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PRO Citations

  1. Ai J, Smith B, Wong DT: Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. BMC Bioinformatics 2010, 11:302-2105-11-302.
  2. Ai JY, Smith B, Wong DT: Bioinformatics advances in saliva diagnostics. Int J Oral Sci 2012, 4(2):85-87.
  3. Anguita A, Garcia-Remesal M, de la Iglesia D, Maojo V: NCBI2RDF: enabling full RDF-based access to NCBI databases. Biomed Res Int 2013, 2013:983805.
  4. Arighi CN, Roberts PM, Agarwal S, Bhattacharya S, Cesareni G, Chatr-Aryamontri A, Clematide S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais LJ, Okazaki N, Perfetto L, Rinaldi F, Saetre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman L, Wu CH: BioCreative III interactive task: an overview. BMC Bioinformatics 2011, 12 Suppl 8:S4-2105-12-S8-S4.
  5. Avram S, Milac A, Mernea M, Mihailescu D, Putz MV, Buiu C. Structure-biological function relationship extended to mitotic arrest-deficient 2-like protein Mad2 native and mutants-new opportunity for genetic disorder control. Int J Mol Sci. 2014 Nov 18;15(11):21381-400.
     
  6. Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA,Jr, Cohen KB, Verspoor K, Blake JA, Hunter LE: Concept annotation in the CRAFT corpus. BMC Bioinformatics 2012, 13:161-2105-13-161.
  7. Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT, Mouse Genome Database Group: The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 2011, 39(Database issue):D842-8.
  8. Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME: The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 2008, 6(3):175-194.
  9. Burgun A, Bodenreider O: Accessing and integrating data and knowledge for biomedical research. Yearb Med Inform 2008, :91-101.
  10. Chen B, Ding Y, Wild DJ: Improving integrative searching of systems chemical biology data using semantic annotation. J Cheminform 2012, 4(1):6-2946-4-6.
  11. Chowdhary R, Tan SL, Zhang J, Karnik S, Bajic VB, Liu JS: Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PLoS One 2012, 7(4):e34480.
  12. Ciccarese P, Ocana M, Clark T: Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics 2012, 3 Suppl 1:S1-1480-3-S1-S1.
  13. Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T: An open annotation ontology for science on web 3.0. J Biomed Semantics 2011, 2 Suppl 2:S4-1480-2-S2-S4.
  14. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7.
     
  15. de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P: The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res Notes 2011, 4:313-0500-4-313.
  16. Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondre-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ: Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform 2011, 44(1):75-79.
  17. Ding R, Arighi CN, Lee, J, Wu, CH, Vijay-Shanker, K: pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature. PLoS One. 2015 Aug 10;10(8):e0135305.
     
  18. Drabkin HJ, Blake JA, Mouse Genome Informatics Database: Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. Database (Oxford) 2012, 2012:bas045.
  19. Fu X, Batista-Navarro R, Rak R, Ananiadou S: Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. J Biomed Semantics. 2015 Mar 14;6:8
  20. Funk C, Baumgartner W Jr, Garcia B, Roeder C, Bada M, Cohen KB, Hunter LE, Verspoor K. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics. 2014 Feb 26;15:59.
  21. Gosal G, Kochut KJ, Kannan N: ProKinO: an ontology for integrative analysis of protein kinases in cancer. PLoS One 2011, 6(12):e28782.
  22. Guardia GD, Vencio RZ, de Farias CR: A UML profile for the OBO relation ontology. BMC Genomics 2012, 13 Suppl 5:S3-2164-13-S5-S3. Epub 2012 Oct 19.
  23. Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E: eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. J Biomed Semantics. 2015 Mar 21;6:10.
     
  24. Hoehndorf R, Dumontier M, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV: Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PLoS One 2011, 6(7):e22006.
  25. Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M: OMIT: dynamic, semi-automated ontology development for the microRNA domain. PLoS One. 2014 Jul 15;9(7):e100855.
  26. Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15:155.
  27. Jayapandian CP, Zhao M, Ewing RM, Zhang GQ, Sahoo SS: A semantic proteomics dashboard (SemPoD) for data management in translational research. BMC Syst Biol 2012, 6 Suppl 3:S20-0509-6-S3-S20. Epub 2012 Dec 17.
  28. Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD. The neurological disease ontology. J Biomed Semantics. 2013 Dec 6;4(1):42. doi:   10.1186/2041-1480-4-42. PubMed PMID:24314207
  29. Kah Wai Lin, Min Jia and Serhiy Souchelnytskyi (2012). Application of Bioinformatics Tools in Gel-Based Proteomics, Integrative Proteomics, Dr. Hon-Chiu Leung (Ed.), ISBN: 978-953-51-0070-6, InTech, DOI: 10.5772/31275. Available from: http://www.intechopen.com/books/integrative-proteomics/application-of-bioinformatics-tools-in-gel-based-proteomics
  30. Laukens K, Naulaerts S, Berghe WV: Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis. Proteomics. 2015 Mar;15(5-6):981-96.
     
  31. Lin Y, Xiang Z, He Y: Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. J Biomed Semantics 2011, 2(1):9-1480-2-9.
  32. McKeever S, Johnson D: The role of markup for enabling interoperability in health informatics.
     
  33. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG: An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics 2009, 10:70-2105-10-70. Front Physiol. 2015 May 18;6:152.
  34. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P: Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009, 37(Database issue):D619-22.
  35. Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S. The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 2015 Jan;43(Database issue):D479-84.
     
  36. Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD: Logical development of the cell ontology. BMC Bioinformatics 2011, 12:6-2105-12-6.
  37. Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013 Aug 30;14:263. doi: 10.1186/1471-2105-14-263. PubMed PMID: 24004649; PubMed Central PMCID: PMC3844401.
  38. Mi H, Thomas PD: Ontologies and standards in bioscience research: for machine or for human. Front Physiol 2011, 2:5.
  39. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J: Cross-product extensions of the Gene Ontology. J Biomed Inform 2011, 44(1):80-86.
  40. Mungall CJ, Batchelor C, Eilbeck K: Evolution of the Sequence Ontology terms and relationships. J Biomed Inform 2011, 44(1):87-93.
  41. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M: Integrating phenotype ontologies across multiple species. Genome Biol 2010, 11(1):R2-2010-11-1-r2.
  42. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA: Uberon, an integrative multi-species anatomy ontology. Genome Biol 2012, 13(1):R5-2012-13-1-r5.
  43. Pál G, Lovas G, Dobolyi A. Induction of transforming growth factor beta receptors following focal ischemia in the rat brain. PLoS One. 2014 Sep 5;9(9):e106544.
     
  44. Pal G, Vincze C, Renner E, Wappler EA, Nagy Z, Lovas G, Dobolyi A: Time course, distribution and cell types of induction of transforming growth factor betas following middle cerebral artery occlusion in the rat brain. PLoS One 2012, 7(10):e46731.
  45. Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A: Initial implementation of a comparative data analysis ontology. Evol Bioinform Online 2009, 5:47-66.
  46. Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM: The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics 2008, 24(23):2767-2772.
  47. Robinson PN, Webber C.Phenotype ontologies and cross-species analysis for translational research.PLoS Genet. 2014 Apr 3;10(4):e1004268.
     
  48. Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A: Sharing and archiving nucleic acid structure mapping data. RNA 2011, 17(7):1204-1212.
  49. Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J: The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics 2013, 4(1):20.
  50. Ruttenberg A, Rees JA, Samwald M, Marshall MS: Life sciences on the Semantic Web: the Neurocommons and beyond. Brief Bioinform 2009, 10(2):193-204.
  51. Smith B, Ceusters W: Ontological realism: A methodology for coordinated evolution of scientific ontologies. Appl Ontol 2010, 5(3-4):139-188.
  52. Steinert-Threlkeld S, Ardekani S, Mejino JL, Detwiler LT, Brinkley JF, Halle M, Kikinis R, Winslow RL, Miller MI, Ratnanather JT: Ontological labels for automated location of anatomical shape differences. J Biomed Inform 2012, 45(3):522-527.
  53. Torii M, Arighi CN, Gang Li, Qinghua Wang, Wu CH, Vijay-Shanker K: RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):17-29.
     
  54. Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K: The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database (Oxford) 2012, 2012:bas044.
  55. UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8. doi: 10.1093/nar/gkt1140. Epub 2013 Nov 18.
  56. Vazquez-Naya JM, Martinez-Romero M, Porto-Pazos AB, Novoa F, Valladares-Ayerbes M, Pereira J, Munteanu CR, Dorado J: Ontologies of drug discovery and design for neurology, cardiology and oncology. Curr Pharm Des 2010, 16(24):2724-2736.
  57. Vita R, Overton JA, Greenbaum JA, Sette A, OBI consortium, Peters B: Query enhancement through the practical application of ontology: the IEDB and OBI. J Biomed Semantics 2013, 4 Suppl 1:S6-1480-4-S1-S6. Epub 2013 Apr 15.
  58. Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW: Ontologies as integrative tools for plant science. Am J Bot 2012, 99(8):1263-1275.
  59. Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ: The ChEMBL database as linked open data. J Cheminform 2013, 5(1):23-2946-5-23.
  60. Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y: OntoFox: web-based support for ontology reuse. BMC Res Notes 2010, 3:175-0500-3-175.
  61. Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T: INOH: ontology-based highly structured database of signal transduction pathways. Database (Oxford) 2011, 2011:bar052.

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