AgeMiner logo

AgeMiner: interactive text mining resource for research in neuronal ageing

Released online on 10th March 2021

My latest literature mining project looks at the ageing neuron. After a lot of reading of over 10000 manuscripts and 17000 abstracts, the database is now online and freely accessible. This project includes all the new miner features such as semantic tagging and an RSS feed of latest papers. API access is coming soon.

For more information, visit the website:
https://rupertoverall.net/ageminer



Screenshot of the CovidMiner API running in RStudio

COVIDminer API: advanced search tools for the COVIDminer database

Released on 5th March 2021

The COVIDminer project now uses semantic tagging to filter literature evidence and better navigate through the (now very extensive) database. There is also an API allowing programmatic access to the database and its search features as well as an R package enabling all this to be performed from within your analysis workflow.

The COVIDminerAPI R package is hosted on github:
https://github.com/rupertoverall/COVIDminerAPI



Visual abstract for the manuscript 'ROS Dynamics Delineate Functional States of Hippocampal Neural Stem Cells and Link to Their Activity-Dependent Exit from Quiescence'

ROS Dynamics Delineate Functional States of Hippocampal Neural Stem Cells and Link to Their Activity-Dependent Exit from Quiescence

Published on 4th February 2021

Our study on the role of reactive oxygen species as signalling molecules directing the exit of adult hippocampal neural stem cells from quiescence has been published in Cell Stem Cell.

See the paper at:
https://doi.org/10.1016/j.stem.2020.10.019



NeurogenesisMiner logo

NeurogenesisMiner: interactive text mining resource for research in adult neurogenesis

Released online on 23rd September 2020

I have applied my text mining workflow to another of my research interests - adult neurogenesis. All of the adult neurogenesis literature has been read and condensed into a browsable network of interactions between molecules and biological processes.

For more information, visit the website:
https://rupertoverall.net/neurogenesis-miner



Screenshot of the CovidMiner interface

COVIDminer: interactive text mining resource for COVID-19 research

Released online on 13th April 2020

In response to the COVID-19 crisis, I have created a resource to make text mining results of the enormous flood of published literature accessible to researchers. Primarily aimed at curators of molecular pathway models, this freely-available resource can be helpful to anyone trying to rapidly process the COVID-19 literature.

For more information, visit the website:
https://rupertoverall.net/covidminer



Systems Genetics of Neural Ageing logo

Summer School: Systems Genetics of Neural Ageing

21st – 28th August 2020

POSTPONED TO 2021

I am running a summer school in systems medicine this year. Aimed at PhD students and postdocs working in neuroscience and medicine who want to know more about using 'big data' in their research. We ask the question: how can we use public data and system genetics tools to understand the functional decline in neural cells in advanced age?

For more information, visit the website:
https://sysgenschool.org/sgn2020



Rtrack: an R package for spatial navigation analysis

Version 0.9.6 released on 28th January 2020

I have published a package for the analysis of spatial navigation data (e.g. water maze). This is now on CRAN and there is a website full of background information and step-by-step tutorials.

For more information, visit the website:
https://rupertoverall.net/Rtrack