I have just submitted my PhD in Biomedical Sciences at VIB and Ghent University (Belgium), with a thesis entitled “An open data exchange ecosystem: forging a new path for cell migration data analysis and mining”. During my PhD I have tried to make cell migration research more ‘open’: I have developed computational open source tools and algorithms for the storage, management, dissemination and analysis of cell migration experiments. Furthermore, I have tried to push this ‘open’ concept a bit beyond my own PhD, and have succeeded in engaging a few researchers in this fight: I am now working in MULTIMOT, an EU-H2020 funded project that aims to build an open data ecosystem for cell migration research, with the ultimate goal to increase reproducibility, and allow analyses to take place on rich datasets that would otherwise remain unused.
As a ContentMine fellow, I want to text mine literature around cell migration and invasion, because I believe that there is a huge amount of information in all the papers continuously published in the field, and that this information simply cannot be processed by the human eye. Specifically, text mine cell migration articles will hopefully help in the following tasks:
- automatically detect a set of core information reported when describing experiments in the field, and therefore construct a collection of minimum reporting requirements from these. These requirements can then be used to aid experimental and computational reproducibility.
- check for nomenclature consistency, the use of common terms or ontologies to describe the same concept, again with the goal to increase reproducibility, and allow meta-analyses to take place.
- construct a knowledge map that could capture the current status of information in the field, especially in terms of cell motility-related compounds and (cancer) cell lines.