Literature DB >> 20139945

Ontology engineering.

Gil Alterovitz, Michael Xiang, David P Hill, Jane Lomax, Jonathan Liu, Michael Cherkassky, Jonathan Dreyfuss, Chris Mungall, Midori A Harris, Mary E Dolan, Judith A Blake, Marco F Ramoni.   

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Year:  2010        PMID： 20139945      PMCID： PMC4829499          DOI： 10.1038/nbt0210-128

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  17 in total

1.  The Gene Ontology (GO) database and informatics resource.

Authors:  M A Harris; J Clark; A Ireland; J Lomax; M Ashburner; R Foulger; K Eilbeck; S Lewis; B Marshall; C Mungall; J Richter; G M Rubin; J A Blake; C Bult; M Dolan; H Drabkin; J T Eppig; D P Hill; L Ni; M Ringwald; R Balakrishnan; J M Cherry; K R Christie; M C Costanzo; S S Dwight; S Engel; D G Fisk; J E Hirschman; E L Hong; R S Nash; A Sethuraman; C L Theesfeld; D Botstein; K Dolinski; B Feierbach; T Berardini; S Mundodi; S Y Rhee; R Apweiler; D Barrell; E Camon; E Dimmer; V Lee; R Chisholm; P Gaudet; W Kibbe; R Kishore; E M Schwarz; P Sternberg; M Gwinn; L Hannick; J Wortman; M Berriman; V Wood; N de la Cruz; P Tonellato; P Jaiswal; T Seigfried; R White
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.

Authors:  Fátima Al-Shahrour; Ramón Díaz-Uriarte; Joaquín Dopazo
Journal:  Bioinformatics       Date:  2004-01-22       Impact factor: 6.937

3.  Solving the information overload problem: a letter from Canada.

Authors:  David A Davis; Ileana Ciurea; Tanya M Flanagan; Laure Perrier
Journal:  Med J Aust       Date:  2004-03-15       Impact factor: 7.738

4.  Implications of compositionality in the gene ontology for its curation and usage.

Authors:  Philip V Ogren; K Bretonnel Cohen; Lawrence Hunter
Journal:  Pac Symp Biocomput       Date:  2005

5.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Authors:  Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Christopher J Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
Journal:  Nat Biotechnol       Date:  2007-11       Impact factor: 54.908

6.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

7.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; Vivian Lee; Emily Dimmer; John Maslen; David Binns; Nicola Harte; Rodrigo Lopez; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  The Gene Ontology project in 2008.

Authors: 
Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

9.  MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data.

Authors:  Scott W Doniger; Nathan Salomonis; Kam D Dahlquist; Karen Vranizan; Steven C Lawlor; Bruce R Conklin
Journal:  Genome Biol       Date:  2003-01-06       Impact factor: 13.583

10.  Strategy for encoding and comparison of gene expression signatures.

Authors:  Yajun Yi; Chun Li; Clay Miller; Alfred L George
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
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  34 in total

1.  Siri of the cell: what biology could learn from the iPhone.

Authors:  Anne-Ruxandra Carvunis; Trey Ideker
Journal:  Cell       Date:  2014-04-24       Impact factor: 41.582

2.  Marco Ramoni: an appreciation of academic achievement.

Authors:  Isaac S Kohane; Peter Szolovits
Journal:  J Am Med Inform Assoc       Date:  2011-04-07       Impact factor: 4.497

3.  An ontology-neutral framework for enrichment analysis.

Authors:  Rob Tirrell; Uday Evani; Ari E Berman; Sean D Mooney; Mark A Musen; Nigam H Shah
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

4.  Automating the construction of gene ontologies.

Authors:  Kara Dolinski; David Botstein
Journal:  Nat Biotechnol       Date:  2013-01       Impact factor: 54.908

5.  Design and Development of a Sharable Clinical Decision Support System Based on a Semantic Web Service Framework.

Authors:  Yi-Fan Zhang; Ling Gou; Yu Tian; Tian-Chang Li; Mao Zhang; Jing-Song Li
Journal:  J Med Syst       Date:  2016-03-22       Impact factor: 4.460

6.  Coordinated Action of Biological Processes during Embryogenesis Can Cause Genome-Wide Linkage Disequilibrium in the Human Genome and Influence Age-Related Phenotypes.

Authors:  Irina Culminskaya; Alexander M Kulminski; Anatoli I Yashin
Journal:  Ann Gerontol Geriatr Res       Date:  2016-05-04

Review 7.  Pathway analysis of genomic data: concepts, methods, and prospects for future development.

Authors:  Vijay K Ramanan; Li Shen; Jason H Moore; Andrew J Saykin
Journal:  Trends Genet       Date:  2012-04-03       Impact factor: 11.639

Review 8.  Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.

Authors:  David P Hill; Tanya Z Berardini; Douglas G Howe; Kimberly M Van Auken
Journal:  Mol Reprod Dev       Date:  2010-04       Impact factor: 2.609

9.  An Independent Filter for Gene Set Testing Based on Spectral Enrichment.

Authors:  H Robert Frost; Zhigang Li; Folkert W Asselbergs; Jason H Moore
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2015 Sep-Oct       Impact factor: 3.710

10.  Modeling the autism spectrum disorder phenotype.

Authors:  Alexa T McCray; Philip Trevvett; H Robert Frost
Journal:  Neuroinformatics       Date:  2014-04
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