Gene Function Prediction by Mining Bioimedical Literature
Pooja Jain,
Faculdade de Ciências de Universidade de Lisboa –
Abstract:
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:
Upcoming Events
Mathematics, Physics & Machine Learning Seminar Series (Online)

The Mathematics, Physics & Machine Learning seminar series has started on October 2020 and runs until March 2021.
The seminars aim to bring together mathematicians and physicists interested in machine learning (ML) with ML and AI experts interested in mathematics and physics, with the goal of introducing innovative Mathematics and Physics-inspired techniques in Machine Learning and, reciprocally, applying Machine Learning to problems in Mathematics and Physics.
Attendance is free but registration is required.
More information is available here.
International European Conference on Parallel and Distributed Computing

The 27th International European Conference on Parallel and Distributed Computing (Euro-Par 2021) will take from August 30 to September 3 2021 in Lisbon.
Euro-Par is the prime European conference covering all aspects of parallel and distributed processing, ranging from theory to practice, from small to the largest parallel and distributed systems and infrastructures, from fundamental computational problems to full-fledged applications, from architecture, compiler, language and interface design and implementation, to tools, support infrastructures, and application performance aspects.
The 2021 edition of Euro-Par will be organized as a collaboration between INESC-ID and Instituto Superior Técnico (IST).
Important Dates:
– Abstract Submission: February 5, 2021
– Paper Submission Deadline: February 12, 2021
– Author Notification: April 30, 2021
– Camera-Ready Papers: June 6, 2021
More information is available here.