"May we show you something in a gene?"


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Content Discovery features in PubMed

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  • **GO THERE: tinyurl.com/bones-and-cartilage**Amazon.com is a very popular model for all types of Web sites b/c it does such a good job of offering “hooks”Pts of entry, ways to draw you in.On this page, we can:Look inside the book or even search its contents (mouseover cover image)Read a customer reviewClick on one of the book’s key phrases to search on itIf you scroll down:Customers Who Bought This Item Also BoughtEditorial ReviewsKey Phrases – Statistically Improbable PhrasesBooks on Related TopicsWhat Do Customers Ultimately Buy After Viewing This Item?Add a tag (keyword) of your ownStart a discussion 
  • NCBI=National Center for Biotechnology Information – part of National Library of Medicine, which is one of the National Institutes of Health
  • http://www.ncbi.nlm.nih.gov/sites/gquery
  • **BE IN PUBMED.** Show NCBI Resources dropdown menuOther NCBI literature databases (which may be familiar to you)PubMed Central (free digital archive of biomedical and health sciences journal literature)Bookshelf (full-text biomedical books)
  • Appears pretty reliably, especially if you include date.
  • PAH (associated with phenylketonuria)too ambiguous? (polycyclic aromatic hydrocarbons, Pretoria Academic Hospital, pulmonary arterial hypertension)
  • Comparing multiple drugs of same type (statins, antihistamines) Comparing multiple drugs for same diagnosis (insomnia, antidepressants)Point out paucity of content-----------------------------------------------------------------------------------simva=Zocor;atorva=Lipitor; simva/ezetimibe=Vytorindonepezil=Aricept -- donEH pehzilsertraline=Zoloft
  • When NCBI started introducing sensors and ads a while back, they appeared only randomly and only 1% of the time, so you sometimes had to do the same search over and over again before the information you wanted showed up. Now most seem to appear reliably when you might expect them. With Drug Sensorand Hot Topic Sensor, big constraint as mentioned earlier is limited amount of content. Originally, NCBI also said that they were experimenting with these features and that they would not necessarily be permanent. In preparing for today’s talk, I did discover that one of the sensors seems to have been taken out of service: (next page)
  • Seems to be MIA: Patient Drug InformationIt links to AHFS Consumer Medication Information (on Entrez Bookshelf)Now covers >1,000 drugsSwitch to Abstract display (single article view) for this one.Examples:diphenhydramine AND loratadineacetominophen ibuprofen headache
  • NCBI did say, as they were introducing
  • Explain PMC
  • PMID 16543414
  • Explain PMC
  • Auto Suggest and Also try are SOCIAL – “Searches done by other users on the same topic” ~ “People who bought this bought that” Some, like Find Related Data, always appear.Others are triggered by specific circumstances, such as existence of a retrieved article in PMC or related searches that other people have done.
  • Here’s AutoSearch.As you search, PubMed displays corresponding list of searches others have done.You can turn off feature, but have to do it or every search session.
  • Even though the ads and sensors are easily evoked these days, being on the lookout for them still reminds me of birdwatching.You never know what combinations of features you’ll see in your search results.Think about pictures taken at your last big family gathering.As people socialize, groupings of relatives change in size and content in the course of the day or evening.One of the relatives in this happy group is cousin John.
  • Here’s John again, sitting next to cousinNathaniel.
  • Here’s Nathaniel with Grandpa.
  • Here’s Grandpa with Uncle Tim…
  • …and Uncle Tim with cousin Chloe.Not knowing what kind of birdwatching luck I’d have with PubMed today, I took some PubMed family pictures to show you how different combinations of test features look in actual search results.
  • Search: hirschpnas 2005Citation SensorFree article linksFree full-text articles in PMCFind related data
  • Drug Sensor search: memantine AND rivastigmineFree article linkDrug SensorTitles with your search termsFree full-text articles in PMC(Find related data there but not included)
  • Search: BRCA2 ovarian cancerGene SensorAlso tryTitles with your search termsFree full-text articles in PMC(Find related data – off stage)
  • Again, features appearing in search results are different from features that appear in Abstract display of a single record.Abstract display for single article:Cited by PMC articlesAll links from this record including
  • The latest news, just this past week, is the addition of books and book chapter records to PubMed.Since 1966, MEDLINE (the database underlying PubMed) has indexed only journal articles.But PubMed’s sister literature databases on NCBI include a collection of Books.It’s called Bookshelf.
  • SEARCH <feingold syndrome>.To start, only 2 books will be cited: GeneReviews and Essentials of Glucobiology.Records for these
  • My NCBI is a feature that lets you store searches and data from PubMed and other NCBI databases.It had a facelift a while back. My NCBI “lives” in the upper right corner of every page on the NCBI Web site.It’s easy to set up a My NCBI account. Once you log in, you stay logged in through multiple sessions on that computer unless you sign out.
  • No PubMed searcher should be without it! Like other Web-based utilities, you can use it anywhere.Even if you don’t routinely save a lot of your work, it’s perfect for those rushed situations in which you can’t finish a task and want to resume it later.
  • SearchesSave searchlink appears above search box.Can set up saved searches to act as alerts, so that you automatically get updates.Collections of articlesSave from Send to dropdownmenu on results page.[Can also save bibliographies (in addition to articles, you can also add books, chapters, other non-journal article items and share)]
  • PubMed filters – Saved Preferences that will always apply when searching from a computer you’re logged into My NCBI on. So if you always only want English language articles or articles with abstracts, you can make that your default.Bibliographies (can add books, chapters, other non-journal article items and share)
  • We have already seen lots of badges in PubMed that link to PubMed Central.
  • PubMed Central (PMC) = Another Entrez literature database
  • PMC is NIH’s free digital archive of biomedical and life sciences journal literature.All peer-reviewed articles arising from NIH-funded projects and published ≥4/7/2008:… must be submitted to PMC.… must be publicly by 12 months after publication.PMCID #s must be added to the end of journal citations in NIH grant applications, proposals, and progress reports (≥ 5/25/2008).
  • Here we see a PubMed record with both PMID and PMCID displayed in Abstract display of single record.Not all articles in PubMed are in PubMed Central (and vice versa).Even when an article is in both, PMCID may not show in corresponding PubMed record because publishers can impose a 12-month embargo.But… say you’re writing a grant and need PMCID numbers for the references you plan to cite. How would you go about do that in an efficient way?
  • Use the PMID : PMCID Converter to get an article’s PubMed Central ID from its PubMed ID (or vice versa)Start in PubMed:Select articles.Use Send to:link to add them to Clipboard.In NCBI Resources menu, choose Literature, PubMed Central.In PubMed Central:From Utilities, click on PMID to PMCID Converter.Click on Get IDs from PubMed Clipboard, then on Convert.
  • "May we show you something in a gene?"

    1. 1. “May we show you something in a gene?” <br />Content Discovery Features in PubMed<br />Patricia Weiss, MLIS<br />Health Sciences Library System<br />University of Pittsburgh<br />April 15, 2010<br />
    2. 2. Copyright 2009-2010 Health Sciences Library System, University of Pittsburgh <br />
    3. 3.
    4. 4. NCBI Discovery Initiative<br />Goal: Serendipitous searching that takes advantage of NCBI’s highly integrated system of databases. <br />Builds ways to relate your search to information in other NCBI databases.<br />Use ad-like features in search results to draw you beyond PubMed to related data in other databases. <br />
    5. 5. PubMed Discovery Components<br />Sensors<br />Database ads<br />Generic discovery aids<br />
    6. 6. NCBI<br />National Center for Biotechnology Information<br />|<br />NLM<br />National Library of Medicine<br />|<br />NIH<br />National Institutes of Health<br />
    7. 7.
    8. 8. Entrez: Search Engine for Many NCBI Databases<br />Literature databases such as:<br />PubMed<br />PubMed Central<br />Bookshelf<br />Molecular biology and genetics databases such as:<br />Gene<br />SNP<br />Structure<br />
    9. 9.
    10. 10. Content Discovery with “Sensors” and “Ads”<br />
    11. 11. Sensors<br />Citation Sensor<br />Accession Sensor<br />Gene Sensor<br />Hot Topic Sensor<br />Drug Sensor<br />Patient Drug Information<br />
    12. 12. Citation Sensor<br />Examples: <br />obama 2008<br />choi blood 2008<br />attiajama 2009<br />Appears if you do a search that suggests a citation<br />
    13. 13. Search: obama 2008<br />
    14. 14. Accession Sensor<br />Examples:<br />X51362<br />NM_000059<br />NM_000128<br />Appears if you search with an NCBI sequence identifier<br />Links to NCBI sequence databases <br />
    15. 15. Search: NM_000059<br />
    16. 16. Related Record in Entrez Nucleotide<br />
    17. 17. Gene Sensor<br />Examples:<br />BRCA1(associated with early onset breast cancer)<br />IDDM2(associated with insulin-dependent diabetes mellitus type 2)<br />CFTR(associated with cystic fibrosis)<br />F8(associated with hemophilia)<br />Links to Entrez Gene database<br />
    18. 18. Search: cftr AND respiratory infection<br />
    19. 19. Related Record in Entrez Gene<br />
    20. 20. Hot Topic Sensor<br />Inspired by rapidly changing data for H1N1 during current outbreak<br />Appears for searches including terms H1N1or swine flu/influenza<br />Appears as 2009 H1N1 Flu Sequences link, which links to NCBI’s Influenza Virus Resource page.<br />
    21. 21. Search: h1n1 resistance oseltamivir<br />
    22. 22. Influenza Virus Resource<br />
    23. 23. Drug Sensor<br />Examples:<br />simvastatin AND atorvastatin<br />anxiety AND sertraline<br />Prompted by search corresponding to topic in PubMed Clinical Q&A(Entrez Bookshelf).<br />Q&A has 2 types of systematic reviews:<br />Comparing multiple drugs of same type<br />Comparing multiple drugs for same diagnosis<br />Limited coverage (currently, 26 drug classes)<br />
    24. 24. Search: simvastatin AND atorvastatin<br />
    25. 25. Related Record in PubMed Clinical Q&A<br />
    26. 26. Patient Drug Information (in Abstract Display of Single Article)<br />
    27. 27. Related Record in AHFS Consumer Medication Information <br />
    28. 28. Database Ads<br />Structure (in Abstract display)<br />
    29. 29. Article Reporting a Structure<br />
    30. 30. Reported Structure in Molecular Modeling DB<br />
    31. 31. More Database Ads<br />Titles with Your Search Terms<br />For PubMed Central (PMC)<br />Free full-text articles in PMC<br />Cited by articles in PMC(in Abstract display)<br />
    32. 32. Generic Discovery Aids<br />During search: Auto Suggest <br />Has turn off feature (for current session only) <br />Always in Abstract display of an article: Find related data<br />Sometimes in Abstract display of an article: <br />Also try<br />All links from this record<br />
    33. 33. Auto Suggest<br />
    34. 34. Find related data on Search Results Page<br />
    35. 35. Find related data: how it works<br />Data description<br />Database menu<br />
    36. 36. All links from this record: what it tells you<br />Which NCBI resources does this article cite?<br />Which resources cite it?<br />Other associations with resources?<br />
    37. 37. PubMed as Birdwatching<br />Sensors and ads depend on your search terms.<br />They are not necessarily permanent in PubMed.<br />Features appearing in search results are different from features that appear in Abstract display of a single record.<br />
    38. 38.
    39. 39.
    40. 40.
    41. 41.
    42. 42.
    43. 43.
    44. 44.
    45. 45.
    46. 46.
    47. 47. Any other goodies I show know about?<br />
    48. 48.
    49. 49. New! Books & DocumentsLabel + Free textlink<br />
    50. 50. My NCBI on PubMed Home Page<br />
    51. 51.
    52. 52. Saving My NCBI data from PubMed<br />Searches<br />Collections of articles <br /> (can be shared)<br />
    53. 53. PubMed Filters in My NCBI<br />
    54. 54.
    55. 55.
    56. 56.
    57. 57.
    58. 58. PMID : PMCID Converter<br />