Rutabaga by any other name: extracting biological names

Journal of Biomedical Informatics
Lynette HirschmanAlexander Yeh

Abstract

As the pace of biological research accelerates, biologists are becoming increasingly reliant on computers to manage the information explosion. Biologists communicate their research findings by relying on precise biological terms; these terms then provide indices into the literature and across the growing number of biological databases. This article examines emerging techniques to access biological resources through extraction of entity names and relations among them. Information extraction has been an active area of research in natural language processing and there are promising results for information extraction applied to news stories, e.g., balanced precision and recall in the 93-95% range for identifying person, organization and location names. But these results do not seem to transfer directly to biological names, where results remain in the 75-80% range. Multiple factors may be involved, including absence of shared training and test sets for rigorous measures of progress, lack of annotated training data specific to biological tasks, pervasive ambiguity of terms, frequent introduction of new terms, and a mismatch between evaluation tasks as defined for news and real biological problems. We present evidence from a simple le...Continue Reading

References

Jul 27, 2001·Bioinformatics·V HatzivassiloglouA Rzhetsky
Jul 26, 2002·Briefings in Bioinformatics·Christian BlaschkeAlfonso Valencia
Aug 10, 2002·Bioinformatics·Michael KrauthammerAndrey Rzhetsky
Aug 15, 2002·Bioinformatics·Lorraine Tanabe, W John Wilbur

❮ Previous
Next ❯

Citations

Jun 17, 2011·Briefings in Bioinformatics·Alberto FaroConcetto Spampinato
Aug 31, 2004·Bioinformatics·Lifeng ChenCarol Friedman
Feb 5, 2005·Bioinformatics·Anna Divoli, Teresa K Attwood
Oct 27, 2005·Bioinformatics·Ted SandlerLyle H Ungar
Nov 20, 2012·Database : the Journal of Biological Databases and Curation·Sun KimW John Wilbur
Dec 22, 2011·BMC Bioinformatics·Chih-Hsuan Wei, Hung-Yu Kao
Jun 18, 2005·BMC Bioinformatics·Katrin FundelJoannis Apostolakis
Jun 18, 2005·BMC Bioinformatics·Alexander YehLynette Hirschman
Jun 18, 2005·BMC Bioinformatics·Jenny FinkelClaire Grover
Apr 25, 2006·BMC Bioinformatics·Aditya K Sehgal, Padmini Srinivasan
Aug 11, 2006·BMC Bioinformatics·Katrin Fundel, Ralf Zimmer
May 9, 2012·BMC Medical Informatics and Decision Making·Son DoanMinh Phuong Tu
Oct 20, 2005·BMC Medical Informatics and Decision Making·Jules J Berman
Aug 31, 2012·BioData Mining·Vida AbediFazle Elahi Faisal
May 17, 2011·Journal of Biomedical Semantics·Tamara PolajnarMark Girolami
Oct 18, 2008·Genome Biology·Fabio RinaldiTherese Vachon
Aug 4, 2009·PLoS Computational Biology·Andrey RzhetskyMark B Gerstein
Feb 1, 2005·Indian Journal of Medical Sciences·Hariom YadavGbks Prasad
Feb 29, 2008·Bioinformation·Hui YangJohn A Keane
Feb 1, 2006·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Byron MarshallHsinchun Chen
Oct 19, 2006·Trends in Biotechnology·Sophia AnaniadouJun-ichi Tsujii
Nov 8, 2011·Journal of Biomedical Informatics·Lishuang LiJing Sun
Apr 19, 2015·BMC Bioinformatics·Sun KimW John Wilbur
Mar 16, 2004·Journal of Biomedical Informatics·Andrey RzhetskyCarol Friedman
Nov 16, 2004·Journal of Biomedical Informatics·Michael Krauthammer, Goran Nenadic
Nov 16, 2004·Journal of Biomedical Informatics·Alexander A MorganJeff B Colombe
Dec 9, 2008·Briefings in Bioinformatics·Rainer WinnenburgMichael Schroeder
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Lorraine Tanabe, W John Wilbur
Jul 17, 2008·Comparative and Functional Genomics·Henk HarkemaMark Hepple
May 14, 2011·The Journal of Biological Chemistry·James A Evans, Andrey Rzhetsky
May 6, 2017·Chemical Reviews·Martin KrallingerAlfonso Valencia

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.