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:3/24/2015)... , March 24, 2015   Crossmatch ... solutions, today announced that its U.are.U ® ... retailer Goorin Bros . to achieve PCI ... solution secures access to the POS terminal, protecting ... risk of data breaches. With ...
(Date:3/20/2015)... Mar. 20, 2015 Research and Markets ... of the "India Sensors Market Forecast and ... The sensor market is projected to grow ... Consumer electronics, automotive, industrial and healthcare sectors ... the country. In addition, adoption of MEMS technology ...
(Date:3/18/2015)... 2015 As mobile payments become more ... wallets and apps continue to be introduced into the market ... mobile payment industry in focus today are:  NXT-ID, Inc. (NASDAQ: ... BABA ), Apple Inc. (NASDAQ: AAPL ), ... (NASDAQ: FB ) NXT-ID, Inc. (NASDAQ: ...
Breaking Biology News(10 mins):Crossmatch Fingerprint Readers Help Retailer Prevent Data Breaches at Point-of-Sale 2India Sensors Market Forecast and Opportunities 2020 - STMicroelectronics held the largest share in 2014 2India Sensors Market Forecast and Opportunities 2020 - STMicroelectronics held the largest share in 2014 3Revolutionary Smart Wallet & Mobile Payment Choices Change the Game for Consumers - Company Begins Shipping Newest Digital Wallet to Customers 2Revolutionary Smart Wallet & Mobile Payment Choices Change the Game for Consumers - Company Begins Shipping Newest Digital Wallet to Customers 3Revolutionary Smart Wallet & Mobile Payment Choices Change the Game for Consumers - Company Begins Shipping Newest Digital Wallet to Customers 4Revolutionary Smart Wallet & Mobile Payment Choices Change the Game for Consumers - Company Begins Shipping Newest Digital Wallet to Customers 5Revolutionary Smart Wallet & Mobile Payment Choices Change the Game for Consumers - Company Begins Shipping Newest Digital Wallet to Customers 6
... and vegetation allowed human ancestors to evolve in Africa. ... to the idea that ground movements formed mountains and ... Tectonics [movement of Earths crust] was ultimately responsible ... of the universitys Energy and Geoscience Institute write in ...
... Viticulture, the growing of grapes (Vitis vinifera) chiefly to make ... has been found from the Neolithic and Early Bronze Ages. ... qualities of a grape harvest leading to the concept of ... a wine). The nature of the grapes themselves has been ...
... 18, 2007)Researchers at The University of Texas Medical School ... glucose metabolism and spina bifida. The decade-long study looked ... their children with that birth defect. UT Medical ... take part in glucose metabolism to look for a ...
Cached Biology News:Evolution tied to Earth movement 2Evolution tied to Earth movement 3Evolution tied to Earth movement 4Plant geneticists find veritas in vino 2Plant geneticists find veritas in vino 3UT-Houston's Northrup and colleagues uncover genetic link to spina bifida 2
(Date:3/30/2015)... 30, 2015 PMG Research, Benchmark ... announce the formation of VaxCorps, a network of ... in the conduct of vaccine trials in healthy ... sites have successfully conducted over 500 phase I-III ... and pandemic influenza as well as a vast ...
(Date:3/30/2015)... , March 30, 2015  New Jersey Health ... projects in the state of New Jersey ... round of grant funding, announced James M. Golubieski ... Health Foundation Research Grants program, an additional $500,000 will ... to fund early stage research projects that demonstrate exciting ...
(Date:3/30/2015)... 30, 2015    Intrexon Corporation (NYSE: ... and Merck Serono, the biopharmaceutical business of Merck ... announced an exclusive strategic collaboration and license agreement ... (CAR-T) cancer therapies. This collaboration advances Merck Serono,s ... modulate the immune system,s natural ability to fight ...
(Date:3/30/2015)... 2015  Naldemedine, an investigational peripherally acting mu-opioid ... Co., Ltd., met its primary and secondary endpoints ... the treatment of opioid-induced constipation (OIC) in adult ... Study results showed that naldemedine (0.2 mg tablet ... of spontaneous bowel movement (SBM) compared with placebo ...
Breaking Biology Technology:PMG Research announces formation of VaxCorps with two industry-leading vaccine site networks 2New Jersey Health Foundation Announces An Additional $1 Million To Fund Innovation and Research Grants in New Jersey 2Intrexon and Merck Serono Announce Agreement for the Development and Commercialization of CAR-T Therapy 2Intrexon and Merck Serono Announce Agreement for the Development and Commercialization of CAR-T Therapy 3Intrexon and Merck Serono Announce Agreement for the Development and Commercialization of CAR-T Therapy 4Shionogi & Co., Ltd. Announces That Naldemedine Meets Primary Endpoint In A Phase 3 Study For The Treatment Of Opioid-Induced Constipation 2Shionogi & Co., Ltd. Announces That Naldemedine Meets Primary Endpoint In A Phase 3 Study For The Treatment Of Opioid-Induced Constipation 3
... North Carolina Sen. John Edwards polled well in last weeks ... Free Trade Agreement has been a raw deal. It was ... to blame the states economic troubles on those dastardly Canadians ... Free trade is a part of saving Wisconsin, not ruining ...
... Wis.- Gundersen Lutheran Health System is reducing surgery delays ... management of its surgical instruments and trays by using ... Minn.- based Lawson Software. , ,Gundersen Lutheran operates ... of the nation's largest group medical practices, community clinics, ...
... Muskego, Wis - The City of Muskego, Wis., has ... intranet site and their public Web site . ... Software , an Australian software company specializing in knowledge ... government. , ,Prior to choosing ISYS, the City evaluated ...
Cached Biology Technology:A Vote Against Free Trade is a Vote Against Wisconsins Long-Term Interests 2Gunderson Lutheran Implements Instrument Management Systems 2
Sprague-Dawley rats, 7-8 weeks old, mixed gender; tissue is collected fresh, frozen on dry ice within minutes of sacrifice and stored at -20C; individual tissue weight approx. 0.05 gram....
...
Contains L-glutamine...
EMBP (FL-222)...
Biology Products: