Search Tutorial

Overview

This page provides the search syntax for the BioMedSearch.com website.
The basic structure for the syntax query on BioMedSearch is: term [FIELD]

Terms

A query is broken up into terms and Boolean operators. There are two types of terms: Single Terms and Phrases.
A Single Term is a single word such as "test" or "hello."
Multiple terms can also be combined using parentheses.
A Phrase is a group of words surrounded by double quotes such as "hello world."

Common Search

This would search the system database for user term based on common fields including PMID, author name, article title or journal title.

Quick Search

Quick search lists the most common search fields. You can search for a word or a simple phrase or document number in any of the listed fields. You can search in more than one field at a time. You can also use wildcards to enhance your searches in quick search (see wildcards for tips and examples for searching with wildcards). Boolean operators and nesting are not allowed in quick search. Quick search also has additional features like word stemming, sort order and date range to further enhance your search.

Expert Search

Expert search helps you create complex queries to search multiple fields using field abbreviations. You can also include Boolean operators, nesting and wildcards in your expert search query. To add value to your searches, BioMedSearch incorporates proximity searching and search term weighting features in expert search. Word stemming, sort order and date range options are available to further enhance your search.

Sort Order

You can select to sort the documents in your results list either chronologically or according to their relevancy. If you select chronological sort order, documents in the results list would be arranged chronologically, with most recently published documents on the top of the list. You can also select to sort the documents in the results list according to their relevancy. Relevancy sorting is based on a "relevancy score" assigned to each document. Relevancy score is based on frequency and positioning of keyword(s) in the document. Relevancy score ranges from 0 to 1000. Documents with higher relevancy score would be placed at the top of the list.

Boolean Operators

Boolean operators allow terms to be combined through logic operators. BioMedSearch supports AND, "+", OR, NOT and "-" as Boolean operators (Note: Boolean operators can be lower case as well).
The AND operator is the default conjunction operator. This means that if there is no Boolean operator between two terms, the AND operator is used. The AND operator links two terms and finds a matching document if both terms exist anywhere in a document. This is equivalent to an intersection using sets. The symbol && can be used in place of the word AND.
To search for document that contain all the words water, borne, disease use the query:
water borne disease
or
water AND borne AND disease
This also works with fielded search:
water[TIAB] AND borne[TIAB] AND disease[TIAB]
Note, that the above query IS NOT the same as:
water AND borne AND disease[TIAB]
The above query would search for water and borne in any of the fields, and only restrict the word disease to the Title/Abstract field.
Boolean Operator Example Function
AND Mobile and Telephone Finds documents which have both mobile and telephone.
OR Mobile or Telephone Finds documents which have either mobile or telephone or both.
NOT Mobile not Telephone Finds documents which have only mobile. The NOT operator excludes telephone completely.

Order of precedence for Boolean operators is:

1. NOT

2. AND

3. OR

Which means that in a query with NOT, AND and OR, terms connected by NOT would be processed first, followed by terms connected by AND and lastly, those connected with OR. Example: auto or manual and gear - Since AND is processed before OR, the query would be interpreted as auto or (manual and gear). Note: BioMedSearch search engine is not case sensitive for boolean operators.

Nested Queries/Creating queries with Parentheses or Brackets

You can enclose search terms and their operators in parentheses or brackets to specify the order in which they should be processed. Information within parentheses is read first and then information outside parentheses. If there are more than one set of parentheses, the innermost set of parentheses would be read first, then the next and so on until the whole query is interpreted. The order of precedence for parenthesis and Boolean operators is:

1.     Parentheses

2.     NOT

3.     AND

4.     OR

Nested query How it is interpreted (following order of precedence)
Water and borne or disease (Water and borne) or disease
(water or borne and resistant) and disease (water or (borne and resistant)) and disease

Proximity Searching

Proximity searching helps you to specify how near/distant you want your search terms to be. You can specify the distance or nearness of the terms searched as whole numbers. The proximity operator in BioMedSearch is "~". The proximity operator should be followed by a whole number indicating the proximity of the search terms. For example, "~10" means within ten words of each other. Note: Ensure that your keywords are enclosed in double-quotation marks, and there is no space left between the end-quotation mark and the proximity operator.
Query Results list would have
"Enzyme peptide"~3 Documents with both enzyme and peptide, where both are within 3 words of each other.
"fermentation bacteria milk"~5 Documents where the words fermentation, bacteria and milk, are present within 5 words of each other.

Fuzzy Searching

BioMedSearch supports fuzzy searches based on the Levenshtein Distance, or Edit Distance algorithm. To do a fuzzy search use the tilde, "~", symbol at the end of a single word term.
Query Results list would have
roam~[ti] Documents with the word "foam" or "roams" in the title field.

Date Ranges

BioMedSearch allows date range searches using the appropriate date field, and a colon as a date separator. The following search will result in documents that have a Published Date from January 1, 1999 to March 31, 1999:

1999/01/01:1999/03/31[DP]

Dates can also be truncated at the day and month level, meaning that those parts of the date are not required.  When omitted, logical values are assumed.  The following search will result in the same documents as those in the above example:

1999/01:1999/03[DP]

The following syntax will also work. This search will search for all documents with a Published Date in the year 2008:

2008[DP]

This is logically equivalent to:

2008/01/01:2008/12/31[DP]

Text Ranges

BioMedSearch allows Text range searches, similar to the Date Ranges described above. Instead of using dates, text can be used, and the search will return results that exist between the two terms specified (inclusive).
Query Results list would have
(blood:bloody)[ti] Articles with terms alphabetically between blood and bloody in the title. For example, bloodless, bloodstream, bloodworm, etc.

Wildcard Searching

Truncation or Wildcard searching allows you to retrieve documents containing variations of a search term. Wildcard symbols can be used to replace a single letter or a part of a word, or one or more numbers.

We can use two wildcards: ? to replace exactly one character or number. * to replace zero or multiple characters or numbers.

Query Results list would have
Analy?e Analyse and Analyze
Sul*ur Sulphur and Sulfur
Harbo*r Harbor and harbour

Boosting a Term

BioMedSearch provides the relevance level of matching documents based on the terms found. To boost a term use the caret, "^", symbol with a boost factor (a number) at the end of the term you are searching. The higher the boost factor, the more relevant the term will be.

Boosting allows you to control the relevance of a document by boosting its term. For example, if you are searching for water disease and you want the term disease to be more relevant, boost it using the ^ symbol along with the boost factor next to the term. You would type:

water disease^4

This can also be done in fielded searches:

water^4[TIAB] disease^2[TIAB] smith[AU]

By default, the boost factor is 1. Although the boost factor must be positive, it can be less than 1 (e.g. 0.2).

Fielded Searching

BioMedSearch supports fielded data. When performing a search you may either specify a field, or identify no field, in which case the terms will be searched against all indexed fields.

You can execute field searches by typing in the term(s) to be searched, followed by the field name enclosed in brackets.

As an example, let's assume you want to search for the word water in the Title/Abstract field:

water[TIAB]

If you wanted to search for the word water, regardless of which field it was in:

Water

If you wanted to search for multiple words in the same field:

water[TIAB] disease[TIAB]

The following query will result in the word water being searched for in all fields, and the word disease being limited to the Title/Abstract field.

water disease[TIAB]

If you wanted to search for both terms water and disease in the Title/Abstract field:

(water AND disease)[TIAB]

or

(water disease)[TIAB]

To search for water or disease in the Title/Abstract:

(water OR disease)[TIAB]

Multiple fields can also be searched.  The following query will search for the word disease in the Title/Abstract field and the word smith in the Author field.

disease[TIAB] AND smith[AU]

Escaping Special Characters

Whenever special characters are used in expressions, there is a need to provide an escaping mechanism so that the special characters themselves can be used in a normal fashion. BioMedSearch uses a backslash to escape special characters within terms. The list of escapable characters is:

* *  +   -   !   (   )   :   ^   ]   {   }   ~   *   ?

To escape these character use the \ before the character. For example to search for (1+1):2 use the query:

(1+1)\:2

Syntax Examples

Data Element Description
water Find all documents containing the word 'water' in any field.
water[AB] Find all documents containing the word 'water' in only the abstract.
Water AND disease Find all documents containing both the word 'water' and the word 'disease' in any fields (e.g., title, abstract, or specification/description). The two words may be in different fields.
water[AB] AND disease Find all documents containing the word 'water' in the abstract, and the word 'disease' in any field (e.g.,title, abstract, or specification/description).
water[AB] AND 2000/12/14:2005/12/31[DP] Find all documents containing the word 'water' in the abstract which have a Publication Date between Dec 14, 2000 and Dec 31, 2005.
water[TI] NOT disease Find all documents containing the word 'water' in the title, but do not include any documents which have the word 'disease' in any field (e.g., title, abstract, or specification/description).
(water OR disease) AND (borne OR resistant) Find all documents that contain either the word 'water' or the word 'disease', and which also contain either the word 'borne' or the word 'resistant.' Note that without the parenthesis this query would be interpreted in an entirely different manner.
[with word stemming on] electroplate Find all forms of the word 'electroplate', including 'electroplated', 'electroplating', and 'electroplater'.
"Water disease"~5 Find all documents containing the word 'water' within 5 words of 'disease', in any fields (e.g., title, abstract, or body). The "5" may be replaced with any whole number.
cat^5 OR disease Water is 5 times more important to the relevancy of documents than disease. Find all documents containing the word 'water' or 'disease' but, all other things being equal, rank the documents containing water higher. The "5" may be replaced with any whole number.
electron* Find all documents containing words starting with electron like electron, electrons, electronic, electronics, etc.
su? Find all documents containing words that has only one character after 'su' like sub, sun, sum, etc.

Search Fields

List of Search Fields
Field Abbreviation Field Name Description
Example Search
1AU First Author The first personal author name listed for a record.
  • Smith [1AU]
  • (J Smith) [1AU]
  • (Smith John) [1AU]
  • "John Smith"[1AU]
AB Abstract Text Text included in the  "abstract" and "other abstract" (if supplied) fields of a record. For PubMed articles, English language abstracts are taken directly from the published article. If an article does not have a published abstract, PubMed does not create one.
  • "skin cancer" [AB]
  • (skin OR cancer) [AB]
AD Affiliation The institutional affiliation and address (including e-mail address) of the first author of the article as it appears in the journal. This field can be used to search for work done at specific institutions.
  • (cleveland clinic) [AD]
  • mayo [AD]
ADP Article Date Published This is typically a date the article was published in electronic format, often times before the Journal Date Published.
  • 2009/1/30[ADP]
  • 2001/3:2009/3[ADP]
  • 2009[ADP]
ALL All Fields Searches against all search fields.  NOTE: This is the default search field if no field is specified.
  • "skin cancer"
  • microbiology OR (bacteria AND microbial)
  • device [ALL]
AU Author Searches all authors for an article.  To search just the first author of a record, use [1AU].  Note: The [AU] behaves exactly the same as the [FAU] field.
  • Smith [AU]
  • (J Smith) [AU]
  • (Smith John) [AU]
  • "John Smith"[AU]
CN Corporate Author The corporate or collective authorship of an article. Corporate names display exactly as they appear in the journal.
  • CDC [CN]
  • Centers for Disease Control and Prevention" [CN]
DP Publication Date The date that the article was published.
  • 2007/1/31[DP]
  • 2001/3:2001/10[DP]
  • 2009[DP]
DTRE Date Revised The date a change was last made to a record as a result of NLM's individual or global maintenance. NOTE: This date is supplied by the NLM and they inform users not to "depend on [the] initial presence of [this date] or [a] change to [this date's] value to indicate that a record has been maintained."
  • 2001/3/23[DTRE]
  • 2001/3:2001/10[DTRE]
  • 2009[DTRE]
EDP Earlier Date Published This is the earlier of the Print Publication Date or the Electronic Publication Date.
  • 2009/1/15[EDP]
  • 2001/3:2009/3[EDP]
  • 2009[EDP]
FAU Full Author Name Searches all authors for each record.  To search just the first author of a record, use [1AU].  Note: The [FAU] field behaves exactly the same as the [AU] field.
  • Smith [FAU]
  • (J Smith) [FAU]
  • (Smith John) [FAU]
  • "John Smith" [FAU]
FIR Investigator/Collaborator Name The full investigator or collaborator name for articles, if available.
  • "harry james" [FIR]
  • (h james) [FIR]
GR Grant Number Research grant numbers, contract numbers, or both that designate financial support by any agency of the US PHS (Public Health Service), several United Kingdom granting agencies and other funding sources.
  • 5R01CA101211-03 [GR]
IP Issue The number of the journal issue in which the article was published.
  • 12 [IP]
JIDP Journal Date Published This is the date the document appeared in a printed journal.
  • 2009/1/15[JIDP]
  • 2001/3:2009/3[JIDP]
  • 2009[JIDP]
IR Investigator/Collaborator Name Names of principal investigator(s) or collaborators who contributed to the research.
  • Smith [IR]
  • (J Smith) [IR]
  • (Smith John) [IR]
  • "John Smith" [IR]
JID NLM Unique Identifier The alpha-numeric identifier for the cited journal that was assigned by NLM's Integrated Library System.
  • 0375267 [jid].
LA Language The language in which the article was published. Note: Many non-English articles have English language abstracts. You can either enter the language or enter just the first three characters of most languages, e.g., chi [la] retrieves the same as chinese [la]. The most notable exception is jpn [la] for Japanese.
  • eng [LA]
  • english [LA]
  • chi [LA]
  • chinese [LA]
LASTAU Last Author The last personal author name in a citation.
  • Smith [LASTAU]
  • (J Smith) [LASTAU]
  • (Smith John) [LASTAU]
  • "John Smith" [LASTAU]
LID Location ID The DOI or publisher ID that serves the role of pagination to locate an online article.
  •  "s0212 16112008000100001" [LID]
MAJR MeSH Major Topic A MeSH term that is one of the main topics discussed in the article.
  •  Neuropsychology [MAJR]
MH MeSH Terms All MeSH terms related to the article.
  • "Blood Pressure" [MH]
  • (epidemiology AND humans) [MH]
NM Substance Name The name of a chemical discussed in the article.
  •  tiadenol [NM]
OT Other Term Mostly non-MeSH subject terms (keywords), including NASA Space Flight Mission, assigned by an organization other than NLM.
  • cancer [OT]
  • "APEX Project" [OT]
OWNER Owner Acronym that identifies the organization that supplied the citation data.
  •  NASA [OWNER]
PG Pagination Enter only the first page number on wihch the article appears. The citation will display the full pagination of the article but this field is searchable using only the first page number.
  • "1, 4" [PG]
  • 304 [PG]
  • "E101-6" [PG]
PL Place of Publication 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 included in All Fields or Text Word retrieval.
  •  nigeria [PL]
  • ("United States" OR US*) [PL]
PMID Unique ID PubMed Unique Identifier PMID.
  •  12343555[PMID]
PS Personal Name as Subject Use this search field tag to limit retrieval to where the name is the subject of the article
  • Smith [LASTAU]
  • (J Smith) [LASTAU]
  • (Smith John) [LASTAU]
  • "John Smith" [LASTAU]
PT Publication Type Describes the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter.)
  • Addresses [PT]
RN EC/RN Number Number assigned by the Enzyme Commission (EC) to designate a particular enzyme or by the Chemical Abstracts Service (CAS) for Registry Numbers
  • "69-93-2" [RN]
  • "3.1.1.34" [RN]
  • "3.1.1.34" [RN]
SB Subset Method of restricting retrieval by topic, citation status and journal/citation subsets.
  • AIDS [SB]
SFM Space Flight Mission The Space Flight Mission identifier for the record.
  • "APEX Project" [SFM]
SH MeSH Subheadings MeSH terms flagged as subheadings in the record.
  • "Blood Pressure" [SH]
  • (epidemiology AND humans) [SH]
SI Secondary Source ID The SI field identifies secondary source databanks and accession numbers, e.g., GenBank, GEO, PubChem, ClinicalTrials.gov, ISRCTN. 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.
  • genbank [si]
  • AF001892 [si]
  • genbank/AF001892 [si]. | |
TA Journal Title The journal title abbreviation, full journal title, or ISSN number.
  • J Biol Chem
  • Journal of Biological Chemistry
  • 0021-9258 | |
TI Title Words and numbers included in the title of a citation.
  • "The Kleine-Levin syndrome as a neuropsychiatric disorder: a case report" [TI]
TIAB Title/Abstract Words and numbers included in the title, abstract, and other abstract of a citation. English language abstracts are taken directly from the published article. If an article does not have a published abstract, PubMed does not create one.
  • AIDS [TIAB]
TT Transliterated Title Words and numbers in title originally published in a non-English language, in that language. Non-Roman alphabet language title are transliterated.
  • dystalnego [TT]
TW Text Words Searches against all search fields.  Note: This is the same as the [ALL] field.
  • (humans AND cancer) [TW]
VI Volume The number of the journal volume in which an article is published.
  • 1 [VI]
  • "49 Suppl 20" [VI]
Fields related to comments and correction
Field Abbreviation Field Name Description
Example Search
partialretractionin Partial Retraction In Cites the reference containing a partial retraction of the article; began use in 2007.
  • Surg. 2007 [partialretractionin]
partialretractionof Partial Retraction Of Cites the article being partially retracted; began use in 2007.
  • Organ Transplant. 2001 [partialretractionof]
republishedfrom Republished From Cites the original article subsequently corrected and republished; began use in 1987.
  • Med. 2009 [republishedfrom]
republishedin Republished In Cites the final, correct version of a corrected and republished article; began use in 1987.
  • Nutr. 2009 [republishedin]
retractionof Retraction Of Cites the article being retracted; began use in August 1984.
  • Med Assoc. 2008 [retractionof]
retractionin Retraction In Cites the reference containing a retraction of the article; began use in August 1984.
  • Chemphyschem. 2009 [retractionin]
updatein Update In Cites the reference containing an update to the article; began limited use in 2001.
  • Rev 2007 [updatein]
updateof Update Of Cites the article being updated; limited use; began limited use in 2001.
  • Rev 2007 [updateof]
summaryforpatientsin Summary For Patients In Cites the reference containing a patient summary article; began use in Nov. 2001
  • Ethn Dis. 2009 [summaryforpatientsin]
originalreportin Original Report In Cites a scientific article associated with a patient summary.
  • Ethn Dis. 2009 [originalreportin]
republishedin Republished In Cites the subsequent (and possibly abridged) version of a republished article; began use in 2006.
  • Dermatol Nurs. 2009 [republishedin]
republishedfrom Republished From Cites the first, originally published article; began use in 2006.
  • N Engl J Med. 2008 [republishedfrom]
commentin Comment In Cites the reference containing a comment about the article; began use with journal issues published in 1989.
  • Paediatr Respir Rev. 2008 [commentin]
commenton Comment On Cites the reference upon which the article comments; began use with journal issues published in 1989.
  • Paediatr Respir Rev. 2008 [commenton]
erretumin Erratum In Cites the reference containing a published erratum to the article; began use in 1987.
  • ANS Adv Nurs Sci. 2008 [erretumin]
erratumfor Erratum For Cites the original article for which there is a published erratum.
  • ANS Adv Nurs Sci. 2008 [erratumfor]