MalaCards: An amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D877-D887

  Rappaport, Noa ^a   Twik, Michal ^a   Plaschkes, Inbar ^a   Nudel, Ron ^a   Stein, Tsippi Iny ^a   Levitt, Jacob ^a   Gershoni, Moran ^a   Morrey, C Paul ^b   Safran, Marilyn ^a   Lancet, Doron ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UTAH VALLEY UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOMEDICINE; CLINICAL ANNOTATION; COMPARATIVE STUDY; COMPUTER INTERFACE; DATA EXTRACTION; DATA MINING; DATA PROCESSING; DISEASE CLASSIFICATION; DISEASE COURSE; DISEASE NAME INTEGRATION; DISEASE RELATEDNESS; DISEASE UNIFICATION; FACTUAL DATABASE; GENE ONTOLOGY; GENE RELATED DISEASE ANNOTATION; GENETIC ANNOTATION; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIATION; HUMAN; INFORMATION PROCESSING; MALACARD; MEDICAL TERMINOLOGY; NEXT GENERATION SEQUENCING; ONLINE SYSTEM; ONTOLOGY; PHENOTYPE; PUBLICATION; QUALITY CONTROL; REGISTER; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURED SEARCH; SYMPTOM; SYSTEMS MEDICINE; TRANSCRIPTOMICS; UNIFIED MEDICAL LANGUAGE SYSTEM; BIOLOGY; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; GENOMICS; MOLECULAR GENETICS; PROCEDURES; WEB BROWSER;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOMICS; HUMANS; MOLECULAR SEQUENCE ANNOTATION; WEB BROWSER;

EID: 85016157457     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1012     Document Type: Article

References (42)

1. Rappaport, N., Nativ, N., Stelzer, G., Twik, M., Guan-Golan, Y., Stein, T.I., Bahir, I., Belinky, F., Morrey, C.P., Safran, M. et al. (2013) MalaCards: an integrated compendium for diseases and their annotation. Database, 2013, bat018.
2. Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H. et al. (2010) GeneCards Version 3: the human gene integrator. Database, 2010, baq020.
3. Stelzer, G., Rosen, N., Plaschkes, I., Zimmerman, S., Twik, M., Fishilevich, S., Stein, T.I., Nudel, R., Lieder, I., Mazor, Y. et al. (2016) The GeneCards Suite: from gene data mining to disease genome sequence analyses. Curr. Protoc. Bioinformatics, 54, 1.30.1-1.30.33.
4. Aronson, A.R. and Lang, F.M. (2010) An overview of MetaMap: historical perspective and recent advances. J. Am. Med. Inform. Assoc., 17, 229-236.
5. Pinero, J., Queralt-Rosinach, N., Bravo, A., Deu-Pons, J., Bauer-Mehren, A., Baron, M., Sanz, F. and Furlong, L.I. (2015) DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database, 2010, bav028.
6. Amberger, J.S., Bocchini, C.A., Schiettecatte, F., Scott, A.F. and Hamosh, A. (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
7. Ben-Ari Fuchs, S., Lieder, I., Stelzer, G., Mazor, Y., Buzhor, E., Kaplan, S., Bogoch, Y., Plaschkes, I., Shitrit, A., Rappaport, N. et al. (2016) Gene Analytics: an integrative gene set analysis tool for next generation sequencing, RNAseq and microarray data. OMICS, 20, 139-151.
8. Rappaport, N., Twik, M., Nativ, N., Stelzer, G., Bahir, I., Stein, T.I., Safran, M. and Lancet, D. (2014) MalaCards: a comprehensive automatically-mined database of human diseases. Curr. Protoc. Bioinformatics, 47, doi:10.1002/0471250953.bi0124s47.
9. Belinky, F., Nativ, N., Stelzer, G., Zimmerman, S., Iny Stein, T., Safran, M. and Lancet, D. (2015) PathCards: multi-source consolidation of human biological pathways. Database: J. Biol. Dtabases Curation, 2015, bav006.
10. Hidalgo, C.A., Blumm, N., Barabasi, A.L. and Christakis, N.A. (2009) A dynamic network approach for the study of human phenotypes. PLoS Comput. Biol., 5, e1000353.
11. Kohler, S., Doelken, S.C., Mungall, C.J., Bauer, S., Firth, H.V., Bailleul-Forestier, I., Black, G.C., Brown, D.L., Brudno, M., Campbell, J. et al. (2014) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res., 42, D966-D974.
12. Kibbe, W.A., Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C.J., Binder, J.X., Malone, J., Vasant, D. et al. (2015) Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res., 43, D1071-D1078.
13. Maiella, S., Rath, A., Angin, C., Mousson, F. and Kremp, O. (2013) [Orphanet and its consortium: where to find expert-validated information on rare diseases]. Rev Neurol (Paris), 169 (Suppl. 1), S3-S8.
14. Eppig, J.T., Richardson, J.E., Kadin, J.A., Ringwald, M., Blake, J.A. and Bult, C.J. (2015) Mouse Genome Informatics (MGI): reflecting on 25 years. Mamm. Genome, 26, 272-284.
15. Chute, C.G., Carter, J.S., Tuttle, M.S., Haber, M. and Brown, S.H. (2003) Integrating pharmacokinetics knowledge into a drug ontology: as an extension to support pharmacogenomics. AMIA Annu. Symp. Proc., 2003, 170-174.
16. Edgar, R., Mazor, Y., Rinon, A., Blumenthal, J., Golan, Y., Buzhor, E., Livnat, I., Ben-Ari, S., Lieder, I., Shitrit, A. et al. (2013) LifeMap Discovery: the embryonic development, stem cells, and regenerative medicine research portal. PLoS One, 8, e66629.
17. Roberts, I. and Ker, K. (2016) Cochrane: the unfinished symphony of research synthesis. Syst. Rev., 5, 115.
18. Bramer, G.R. (1988) International statistical classification of diseases and related health problems. Tenth revision. World Health Stat. Q, 41, 32-36.
19. McEntyre, J. (1998) Linking up with Entrez. Trends Genet., 14, 39-40.
20. Pletscher-Frankild, S., Palleja, A., Tsafou, K., Binder, J.X. and Jensen, L.J. (2015) DISEASES: text mining and data integration of disease-gene associations. Methods, 74, 83-89.
21. Allende, R.A. (2009) Accelerating searches of research grants and scientific literature with novo|seek SM. Nat. Methods, 6, http://www.nature.com/nmeth/journal/v6/n5/full/nmeth.f.250.html.
22. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N. and Stratton, M.R. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
23. Pagon, R.A. (2007) Gene Tests: integrating genetic services into patient care. Am. J. Hum. Genet., 81, 658-659.
24. Rubinstein, W.S., Maglott, D.R., Lee, J.M., Kattman, B.L., Malheiro, A.J., Ovetsky, M., Hem, V., Gorelenkov, V., Song, G., Wallin, C. et al. (2013) The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. Nucleic Acids Res., 41, D925-D935.
25. Gene Ontology, C. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
26. Stelzer, G., Inger, A., Olender, T., Iny-Stein, T., Dalah, I., Harel, A., Safran, M. and Lancet, D. (2009) Gene Decks: paralog hunting and gene-set distillation with Gene Cards annotation. OMICS, 13, 477-487.
27. Landrum, M.J., Lee, J.M., Benson, M., Brown, G., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Hoover, J. et al. (2016) Clin Var: public archive of interpretations of clinically relevant variants. Nucleic Acids Res., 44, D862-D868.
28. Forbes, S.A., Beare, D., Gunasekaran, P., Leung, K., Bindal, N., Boutselakis, H., Ding, M., Bamford, S., Cole, C., Ward, S. et al. (2015) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 43, D805-D811.
29. Sonabend, A.M., Zacharia, B.E., Cloney, M.B., Sonabend, A., Showers, C., Ebiana, V., Nazarian, M., Swanson, K.R., Baldock, A., Brem, H. et al. (2016) Defining Glioblastoma resectability through the wisdom of the crowd: a proof-of-principle study. Neurosurgery, 2016, doi:10.1227/NEU.0000000000001374.
30. Davis, A.P., Grondin, C.J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B.L., Wiegers, T.C. and Mattingly, C.J. (2015) The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res., 43, D914-D920.
31. Famiglietti, M.L., Estreicher, A., Gos, A., Bolleman, J., Gehant, S., Breuza, L., Bridge, A., Poux, S., Redaschi, N., Bougueleret, L. et al. (2014) Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation. Hum. Mutat., 35, 927-935.
32. Imbert, G., Saudou, F., Yvert, G., Devys, D., Trottier, Y., Garnier, J.M., Weber, C., Mandel, J.L., Cancel, G., Abbas, N. et al. (1996) Cloning of the gene for spinocerebellar ataxia 2 reveals a locus with high sensitivity to expanded CAG/glutamine repeats. Nat. Genet., 14, 285-291.
33. Lohmann, K. and Klein, C. (2014) Next generation sequencing and the future of genetic diagnosis. Neurotherapeutics, 11, 699-707.
34. Stelzer, G., Plaschkes, I., Oz-Levi, D., Alkelai, A., Olender, T., Zimmerman, S., Twik, M., Belinky, F., Fishilevich, S., Nudel, R. et al. (2016) VarElect: the phenotype-based variation prioritizer of the GeneCards Suite. BMC Genomics, 17(Suppl. 2), 444.
35. Rabbani, B., Nakaoka, H., Akhondzadeh, S., Tekin, M. and Mahdieh, N. (2016) Next generation sequencing: implications in personalized medicine and pharmacogenomics. Mol. Biosyst., 12, 1818-1830.
36. Zhao, C., Eisinger, B.E., Driessen, T.M. and Gammie, S.C. (2014) Addiction and reward-related genes show altered expression in the postpartum nucleus accumbens. Front. Behav. Neurosci., 8, 388.
37. Zhao, M., Wang, K.J., Tan, Z., Zheng, C.M., Liang, Z. and Zhao, J.Q. (2016) Identification of potential therapeutic targets for papillary thyroid carcinoma by bioinformatics analysis. Oncol. Lett., 11, 51-58.
38. Hashemikhabir, S., Xia, R., Xiang, Y. and Janga, S. (2015) A framework for identifying genotypic information from clinical records: exploiting integrated ontology structures to transfer annotations between ICD codes and Gene Ontologies. IEEE/ACM Trans. Comput. Biol. Bioinform., 2015, doi:10.1109/TCBB.2015.2480056.
39. Hashemikhabir, S., Neelamraju, Y. and Janga, S.C. (2015) Database of RNA binding protein expression and disease dynamics (READ DB). Database, 2015, bav072.
40. Zhou, X., Menche, J., Barabasi, A.L. and Sharma, A. (2014) Human symptoms-disease network. Nat. Commun., 5, 4212.
41. Speir, M.L., Zweig, A.S., Rosenbloom, K.R., Raney, B.J., Paten, B., Nejad, P., Lee, B.T., Learned, K., Karolchik, D., Hinrichs, A.S. et al. (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Res, 44, D717-D725.
42. Lopes, P. and Oliveira, J.L. (2013) An innovative portal for rare genetic diseases research: the semantic Diseasecard. J. Biomed. Inform., 46, 1108-1115.