Navigation Links
Automatic extraction of gene/protein biological functions from biomedical text

With the rapid advancement of biomedical science and the development of high-throughput analysis methods, the extraction of various types of information from biomedical text has become critical. Since automatic functional annotations of genes are quite useful for interpreting large amounts of high-throughput data efficiently, the demand for automatic extraction of information related to gene functions from text has been increasing.

Results: We have developed a method for automatically extracting the biological process functions of genes/protein/families based on Gene Ontology (GO) from text using a shallow parser and sentence structure analysis techniques. When the gene/protein/family names and their functions are described in ACTOR (doer of action) and OBJECT (receiver of action) relationships, the corresponding GO-IDs are assigned to the genes/proteins/families. The gene/protein/family names are recognized using the gene/protein/family name dictionaries developed by our group. To achieve wide recognition of the gene/protein/family functions, we semi-automatically gather functional terms based on GO using co-occurrence, collocation similarities and rule-based techniques. A preliminary experiment demonstrated that our method has an estimated recall of 54?4% with a precision of 91?4% for actually described functions in abstracts. When applied to the PUBMED, it extracted over 190 000 gene–GO relationships and 150 000 family–GO relationships for major eukaryotes.
Availability: The extracted gene functions are available at http://prime.ontology.ims.u-tokyo.ac.jp


'"/>

Source:Bioinformatics


Page: 1

Related biology news :

1. Automatic identification of proteins critical features from the structure
2. Building a protein name dictionary from full text: a machine learning term extraction approach
3. NYU researchers simulate molecular biological clock
4. DuPonts first biologically derived polymer receives global recognition
5. Glow-in-the-dark zebrafish at UH hold keys to biological clocks
6. Discovery clarifies role of peptide in biological clock
7. A new way to share models of biological systems
8. Engineers improve plastics potential for use in implants by linking it to biological material
9. New book expands biological classifications to account for alien life
10. Technique offers new view of dynamic biological landscape
11. UC Berkeley researchers create a biologically-inspired artificial compound eye
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:6/1/2016)... , June 1, 2016 ... in Election Administration and Criminal Identification to Boost Global ... a recently released TechSci Research report, " Global Biometrics ... Region, Competition Forecast and Opportunities, 2011 - 2021", the ... billion by 2021, on account of growing security concerns ...
(Date:5/16/2016)...   EyeLock LLC , a market leader of ... an IoT Center of Excellence in Austin, ... of embedded iris biometric applications. EyeLock,s iris ... security with unmatched biometric accuracy, making it the most ... EyeLock,s platform uses video technology to deliver a fast ...
(Date:5/3/2016)... VILNIUS, Lithuania , May 3, 2016 /PRNewswire/ ... today released the MegaMatcher Automated Biometric Identification ... deployment of large-scale multi-biometric projects. MegaMatcher ABIS can ... and accuracy using any combination of fingerprint, face ... of MegaMatcher SDK and MegaMatcher ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... on a range of subjects including policies, debt and investment ... Speaking at a lecture to the Canadian Economics ... the country,s inflation target, which is set by both the ... "In certain areas there needs to be frequent ... not sit down and address strategy together?" He ...
(Date:6/24/2016)... (PRWEB) , ... June 24, 2016 , ... While the ... such as the Cary 5000 and the 6000i models are higher end machines that ... the height of the spectrophotometer’s light beam from the bottom of the cuvette holder. ...
(Date:6/23/2016)... , ... June 23, 2016 , ... ... release of its second eBook, “Clinical Trials Patient Recruitment and Retention Tips.” Partnering ... retention in this eBook by providing practical tips, tools, and strategies for clinical ...
(Date:6/23/2016)... 2016   Boston Biomedical , an industry ... to target cancer stemness pathways, announced that its ... Drug Designation from the U.S. Food and Drug ... including gastroesophageal junction (GEJ) cancer. Napabucasin is an ... cancer stemness pathways by targeting STAT3, and is ...
Breaking Biology Technology: