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Literature DB >> 11825233

A model for data integration systems of biomedical data applied to online genetic databases.

Abstract

We present a general model for data integration systems using a mediated schema to represent commonalities in the underlying sources. These sources are mapped to the mediated schema using source descriptions. Users can pose queries against the mediated schema, allowing the system to generate automatically a query plan that enumerates and ranks all possible ways in which the query could be answered. We apply this approach to the domain of online genetic databases, demonstrating the system s ability to answer relevant queries across multiple sources.

Mesh：

Year: 2001 PMID： 11825233 PMCID： PMC2243562

Source DB: PubMed Journal: Proc AMIA Symp ISSN： 1531-605X

12 in total

1. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

2. Genomics. Are you ready for the revolution?

Authors: D Butler
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

3. Computational biology. Bioinformatics--trying to swim in a sea of data.

Authors: D S Roos
Journal: Science Date: 2001-02-16 Impact factor: 47.728

4. Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base.

Authors: C Rosse; J L Mejino; B R Modayur; R Jakobovits; K P Hinshaw; J F Brinkley
Journal: J Am Med Inform Assoc Date: 1998 Jan-Feb Impact factor: 4.497

5. SRS: information retrieval system for molecular biology data banks.

Authors: T Etzold; A Ulyanov; P Argos
Journal: Methods Enzymol Date: 1996 Impact factor: 1.600

6. Reports from the Eighth Annual Conference on Retroviruses and Opportunistic Infections. Chicago, February 4-8, 2001.

Authors:
Journal: Body Posit Date: 2001-04

Review 7. Internet resources for the clinical geneticist.

Authors: F Ouellette
Journal: Clin Genet Date: 1999-09 Impact factor: 4.438

8. Database resources of the National Center for Biotechnology Information.

Authors: D L Wheeler; D M Church; A E Lash; D D Leipe; T L Madden; J U Pontius; G D Schuler; L M Schriml; T A Tatusova; L Wagner; B A Rapp
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

9. Creation and maintenance of Helix, a Web based database of medical genetics laboratories, to serve the needs of the genetics community.

Authors: P Tarczy-Hornoch; M L Covington; J Edwards; P Shannon; S Fuller; R A Pagon
Journal: Proc AMIA Symp Date: 1998

10. The sequence of the human genome.

Authors: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal: Science Date: 2001-02-16 Impact factor: 47.728

17 in total

1. A knowledge framework for computational molecular-disease relationships in cancer.

Authors: Michael N Cantor; Yves A Lussier
Journal: Proc AMIA Symp Date: 2002

2. PQL: a declarative query language over dynamic biological schemata.

Authors: P Mork; R Shaker; A Halevy; P Tarczy-Hornoch
Journal: Proc AMIA Symp Date: 2002

3. Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform.

Authors: H Mei; P Tarczy-Hornoch; P Mork; A J Rossini; R Shaker; L Donelson
Journal: AMIA Annu Symp Proc Date: 2003

A model for data integration systems of biomedical data applied to online genetic databases.

1. Initial sequencing and analysis of the human genome.

2. Genomics. Are you ready for the revolution?

3. Computational biology. Bioinformatics--trying to swim in a sea of data.

4. Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base.

5. SRS: information retrieval system for molecular biology data banks.

6. Reports from the Eighth Annual Conference on Retroviruses and Opportunistic Infections. Chicago, February 4-8, 2001.

Review 7. Internet resources for the clinical geneticist.

8. Database resources of the National Center for Biotechnology Information.

9. Creation and maintenance of Helix, a Web based database of medical genetics laboratories, to serve the needs of the genetics community.

10. The sequence of the human genome.

1. A knowledge framework for computational molecular-disease relationships in cancer.

2. PQL: a declarative query language over dynamic biological schemata.

3. Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform.

4. QIS: A framework for biomedical database federation.

5. Automating terminological networks to link heterogeneous biomedical databases.

6. Supporting retrieval of diverse biomedical data using evidence-aware queries.

7. BioMediator data integration: beyond genomics to neuroscience data.

8. Automated database mediation using ontological metadata mappings.

9. Explorative search of distributed bio-data to answer complex biomedical questions.

10. Evaluation of probabilistic and logical inference for a SNP annotation system.