Searching PubMed

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  • 1. Texas Tech UniversityHealth Sciences Center Library presentsSearching PubMed® Rev. 12/8/11
  • 2. To begin...
  • 3. Mouse-over Databases
  • 4. Click PubMed
  • 5. PubMed Home Page
  • 6. Searching PubMed
  • 7. Click MeSH Database
  • 8. MeSH DatabaseTerms in the database are called Medical Subject Headings or a “controlled vocabulary list” of more than 25,000 subject headings.10-15 MeSH are assigned to each article in PubMed.The MeSH index of 10-15 subject headings is like a keyword abstract of the article.MeSH are updated annually in December.
  • 9. Frequently Used Mesh Categories – 2011 A Anatomy C Diseases D Chemicals & DrugsA1 Body Regions C1 Bacterial Infections & Mycoses D1 Inorganic ChemicalsA2 Musculoskeletal System C2 Virus Diseases D2 Organic ChemicalsA3 Digestive System C3 Parasitic Diseases D3 Heterocyclic CompoundsA4 Respiratory System C4 Neoplasms D4 Polycyclic CompoundsA5 Urogenital System C5 Musculoskeletal Diseases D5 Macromolecular SubstancesA6 Endocrine System C6 Digestive System Diseases D6 Hormones, Hormone Substitutes,A7 Cardiovascular System C7 Stomatognathic Diseases & Hormone AntagonistsA8 Nervous System C8 Respiratory Tract Diseases D8 Enzymes, & CoenzymesA9 Sense Organs C9 Otorhinolaryngologic Diseases D9 CarbohydratesA10 Tissues C10 Nervous System Diseases D10 LipidsA11 Cells C11 Eye Diseases D12 Amino Acids, Peptides,A12 Fluids and Secretions C12 Male Urogenital Diseases & ProteinsA13 Animal Structures C13 Female Urogenital Diseases D13 Nucleic Acids, Nucleotides,A14 Stomatognathic System & Pregnancy Complications & NucleosidesA15 Hemic and Immune Systems C14 Cardiovascular Diseases D20 Complex MixturesA16 Embryonic Structures C15 Hemic & Lymphatic Diseases D23 Biologic FactorsA17 Integumentary System C16 Congenital, Hereditary, & D25 Biomedical and Dental MaterialsA18 Plant Structures Neonatal Diseases & Abnormalities D26 Pharmaceutical PreparationsA19 Fungal Structures C17 Skin & Connective Tissue Diseases D27 Chemical Actions and UsesA20 Bacterial Structures C18 Nutritional & Metabolic DiseasesA21 Viral Structures C19 Endocrine System Diseases C20 Immune System Diseases C21 Disorders of Environmental Origin C22 Animal Diseases B Organisms C23 Pathologic Conditions, Signs, and SymptomsB1 Eukaryota C24 Occupational DiseasesB2 Archaea C25 Substance-Related DisordersB3 Bacteria C26 Wounds and InjuriesB4 VirusesB5 Organism Forms
  • 10. Other Categories Include :Analytical, Diagnostic, & Therapeutic Techniques & Equipment Psychiatry and Psychology Biological Sciences Natural Sciences Anthropology, Education, Sociology & Social Phenomena Technology, Industry, Agriculture Information Science Named Groups Health Care Publication Characteristics Geographic Locations
  • 11. Create a Search Strategy PlanIdentify the question and key concepts: alanine or threonine in the genetics of neoplasms Write the search program using medical subject headings (MeSH)
  • 12. alanine Search Enter and click aa (Note: If there is a Boolean OR relationship, start with the “OR” statement first.)
  • 13. Term Definitions
  • 14. 1) Check the box next to the MeSH heading a✔ 2) Then click Add to search builder
  • 15. The first MeSH term is in the search program “box”
  • 16. threonine Search Enter and click aa (Note: If there is a Boolean OR relationship, start with the “OR” statement first.)
  • 17. 1) Check the box next 2) Select OR to the MeSH heading a✔ 3) Then click Add to search builder
  • 18. The second MeSH term is in the search program “box”
  • 19. Boolean Logic - OR alanine OR threonine
  • 20. aa Enter neoplasms and click Search
  • 21. Click the underlined term
  • 22. Scroll screen down to view…
  • 23. MeSH terms arranged in tree structure hierarchy Terms are listed from broadest to narrowest. If Abdominal Neoplasms yields zero results, try using abroader term: Neoplasms by Site.
  • 24. Scroll screen back up
  • 25. Sub-headings narrow the “meaning” of a MeSH term. They are a “subset” of all the Marticles under the MeSH term: Neoplasms.
  • 26. 83SUBHEADINGS:abnormalities embryology enzymology physiology physiopathologyadministrations & dosage epidemiology poisoningadverse effects ethics prevention & controlagonists ethnology psychologyanalogs & derivatives etiology radiation effectsanalysis radiographyanatomy & histology genetics radionuclide imagingantagonists & inhibitors radiotherapybiosynthesis growth & development rehabilitationblood history secondaryblood supply immunology secretioncerebrospinal fluid injuries standardschemical synthesis innervation statistics & numerical datachemically induced instrumentation supply & distributionchemistry isolation & purification surgeryclassification legislation & jurisprudence therapeutic usecomplications manpower therapycongenital metabolism toxicitycontraindications methods transmissioncytology microbiology transplantationdeficiency mortality trendsdiagnosis nursing ultrasonographydiagnostic use organization & administration ultrastructurediet therapy parasitology urinedrug effects pathogenicity utilizationdrug therapy pathology veterinaryeconomics pharmacokinetics virologyeducation pharmacology
  • 27. 2) Select AND ✔1) Check the box next to the subheading a 3) Then click Add to search builder
  • 28. Boolean Logic - AND alanine OR and neoplasms/ genetics threonine
  • 29. The search program is complete. Click Search PubMed
  • 30. Search Results
  • 31. PubMed identifies 231 articles
  • 32. Click Limits
  • 33. Limits include:a A LanguageHuman or Animal Publication Date Gender Type of Article Subsets Ages
  • 34. Limit to articles that are human studies and written in English. ✔✔ Click Search
  • 35. Results are reduced From 231 to 207
  • 36. AAScroll to article #19
  • 37. AA Scroll back upX Select X article(s).
  • 38. Click Display Settings
  • 39. Select Abstract, change to Pub Date tosort to most recent articles appearing first, then click Apply
  • 40. Click + for MeSH terms.
  • 41. MeSH Database searches onlythe MeSH terms for: alanine OR threonine AND neoplasms/genetics
  • 42. Look at subject headings in the MeSH Terms Index for additional terms. You may want to write a new search program using: Polymorphism, Genetic*
  • 43. Links from this record to NCBI databases. Click Gene.
  • 44. Entrez Gene recordClick the back button.
  • 45. Click Send to: and selectFile to save citations to a file on your computer or .Clipboard to temporarily store selected citations orE-mail to send citations to self or colleague
  • 46. …or click icon for full text.
  • 47. Linking to Full-Text Articlesin Electronic Journals
  • 48. TTUHSC Libraries - Proxy Server When Searching from Off Campus: Enter the Eraider username and password assigned to you by Information Services. A Problems with eRaider call: Amarillo: (806) 354-5404 El Paso: (915) 545-6800 Odessa: (432) 335-5108 Lubbock: (806) 743-1234
  • 49. Click PDF
  • 50. Full Text Article Close Article
  • 51. Other Searching Features aa 1) MeSH, phrase, & title word searching 2) Truncation
  • 52. Enter human genome and click aSearcha
  • 53. 1) Check the box next 2) Select AND to the MeSH heading✔ 3) Then click Add to search builder
  • 54. Enter “dark matter” and click Search
  • 55. PubMed identifies 6 articles
  • 56. Enter “dark matter” [ti] and click Search
  • 57. Results are narrowed to 4
  • 58. Truncation
  • 59. Enter gene* to truncate.
  • 60. PubMed locates: gene generation generated genetic
  • 61. My NCBI
  • 62. About a My NCBI AccountA My NCBI account will allow you to: * Save search strategies * Receive automatic search updates via email * Create “search filters”NOTE: you will NOT receive any spam as a result of this account.This account is for databases from the National Library of Medicine including PubMed.
  • 63. Click My NCBI
  • 64. Follow instructions to fill out formClick Register
  • 65. Do provide an email so you can receive automatic search updatesClick Register
  • 66. Verifying YourMy NCBI Account
  • 67. Verifying Your My NCBI Account1) Open your email.2) There will be message from NCBI.3) Copy and paste the verification URL into the web address bar and return.4) Your account will be verified by the National Library of Medicine.
  • 68. A Visit this web site to verify you’re My NCBI account.
  • 69. Search Filters
  • 70. Click Manage Filters.
  • 71. Select filters – no limit. These selections override thedefault filters of Review and Free Full Text. These filters apply to searches run while signed into you’re My NCBI account.
  • 72. Example of results with customized filters
  • 73. Save Search
  • 74. Click Save search
  • 75. Click Save to receive automatic email updates of newlypublished articles on this topic.
  • 76. Set up an e-mail address if you have not done so. Select when and how often you wish to receive updates, report format, and number of results.Click Save
  • 77. Click PubMed
  • 78. Click Remove
  • 79. Online Tutorial
  • 80. Click Training & Tutorials for hands-on learning.
  • 81. Please contact us at:Lubbock (806) 743-2200Amarillo (806) 354-5448El Paso (915) 545-6652Odessa (432) 335-5171
  • 82. The End