Gene Function Prediction by Mining Bioimedical Literature
Faculdade de Ciências de Universidade de Lisboa –
This seminar will discuss the application of text mining to automate the identiﬁcation
of the function of large sets of genes from the biomedical literature. An approach
will be presented to obtain this knowledge as annotations that associate biologic entities
to Gene Ontology terms. This approach was validated by building the APEG
(Arabidopsis Pollen Expressed Genes) database system, which integrates information
about 147 pollen selectively expressed genes of Arabidopsis thaliana, from various public
databases available on the Web. APEG operates with ProFAL, a text mining and
automatic database annotation tool. The eﬀectiveness of the automatic annotation
of the genes was evaluated by comparing the set of annotations discovered by Pro-
FAL with those obtained by domain experts scanning the same literature. Functional
annotations were extracted with an average precision and recall of 61% and 78%, respectively.
ProFAL has also identiﬁed 21 probable functions for 8 genes, which, to
the best of my knowledge, have not been documented. The validation of the proposed
approach was done using an interactive web interface with curator speciﬁc features.
The results show that mining the biomedical literature can eﬀectively increase our
knowledge about a set of genes or proteins of interest, leading to more conclusive
answers to the underlying biological problems.
Date: 2004-Oct-07 Time: 16:00:00 Room: 336
For more information:
Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.