KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes
<p>Abstract</p> <p>Background</p> <p>The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biolo...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-07-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/375 |
| _version_ | 1811299350283812864 |
|---|---|
| author | Schomburg Dietmar Thielen Bernhard Heinen Stephanie |
| author_facet | Schomburg Dietmar Thielen Bernhard Heinen Stephanie |
| author_sort | Schomburg Dietmar |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed.</p> <p>Description</p> <p>Here we present a text mining algorithm for the extraction of kinetic information such as K<sub>M</sub>, K<sub>i</sub>, k<sub>cat </sub>etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (K<sub>M</sub>, K<sub>i</sub>, k<sub>cat</sub>, k<sub>cat</sub>/K<sub>M</sub>, V<sub>max</sub>, IC<sub>50</sub>, S<sub>0.5</sub>, K<sub>d</sub>, K<sub>a</sub>, t<sub>1/2</sub>, pI, n<sub>H</sub>, specific activity, V<sub>max</sub>/K<sub>M</sub>) from about 17 million PubMed abstracts and combine them with other data in the abstract.</p> <p>A manual verification of approx. 1,000 randomly chosen results yielded a recall between 51% and 84% and a precision ranging from 55% to 96%, depending of the category searched.</p> <p>The results were stored in a database and are available as "KID the KInetic Database" via the internet.</p> <p>Conclusions</p> <p>The presented algorithm delivers a considerable amount of information and therefore may aid to accelerate the research and the automated analysis required for today's systems biology approaches. The database obtained by analysing PubMed abstracts may be a valuable help in the field of chemical and biological kinetics. It is completely based upon text mining and therefore complements manually curated databases.</p> <p>The database is available at <url>http://kid.tu-bs.de</url>. The source code of the algorithm is provided under the GNU General Public Licence and available on request from the author.</p> |
| first_indexed | 2024-04-13T06:33:55Z |
| format | Article |
| id | doaj.art-944d9563a63d40f1b844ee10884f4c83 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T06:33:55Z |
| publishDate | 2010-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-944d9563a63d40f1b844ee10884f4c832022-12-22T02:57:59ZengBMCBMC Bioinformatics1471-21052010-07-0111137510.1186/1471-2105-11-375KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymesSchomburg DietmarThielen BernhardHeinen Stephanie<p>Abstract</p> <p>Background</p> <p>The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed.</p> <p>Description</p> <p>Here we present a text mining algorithm for the extraction of kinetic information such as K<sub>M</sub>, K<sub>i</sub>, k<sub>cat </sub>etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (K<sub>M</sub>, K<sub>i</sub>, k<sub>cat</sub>, k<sub>cat</sub>/K<sub>M</sub>, V<sub>max</sub>, IC<sub>50</sub>, S<sub>0.5</sub>, K<sub>d</sub>, K<sub>a</sub>, t<sub>1/2</sub>, pI, n<sub>H</sub>, specific activity, V<sub>max</sub>/K<sub>M</sub>) from about 17 million PubMed abstracts and combine them with other data in the abstract.</p> <p>A manual verification of approx. 1,000 randomly chosen results yielded a recall between 51% and 84% and a precision ranging from 55% to 96%, depending of the category searched.</p> <p>The results were stored in a database and are available as "KID the KInetic Database" via the internet.</p> <p>Conclusions</p> <p>The presented algorithm delivers a considerable amount of information and therefore may aid to accelerate the research and the automated analysis required for today's systems biology approaches. The database obtained by analysing PubMed abstracts may be a valuable help in the field of chemical and biological kinetics. It is completely based upon text mining and therefore complements manually curated databases.</p> <p>The database is available at <url>http://kid.tu-bs.de</url>. The source code of the algorithm is provided under the GNU General Public Licence and available on request from the author.</p>http://www.biomedcentral.com/1471-2105/11/375 |
| spellingShingle | Schomburg Dietmar Thielen Bernhard Heinen Stephanie KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes BMC Bioinformatics |
| title | KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes |
| title_full | KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes |
| title_fullStr | KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes |
| title_full_unstemmed | KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes |
| title_short | KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes |
| title_sort | kid an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes |
| url | http://www.biomedcentral.com/1471-2105/11/375 |
| work_keys_str_mv | AT schomburgdietmar kidanalgorithmforfastandefficienttextminingusedtoautomaticallygenerateadatabasecontainingkineticinformationofenzymes AT thielenbernhard kidanalgorithmforfastandefficienttextminingusedtoautomaticallygenerateadatabasecontainingkineticinformationofenzymes AT heinenstephanie kidanalgorithmforfastandefficienttextminingusedtoautomaticallygenerateadatabasecontainingkineticinformationofenzymes |