{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:27:29Z","timestamp":1725992849482},"reference-count":84,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128114322"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20496-2","type":"book-chapter","created":{"date-parts":[[2018,3,15]],"date-time":"2018-03-15T19:01:54Z","timestamp":1521140514000},"page":"1071-1084","source":"Crossref","is-referenced-by-count":5,"title":["Two Decades of Biological Pathway Databases: Results and Challenges"],"prefix":"10.1016","author":[{"given":"Sara","family":"Rahmati","sequence":"first","affiliation":[]},{"given":"Chiara","family":"Pastrello","sequence":"additional","affiliation":[]},{"given":"Andrea E.M.","family":"Rossos","sequence":"additional","affiliation":[]},{"given":"Igor","family":"Jurisica","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib1","doi-asserted-by":"crossref","first-page":"e-151","DOI":"10.1093\/nar\/gkx642","article-title":"De novo pathway-based biomarker identification","author":"Alcaraz","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20496-2_bib2","first-page":"D504-6","article-title":"Pathguide: A pathway resource list","volume":"34","author":"Bader","year":"2006","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib3","first-page":"1","article-title":"PathwayMapper: A collaborative visual web editor for cancer pathways and genomic data","author":"Bahceci","year":"2017","journal-title":"Bioinformatics"},{"issue":"C","key":"10.1016\/B978-0-12-809633-8.20496-2_bib4","first-page":"1","article-title":"Map Construction in Neurospora Crassa","volume":"6","author":"Barratt","year":"1954","journal-title":"Advances in Genetics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib5","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41540-017-0007-2","article-title":"On the performance of de novo pathway enrichment","volume":"3","author":"Batra","year":"2017","journal-title":"NPJ Systems Biology and Applications"},{"issue":"0","key":"10.1016\/B978-0-12-809633-8.20496-2_bib6","article-title":"PathCards: Multi-source consolidation of human biological pathways","volume":"2015","author":"Belinky","year":"2015","journal-title":"Database"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib7","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-1-4939-2095-2_8","article-title":"Systems analysis of high-throughput data","volume":"844","author":"Braun","year":"2014","journal-title":"Advances in Experimental Medicine and Biology"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20496-2_bib8","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1586\/eci.13.9","article-title":"Systems level immune response analysis and personalized medicine","volume":"9","author":"Brodin","year":"2013","journal-title":"Expert Review of Clinical Immunology"},{"issue":"SUPPL. 1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib9","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1111\/j.1463-1326.2008.01004.x","article-title":"Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data","volume":"11","author":"Brorsson","year":"2009","journal-title":"Diabetes, Obesity and Metabolism"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib10","doi-asserted-by":"crossref","DOI":"10.1038\/msb.2008.7","article-title":"A comprehensive modular map of molecular interactions in RB\/E2F pathway","volume":"4","author":"Calzone","year":"2008","journal-title":"Molecular Systems Biology"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20496-2_bib11","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.gde.2013.10.003","article-title":"Genotype to phenotype via network analysis","volume":"23","author":"Carter","year":"2013","journal-title":"Current Opinion in Genetics and Development"},{"issue":"Database","key":"10.1016\/B978-0-12-809633-8.20496-2_bib12","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway Commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20496-2_bib13","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nn.3907","article-title":"Genotype to phenotype relationships in autism spectrum disorders","volume":"18","author":"Chang","year":"2015","journal-title":"Nature Neuroscience"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib14","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100180","article-title":"Network-based classification of breast cancer metastasis","volume":"3","author":"Chuang","year":"2007","journal-title":"Molecular Systems Biology"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20496-2_bib15","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1038\/nbt861","article-title":"Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages","volume":"21","author":"Date","year":"2003","journal-title":"Nature Biotechnology"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20496-2_bib16","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003194","article-title":"Using Biological Pathway Data with Paxtools","volume":"9","author":"Demir","year":"2013","journal-title":"PLOS Computational Biology"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20496-2_bib17","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"The BioPAX community standard for pathway data sharing","volume":"28","author":"Demir","year":"2010","journal-title":"Nature Biotechnology"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20496-2_bib18","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/sj.cdd.4401230","article-title":"The apoptosis database","volume":"10","author":"Doctor","year":"2003","journal-title":"Cell Death and Differentiation"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib19","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The reactome pathway knowledgebase","volume":"44","author":"Fabregat","year":"2016","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib20","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1752-0509-7-7","article-title":"SignaLink 2 \u2013 A signaling pathway resource with multi-layered regulatory networks","volume":"7","author":"Fazekas","year":"2013","journal-title":"BMC Systems Biology"},{"issue":"8","key":"10.1016\/B978-0-12-809633-8.20496-2_bib21","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","article-title":"CellDesigner 3.5: A versatile modeling tool for biochemical networks","volume":"96","author":"Funahashi","year":"2008","journal-title":"Proceedings of the IEEE"},{"issue":"269","key":"10.1016\/B978-0-12-809633-8.20496-2_bib22","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.2004088","article-title":"Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal","volume":"6","author":"Gao","year":"2013","journal-title":"Science Signaling"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib23","doi-asserted-by":"crossref","DOI":"10.3389\/fphys.2015.00383","article-title":"Pathway analysis: State of the art","volume":"6","author":"Garc\u00eda-Campos","year":"2015","journal-title":"Frontiers in Physiology"},{"issue":"18","key":"10.1016\/B978-0-12-809633-8.20496-2_bib24","doi-asserted-by":"crossref","first-page":"i451","DOI":"10.1093\/bioinformatics\/bts389","article-title":"EnrichNet: Network-based gene set enrichment analysis","volume":"28","author":"Glaab","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib25","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1186\/1471-2105-11-597","article-title":"Extending pathways and processes using molecular interaction networks to analyse cancer genome data","volume":"11","author":"Glaab","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib26","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1111\/j.1749-6632.2002.tb04532.x","article-title":"Science\u2019s Signal Transduction Knowledge Environment","volume":"971","author":"Gough","year":"2002","journal-title":"Annals of the New York Academy of Sciences"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib27","doi-asserted-by":"crossref","first-page":"D1079","DOI":"10.1093\/nar\/gku1071","article-title":"Genenames.org: The HGNC resources in 2015","volume":"43 (Database issue)","author":"Gray","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib28","article-title":"TRRUST: A reference database of human transcriptional regulatory interactions","volume":"5","author":"Han","year":"2015","journal-title":"Scientific Reports"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20496-2_bib29","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1038\/nprot.2016.117","article-title":"Analyzing and interpreting genome data at the network level with ConsensusPathDB","volume":"11","author":"Herwig","year":"2016","journal-title":"Nature Protocols"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib30","doi-asserted-by":"crossref","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: Mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20496-2_bib31","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1074\/mcp.M700550-MCP200","article-title":"Targeting the human cancer pathway protein interaction network by structural genomics","volume":"7","author":"Huang","year":"2008","journal-title":"Mol Cell Proteomics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib32","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bib\/bbv024","article-title":"Community challenges in biomedical text mining over 10 years: Success, failure and the future","volume":"17","author":"Huang","year":"2016","journal-title":"Briefings in Bioinformatics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20496-2_bib33","doi-asserted-by":"crossref","first-page":"R23","DOI":"10.1186\/gb-2010-11-2-r23","article-title":"Identification of functional modules that correlate with phenotypic difference: the influence of network topology","volume":"11","author":"Hung","year":"2010","journal-title":"Genome Biology"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib34","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1093\/bioinformatics\/btq615","article-title":"dmGWAS: Dense module searching for genome-wide association studies in protein-protein interaction networks","volume":"27","author":"Jia","year":"2011","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib35","doi-asserted-by":"crossref","first-page":"R3","DOI":"10.1186\/gb-2010-11-1-r3","article-title":"NetPath: A public resource of curated signal transduction pathways","volume":"11","author":"Kandasamy","year":"2010","journal-title":"Genome Biology"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20496-2_bib36","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/S0168-9525(97)01223-7","article-title":"A database for post-genome analysis","volume":"13","author":"Kanehisa","year":"1997","journal-title":"Trends in Genetics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib37","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Research"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib38","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Kanehisa","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib39","unstructured":"Karp, P.D., Paley, S.M., 1994. Representations of metabolic knowledge: pathways. In: Proceedings of the International Conference on Intelligent Systems for Molecular Biology; ISMB., 2, pp. 203\u201311. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/7584392."},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20496-2_bib40","doi-asserted-by":"crossref","first-page":"i374","DOI":"10.1093\/bioinformatics\/btq221","article-title":"PathText: A text mining integrator for biological pathway visualizations","volume":"26","author":"Kemper","year":"2010","journal-title":"Bioinformatics"},{"issue":"818","key":"10.1016\/B978-0-12-809633-8.20496-2_bib41","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1086\/281636","article-title":"Semi-Allelic Genes","volume":"84","author":"Komai","year":"1950","journal-title":"American Naturalist"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20496-2_bib42","doi-asserted-by":"crossref","first-page":"e160","DOI":"10.1038\/oncsis.2015.19","article-title":"Atlas of Cancer Signalling Network: A systems biology resource for integrative analysis of cancer data with Google Maps","volume":"4","author":"Kuperstein","year":"2015","journal-title":"Oncogenesis"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib44","doi-asserted-by":"crossref","first-page":"D488","DOI":"10.1093\/nar\/gkv1024","article-title":"WikiPathways: Capturing the full diversity of pathway knowledge","volume":"44","author":"Kutmon","year":"2016","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20496-2_bib45","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004085","article-title":"PathVisio 3: An Extendable Pathway Analysis Toolbox","volume":"11","author":"Kutmon","year":"2015","journal-title":"PLoS Computational Biology"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20496-2_bib46","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database Hallmark Gene Set Collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Systems"},{"issue":"Suppl 1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib47","first-page":"69","article-title":"Text mining in cancer gene and pathway prioritization","volume":"13","author":"Luo","year":"2014","journal-title":"Cancer Informatics"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib48","first-page":"3","article-title":"The Edinburgh human metabolic network reconstruction and its functional analysis","author":"Ma","year":"2007","journal-title":"Molecular Systems Biology"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib49","first-page":"1","article-title":"Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases","author":"Marbach","year":"2016","journal-title":"Nature methods"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20496-2_bib50","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1093\/bioinformatics\/btq143","article-title":"Payao: A community platform for SBML pathway model curation","volume":"26","author":"Matsuoka","year":"2010","journal-title":"Bioinformatics"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib51","doi-asserted-by":"crossref","first-page":"D336","DOI":"10.1093\/nar\/gkv1194","article-title":"PANTHER version 10: Expanded protein families and functions, and analysis tools","volume":"44","author":"Mi","year":"2016","journal-title":"Nucleic Acids Research"},{"issue":"13","key":"10.1016\/B978-0-12-809633-8.20496-2_bib52","doi-asserted-by":"crossref","first-page":"i44","DOI":"10.1093\/bioinformatics\/btt227","article-title":"A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text","volume":"29","author":"Miwa","year":"2013","journal-title":"Bioinformatics"},{"issue":"(SUPPL.2","key":"10.1016\/B978-0-12-809633-8.20496-2_bib53","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: An automatic genome annotation and pathway reconstruction server","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib54","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-14-235","article-title":"The KUPNetViz: A biological network viewer for multiple-omics datasets in kidney diseases","volume":"14","author":"Moulos","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20496-2_bib55","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1089\/152791601750294344","article-title":"BioCarta","volume":"2","author":"Nishimura","year":"2001","journal-title":"Biotech Software & Internet Report"},{"issue":"6770","key":"10.1016\/B978-0-12-809633-8.20496-2_bib56","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/35001165","article-title":"Guilt-by-association goes global","volume":"403","author":"Oliver","year":"2000","journal-title":"Nature"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20496-2_bib57","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/nmeth0612-626a","article-title":"Protein interaction data curation: The International Molecular Exchange (IMEx) consortium","volume":"9","author":"Orchard","year":"2012","journal-title":"Nature Methods"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20496-2_bib58","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/S1367-5931(03)00027-9","article-title":"Missing genes in metabolic pathways: A comparative genomics approach","volume":"7","author":"Osterman","year":"2003","journal-title":"Current Opinion in Chemical Biology"},{"issue":"SUPPL. 1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib59","doi-asserted-by":"crossref","first-page":"D793","DOI":"10.1093\/nar\/gkq1167","article-title":"SPIKE: A database of highly curated human signaling pathways","volume":"39","author":"Paz","year":"2011","journal-title":"Nucleic Acids Research"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib60","doi-asserted-by":"crossref","first-page":"D548","DOI":"10.1093\/nar\/gkv1048","article-title":"\u2018SIGNOR: A database of causal relationships between biological entities","volume":"44","author":"Perfetto","year":"2016","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib61","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/2041-1480-5-7","article-title":"The pathway ontology \u2013 updates and applications","volume":"5","author":"Petri","year":"2014","journal-title":"Journal of Biomedical Semantics"},{"issue":"W1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib62","doi-asserted-by":"crossref","first-page":"W154","DOI":"10.1093\/nar\/gku455","article-title":"StemCellNet: An interactive platform for network-oriented investigations in stem cell biology","volume":"42","author":"Pinto","year":"2014","journal-title":"Nucleic Acids Research"},{"issue":"503","key":"10.1016\/B978-0-12-809633-8.20496-2_bib63","first-page":"1","article-title":"Identification of G protein-coupled receptor signaling pathway proteins in marine diatoms using comparative genomics","volume":"14","author":"Port","year":"2013","journal-title":"BMC genomics"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20496-2_bib64","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gkw1082","article-title":"pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis","volume":"45","author":"Rahmati","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib65","doi-asserted-by":"crossref","unstructured":"Ravikumar, K.E., Wagholikar, K.B., Liu, H., 2014a. Challenges in adapting text mining for full text articles to assist pathway curation. ACM BCB 2014 \u2013 Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 551\u2013558. doi:10.1145\/2649387.2649444.","DOI":"10.1145\/2649387.2649444"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib66","first-page":"352","article-title":"Towards pathway curation through literature mining \u2013 a case study using pharmgkb","volume":"19","author":"Ravikumar","year":"2014","journal-title":"Pac Symp Biocomput"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib67","doi-asserted-by":"crossref","first-page":"R2","DOI":"10.1186\/gb-2004-6-1-r2","article-title":"Computational prediction of human metabolic pathways from the complete human genome","volume":"6","author":"Romero","year":"2005","journal-title":"Genome Biology"},{"issue":"Database","key":"10.1016\/B978-0-12-809633-8.20496-2_bib68","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: The Pathway Interaction Database","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Research"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20496-2_bib69","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000605","article-title":"Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies","volume":"5","author":"Schnoes","year":"2009","journal-title":"PLoS Computational Biology"},{"issue":"19","key":"10.1016\/B978-0-12-809633-8.20496-2_bib70","doi-asserted-by":"crossref","first-page":"4188","DOI":"10.1016\/j.physa.2010.05.051","article-title":"Modeling the human genome maintenance network","volume":"389","author":"Sim\u00e3o","year":"2010","journal-title":"Physica A: Statistical Mechanics and its Applications"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib71","doi-asserted-by":"crossref","first-page":"D803","DOI":"10.1093\/nar\/gkr1208","article-title":"IPAVS: Integrated pathway resources, analysis and visualization system","volume":"40","author":"Sreenivasaiah","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib72","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.jbi.2015.01.006","article-title":"HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways","volume":"54","author":"Subramani","year":"2015","journal-title":"Journal of Biomedical Informatics"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20496-2_bib73","doi-asserted-by":"crossref","first-page":"e18","DOI":"10.1093\/nar\/gkr1103","article-title":"An iterative network partition algorithm for accurate identification of dense network modules","volume":"40","author":"Sun","year":"2012","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20496-2_bib74","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/clpt.2012.96","article-title":"Pharmacogenomics knowledge for personalized medicine","volume":"92","author":"Whirl-Carrillo","year":"2012","journal-title":"Clinical Pharmacology & Therapeutics"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib75","doi-asserted-by":"crossref","first-page":"D801","DOI":"10.1093\/nar\/gks1065","article-title":"HMDB 3.0 \u2013 The Human Metabolome Database in 2013","volume":"41","author":"Wishart","year":"2013","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20496-2_bib76","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1038\/ncb1007-1102","article-title":"Autophagosome formation: Core machinery and adaptations","volume":"9","author":"Xie","year":"2007","journal-title":"Nature cell biology"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_bib77","first-page":"2011","article-title":"INOH: Ontology-based highly structured database of signal transduction pathways","author":"Yamamoto","year":"2011","journal-title":"Database"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib78","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.gde.2012.01.003","article-title":"Recent advances in pathway-targeted cancer drug therapies emerging from cancer genome analysis","volume":"22","author":"Yauch","year":"2012","journal-title":"Current Opinion in Genetics & Development"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20496-2_bib79","doi-asserted-by":"crossref","first-page":"e86","DOI":"10.1093\/nar\/gkx089","article-title":"Discovery of cancer common and specific driver gene sets","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20496-2_bib80","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1186\/s13059-016-1044-7","article-title":"Gene name errors are widespread in the scientific literature","volume":"17","author":"Ziemann","year":"2016","journal-title":"Genome Biology"},{"year":"2014","series-title":"Intelligent strategies for pathway mining; models and pattern identification (Lecture notes in Artificial Intelligence)","author":"Chen","key":"10.1016\/B978-0-12-809633-8.20496-2_fur1"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_fur2","doi-asserted-by":"crossref","DOI":"10.1016\/j.ymben.2017.02.002","article-title":"Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis","author":"Dong","year":"2017","journal-title":"Metabolic Engineering"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20496-2_fur3","article-title":"Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks","volume":"38","author":"Emmert-Streib","year":"2014","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20496-2_fur4","first-page":"1","article-title":"Comparison of human cell signaling pathway databases \u2013 evolution, drawbacks and challenges","author":"Saikat","year":"2015","journal-title":"Database (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20496-2_fur5","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/1752-0509-5-165","article-title":"Critical assessment of human metabolic pathway databases: A stepping stone for future integration","volume":"5","author":"Stobbe","year":"2011","journal-title":"BMC Systems Biology"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338204962?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338204962?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T20:05:29Z","timestamp":1548101129000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338204962"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":84,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20496-2","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}