This webpage is a demonstration application of a conceptual semi-automatic indexer. This project is funded by the LGI2P laboratory of the École des mines d'Alès.

The use case presented here relies on an ontology – the MeSH – and a corpus previously created in the LGI2P – 38.000 documents annotated by MeSH concepts. If you just want to quickly try out this tool, follow the "How to" instructions. When the form is displayed, click "Load example".

This front-end application is developped and maintained by Nicolas Fiorini, PhD candidate at the École des mines d'Alès. Sylvie Ranwez, Jacky Montmain and Vincent Ranwez supervise this project through the whole PhD project supervision.



This prototype shows how USI can annotate a document when a neighborhood is identified. In this application, the neighborhood is implicitly defined by a click on the map. The map creation relies on independent tools to get MeSH concepts for each document on the map, from a list of authors, a title and a list of references. These tools are the Europe PMC web service and the E-utilities:

Sayers E. E-utilities Quick Start. 2008 Dec 12 [Updated 2013 Aug 9]. In: Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. Available from: http://www.ncbi.nlm.nih.gov/books/NBK25500/

Once the resources are loaded, the proper map creation relies on the Multi-Dimensional Scaling by using the MDSJ library:

Algorithmics Group. MDSJ: Java Library for Multidimensional Scaling (Version 0.2). Available at http://www.inf.uni-konstanz.de/algo/software/mdsj/. University of Konstanz, 2009.

The Semantic Measures Library is a keystone in this project, allowing USI to compute semantic similarities:

The Semantic Measures Library and Toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. Sébastien Harispe; Sylvie Ranwez; Stefan Janaqi; Jacky Montmain. Bioinformatics 2014 30(5): 740-742. doi: 10.1093/bioinformatics/btt581


Annotation suggestion



Here is a semi-automatic indexer for annotating entities. This tool allows you to annotate biomedical related papers with MeSH concepts.


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