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:
(Date:4/2/2015)... 2, 2015 In the ... far outperforms the strongest competitors, showing outstanding performance ... the system is capable of a throughput of ... up to be ten times faster than most ... performance.      (Photo: http://photos.prnewswire.com/prnh/20150402/738673-a ...
(Date:4/2/2015)... Fingerprint Cards (FPC) has received ... the distributor World Peace Industrial Group (WPI), part of ... the major part of the shipments will take place ... smartphone manufacturers in China . The ... communicated revenue guidance of + 1 000 MSEK for 2015.  ...
(Date:3/31/2015)... March 31, 2015  Elephant Talk Communications Corp. (NYSE ... provider of Software Defined Network Architecture (ET Software DNA® ... revenue of approximately $20.4 million for the year ended ... million for the year ended December 31, 2013. ... Company had completed its multi-year transition away from its ...
Breaking Biology News(10 mins):DERMALOG AFIS Emerges as Performance Winner in NIST Benchmark Test 2DERMALOG AFIS Emerges as Performance Winner in NIST Benchmark Test 3Fingerprint Cards Receives Touch Fingerprint Sensor Order of SEK 110 Million 2Elephant Talk Reports 2014 Fourth Quarter and Year End Financial Results 2Elephant Talk Reports 2014 Fourth Quarter and Year End Financial Results 3Elephant Talk Reports 2014 Fourth Quarter and Year End Financial Results 4Elephant Talk Reports 2014 Fourth Quarter and Year End Financial Results 5Elephant Talk Reports 2014 Fourth Quarter and Year End Financial Results 6
... removes excess signaling molecules to prevent them from damaging cilia, ... published in the December 28 issue of the Journal ... cause a range of diseases including Bardet-Biedl syndrome (BBS), a ... Seven of these form a complex called the BBSome, but ...
... 2009. Emerald BioStructures (formerly deCODE biostructures) announced ... advance online issue of Nature Biotechnology , ... to engineer new allosteric small molecule modulators of ... According to the paper, the researchers established the ...
... the first time that insects, like mammals, use vision rather ... to high-speed video cameras technology the BBC uses to ... film desert locusts stepping along the rungs of a miniature ... to perform complex tasks, such as visually-guided limb control, usually ...
Cached Biology News:Emerald BioStructures announces discovery of small molecule modulators of PDE4 2Ladder-walking locusts show big brains aren't always best 2
(Date:5/4/2015)... PHILADELPHIA , May 4, 2015 ... help thousands of med students prepare for the United ... a world-leading provider of scientific, technical and medical information ... a free MOOC (Massive Open Online Course) designed to ... Licensing Examination (USMLE) Step 1, the first and most ...
(Date:5/4/2015)...   Intrexon Corporation (NYSE: XON ) ... results after the market closes on May 11, 2015.  ... at 5:30 PM ET to discuss the results and ... call may be accessed by dialing 1-888-346-3959 (Domestic US) ... Conference Call."  Participants may also access the live webcast ...
(Date:5/4/2015)... Wheaton, Illinois (PRWEB) May 04, 2015 ... treatment options for patients with arm and hand ... rehabilitation exoskeleton at its Oakbrook Terrace network site. ... foundation, the Armeo®Spring is a highly-regarded treatment option ... In acquiring the Armeo®Spring, Marianjoy becomes one of ...
(Date:5/1/2015)... 01, 2015 OncoTAb, Inc., ... spin-out company, announced that Pinku Mukherjee, Ph.D. has received ... Board of Governors’ highest faculty honor. Mukherjee received the ... , for her innovative research and development of cancer ... represents a crowning moment in my scientific career,” said ...
Breaking Biology Technology:Elsevier's Free MOOC Prepares Med Students for Licensing Exam 2Elsevier's Free MOOC Prepares Med Students for Licensing Exam 3Intrexon to Announce First Quarter 2015 Financial Results on Monday, May 11, 2015 2Marianjoy Acquires Armeo®Spring Arm and Hand Rehabilitation Exoskeleton at Oakbrook Terrace Facility 2OncoTAb CSO Awarded the University of North Carolina’s O. Max Gardner Award 2
... - Employers who are looking for health information technology ... have to wait a while longer, according to the ... ,Stephen Lieber, president and CEO of the Healthcare ... electronic health records and improving interoperability between facilities remain ...
... - Wisconsin attracts far fewer defense research dollars annually ... of public and private initiatives are quietly positioning the ... , ,These projects and others like them could thrive ... responds to the unique threats it poses. Tom Still, ...
... - Last Sunday morning, in the free-wheeling environment ... shared secrets and strategies from her forthcoming book, titled ... she expects to publish next year. , ,In her ... Huber provided advice about maximizing efficiency and minimizing hurt ...
Cached Biology Technology:CEO of healthcare group still hopeful IT will save employers money 2CEO of healthcare group still hopeful IT will save employers money 3Chippewa Valley firms land more defense work 2Chippewa Valley firms land more defense work 3Chippewa Valley firms land more defense work 4Chippewa Valley firms land more defense work 5Chippewa Valley firms land more defense work 6Chippewa Valley firms land more defense work 7BarCamp talk turns to Internet dating 2BarCamp talk turns to Internet dating 3
Tissue culture grade....
Tris-Hepes kit of BG-163 & BG-165 (order number BG-166)...
... Translation System is ideal for both radioactive ... Translation System: Provides five pre-mixed nucleotide ... Yields >10 8 cpm/g control ... to monitor the performance of the system ...
Activating Agents, 7-azabenzotriazol-1-yloxy-tris-(pyrrolidino)phosphonium hexafluorophosphate...
Biology Products: