Great Link for PubMed Help

http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html

 

1.      Create a Cubby to store your search strategies. 

o        Saving Entire Search Results:

§         The default for the Save feature is to save the entire retrieval, up to 10,000 items, unless you specifically select citations. For example, if you use the Send to File on a screen displaying 1-20 items of 30, your saved file will contain all 30 citations.

§         Use the Display pull-down menu to select a format.

§         Click Send to File and your items will be saved in this format as plain text.

o       Saving Selected Citations from a Single Search:

§         Use the Display pull-down menu to select a format.

§         Click in the check boxes next to each citation you want to save.

§         You can move to other pages within the search results to make more selections.

§         Click Send to File and your selected items will be saved in the Display format as plain text.

o       Saving Citations from Multiple Searches:

§         Use the Send to Clipboard selection to add either entire search results or selected items to the Clipboard.

§         The Clipboard can contain up to 500 items.

§         After adding citations to the Clipboard, click on the Clipboard link to go to that screen.

§         Use the Display pull-down menu to select a format.

§         Choose File and click Send to and your items will be saved in this format as plain text.

 

2.      For this part of the assignment, do your searches and then bring down the History menu and use the clipboard to summarize your efforts. 

o        Write a simple term search to find articles about HIV RNA dependent DNA polymerase.  What search terms did you select?

o        Select the first 10 articles published in 2004 and send them to the clipboard.  Save them as text.  Score each for relevance (e.g. highly relevant, somewhat relevant or irrelevant).

o        Try your search delimited by quotation marks around “RNA dependant” “DNA polymerase” and “human immunodeficiency virus”.  Try hyphens too.  What are some differences and why?

o        What description do you get of your search when you click “Details”?  Is this what you expected?

o        Search using all three of the Boolean operators (AND, OR, NOT).

o        Demonstrate that you can search in PubMed using the parentheses to make an ordered series of searches.

3.      Read the section on MeSH terms.  http://www.nlm.nih.gov/mesh/introduction2004.html. 

o        What is a descriptor? 

o        A qualifier? 

o        An entry term?

4.      Write a search strategy for the same search using MeSH headings related to the term on the Main Heading. 

o        What is a MeSH tree?  Where on a MeSH tree is your term?

o        What happens with Find Exact Term? 

o        What happens with “Find terms with ALL fragments”? 

o        Find terms with ANY fragment.” 

o        How many articles do you find using the MeSH terms instead of the terms you thought of?

o        Score the first 10 articles published in 2003 for relevance as above.

5.      Use “Related Articles” to find articles similar to those retrieved in #4.

o        How many articles do you find? 

o        Score the first 10 articles in 2003 for relevance as above.

o        Use the History function and combine two searches. 

o        Select the “links for one or more of your articles.  Can you locate a “linkout” resource for HIV?

6.      Use “limits” focus your searches.

o        Find review articles on HIV RNA dependent DNA polymerase.  Export 10 articles and rank for relevance as above.

o        Find clinical trials on food allergies limited to human infants. Export 10 articles and rank for relevance as above.

7.      Compare the precision and recall of these searches.  What are some issues in assessing performance of the searches?   

8.      Try Google with the same search term.  What are some of the differences in what you hit?  Number of hits?

9.      Try using some of the subfields in PubMed listed below. 

o        Find local or regional experts on HIV (Marshall, WVU, Ohio State etc.?  What was your search strategy?  

o        Search for a paper written by someone with your last name.

o        Search for a method used in a paper, such as rtPCR or PCR?

o        Find a free full text article on HIV.

o        Find a paper on Canis familiaris published in Proceedings of the National Academy of Science USA

10.  Create a search strategy for a topic you are interested in.  Tell me the topic, describe you strategy and save it in your cubby.  Exercise your search more than once during the course of the class to look for new papers.

 

 

Search Field Descriptions and Tags (in alphabetical order)

  • Affiliation [ad] - Includes the institutional affiliation and address (including email address) of the authors of the article as it appears in the journal. This field can be used to search for work done at specific institutions (e.g., "cleveland [ad] AND clinic [ad]").
  • All Fields [all] - Includes all searchable PubMed Central fields. However, only terms where there is no match found in one of the Translation tables or Indexes via the Automatic Term Mapping process will be searched in All Fields. PubMed Central ignores stopwords from search queries.
  • Abstract [ab] - Includes all words and numbers in the abstract of an article.
  • Accession [accn] - Accession numbers from the GenBank sequence database that are cited in PMC articles.
  • Author [au] - PubMed Central citations do not list the full author name. The format to search for an author is: last name followed by a space and up to the first two initials followed by a space and a suffix abbreviation, if applicable, all without periods or a comma after the last name (e.g., "fauci as or o'brien jc jr"). Initials and suffixes may be omitted when searching. PubMed Central automatically truncates on an author's name to account for varying initials, e.g., o'brien j [au] will retrieve o'brien ja, o'brien jb, o'brien jc jr, as well as o'brien j. To turn off this automatic truncation, enclose the author's name in double quotes and qualify with [au] in brackets, e.g., "o'brien j" [au] to retrieve just o'brien j.
  • Body - All Words [articlebody] - Includes all words and numbers in the body of a article except for the Abstract and References.
  • Body - Key Terms [body - key terms] - Key terms from the article body.
  • EC/RN Number [rn] - Number assigned by the Enzyme Commission to designate a particular enzyme or by the Chemical Abstracts Service (CAS) for Registry Numbers.
  • Electronic Publication Date [epubdat] - The date of the electronic publication. Dates or date ranges must be entered using the format YYYY/MM/DD [edat], e.g. 1998/04/06 [edat] . The month and day are optional (e.g., 1998 [edat] or 1998/03 [epubdat]). To enter a date range, insert a colon (:) between each date (e.g., 1996:1997 [epubdat] or 1998/01:1998/04 [epubdat])
  • Figure/Table Caption [figure/table caption] - Includes all words and numbers in the figure and table captions of an article.
  • Filter [filter] - Technical tags used by PubMed Central to qualify citations.
  • Issue [ip] - The number of the journal issue in which the article is published.
  • Journal [ta] - The journal title abbreviation, full journal title, or ISSN number (e.g., J Biol Chem, Journal of Biological Chemistry, 0021-9258). The Journal Database is also available to look up the full name, abbreviation, and ISSN number of a journal. If a journal title contains parentheses or brackets, enter the name without the parentheses or brackets, e.g., enter J Hand Surg [Am] as j hand surg am.
  • MeSH Major Topic [majr] - A MeSH term that is one of the main topics discussed in the article..
  • MeSH Subheadings [sh] - MeSH Subheadings are used with MeSH terms to help describe more completely a particular aspect of a subject. For example, the drug therapy of asthma is displayed as asthma/drug therapy, see MeSH/Subheading Combinations. The MeSH Subheading field allows users to "free float" Subheadings, e.g., "hypertension [mh] AND toxicity [sh]". MeSH Subheadings automatically include the more specific Subheading terms under the term in a search. To turn off this automatic feature, use the search syntax [sh:noexp], e.g., "therapy [sh:noexp]". In addition, you can enter the MEDLINE two-letter MeSH Subheading abbreviations rather than spelling out the Subheading, e.g., "dh [sh] = diet therapy [sh]".
  • MeSH Terms [mh] - NLM's Medical Subject Headings controlled vocabulary of biomedical terms is used to describe the subject of each journal article in MEDLINE. MeSH contains more than 19,000 terms and is updated annually to reflect changes in medicine and medical terminology. MeSH terms are arranged hierarchically by subject categories with more specific terms arranged beneath broader terms.
  • Methods - Key Terms [methods - key terms] - Key terms from the "methods" section of the article abstract.
  • Organism [orgn] - Contains the scientific and common names for the organisms in the NCBI taxonomy database that are found in PMC articles. The NCBI taxonomy database only includes species that are represented in the public sequence databases, so many of the organisms mentioned in PMC articles will not be found in this index. To cut down on false hits, matches to scientific names are required to add PMC articles to this index - common names in this field will only retrieve articles that mention the corresponding scientific name. By default the PMC organism index is 'unexploded' - the query "Mammalia[orgn]" will only retrieve articles that explicitly mention the Mammalia. The query "Mammalia[orgn:exp]" will retrieve articles that mention any of the species of mammals.
  • Organism Unsynonymized [orgn_nosyn] - Organism names that are identified as Synonyms in the NCBI taxonomy database will retrieve the same set of articles in the PMC Organism index (e.g "Danio rerio[orgn]" = "Brachydanio rerio[orgn]"). The Organism unsynonymized index will only retrieve articles that use the name in question.
  • NLM Unique ID [JID] The alpha-numeric identifier for the cited journal that was assigned by NLM's Integrated Library System LOCATORplus, e.g., 0375267 [jid].
  • Other Term [OT] Mostly non-MeSH subject terms (keywords), including NASA Space Flight Mission, assigned by an organization other than NLM. The Other Term data may be marked with an asterisk to indicate a major concept, however asterisks are for display only. You cannot search Other Terms with a major concept tag. The OT field is searchable with the Text Word [tw] and Other Term [ot] search tags.
  • Owner Acronym that identifies the organization that supplied the citation data. Search using owner + the owner acronym, e.g. ownernasa.
  • Pagination [PG] Enter only the first page number that the article appears on. The citation will display the full pagination of the article but this field is searchable using only the first page number. See Single Citation Matcher.
  • Personal Name as Subject [PS] Use this search field tag to limit retrieval to where the name is the subject of the article, e.g., varmus h [ps]. Search names following the Author field format, e.g., varmus h[ps].
  • Pharmacologic Action MeSH Terms [PA]  Substances known to have a particular pharmacologic action. Each pharmacologic action term index is created with the drug/substance terms known to have that affect. This includes both MeSH terms and terms for Supplementary Concept Records.
  • Place of Publication [PL] Indicates the cited journal's country of publication. Geographic Place of Publication regions are not searchable. In order to retrieve records for all countries in a region (e.g., North America) it is necessary to OR together the countries of interest. Note: This field is not included in All Fields or Text Word retrieval.
  • PMC Live Date [pmcdat] - Date the citation was first available in PubMed Central. Dates or date ranges must be entered using the format YYYY/MM/DD, e.g. "1998/04/06 [pmcdat]". The month and day are optional (e.g., "1998 [pmcdat]" or "1998/03 [pmcdat]"). To enter a date range, insert a colon (:) between each date (e.g., "1996:1997 [pmcdat]" or "1998/01:1998/04 [pmcdat]").
  • Publication Date [dp] - The date that the article was published. Dates or date ranges must be searched using the format YYYY/MM/DD, e.g. "1998/03/06 [dp]". The month and day are optional (e.g., "1998 [dp]" or "1998/03 [dp]"). To enter a date range, insert a colon (:) between each date (e.g., "1996:1998 [dp]" or "1998/01:1998/04 [dp]").
  • Publication Type [PT] Describes the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter); see full listing, e.g., review[pt].
  • Secondary Source ID [SI] The SI field identifies secondary source databanks and accession numbers of molecular sequences discussed in MEDLINE articles.  The field is composed of the source followed by a slash followed by an accession number and can be searched with one or both components, e.g., genbank [si], AF001892 [si], genbank/AF001892 [si]. The SI field and the Entrez sequence database links are not related. The PubMed links to these databases are created from the reference field of the GenBank or GenPept flatfile. These references include citations that discuss the specific sequence presented in these flatfiles.
  • Subset [SB] Method of restricting retrieval by Subject Subsets and Citation Status Subsets. Searchable with [SB]. Other Subsets are available for searching that do not use this search tag. See also Limits and LinkOut.
  • Substance Name [NM] The name of a chemical discussed in the article. Synonyms to the Supplementary Concept Substance Name will automatically map when qualified with [nm]. This field was implemented in mid-1980. Many chemical names are searchable as MeSH terms before that date.
  • Text Words [TW] Includes all words and numbers in the title, abstract, other abstract, MeSH terms, MeSH Subheadings, chemical substance names, personal name as subject, MEDLINE Secondary Source, and Other Terms typically non-MeSH subject terms (keywords), including NASA Space Flight Mission, assigned by an organization other than NLM.
  • Title [TI] Words and numbers included in the title of a citation.
  • Title/Abstract [TIAB] Words and numbers included in the title, abstract, and other abstract of a citation.
  • Unique Identifier [UID]  PubMed Unique Identifier PMID. To search for the PMID type in the number with or without the search field tag [uid]. You can search for several ID numbers by entering each number in the query box separated by a space (e.g., 95091318 97465762); PubMed will OR the terms together. To search in combination with other terms, you must enter the search field tag, e.g., smith [au] AND (10403340 [uid] OR vaccines [mh]).
  • Volume [VI] The number of the journal volume in which an article is published. See Single Citation Matcher.