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 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. Valuable solutions to these problems lie at the intersection of Machine learning and sentiment analysis; through ontologies, semantic similarity, and clustering.
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 project: PatientFORUM embedding model & Combined Ontology for Inflammatory Diseases (COID) Semantic similarity builds upon the patient voice in understanding the sort of terms patients are using. Not only can semantics help us better undertand the patient, but also the clinician.
Patients may struggle with clinical terms (jargon) but domain experts may also be unfamiliar with the terms patients are using. Highlighting gaps in communication and understanding.
Resources for secondary research use This projet presents two resources of novel data for seconday research use.
OcIMIDo
Development and application of the Ocular Immune-Mediated Inflammatory Diseases ontology (OcIMIDo) enhanced with synonyms from online patient support forum conversation GitHub Manuscript Bioportal MIRO guidelines Uveitis and other ocular immune-mediated inflammatory diseases (IMIDs) are chronic conditions and in many cases life threatening. Uveitis itself is one of the top causes of blindness and often undifferentiated: no identifiable cause.
Having good vision is important to our everyday lives and these ocular IMIDs cause problems, such as pain or blurriness.
Jabberwocky
Jabberwocky: a Python toolkit for NLP tasks and manipulation of those nonsensical Ontologies 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 as they condense a domain of knowledge in a structured manner. Concepts in an ontology have a label and possibly synonyms, yet in cases there lacks this vital information.
ResearcHers Code takeover
I ran the ResearcHers Twitter account from the 8th until the 12th February 2021 - the below are Tweets I copied over and edited/shortened for the blog & update the reader. Monday: history Hello! I’m Samantha, and I’ll be tweeting from this account for the week! I’m a 3rd year PhD student at the University of Birmingham in the UK. My field is Clinical Informatics, and I am looking at inflammation!
Applying for a PhD
My experience of the PhD application process 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.
The following advice could be helpful, if not: that’s OK. Please note: the advice below was not mine alone as I had asked fellow PhD students and others.
Colours
Rainbow project All fun little Python projects via command line interface.
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. And so, I made indigo to make my note-taking easier: I can Alt+Tab to switch between the window of results to the window of notes.