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:5/23/2017)...  Hunova, the first robotic gym for the rehabilitation and functional motor ... Genoa, Italy . The first 30 robots will be ... USA . The technology was developed and patented at the ... spin-off Movendo Technology thanks to a 10 million euro investment from entrepreneur ... ...
(Date:5/6/2017)... , May 5, 2017 ... just announced a new breakthrough in biometric authentication ... exploits quantum mechanical properties to perform biometric authentication. These ... smart semiconductor material created by Ram Group and ... finance, entertainment, transportation, supply chains and security. Ram ...
(Date:4/18/2017)... SUNNYVALE, Calif. , April 18, 2017  Socionext Inc., a ... prototype of a media edge server, the M820, which features the ... face recognition software provided by Tera Probe, Inc., will be showcased ... and at the NAB show at the Las Vegas ... ...
Breaking Biology News(10 mins):
(Date:10/12/2017)... ... October 12, 2017 , ... BioMedGPS ... the addition of its newest module, US Hemostats & Sealants. , SmartTRAK’s US ... absorbable hemostats, fibrin sealants, synthetic sealants and biologic sealants used in surgical applications. ...
(Date:10/11/2017)... ... ... eye wash is a basic first aid supply for any work environment, but most personal ... rinse first if a dangerous substance enters both eyes? It’s one less decision, and likely ... dual eye piece. , “Whether its dirt and debris, or an acid or alkali, getting ...
(Date:10/11/2017)... , ... October 11, 2017 , ... Disappearing forests and ... lives of over 5.5 million people each year. Especially those living in larger cities ... Treepex - based in one of the most pollution-affected countries globally - decided to ...
(Date:10/10/2017)... ... October 10, 2017 , ... For ... has won a US2020 STEM Mentoring Award. Representatives of the FirstHand program travelled ... Volunteer Experience from US2020. , US2020’s mission is to change the trajectory of ...
Breaking Biology Technology: