title: LiverAtlas: a unique integrated knowledge database for systems-level research of liver and hepatic disease.
abstract: BACKGROUND
  A large amount of liver-related physiological and pathological data exist in publicly available biological and bibliographic databases, which are usually far from comprehensive or integrated. Data collection, integration and mining processes pose a great challenge to scientific researchers and clinicians interested in the liver.
  
  
  METHODS
  To address these problems, we constructed LiverAtlas (http://liveratlas.hupo.org.cn), a comprehensive resource of biomedical knowledge related to the liver and various hepatic diseases by incorporating 53 databases.
  
  
  RESULTS
  In the present version, LiverAtlas covers data on liver-related genomics, transcriptomics, proteomics, metabolomics and hepatic diseases. Additionally, LiverAtlas provides a wealth of manually curated information, relevant literature citations and cross-references to other databases. Importantly, an expert-confirmed Human Liver Disease Ontology, including relevant information for 227 types of hepatic disease, has been constructed and is used to annotate LiverAtlas data. Furthermore, we have demonstrated two examples of applying LiverAtlas data to identify candidate markers for hepatocellular carcinoma (HCC) at the systems level and to develop a systems biology-based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC differential diagnosis.
  
  
  CONCLUSIONS
  LiverAtlas is the most comprehensive liver and hepatic disease resource, which helps biologists and clinicians to analyse their data at the systems level and will contribute much to the biomarker discovery and diagnostic performance enhancement for liver diseases.
authors.affiliation: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
authors.forename: Yanqiong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Chunyuan
authors.initials: C
authors.lastname: Yang
authors.forename: Shaochuang
authors.initials: S
authors.lastname: Wang
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.forename: Mansheng
authors.initials: M
authors.lastname: Li
authors.forename: Xue
authors.initials: X
authors.lastname: Wang
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Li
authors.forename: Kang
authors.initials: K
authors.lastname: Wang
authors.forename: Jie
authors.initials: J
authors.lastname: Ma
authors.forename: Songfeng
authors.initials: S
authors.lastname: Wu
authors.forename: Xueli
authors.initials: X
authors.lastname: Zhang
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Wu
authors.forename: Fuchu
authors.initials: F
authors.lastname: He
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D006528:Carcinoma, Hepatocellular / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D057225:Data Mining; D016208:Databases, Factual; D030541:Databases, Genetic; D003937:Diagnosis, Differential; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D005820:Genetic Testing; D006801:Humans; D051188:Knowledge Bases; D008099:Liver / Q000378:metabolism / Q000473:pathology / Q000503:physiopathology; D008107:Liver Diseases / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism / Q000503:physiopathology / Q000628:therapy; D008113:Liver Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D011237:Predictive Value of Tests; D011379:Prognosis; D060066:Protein Interaction Maps; D049490:Systems Biology; D018511:Systems Integration
chemical_list: D014408:Biomarkers, Tumor
keywords: biomarker discovery; database; liver; liver pathology; liver physiology; omics