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1. Söhngen C, Chang A, Schomburg D: Development of a classification scheme for disease-related enzyme information. BMC Bioinformatics; 2011;12:329
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Development of a classification scheme for disease-related enzyme information.
  • BACKGROUND: BRENDA (BRaunschweig ENzyme DAtabase, http://www.brenda-enzymes.org) is a major resource for enzyme related information.
  • First and foremost, it provides data which are manually curated from the primary literature.
  • DRENDA (Disease RElated ENzyme information DAtabase) complements BRENDA with a focus on the automatic search and categorization of enzyme and disease related information from title and abstracts of primary publications.
  • In a two-step procedure DRENDA makes use of text mining and machine learning methods.
  • RESULTS: Currently enzyme and disease related references are biannually updated as part of the standard BRENDA update.
  • 910,897 relations of EC-numbers and diseases were extracted from titles or abstracts and are included in the second release in 2010.
  • The enzyme and disease entity recognition has been successfully enhanced by a further relation classification via machine learning.
  • The classification step has been evaluated by a 5-fold cross validation and achieves an F1 score between 0.802 ± 0.032 and 0.738 ± 0.033 depending on the categories and pre-processing procedures.
  • In the eventual DRENDA content every category reaches a classification specificity of at least 96.7% and a precision that ranges from 86-98% in the highest confidence level, and 64-83% for the smallest confidence level associated with higher recall.
  • CONCLUSIONS: The DRENDA processing chain analyses PubMed, locates references with disease-related information on enzymes and categorises their focus according to the categories causal interaction, therapeutic application, diagnostic usage and ongoing research.
  • The categorisation gives an impression on the focus of the located references.
  • Thus, the relation categorisation can facilitate orientation within the rapidly growing number of references with impact on diseases and enzymes.
  • The DRENDA information is available as additional information in BRENDA.
  • [MeSH-major] Data Mining. Databases, Protein. Disease / genetics. HIV Infections / enzymology. Neoplasms / enzymology
  • [MeSH-minor] Artificial Intelligence. Humans. PubMed

  • MedlinePlus Health Information. consumer health - HIV/AIDS.
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  • [Cites] Nat Genet. 2004 Jul;36(7):664 [15226743.001]
  • [Cites] Clin Cancer Res. 2004 Jun 15;10(12 Pt 2):4227s-4232s [15217963.001]
  • [Cites] Antimicrob Agents Chemother. 1998 Feb;42(2):332-8 [9527781.001]
  • [Cites] Bull Med Libr Assoc. 1964 Jan;52:164-70 [14119288.001]
  • [Cites] Bioinformatics. 2005 May 1;21(9):2059-66 [15661799.001]
  • [Cites] Bioinformatics. 2005 Oct 15;21(20):3940-1 [16096348.001]
  • [Cites] Nat Rev Genet. 2006 Feb;7(2):119-29 [16418747.001]
  • [Cites] Acta Pharmacol Sin. 2007 Sep;28(9):1409-21 [17723174.001]
  • [Cites] Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6 [18048412.001]
  • [Cites] Bioinformatics. 2008 Jun 1;24(11):1410-2 [18400773.001]
  • [Cites] BMC Bioinformatics. 2009;10 Suppl 8:S1 [19758464.001]
  • [Cites] BMC Bioinformatics. 2009;10 Suppl 8:S2 [19758466.001]
  • [Cites] Methods Mol Biol. 2010;593:341-82 [19957157.001]
  • [Cites] Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16 [19910364.001]
  • [Cites] BioDrugs. 2010 Feb 1;24(1):41-7 [20055531.001]
  • [Cites] Curr Med Chem. 2010;17(32):3769-805 [20858219.001]
  • [Cites] Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6 [21062828.001]
  • [Cites] Orphanet J Rare Dis. 2010;5:30 [21092187.001]
  • [Cites] Pathology. 2000 Nov;32(4):245-9 [11186419.001]
  • [Cites] Crit Rev Clin Lab Sci. 2001 Aug;38(4):263-355 [11563810.001]
  • [Cites] Clin Immunol. 2002 Jul;104(1):73-6 [12139950.001]
  • [Cites] Br J Cancer. 2002 Sep 23;87(7):751-5 [12232759.001]
  • [Cites] AIDS Res Hum Retroviruses. 1992 Feb;8(2):153-64 [1540403.001]
  • (PMID = 21827651.001).
  • [ISSN] 1471-2105
  • [Journal-full-title] BMC bioinformatics
  • [ISO-abbreviation] BMC Bioinformatics
  • [Language] eng
  • [Publication-type] Journal Article; Research Support, Non-U.S. Gov't
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3166944
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2. Samwald M, Stenzhorn H: Establishing a distributed system for the simple representation and integration of diverse scientific assertions. J Biomed Semantics; 2010;1 Suppl 1:S5
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Establishing a distributed system for the simple representation and integration of diverse scientific assertions.
  • BACKGROUND: Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information.
  • There are numerous projects that employ ontologies and Semantic Web technologies towards this goal.
  • However, the number of applications that have found widespread use among biomedical researchers is still surprisingly small.
  • In this paper we present the aTag ('associative tags') convention, which aims to drastically lower the entry barriers to the biomedical Semantic Web. aTags are short snippets of HTML+RDFa with embedded RDF/OWL based on the Semantically Interlinked Online Communities (SIOC) vocabulary and domain ontologies and taxonomies, such as the Open Biomedical Ontologies and DBpedia.
  • The structure of aTags is very simple: a short piece of human-readable text that is 'tagged' with relevant ontological entities.
  • This paper describes our efforts for seeding the creation of a viable ecosystem of datasets, tools and services around aTags.
  • RESULTS: Numerous biomedical datasets in aTag format and systems for the creation of aTags have been set-up and are described in this paper.
  • Prototypes of some of these systems are accessible at http://hcls.deri.org/atag CONCLUSIONS: The aTags convention enables the rapid development of diverse, integrated datasets and semantically interoperable applications.
  • More work needs to be done to study the practicability of this approach in different use-case scenarios, and to encourage uptake of the convention by other groups.

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  • [Cites] J Biomed Inform. 2008 Oct;41(5):739-51 [18583197.001]
  • [Cites] Nat Genet. 2008 Sep;40(9):1047-51 [18728691.001]
  • [Cites] AMIA Annu Symp Proc. 2008;:1223-4 [18999306.001]
  • [Cites] Stud Health Technol Inform. 2009;150:317-21 [19745321.001]
  • [Cites] Bioinformatics. 2008 Jun 1;24(11):1410-2 [18400773.001]
  • [Cites] Bioinformatics. 2005 Sep 1;21 Suppl 2:ii252-8 [16204114.001]
  • [Cites] Nat Biotechnol. 2007 Nov;25(11):1251-5 [17989687.001]
  • [Cites] Bioinformatics. 2008 Jan 15;24(2):296-8 [18006544.001]
  • [Cites] FEBS Lett. 2008 Apr 9;582(8):1169 [18328821.001]
  • [Cites] Genome Biol. 2005;6(5):R46 [15892874.001]
  • (PMID = 20626925.001).
  • [ISSN] 2041-1480
  • [Journal-full-title] Journal of biomedical semantics
  • [ISO-abbreviation] J Biomed Semantics
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC2903724
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3. Lu Z: PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford); 2011;2011:baq036
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] PubMed and beyond: a survey of web tools for searching biomedical literature.
  • The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature.
  • This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters.
  • However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth.
  • In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement.
  • Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications.
  • These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed.
  • In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development.
  • Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search.
  • Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field.
  • Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.

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  • [Cites] Trends Genet. 1999 Nov;15(11):471-2 [10529811.001]
  • [Cites] J Biomed Inform. 2011 Apr;44(2):310-8 [21094696.001]
  • [Cites] J Am Med Inform Assoc. 2000 Nov-Dec;7(6):605-17 [11062234.001]
  • [Cites] Trends Biochem Sci. 2001 Sep;26(9):573-5 [11551795.001]
  • [Cites] Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W16-9 [15215341.001]
  • [Cites] BMC Bioinformatics. 2004 Oct 8;5:147 [15473905.001]
  • [Cites] Drug Discov Today. 2005 Mar 15;10(6):439-45 [15808823.001]
  • [Cites] BMC Med Inform Decis Mak. 2005;5:5 [15760470.001]
  • [Cites] Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W774-8 [15980583.001]
  • [Cites] Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W783-6 [15980585.001]
  • [Cites] In Silico Biol. 2005;5(2):199-208 [15972015.001]
  • [Cites] Genome Biol. 2005;6(9):R80 [16168087.001]
  • [Cites] BMC Med Inform Decis Mak. 2005;5:37 [16321145.001]
  • [Cites] Nat Rev Genet. 2006 Feb;7(2):119-29 [16418747.001]
  • [Cites] Bioinformatics. 2006 Feb 1;22(3):378-80 [16332704.001]
  • [Cites] Mol Cell. 2006 Mar 3;21(5):589-94 [16507357.001]
  • [Cites] Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W745-7 [16845111.001]
  • [Cites] Bioinformatics. 2006 Oct 1;22(19):2444-5 [16870931.001]
  • [Cites] BMC Bioinformatics. 2006;7:424 [17014720.001]
  • [Cites] AMIA Annu Symp Proc. 2006;:923 [17238542.001]
  • [Cites] AMIA Annu Symp Proc. 2006;:1012 [17238631.001]
  • [Cites] Bioinformatics. 2007 Jan 15;23(2):e237-44 [17237098.001]
  • [Cites] BMC Med Inform Decis Mak. 2007;7:1 [17214888.001]
  • [Cites] J Biomed Inform. 2007 Apr;40(2):114-30 [16996316.001]
  • [Cites] BMC Med Inform Decis Mak. 2007;7:16 [17573961.001]
  • [Cites] Nucleic Acids Res. 2007 Jul;35(Web Server issue):W12-5 [17452348.001]
  • [Cites] Nucleic Acids Res. 2007 Jul;35(Web Server issue):W21-6 [17485473.001]
  • [Cites] Bioinformatics. 2007 Aug 15;23(16):2196-7 [17545178.001]
  • [Cites] BMC Bioinformatics. 2007;8:423 [17971238.001]
  • [Cites] PLoS Comput Biol. 2008 Jan;4(1):e20 [18225946.001]
  • [Cites] BMC Bioinformatics. 2008;9:108 [18284683.001]
  • [Cites] Bioinformatics. 2008 Jun 1;24(11):1410-2 [18400773.001]
  • [Cites] Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405 [18487273.001]
  • [Cites] Methods Mol Biol. 2008;453:471-91 [18712320.001]
  • [Cites] Bioinformatics. 2008 Sep 1;24(17):1968-70 [18614584.001]
  • [Cites] Genome Biol. 2008;9 Suppl 2:S3 [18834494.001]
  • [Cites] Genome Biol. 2008;9 Suppl 2:S4 [18834495.001]
  • [Cites] Genome Biol. 2008;9 Suppl 2:S8 [18834499.001]
  • [Cites] J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31 [18952929.001]
  • [Cites] Brief Bioinform. 2008 Nov;9(6):452-65 [18660511.001]
  • [Cites] Bioinformatics. 2009 Mar 15;25(6):815-21 [19188193.001]
  • [Cites] Bioinformatics. 2009 Apr 1;25(7):974-6 [18326507.001]
  • [Cites] Nucleic Acids Res. 2009 Jul;37(Web Server issue):W141-6 [19429696.001]
  • [Cites] PLoS Comput Biol. 2009 Jul;5(7):e1000411 [19649304.001]
  • [Cites] Bioinformatics. 2009 Nov 15;25(22):3031-2 [19654114.001]
  • [Cites] Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16 [19910364.001]
  • [Cites] PLoS Comput Biol. 2009 Dec;5(12):e1000597 [20041219.001]
  • [Cites] AMIA Annu Symp Proc. 2009;2009:396-400 [20351887.001]
  • [Cites] BMC Bioinformatics. 2010;11 Suppl 2:S6 [20406504.001]
  • [Cites] EMBO Rep. 2010 May;11(5):345-9 [20428107.001]
  • [Cites] Bioinformatics. 2010 Sep 15;26(18):2321-7 [20624778.001]
  • [Cites] Neural Netw. 2010 Dec;23(10):1208-25 [20674268.001]
  • [Cites] Biotechniques. 1999 Dec;27(6):1210-4, 1216-7 [10631500.001]
  • (PMID = 21245076.001).
  • [ISSN] 1758-0463
  • [Journal-full-title] Database : the journal of biological databases and curation
  • [ISO-abbreviation] Database (Oxford)
  • [Language] ENG
  • [Grant] United States / Intramural NIH HHS / /
  • [Publication-type] Journal Article; Research Support, N.I.H., Intramural; Review
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3025693
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