publication . Article . Other literature type . 2019

VIST-a Variant-Information Search Tool for precision oncology

Reinhold Schäfer;
Open Access English
  • Published: 16 Aug 2019 Journal: BMC Bioinformatics, volume 20 (eissn: 1471-2105, Copyright policy)
  • Publisher: BioMed Central
Abstract
Background Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient’s genome. This analysis relies on previously published information regarding the association of variations to disease progression and possible interventions. Clinicians to a large degree use biomedical search engines to obtain such information; however, the vast majority of scientific publications focus on basic science and have no direct clinical impact. We develop the Variant-Information Search Tool (VIST), a search engine designed for the targeted search of clinically relevant publications given an oncological mutation profil...
Subjects
free text keywords: Research Article, Biomedical information retrieval, Document retrieval, Personalized oncology, Document classification, Clinical relevance, Document triage, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications
Related Organizations
44 references, page 1 of 3

Garraway, LA, Verweij, J, Ballman, KV. Precision Oncology: An Overview. J Clin Oncol. 2013; 31 (15): 1803-5 [OpenAIRE] [PubMed] [DOI]

Topalian, SL, Taube, JM, Anders, RA, Pardoll, DM. Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy. Nat Rev Cancer. 2016; 16 (5): 275-87 [OpenAIRE] [PubMed] [DOI]

Doig, KD, Fellowes, A, Bell, AH, Seleznev, A, Ma, D, Ellul, J, Li, J, Doyle, MA, Thompson, ER, Kumar, A, Lara, L, Vedururu, R, Reid, G, Conway, T, Papenfuss, AT, Fox, SB. PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories. Genome Med. 2017; 9 (1): 38 [OpenAIRE] [PubMed] [DOI]

4 Fiorini N, Lipman DJ, Lu Z. Towards PubMed 2.0. eLife. 2017; 6. 10.7554/eLife.28801.

Thomas, P, Starlinger, J, Vowinkel, A, Arzt, S, Leser, U. GeneView: a comprehensive semantic search engine for PubMed. Nucleic Acids Res. 2012; 40 (W1): 585-91 [OpenAIRE] [DOI]

Wei, C-H, Kao, H-Y, Lu, Z. PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 2013; 41 (W1): 518-22 [OpenAIRE] [PubMed] [DOI]

Köhler, J, Philippi, S, Lange, M. SEMEDA: Ontology based semantic integration of biological databases. Bioinformatics. 2003; 19 (18): 2420-7 [OpenAIRE] [PubMed] [DOI]

Kim, J, So, S, Lee, H-J, Park, JC, Kim, J-j, Lee, H. DigSee: disease gene search engine with evidence sentences (version cancer). Nucleic Acids Res. 2013; 41 (W1): 510-7 [OpenAIRE] [DOI]

Ernst, P, Siu, A, Milchevski, D, Hoffart, J, Weikum, G. DeepLife: An Entity-aware Search, Analytics and Exploration Platform for Health and Life Sciences. Proceedings of ACL-2016 System Demonstrations. 2016

10 Yu H, Kim T, Oh J, Ko I, Kim S. RefMed: relevance feedback retrieval system fo PubMed. In: Proceeding of the 18th ACM Conference on Information and Knowledge Management: 2009. 10.1145/1645953.1646322. [OpenAIRE] [DOI]

Baker, Simon, Ali, Imran, Silins, Ilona, Pyysalo, Sampo, Guo, Yufan, Högberg, Johan, Stenius, Ulla, Korhonen, Anna. Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. Bioinformatics. 2017; 33 (24): 3973-3981 [OpenAIRE] [PubMed] [DOI]

Cotto, Kelsy C, Wagner, Alex H, Feng, Yang-Yang, Kiwala, Susanna, Coffman, Adam C, Spies, Gregory, Wollam, Alex, Spies, Nicholas C, Griffith, Obi L, Griffith, Malachi. DGIdb 3.0: a redesign and expansion of the drug–gene interaction database. Nucleic Acids Research. 2017; 46 (D1): D1068-D1073 [OpenAIRE] [DOI]

Chakravarty, D, Gao, J, Phillips, S, Kundra, R, Zhang, H, Wang, J, Rudolph, JE, Yaeger, R, Soumerai, T, Nissan, MH, Chang, MT, Chandarlapaty, S, Traina, TA, Paik, PK, Ho, AL, Hantash, FM, Grupe, A, Baxi, SS, Callahan, MK, Snyder, A, Chi, P, Danila, DC, Gounder, M, Harding, JJ, Hellmann, MD, Iyer, G, Janjigian, YY, Kaley, T, Levine, DA, Lowery, M, Omuro, A, Postow, MA, Rathkopf, D, Shoushtari, AN, Shukla, N, Voss, MH, Paraiso, E, Zehir, A, Berger, MF, Taylor, BS, Saltz, LB, Riely, GJ, Ladanyi, M, Hyman, DM, Baselga, J, Sabbatini, P, Solit, DB, Schultz, N. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017; 1 (1): 1-16 [DOI]

Landrum, MJ, Lee, JM, Benson, M, Brown, G, Chao, C, Chitipiralla, S, Gu, B, Hart, J, Hoffman, D, Hoover, J, Jang, W, Katz, K, Ovetsky, M, Riley, G, Sethi, A, Tully, R, Villamarin-Salomon, R, Rubinstein, W, Maglott, DR. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016; 44 (D1): 862-8 [OpenAIRE] [DOI]

Griffith, M, Spies, NC, Krysiak, K, McMichael, JF, Coffman, AC, Danos, AM, Ainscough, BJ, Ramirez, CA, Rieke, DT, Kujan, L, Barnell, EK, Wagner, AH, Skidmore, ZL, Wollam, A, Liu, CJ, Jones, MR, Bilski, RL, Lesurf, R, Feng, Y-Y, Shah, NM, Bonakdar, M, Trani, L, Matlock, M, Ramu, A, Campbell, KM, Spies, GC, Graubert, AP, Gangavarapu, K, Eldred, JM, Larson, DE, Walker, JR, Good, BM, Wu, C, Su, AI, Dienstmann, R, Margolin, AA, Tamborero, D, Lopez-Bigas, N, Jones, SJM, Bose, R, Spencer, DH, Wartman, LD, Wilson, RK, Mardis, ER, Griffith, OL. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 2017; 49 (2): 170-4 [OpenAIRE] [PubMed] [DOI]

44 references, page 1 of 3
Abstract
Background Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient’s genome. This analysis relies on previously published information regarding the association of variations to disease progression and possible interventions. Clinicians to a large degree use biomedical search engines to obtain such information; however, the vast majority of scientific publications focus on basic science and have no direct clinical impact. We develop the Variant-Information Search Tool (VIST), a search engine designed for the targeted search of clinically relevant publications given an oncological mutation profil...
Subjects
free text keywords: Research Article, Biomedical information retrieval, Document retrieval, Personalized oncology, Document classification, Clinical relevance, Document triage, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications
Related Organizations
44 references, page 1 of 3

Garraway, LA, Verweij, J, Ballman, KV. Precision Oncology: An Overview. J Clin Oncol. 2013; 31 (15): 1803-5 [OpenAIRE] [PubMed] [DOI]

Topalian, SL, Taube, JM, Anders, RA, Pardoll, DM. Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy. Nat Rev Cancer. 2016; 16 (5): 275-87 [OpenAIRE] [PubMed] [DOI]

Doig, KD, Fellowes, A, Bell, AH, Seleznev, A, Ma, D, Ellul, J, Li, J, Doyle, MA, Thompson, ER, Kumar, A, Lara, L, Vedururu, R, Reid, G, Conway, T, Papenfuss, AT, Fox, SB. PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories. Genome Med. 2017; 9 (1): 38 [OpenAIRE] [PubMed] [DOI]

4 Fiorini N, Lipman DJ, Lu Z. Towards PubMed 2.0. eLife. 2017; 6. 10.7554/eLife.28801.

Thomas, P, Starlinger, J, Vowinkel, A, Arzt, S, Leser, U. GeneView: a comprehensive semantic search engine for PubMed. Nucleic Acids Res. 2012; 40 (W1): 585-91 [OpenAIRE] [DOI]

Wei, C-H, Kao, H-Y, Lu, Z. PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 2013; 41 (W1): 518-22 [OpenAIRE] [PubMed] [DOI]

Köhler, J, Philippi, S, Lange, M. SEMEDA: Ontology based semantic integration of biological databases. Bioinformatics. 2003; 19 (18): 2420-7 [OpenAIRE] [PubMed] [DOI]

Kim, J, So, S, Lee, H-J, Park, JC, Kim, J-j, Lee, H. DigSee: disease gene search engine with evidence sentences (version cancer). Nucleic Acids Res. 2013; 41 (W1): 510-7 [OpenAIRE] [DOI]

Ernst, P, Siu, A, Milchevski, D, Hoffart, J, Weikum, G. DeepLife: An Entity-aware Search, Analytics and Exploration Platform for Health and Life Sciences. Proceedings of ACL-2016 System Demonstrations. 2016

10 Yu H, Kim T, Oh J, Ko I, Kim S. RefMed: relevance feedback retrieval system fo PubMed. In: Proceeding of the 18th ACM Conference on Information and Knowledge Management: 2009. 10.1145/1645953.1646322. [OpenAIRE] [DOI]

Baker, Simon, Ali, Imran, Silins, Ilona, Pyysalo, Sampo, Guo, Yufan, Högberg, Johan, Stenius, Ulla, Korhonen, Anna. Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. Bioinformatics. 2017; 33 (24): 3973-3981 [OpenAIRE] [PubMed] [DOI]

Cotto, Kelsy C, Wagner, Alex H, Feng, Yang-Yang, Kiwala, Susanna, Coffman, Adam C, Spies, Gregory, Wollam, Alex, Spies, Nicholas C, Griffith, Obi L, Griffith, Malachi. DGIdb 3.0: a redesign and expansion of the drug–gene interaction database. Nucleic Acids Research. 2017; 46 (D1): D1068-D1073 [OpenAIRE] [DOI]

Chakravarty, D, Gao, J, Phillips, S, Kundra, R, Zhang, H, Wang, J, Rudolph, JE, Yaeger, R, Soumerai, T, Nissan, MH, Chang, MT, Chandarlapaty, S, Traina, TA, Paik, PK, Ho, AL, Hantash, FM, Grupe, A, Baxi, SS, Callahan, MK, Snyder, A, Chi, P, Danila, DC, Gounder, M, Harding, JJ, Hellmann, MD, Iyer, G, Janjigian, YY, Kaley, T, Levine, DA, Lowery, M, Omuro, A, Postow, MA, Rathkopf, D, Shoushtari, AN, Shukla, N, Voss, MH, Paraiso, E, Zehir, A, Berger, MF, Taylor, BS, Saltz, LB, Riely, GJ, Ladanyi, M, Hyman, DM, Baselga, J, Sabbatini, P, Solit, DB, Schultz, N. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017; 1 (1): 1-16 [DOI]

Landrum, MJ, Lee, JM, Benson, M, Brown, G, Chao, C, Chitipiralla, S, Gu, B, Hart, J, Hoffman, D, Hoover, J, Jang, W, Katz, K, Ovetsky, M, Riley, G, Sethi, A, Tully, R, Villamarin-Salomon, R, Rubinstein, W, Maglott, DR. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016; 44 (D1): 862-8 [OpenAIRE] [DOI]

Griffith, M, Spies, NC, Krysiak, K, McMichael, JF, Coffman, AC, Danos, AM, Ainscough, BJ, Ramirez, CA, Rieke, DT, Kujan, L, Barnell, EK, Wagner, AH, Skidmore, ZL, Wollam, A, Liu, CJ, Jones, MR, Bilski, RL, Lesurf, R, Feng, Y-Y, Shah, NM, Bonakdar, M, Trani, L, Matlock, M, Ramu, A, Campbell, KM, Spies, GC, Graubert, AP, Gangavarapu, K, Eldred, JM, Larson, DE, Walker, JR, Good, BM, Wu, C, Su, AI, Dienstmann, R, Margolin, AA, Tamborero, D, Lopez-Bigas, N, Jones, SJM, Bose, R, Spencer, DH, Wartman, LD, Wilson, RK, Mardis, ER, Griffith, OL. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 2017; 49 (2): 170-4 [OpenAIRE] [PubMed] [DOI]

44 references, page 1 of 3
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