1 / 17

Alternative Tools for Mining the Biomedical Literature Rolando Garcia-Milian

Alternative Tools for Mining the Biomedical Literature Rolando Garcia-Milian Rolando.milian@ufl.edu Biomedical & Health Information Services Department Health Sciences Center Library February 14, 2014. In this session. Introduction Novel online tools for mining the literature

goro
Download Presentation

Alternative Tools for Mining the Biomedical Literature Rolando Garcia-Milian

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Alternative Tools for Mining the Biomedical Literature Rolando Garcia-Milian Rolando.milian@ufl.edu Biomedical & Health Information Services Department Health Sciences Center Library February 14, 2014

  2. In this session • Introduction • Novel online tools for mining the literature • Unified Medical Language System • Quertle • NextBio • Semantic MEDLINE

  3. Problem – Rapid Growth of Biomedical data GenBank Statistics http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/ Compiled from GEO historic data http://www.ncbi.nlm.nih.gov/geo/summary/?type=history

  4. Problem – Growth of the Biomedical Literature Biomedical Literature • Huge volume (PubMed 23132342 citations) • High diversity • High quality (peer review) Compiled by from PubMed http://www.ncbi.nlm.nih.gov/pubmed • Users overwhelmed by long list of search results • 1/3 of Pubmed queries resulted in 100 or more citations (Islamaj, 2009)

  5. Problem – Querying the Biomedical Literature Querying the biomedical literature becomes more difficult Boolean operators Medical Subject Headings Filters

  6. Alternative Tools for Mining the Biomedical Literature Alternative tools for mining the biomedical literature combine: Statistical methods, Ontologies, Natural Language Processing tools, Visualization tools Reduced time for discovering meaningful results.

  7. records records Information Retrieval and Information Extraction Information Retrieval retrieves documents/ records EGFR Information Extraction extracts facts T14D inhibited EGF receptor internalization EGFR regulates tumor cell proliferation EGFR is expressed in SCCHN Modified from OpenHelix

  8. Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Word Query = phenotype ( ) + anatomy ( ): = association = molecular function ontology category tags Sentence 1 Extract = = phenotype Sentence 4 = anatomy etc... Text Processing Sentence 1 Sentence 2 paper Sentence 3 Sentence 4 Sentence 5 Sentence 6 Modified from OpenHelix

  9. The Process of Marking up a Sentence From Müller H-M, Kenny EE, Sternberg PW (2004)

  10. Unified Medical Language System (UMLS) Started in 1986 - National Library of Medicine A set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems (e.g. doctor, pharmacy, billing, biomedical literature mining. Biomedical terminologies: Anatomy (FMA) Drugs (RxNorm) Medical devices (UMD) Clinical terms (SNOMED CT) Information sciences (MeSH) Administrative terminologies (ICD-9-CM, CPT) Data exchange terminologies (HL7, LOINC) From Fitzman, 2011 Presentation at Biomedical Informatics course, MBL Woods Hole

  11. Unified Medical Language System - Integrating Terminologies From Fitzman, 2011 Presentation at Biomedical Informatics course, MBL Woods Hole

  12. Unified Medical Language System - Integrating Terminologies From Fitzman, 2011 Presentation at Biomedical Informatics course, MBL Woods Hole

  13. Semantic Proposition Lexical Look-up Syntactic Analysis SemRep MetaMap Unified Medical Language System (UMLS) - Overview Text Semantic Network Specialist Lexicon Metathesaurus UMLS From Fitzman, 2011 Presentation at Biomedical Informatics course, MBL Woods Hole

  14. Unified Medical Language System (UMLS) - Overview • Pharmamacologic Substance TREATS Sign or Symptom Albuterol (phsu) TREATSDyspnea (sosy) • Gene or Genome ASSOCIATED_WITH Disease or Syndrome BRCA1 gene (gngm) ASSOCIATED_WITHBreast carcinoma (dsyn) Text From Fitzman, 2011 Presentation at Biomedical Informatics course, MBL Woods Hole

  15. Novel Online Tools for Mining the Biomedical Literature From Luz, 2011 http://www.ncbi.nlm.nih.gov/pubmed/21245076

  16. Comparison of three different literature mining tool

  17. References Campillos M*, Kuhn M*, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science. 2008 Jul 11;321(5886):263-6. http://www.ncbi.nlm.nih.gov/pubmed/18621671 IslamajDogan R, Murray GC, Névéol A, Lu Z. (2009) Understanding PubMed user search behavior. Database (Oxford) http://www.ncbi.nlm.nih.gov/pubmed/20157491 Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. MolSyst Biol. 2010;6:343. Epub 2010 Jan 19. http://sideeffects.embl.de/drugs/56338/ Luz C (2011) PubMed and beyond: a survey of web tools for searching biomedical literature Database (Oxford) http://www.ncbi.nlm.nih.gov/pubmed/21245076 http://www.ncbi.nlm.nih.gov/pubmed/21245076 Müller H-M, Kenny EE, Sternberg PW (2004) Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature. PLoSBiol 2(11): e309. doi:10.1371/journal.pbio.0020309 http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020309 Rindflesch, T.C. et al. (2011) Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use, 31, 15-21. http://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdf Jensen LJ, Saric J, and Bor P (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews Genetics 7: 119-129. Retrieved from http://www.nature.com/nrg/journal/v7/n2/pdf/nrg1768.pdf

More Related