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Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network

Yuji Zhang, Cui Tao, Guoqian Jiang, Asha A Nair, Jian Su, Christopher G Chute, Hongfang Liu
2014 Journal of Biomedical Semantics  
The first step is to construct an association network by extracting pair-wise associations between diseases, drugs and genes in Semantic MEDLINE using a domain pattern driven strategy.  ...  Unique associations among drugs, diseases, and genes are extracted for downstream network-based analysis.  ...  We focus on a heterogeneous drug-disease-gene network derived from Semantic MEDLINE and investigated underlying associations using network-based systems biology approaches.  ... 
doi:10.1186/2041-1480-5-33 pmid:25170419 pmcid:PMC4137727 fatcat:uggl3kazqrcubn63achjtgzqtq

Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns

Yuji Zhang, Cui Tao
2014 Cancer Informatics  
In this paper, we proposed a novel network-based computational framework to identify statistically over-expressed subnetwork patterns called network motifs (NMs) in an integrated cancer-specific drug-disease-gene  ...  network extracted from Semantic MEDLINE, a database containing extracted associations from MEDLINE abstracts.  ...  First, we developed a domain pattern-driven approach to construct an integrated cancer-drug-gene network extracted from Semantic MEDLINE Database.  ... 
doi:10.4137/cin.s14033 pmid:25368509 pmcid:PMC4214591 fatcat:okquxnwezrgcbgwzoqgrncypc4

dRiskKB: a large-scale disease-disease risk relationship knowledge base constructed from biomedical text

Rong Xu, Li Li, QuanQiu Wang
2014 BMC Bioinformatics  
Finally, we analyzed the correlations between disease-disease risk pairs and their associated genes and drugs.  ...  The newly created dRiskKB consists of a total of 34,448 unique D1→D2 pairs, representing the risk-specific semantic relationships among 12,981 diseases with each disease linked to its associated genes  ...  patterns and their associated disease-disease risk pairs in the format "D1 pattern D2. " A pattern is correct for a given sentence if the semantic relationship between its associated disease-disease pairs  ... 
doi:10.1186/1471-2105-15-105 pmid:24725842 pmcid:PMC3998061 fatcat:mxm4y7efvrdqjeasb2fe6kthpi

Prioritising Genes with an Artificial Neural Network Comprising Medical Documents to Accelerate Positional Cloning in Biological Research [chapter]

Norio Kobayashi, Tetsuro Toyo
2011 Artificial Neural Networks - Methodological Advances and Biomedical Applications  
In this chapter, we will discuss the development of a web-based tool named Positional Medline (PosMed) that can immediately suggest genes related to a certain phenotype by accessing a Semantic Web based  ...  , co-expression, localisation, disease, drug and metabolite records (Table 1) .  ...  Artificial neural networks may probably be the single most successful technology in the last two decades which has been widely used in a large variety of applications in various areas.  ... 
doi:10.5772/16135 fatcat:vskrgnijpjcjxdzeyrr3gtua5y

Systematic identification of latent disease-gene associations from PubMed articles

Yuji Zhang, Feichen Shen, Majid Rastegar Mojarad, Dingcheng Li, Sijia Liu, Cui Tao, Yue Yu, Hongfang Liu, Vladimir B. Bajic
2018 PLoS ONE  
subnetwork patterns were enriched in the disease-specific association networks; and (4) genes were enriched in topic-specific biological processes.  ...  Our results demonstrate that (1) the LDA-based modeling is able to group similar diseases into disease topics; (2) the diseasespecific association networks follow the scale-free network property; (3) certain  ...  Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases.  ... 
doi:10.1371/journal.pone.0191568 pmid:29373609 pmcid:PMC5786305 fatcat:pqqptau7s5ctnp6iid3roe4q2e

AB0408 SYSTEMIC SCLERODERMA AND ENVIRONMENTAL RISK FACTORS: IDENTIFYING ASSOCIATIONS MINING THE BIOMEDICAL LITERATURE

A. Rodriguez-Pla
2021 Annals of the Rheumatic Diseases  
The Semantic MEDLINE graph supports the kind of patterns that underpin literature-based discovery.Although the pathogenesis of SSc remains elusive, it is accepted that initial vascular damage driven by  ...  Concepts causally linked to fibrosis were rare diseases, HLA genes, other non-HLA genes, such as STAT4, IR4, IR5, TLR4, TLR7 and Rho-associated Kinase, and vinyl chloride monomer.  ...  CHALLENGES IN THE MANAGEMENT OF MIXED CONNECTIVE TISSUE DISEASE: A RETROSPECTIVE ANALYSIS OF THE MCTD COHORT IN A TERTIARY REFERRAL CENTRE A. Wanzenried 1 , A. Garaiman 1 , S. Jordan 1 , O.  ... 
doi:10.1136/annrheumdis-2021-eular.330 fatcat:na2k4isk2fh3zfh34m4kfosh3i

Using literature-based discovery to identify disease candidate genes

Dimitar Hristovski, Borut Peterlin, Joyce A. Mitchell, Susanne M. Humphrey
2005 International Journal of Medical Informatics  
disease as well as the chromosomal location of the candidate genes from resources such as LocusLink and Human Genome Organization (HUGO).  ...  The goal of this system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database MEDLINE ® .  ...  In addition, we would like to thank Tom Rindflesch and Neil Smalheiser for providing valuable comments and insights.  ... 
doi:10.1016/j.ijmedinf.2004.04.024 pmid:15694635 fatcat:gaxffooxwnbjxaycy5y74ebjmm

Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases

Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos
2015 Scientific Reports  
Using a phenotypic similarity measure, we generate a human disease network in which diseases that share signs and symptoms cluster together, and we use this network to identify phenotypic disease modules  ...  We apply a semantic text- mining approach to identify the phenotypes (signs and symptoms) associated with over 8,000 diseases.  ...  The disease network was visualized using the Gephi graph visualization tool 47 , and the disease network browser was generated with Gephi's Sigma-js export plugin (http://blogs.oii.ox.ac.uk/vis/).  ... 
doi:10.1038/srep10888 pmid:26051359 pmcid:PMC4458913 fatcat:7to4snmfk5b7hee3gyfmg6t63i

Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies

Cui Tao, Puqiang Wu, Yi Luo, Yuji Zhang
2014 BioData Mining  
Further statistical analysis and summarization needs to be done before this data can be leveraged.  ...  FDA/CDC Vaccine Adverse Event Reporting System (VAERS) currently contains more than 200,000 reports for post-vaccination events that occur after the administration of vaccines licensed in the United States  ...  For PubMed data, we have created the SemMed-RDF repository for representing associations among genetic factors, diseases, and drugs extracted from PubMED abstracts [15] based on the Semantic MEDLINE  ... 
doi:10.1186/s13040-014-0036-y pmid:25699091 pmcid:PMC4333877 fatcat:taihqwdqybdynkrmdx3o5tyhga

Mining the pharmacogenomics literature--a survey of the state of the art

U. Hahn, K. B. Cohen, Y. Garten, N. H. Shah
2012 Briefings in Bioinformatics  
dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment  ...  Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years.This survey covers efforts  ...  In order to demonstrate the scalability of their approach, the whole GeneRIF database is processed, resulting in a gene-diseases network that contains 34 758 semantic associations between 4939 genes and  ... 
doi:10.1093/bib/bbs018 pmid:22833496 pmcid:PMC3404399 fatcat:por4dnthkrcxjdsir6uc64kdaq

Text analytics for life science using the Unstructured Information Management Architecture

R. Mack, S. Mukherjea, A. Soffer, N. Uramoto, E. Brown, A. Coden, J. Cooper, A. Inokuchi, B. Iyer, Y. Mass, H. Matsuzawa, L. V. Subramaniam
2004 IBM Systems Journal  
Acknowledgments BioTeKS is in large part a systems integration effort that builds on technologies and expertise developed  ...  Both gene names are represented in a gene dictionary based on LocusLink: 32 • "Recent genotype-phenotype correlation studies in familial hypertrophic cardiomyopathy (FHC) have revealed that some mutations  ...  names such as genes, drugs, or diseases contained in MEDLINE abstracts) can be stored (arrow 4) in a relational database for access by upstream text-mining applications using SQL (structured query language  ... 
doi:10.1147/sj.433.0490 fatcat:altfinouzbdy7mrcqx2kzdzecy

In Search of Newer Targets for IBD: A Systems and a Network Medicine Approach [article]

Takashi Kitani, Sushma C. Maddipatla, Ramya Madupuri, James N. Baraniuk, Christopher Greco, Jonathan Hartman, Sona Vasudevan
2021 arXiv   pre-print
The identified genes were then subject to Systems and Network analysis to reveal their molecular processes and shed some light on their pathogenesis.  ...  Through a network medicine approach, we provide a mechanistic view of the diseases and point to newer drugs and targets.  ...  Acknowledgements We thank Ritika Kundra who, as a graduate student at Georgetown University, contributed to data mining for setting up IBD-OMICS.  ... 
arXiv:2006.04181v2 fatcat:ftjp5xsbeveutliqletvh7etie

Recent progress in automatically extracting information from the pharmacogenomic literature

Yael Garten, Adrien Coulet, Russ B Altman
2010 Pharmacogenomics (London)  
, or of distinct kind such as a drug and a gene or a gene and a disease, in the case of pharmacogenomic relationships.  ...  Ahlers et al. used vocabularies and semantic types defined in the UMLS associated with syntactic constraints to extract gene-disease and drug-disease relationships [90] .  ... 
doi:10.2217/pgs.10.136 pmid:21047206 pmcid:PMC3035632 fatcat:7g3jwc4hjfetbb5phmzstzhjeu

Mining Novel Knowledge from Biomedical Literature using Statistical Measures and Domain Knowledge

Kishlay Jha, Wei Jin
2016 Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16  
In this study, to discover interesting and inherent links latent in large corpora, nine distinct methods, comprising variants of statistical information measures and derived semantic knowledge from domain  ...  Overall, our research presents a comprehensive analysis and perspective of how different statistical information measures and semantic knowledge affect the knowledge discovery procedure. iii  ...  It focuses on understanding relationships among drugs, genes, and disease.  ... 
doi:10.1145/2975167.2975200 dblp:conf/bcb/JhaJ16 fatcat:ldtlfdods5hn7n4hxonqbc7fsq

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
Some problems, such as abbreviationhandling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon.  ...  However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  KBC was supported by NIH grants 'Construction of a Full Text Corpus for Biomedical Text Mining' (#1G08LM009639-01) and 'Technology Development for a Molecular Biology Knowledge-base' (#5R01 LM008111-03  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy
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