Navigation Links
Building a protein name dictionary from full text: a machine learning term extraction approach

The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature.

Results
We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text.
Conclusions
This dictionary term lookup method compares favorably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.


'"/>

Source:BMC Bioinformatics


Page: 1

Related biology news :

1. Whats really making you sick? Plant pathologists offer the science behind Sick Building Syndrome
2. Building a human kinase gene repository
3. Building a better mouse model of lung cancer: FHIT counts
4. Protein folding: Building a strong foundation
5. New, automated tool successfully classifies and relates proteins in unprecedented way
6. New binding target for oncogenic viral protein
7. Controversial drug shown to act on brain protein to cut alcohol use
8. Timing is everything: First step in protein building revealed
9. UWs Rosetta software to unlock secrets of many human proteins
10. Researchers find how protein allows insects to detect and respond to pheromones
11. Signaling protein builds bigger, better bones in mice
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:3/7/2017)... England , March 7, 2017 Brandwatch , ... chosen by The Prince,s Trust to uncover insights to ... across The Trust. The UK,s leading youth charity will ... social campaign results and get a better understanding of the topics ... ...
(Date:3/2/2017)... Summary This report provides all ... and its partnering interests and activities since 2010. ... The Partnering Deals and Alliance since 2010 report provides ... of the world,s leading life sciences companies. ... ensure inclusion of the most up to date deal ...
(Date:2/28/2017)... 2017   Acuant , a leading provider of ... enhancements to new and core technologies building upon the ... mobile and desktop Acuant FRM TM facial recognition ... real time manual review of identity documents by accredited ... fastest and most accurate capture software to streamline workflows ...
Breaking Biology News(10 mins):
(Date:3/23/2017)... Mar 23, 2017 Research and Markets ... Markets" report to their offering. ... The Global Market for ... in 2016 at a CAGR of 8.9%, ... non-energetic bioproducts into seven major product segments: bio-derived chemicals, biofuels, ...
(Date:3/23/2017)... , March 23, 2017  SeraCare Life ... global in vitro diagnostics manufacturers and clinical ... industry,s first multiplexed Inherited Cancer reference ... by next-generation sequencing (NGS). The Seraseqâ„¢ Inherited ... with input from industry experts to validate ...
(Date:3/23/2017)... 2017  BioPharmX Corporation (NYSE MKT: BPMX), a ... market, today reported financial results for the quarter ... provide an update on the company,s clinical development ... "We are pleased to report that last year ... President Anja Krammer. "We achieved key clinical milestones ...
(Date:3/23/2017)... SEATTLE , March 23, 2017 ... translational development of novel therapies in immuno-oncology, today ... to lead" small molecule compounds that activate interferon ... (RLR) pathways and demonstrate immune-mediated tumor regression in ... in the study who demonstrated complete tumor regression ...
Breaking Biology Technology: