Mining Complex Biomedical Literature for Actionable Knowledge on Rare Diseases

Complex scientific phenomena and processes underpin drug discovery and development that have historically been addressed through iterative and statistical strategies to derive knowledge from data using labor intensive, inefficient, and costly practices. Complicating the task of data analysis even further, a lot of useful information about drug activities has been historically described in publications and scientific reports in writing. This naturally required reading by the experts to understand the reported facts and extract useful knowledge from publications, a manual, and therefore, non-scalable process. The opportunity now exists to extract knowledge from reading sources using modern text mining to rapidly and affordably identify and develop new or repurposed drug candidates. Nowhere could this be more important than addressing the unmet need in rare diseases.

[1]  J. Brownstein,et al.  Social and news media enable estimation of epidemiological patterns early in the 2010 Haitian cholera outbreak. , 2012, The American journal of tropical medicine and hygiene.

[2]  Ireneus Kagashe,et al.  Enhancing Seasonal Influenza Surveillance: Topic Analysis of Widely Used Medicinal Drugs Using Twitter Data , 2017, Journal of medical Internet research.

[3]  Peter J. Haas,et al.  Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2 , 2018, Proceedings of the National Academy of Sciences.

[4]  Jahan B Ghasemi,et al.  Combating Diseases with Computational Strategies Used for Drug Design and Discovery. , 2018, Current topics in medicinal chemistry.

[5]  Riccardo Bellazzi,et al.  A Network-Based Data Integration Approach to Support Drug Repurposing and Multi-Target Therapies in Triple Negative Breast Cancer , 2016, PloS one.

[6]  Sean Ekins,et al.  A bibliometric review of drug repurposing. , 2018, Drug discovery today.

[7]  K. Bretonnel Cohen,et al.  Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters , 2014, BMC Bioinformatics.

[8]  Peng Sun,et al.  Drug repurposing by integrated literature mining and drug-gene-disease triangulation. , 2017, Drug discovery today.

[9]  Anne R. Pariser,et al.  From scientific discovery to treatments for rare diseases – the view from the National Center for Advancing Translational Sciences – Office of Rare Diseases Research , 2018, Orphanet Journal of Rare Diseases.

[10]  A. Mantel‐Teeuwisse,et al.  Drug repositioning and repurposing: terminology and definitions in literature. , 2015, Drug discovery today.

[11]  A. Marchevsky,et al.  Presence of c-KIT-positive mast cells in obliterative bronchiolitis from diverse causes. , 2009, Archives of pathology & laboratory medicine.

[12]  Nicola Nosengo Can you teach old drugs new tricks? , 2016, Nature.

[13]  P. Sanseau,et al.  Drug repurposing: progress, challenges and recommendations , 2018, Nature Reviews Drug Discovery.

[14]  Colin P O'Banion,et al.  Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed , 2018, J. Chem. Inf. Model..

[15]  A. Tropsha,et al.  Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions , 2018, Drug Safety.

[16]  Sophia Ananiadou,et al.  SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data , 2017, Wellcome open research.

[17]  Sean Ekins,et al.  Industrializing rare disease therapy discovery and development , 2017, Nature Biotechnology.

[18]  Bradley M. Hemminger,et al.  Mining connections between chemicals, proteins, and diseases extracted from Medline annotations , 2010, J. Biomed. Informatics.

[19]  Bruno J. Neves,et al.  In Silico Repositioning-Chemogenomics Strategy Identifies New Drugs with Potential Activity against Multiple Life Stages of Schistosoma mansoni , 2015, PLoS neglected tropical diseases.

[20]  Evan Bolton,et al.  PubChem's BioAssay Database , 2011, Nucleic Acids Res..

[21]  T. Ashburn,et al.  Drug repositioning: identifying and developing new uses for existing drugs , 2004, Nature Reviews Drug Discovery.

[22]  Lawrence Hunter,et al.  Knowledge-based biomedical Data Science , 2017, Data Sci..

[23]  Alexander Tropsha,et al.  Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research , 2010, J. Chem. Inf. Model..

[24]  Abhishek Pandey,et al.  Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review , 2017, J. Biomed. Informatics.

[25]  Christopher M. Danforth,et al.  Forecasting the onset and course of mental illness with Twitter data , 2016, Scientific Reports.

[26]  Yanli Wang,et al.  PubChem BioAssay: 2014 update , 2013, Nucleic Acids Res..

[27]  Bin Chen,et al.  The ChEMBL database as linked open data , 2013, Journal of Cheminformatics.

[28]  Shang Gao,et al.  Integrating text mining, data mining, and network analysis for identifying genetic breast cancer trends , 2016, BMC Research Notes.

[29]  Janine Lewis,et al.  Marking 15 years of the Genetic and Rare Diseases Information Center , 2017, Translational science of rare diseases.

[30]  P. Reichardt The Story of Imatinib in GIST - a Journey through the Development of a Targeted Therapy , 2018, Oncology Research and Treatment.

[31]  Alexander Golbraikh,et al.  Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models , 2018, J. Chem. Inf. Model..

[32]  R. Valdez,et al.  Public Health and Rare Diseases: Oxymoron No More , 2016, Preventing chronic disease.

[33]  Bridget T. McInnes,et al.  Literature Based Discovery: Models, methods, and trends , 2017, J. Biomed. Informatics.

[34]  E. Abraham,et al.  Metformin reverses established lung fibrosis in a bleomycin model , 2018, Nature Medicine.

[35]  John R. Rumble,et al.  Development of the web-based NIST X-ray Photoelectron Spectroscopy (XPS) Database , 2002, Data Sci. J..

[36]  Ross D. King,et al.  Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases , 2015, Journal of The Royal Society Interface.

[37]  Ronald N. Kostoff,et al.  Literature-related discovery (LRD): Potential treatments for Multiple Sclerosis , 2008 .

[38]  Didier Rognan,et al.  The impact of in silico screening in the discovery of novel and safer drug candidates. , 2017, Pharmacology & therapeutics.

[39]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[40]  R. J. Roberts PubMed Central: The GenBank of the published literature. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Yoonjeong Cha,et al.  Pharma Perspective on Drug Repurposing , 2017 .

[42]  M. Might,et al.  Repurposing of Proton Pump Inhibitors as first identified small molecule inhibitors of endo-β-N-acetylglucosaminidase (ENGase) for the treatment of NGLY1 deficiency, a rare genetic disease. , 2017, Bioorganic & medicinal chemistry letters.

[43]  Natalia Novac,et al.  Challenges and opportunities of drug repositioning. , 2013, Trends in pharmacological sciences.

[44]  E. Klann,et al.  Isoform-selective phosphoinositide 3-kinase inhibition ameliorates a broad range of fragile X syndrome-associated deficits in a mouse model , 2018, Neuropsychopharmacology.

[45]  Ronald N. Kostoff,et al.  Literature-Related Discovery (LRD): Potential treatments for Parkinson's Disease , 2008 .

[46]  A. Markham,et al.  Sildenafil: a review of its use in erectile dysfunction. , 1999, Drugs.

[47]  Sophia Ananiadou,et al.  Text mining resources for the life sciences , 2016, Database J. Biol. Databases Curation.

[48]  W. Tong,et al.  Computational drug repositioning for rare diseases in the era of precision medicine. , 2017, Drug discovery today.

[49]  Domenica Taruscio,et al.  Data Quality in Rare Diseases Registries. , 2017, Advances in experimental medicine and biology.

[50]  Doron Lancet,et al.  MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search , 2016, Nucleic Acids Res..

[51]  Zhiyong Lu,et al.  PubTator: a web-based text mining tool for assisting biocuration , 2013, Nucleic Acids Res..

[52]  Xianting Ding,et al.  Drug screening: Drug repositioning needs a rethink , 2016, Nature.

[53]  Rajarshi Guha,et al.  Pharos: Collating protein information to shed light on the druggable genome , 2016, Nucleic Acids Res..

[54]  Michal Brylinski,et al.  Large-scale computational drug repositioning to find treatments for rare diseases , 2018, npj Systems Biology and Applications.

[55]  Alexander Tropsha,et al.  Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation , 2016, J. Chem. Inf. Model..

[56]  Graeme Hirst,et al.  Utility of social media and crowd-intelligence data for pharmacovigilance: a scoping review , 2018, BMC Medical Informatics and Decision Making.

[57]  Chunlei Liu,et al.  ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..

[58]  J. Arrowsmith Trial watch: Phase II failures: 2008–2010 , 2011, Nature Reviews Drug Discovery.

[59]  D. Swanson Migraine and Magnesium: Eleven Neglected Connections , 2015, Perspectives in biology and medicine.

[60]  Leonardo L. G. Ferreira,et al.  Drug repositioning approaches to parasitic diseases: a medicinal chemistry perspective. , 2016, Drug discovery today.

[61]  Alexander Tropsha,et al.  Curation of chemogenomics data. , 2015, Nature chemical biology.

[62]  Sharon F Terry,et al.  An End to the Myth: There Is No Drug Development Pipeline , 2013, Science Translational Medicine.

[63]  George Papadatos,et al.  The ChEMBL database in 2017 , 2016, Nucleic Acids Res..

[64]  Todd J. Bodnar,et al.  Identifying Adverse Effects of HIV Drug Treatment and Associated Sentiments Using Twitter , 2015, JMIR public health and surveillance.

[65]  S. Rees,et al.  Principles of early drug discovery , 2011, British journal of pharmacology.

[66]  R. W. Hansen,et al.  Journal of Health Economics , 2016 .

[67]  Dong-Qing Wei,et al.  Rare Diseases: Drug Discovery and Informatics Resource , 2017, Interdisciplinary Sciences: Computational Life Sciences.

[68]  G. Spyrou,et al.  Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score , 2017, Scientific Reports.

[69]  S. Ekins,et al.  Collaboration for rare disease drug discovery research , 2014, F1000Research.

[70]  Jie Zhou,et al.  The research on gene-disease association based on text-mining of PubMed , 2018, BMC Bioinformatics.

[71]  Polina Mamoshina,et al.  Design of efficient computational workflows for in silico drug repurposing. , 2017, Drug discovery today.

[72]  Sean Ekins,et al.  In silico repositioning of approved drugs for rare and neglected diseases. , 2011, Drug discovery today.

[73]  Aris Angelis,et al.  Socio-economic burden of rare diseases: A systematic review of cost of illness evidence. , 2015, Health policy.

[74]  Mark D. Wilkinson,et al.  Preparing Data at the Source to Foster Interoperability across Rare Disease Resources. , 2017, Advances in experimental medicine and biology.

[75]  Antonio Jimeno-Yepes,et al.  Detection of adverse drug reactions using medical named entities on Twitter , 2017, AMIA.

[76]  S. Papapetropoulos,et al.  Drug repurposing from the perspective of pharmaceutical companies , 2018, British journal of pharmacology.

[77]  Allison Crosby-Thompson,et al.  KIT Inhibition by Imatinib in Patients with Severe Refractory Asthma , 2017, The New England journal of medicine.

[78]  Wei Pan,et al.  The New Hardware Development Trend and the Challenges in Data Management and Analysis , 2018, Data Science and Engineering.

[79]  A. Simeonov,et al.  Drug discovery and development for rare genetic disorders , 2017, American journal of medical genetics. Part A.

[80]  Michael Pryszlak,et al.  Giving Drugs a Second Chance: Overcoming Regulatory and Financial Hurdles in Repurposing Approved Drugs As Cancer Therapeutics , 2017, Front. Oncol..

[81]  F. Goodsaid,et al.  Recommendations for the development of rare disease drugs using the accelerated approval pathway and for qualifying biomarkers as primary endpoints , 2015, Orphanet Journal of Rare Diseases.