding model. COID is the Combined Ontology for Inflammatory Diseases. Background Semantic similarity builds upon the patient voice in understanding synonyms and the sort of terms patients are using. Not only can semantics help to better undertand the patient, but also the clinician. Patients may not use clinical terms (jargon) often and domain experts may be unfamiliar with patient-preferred terms.
OcIMIDo
Development and application of the Ocular Immune-Mediated Inflammatory Diseases ontology (OcIMIDo) enhanced with synonyms from online patient support forum conversation OcIMIDo is the first ontology of its kind in opthamology1. Available open-source on GitHub and other biomedical ontology platforms, including Bioportal.
Background Uveitis and other ocular immune-mediated inflammatory diseases (IMIDs) are chronic conditions (usually life-long) and in many cases, life threatening. Uveitis itself is one of the top causes of blindness and often undifferentiated: no identifiable cause.
Jabberwocky
Jabberwocky Jabberwocky is a Natural Language Processing (NLP) toolkit for those nonsensical ontologies1. Available open-source on GitHub.
Unstructured text is a valuable resource for research, yet text mining is a complicated task. Text mining with key terms can be limited and potentially enhanced with the knowledge of synonyms. Especially synonyms in that domain.
Ontologies are useful - they condense a domain of knowledge in a structured manner and classes may have synonyms.
ResearcHers Code takeover
I ran the ResearcHers Twitter account from the 8th until the 12th February 2021 - below are Tweets I copied over and edited/shortened for the blog/reader. Monday: history I’m a 3rd year PhD student (2021) at the University of Birmingham, UK. My field is Clinical Informatics, and I am looking at inflammation! Today I’ll talk about my experience learning to code throughout education: when it started, how it progressed, and what I can do now!
Applying for a PhD
My experience of the PhD application process tl;dr: be yourself, include things you have learnt (even if not much practical experience), and get some buzz words in the bank (make sure you use them correctly)!
Introduction During my time as a mentor for undergraduates and teaching assistant for Masters students, I have had questions about the PhD application process. Now as a PhD student with a bunch of curated responses, the following post is the advice I gave.
Colours
Rainbow project A set of fun - little - projects developed with Python for the command line interface.
As of 2019 these projects are no longer supported! indigo Simple to-do list: indi-go-ing
indigo is a to-do list tracker (GitHub repo). During my PhD, I often had impromptu meetings which needed my laptop and I found myself unable to multi-task: reading results, listening to others, and trying to write down notes. I usually ended up rushing my notes, which then became unreadable.