The implicitome: A resource for rationalizing gene-disease associations

PLoS ONE

Volumn 11, Issue 2, 2016, Pages

  Hettne, Kristina M ^a   Thompson, Mark ^a   Van Haagen, Herman H H B M ^a   Van Der Horst, Eelke ^a   Kaliyaperumal, Rajaram ^a   Mina, Eleni ^a   Tatum, Zuotian ^a   Laros, Jeroen F J ^a   Van Mulligen, Erik M ^a,b   Schuemie, Martijn ^b   Emmelien, Aten ^a   Li, Tong Shu ^e   Bruskiewich, Richard ^f   Good, Benjamin M ^e   Su, Andrew I ^e   Kors, Jan A ^b   Den Dunnen, Johan ^a   Van Ommen, Gert Jan B ^a   Roos, Marco ^a   T'Hoen, Peter A C ^a   Mons, Barend ^a,c   Schultes, Erik A ^a,d   more..

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

^c Dutch Techcentre for Life Sciences   (Netherlands)

^d LEIDEN UNIVERSITY   (Netherlands)

^e SCRIPPS RESEARCH INSTITUTE   (United States)

^f STAR Informatics   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; EXPLICITOME; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC PARAMETERS; GENOTYPE PHENOTYPE CORRELATION; HUMAN; IMPLICITOME; ONLINE SYSTEM; PATHOPHYSIOLOGY; PUBLICATION; VALIDATION PROCESS; BIOLOGY; GENETIC DATABASE; GENETIC PREDISPOSITION; GENOME-WIDE ASSOCIATION STUDY; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS;

EID: 84960363331     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0149621     Document Type: Article

References (58)

1. Good BM, Ainscough BJ, McMichael JF, Su AI, Griffith OL. Organizing knowledge to enable personalization of medicine in cancer. Genome Biol. 2014; 15: 438. Available: http://genomebiology.com/2014/15/8/438 doi: 10.1186/s13059-014-0438-7 PMID: 25222080
2. Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, et al. Finding our way through phenotypes. PLoS Biol. 2015; 13: e1002033. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4285398&tool=pmcentrez&rendertype=Abstract doi: 10.1371/journal.pbio. 1002033 PMID: 25562316
3. Machado CM, Rebholz-Schuhmann D, Freitas AT, Couto FM. The semantic web in translational medicine: current applications and future directions. Brief Bioinform. 2015; 16: 89-103. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4293377&tool=pmcentrez&rendertype=Abstract doi: 10.1093/bib/bbt079 PMID: 24197933
4. Swanson DR. Complementary structures in disjoint science literatures. Proceedings of the 14th annual international ACM SIGIR conference on Research and development in information retrieval-SIGIR '91. New York, New York, USA: ACM Press; 1991. pp. 280-289. Available: http://dl.acm.org/citation. cfm?id=122860.122889
5. Jelier R, Schuemie MJ, Roes P-J, van Mulligen EM, Kors JA. Literature-based concept profiles for gene annotation: the issue of weighting. Int J Med Inform. 2008; 77: 354-62. Available: http://www.ncbi.nlm. nih.gov/pubmed/17827057 PMID: 17827057
6. van Haagen HHHBM, 't Hoen PAC, Mons B, Schultes EA. Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery. Altmann EG, editor. PLoS One. Public Library of Science; 2013; 8: e78665. Available: http://dx.plos.org/10.1371/journal.pone. 0078665
7. Schuemie M, Chichester C, Lisacek F, Coute Y, Roes P-J, Sanchez JC, et al. Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE. Proteomics. 2007; 7: 921-31. Available: http://www.ncbi.nlm.nih.gov/pubmed/17370270 PMID: 17370270
8. Jelier R, 't Hoen PAC, Sterrenburg E, den Dunnen JT, van Ommen G-JB, Kors JA, et al. Literatureaided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics. 2008; 9: 291. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=2459190&tool=pmcentrez&rendertype=Abstract doi: 10.1186/1471-2105-9-291 PMID: 18577208
9. Jelier R, Goeman JJ, Hettne KM, Schuemie MJ, den Dunnen JT, 't Hoen PAC. Literature-aided interpretation of gene expression data with the weighted global test. Brief Bioinform. 2011; 12: 518-29. Available: http://www.ncbi.nlm.nih.gov/pubmed/21183478 doi: 10.1093/bib/bbq082 PMID: 21183478
10. Jelier R, Jenster G, Dorssers LCJ, Wouters BJ, Hendriksen PJM, Mons B, et al. Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. BMC Bioinformatics. 2007; 8: 14. doi: 10.1186/1471-2105-8-14 PMID: 17233900
11. Jelier R, Schuemie MJ, Veldhoven A, Dorssers LCJ, Jenster G, Kors JA. Anni 2.0: a multipurpose textmining tool for the life sciences. Genome Biol. 2008; 9: R96. PMID: 18549479
12. Hettne KM, Boorsma A, van Dartel DA, Goeman JJ, de Jong E, Piersma AH, et al. Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data. BMC Med Genomics. 2013; 6: 2. doi: 10.1186/1755-8794-6-2 PMID: 23356878
13. van Haagen HHHBM, 't Hoen PAC, Botelho Bovo A, de Morrée A, van Mulligen EM, Chichester C, et al. Novel protein-protein interactions inferred from literature context. PLoS One. 2009; 4: e7894. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 2774517&tool=pmcentrez&rendertype=Abstract doi: 10.1371/journal.pone.0007894 PMID: 19924298
14. Houlden H, Johnson J, Gardner-Thorpe C, Lashley T, Hernandez D, Worth P, et al. Mutations in TTBK2, encoding a kinase implicated in tau phosphorylation, segregate with spinocerebellar ataxia type 11. Nat Genet. 2007; 39: 1434-6. Available: http://www.ncbi.nlm.nih.gov/pubmed/18037885 PMID: 18037885
15. Yu TW, Mochida GH, Tischfield DJ, Sgaier SK, Flores-Sarnat L, Sergi CM, et al. Mutations inWDR62, encoding a centrosome-associated protein, causemicrocephaly with simplified gyri and abnormal cortical architecture. Nat Genet. 2010; 42: 1015-20. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2969850&tool=pmcentrez&rendertype=Abstract doi: 10.1038/ng.683 PMID: 20890278
16. Sajid Hussain M, Marriam Bakhtiar S, Farooq M, Anjum I, Janzen E, Reza Toliat M, et al. Genetic heterogeneity in Pakistani microcephaly families. Clin Genet. 2013; 83: 446-51. Available: http://www.ncbi.nlm.nih.gov/pubmed/22775483 doi: 10.1111/j.1399-0004.2012.01932.x PMID: 22775483
17. Funk C, Baumgartner W, Garcia B, Roeder C, Bada M, Cohen KB, et al. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics. 2014; 15: 59. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4015610&tool=pmcentrez&rendertype=Abstract doi: 10.1186/1471-2105-15-59 PMID: 24571547
18. Wassif CA, Maslen C, Kachilele-Linjewile S, Lin D, Linck LM, Connor WE, et al. Mutations in the human sterol delta7-reductase gene at 11q12-13 cause Smith-Lemli-Opitz syndrome. Am J Hum Genet. 1998; 63: 55-62. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1377256&tool=pmcentrez&rendertype=Abstract PMID: 9634533
19. Fitzky BU, Witsch-Baumgartner M, Erdel M, Lee JN, Paik YK, Glossmann H, et al. Mutations in the Delta7-sterol reductase gene in patients with the Smith-Lemli-Opitz syndrome. Proc Natl Acad Sci U S A. 1998; 95: 8181-6. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=20950&tool=pmcentrez&rendertype=Abstract PMID: 9653161
20. Tint GS, Irons M, Elias ER, Batta AK, Frieden R, Chen TS, et al. Defective cholesterol biosynthesis associated with the Smith-Lemli-Opitz syndrome. N Engl J Med. 1994; 330: 107-13. Available: http://www.ncbi.nlm.nih.gov/pubmed/8259166 PMID: 8259166
21. Cheng JB, Levine MA, Bell NH, Mangelsdorf DJ, Russell DW. Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase. Proc Natl Acad Sci U S A. 2004; 101: 7711-5. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=419671&tool=pmcentrez&rendertype=Abstract PMID: 15128933
22. Hansen L, Tawamie H, Murakami Y, Mang Y, ur Rehman S, Buchert R, et al. Hypomorphic mutations in PGAP2, encoding a GPI-anchor-remodeling protein, cause autosomal-recessive intellectual disability. Am J Hum Genet. 2013; 92: 575-83. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=3617372&tool=pmcentrez&rendertype=Abstract doi: 10.1016/j.ajhg.2013.03.008 PMID: 23561846
23. Krawitz PM, Murakami Y, Rieß A, Hietala M, Krüger U, Zhu N, et al. PGAP2 mutations, affecting the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation syndrome. Am J Hum Genet. 2013; 92: 584-9. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3617374&tool=pmcentrez&rendertype=Abstract doi: 10.1016/j.ajhg.2013.03.011 PMID: 23561847
24. Umemura M, Fujita M, Yoko-O T, Fukamizu A, Jigami Y. Saccharomyces cerevisiae CWH43 is involved in the remodeling of the lipid moiety of GPI anchors to ceramides. Mol Biol Cell. 2007; 18: 4304-16. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2043546&tool=pmcentrez&rendertype=Abstract PMID: 17761529
25. O'Driscoll M, Ruiz-Perez VL, Woods CG, Jeggo PA, Goodship JA. A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome. Nat Genet. 2003; 33: 497-501. Available: http://www.ncbi.nlm.nih.gov/pubmed/12640452 PMID: 12640452
26. Griffith E, Walker S, Martin C-A, Vagnarelli P, Stiff T, Vernay B, et al. Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling. Nat Genet. 2008; 40: 232-6. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2397541&tool=pmcentrez&rendertype=Abstract PMID: 18157127
27. Bond J, Roberts E, Springell K, Lizarraga SB, Lizarraga S, Scott S, et al. A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size. Nat Genet. 2005; 37: 353-5. Available: http://www.ncbi.nlm.nih.gov/pubmed/15793586 PMID: 15793586
28. Qvist P, Huertas P, Jimeno S, Nyegaard M, Hassan MJ, Jackson SP, et al. CtIP Mutations Cause Seckel and Jawad Syndromes. PLoS Genet. 2011; 7: e1002310. Available: http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid=3188555&tool=pmcentrez&rendertype=Abstract doi: 10.1371/journal. pgen.1002310 PMID: 21998596
29. Kalay E, Yigit G, Aslan Y, Brown KE, Pohl E, Bicknell LS, et al. CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet. 2011; 43: 23-6. Available: http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid=3430850&tool=pmcentrez&rendertype=Abstract doi: 10.1038/ng.725 PMID: 21131973
30. Shaheen R, Faqeih E, Ansari S, Abdel-Salam G, Al-Hassnan ZN, Al-Shidi T, et al. Genomic analysis of primordial dwarfism reveals novel disease genes. Genome Res. 2014; 24: 291-9. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3912419&tool=pmcentrez&rendertype=Abstract doi: 10.1101/gr.160572.113 PMID: 24389050
31. Ogi T, Walker S, Stiff T, Hobson E, Limsirichaikul S, Carpenter G, et al. Identification of the first ATRIPdeficient patient and novel mutations in ATR define a clinical spectrum for ATR-ATRIP Seckel Syndrome. PLoS Genet. 2012; 8: e1002945. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=3493446&tool=pmcentrez&rendertype=Abstract doi: 10.1371/journal.pgen.1002945 PMID: 23144622
32. Kirino Y, Bertsias G, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, et al. Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B.51 and ERAP1. Nat Genet. 2013; 45: 202-7. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=3810947&tool=pmcentrez&rendertype=Abstract doi: 10.1038/ng.2520 PMID: 23291587
33. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, et al. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011; 39: W541-5. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3125807&tool=pmcentrez&rendertype=Abstract doi: 10.1093/nar/gkr469 PMID: 21672956
34. Dogan RI, Leaman R, Lu Z. NCBI disease corpus: a resource for disease name recognition and concept normalization. J Biomed Inform. 2014; 47: 1-10. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3951655&tool=pmcentrez&rendertype=Abstract doi: 10.1016/j.jbi.2013.12.006 PMID: 24393765
35. Kang N, Singh B, Afzal Z, van Mulligen EM, Kors JA. Using rule-based natural language processing to improve disease normalization in biomedical text. J Am Med Inform Assoc. 20: 876-81. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3756254&tool=pmcentrez&rendertype=Abstract doi: 10.1136/amiajnl-2012-001173 PMID: 23043124
36. Aronson AR. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp. 2001; 17-21. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2243666&tool=pmcentrez&rendertype=Abstract PMID: 11825149
37. Jimeno Yepes A, Berlanga R. Knowledge based word-concept model estimation and refinement for biomedical text mining. J Biomed Inform. 2015; 53: 300-7. Available: http://www.ncbi.nlm.nih.gov/pubmed/25510606 doi: 10.1016/j.jbi.2014.11.015 PMID: 25510606
38. McInnes BT, Stevenson M. Determining the difficulty of Word Sense Disambiguation. J Biomed Inform. 2014; 47: 83-90. Available: http://www.ncbi.nlm.nih.gov/pubmed/24076369 doi: 10.1016/j.jbi.2013.09. 009 PMID: 24076369
39. Bravo À, Piñero J, Queralt-Rosinach N, Rautschka M, Furlong LI. Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research. BMC Bioinformatics. 2015; 16: 55. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=4466840&tool=pmcentrez&rendertype=Abstract doi: 10.1186/s12859-015-0472-9 PMID: 25886734
40. Rindflesch TC, Fiszman M. The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform. 2003; 36: 462-77. Available: http://www.ncbi.nlm.nih.gov/pubmed/14759819 PMID: 14759819
41. Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC. SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics. 2012; 28: 3158-60. Available: http://bioinformatics.oxfordjournals.org/content/28/23/3158.long doi: 10.1093/bioinformatics/bts591 PMID: 23044550
42. Mons B, Haagen Van H, Chichester C, 't Hoen P-B, Dunnen Den JT, Ommen Van G, et al. The value of data. Nat Genet. Nature Publishing Group; 2011; 43: 281-283. Available: http://www.ncbi.nlm.nih.gov/pubmed/21445068
43. Groth P, Gibson A, Velterop J. The anatomy of a nanopublication. Inf Serv Use. 2010; 30: 51-56. doi: 10.3233/ISU-2010-0613
44. Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, et al. Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. 2015; 55: 206-17. Available: http://www.ncbi.nlm.nih.gov/pubmed/25917055 doi: 10.1016/j.jbi.2015.04.006 PMID: 25917055
45. Ganapathiraju MK, Orii N. Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. Gigascience. BioMed Central Ltd; 2013; 2: 11. doi: 10. 1186/2047-217X-2-11
46. Schuemie MJ, Jelier R, Kors JA. Peregrine: Lightweight gene name normalization by dictionary lookup. Proc of the Second BioCreative Challenge Evaluation Workshop. pp. 131-133. Available: http://schuemie.net/pdf/biocreative-2007.pdf
47. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004; 32: 267D-270. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=308795&tool=pmcentrez&rendertype=Abstract
48. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2010; 39: D52-D57. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013746&tool=pmcentrez&rendertype=Abstract doi: 10.1093/nar/gkq1237 PMID: 21115458
49. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010; 38: D142-8. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2808944&tool=pmcentrez&rendertype=Abstract doi: 10.1093/nar/gkp846 PMID: 19843607
50. Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E. The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res. 2008; 36: D445-8. doi: 10.1093/nar/gkm881 PMID: 17984084
51. Hettne KM, Stierum RH, Schuemie MJ, Hendriksen PJM, Schijvenaars BJA, Mulligen van EM, et al. A dictionary to identify small molecules and drugs in free text. Bioinformatics. 2009; 25: 2983-91. doi: 10. 1093/bioinformatics/btp535 PMID: 19759196
52. Schuemie MJ, Mons B, Weeber M, Kors JA. Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. J Biomed Inform. 2007; 40: 316-24. doi: 10. 1016/j.jbi.2006.09.002 PMID: 17079192
53. Hettne KM, van Mulligen EM, Schuemie MJ, Schijvenaars BJ, Kors JA. Rewriting and suppressing UMLS terms for improved biomedical term identification. J Biomed Semantics. 2010; 1: 5. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2895736&tool=pmcentrez&rendertype=Abstract doi: 10.1186/2041-1480-1-5 PMID: 20618981
54. McCray AT, Srinivasan S, Browne AC. Lexical methods for managing variation in biomedical terminologies. Proc Annu Symp Comput Appl Med Care. 1994; 235-9. Available: http://www.pubmedcentral.nih. gov/articlerender.fcgi?artid=2247735&tool=pmcentrez&rendertype=Abstract PMID: 7949926
55. Goodman LA, Kruskal WH. Measures of Association for Cross Classifications [Internet]. New York, NY: Springer New York; 1979. doi: 10.1007/978-1-4612-9995-0
56. Coulet A, Garten Y, Dumontier M, Altman RB, Musen MA, Shah NH. Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J Biomed Semantics. 2011; 2 Suppl 2: S10. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3102890&tool=pmcentrez&rendertype=Abstract doi: 10.1186/2041-1480-2-S2-S10 PMID: 21624156
57. Hettne KM, van Schouwen R, Mina E, van der Horst E, Thompson M, Kaliyaperumal R, et al. Explain your data by Concept Profile Analysis Web Services. F1000Research. 2014; 3. doi: 10.12688/f1000research.4830.1
58. Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL, et al. Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today. 2012; 17: 1188-98. Available: http://www.ncbi.nlm.nih.gov/pubmed/22683805 doi: 10.1016/j.drudis.2012.05.016 PMID: 22683805