Advanced Search Options

The following are advanced search options you can use to help better target the search results you're looking for. For a list of helpful search tips, visit our search tip information listing:

Gene/Identifier Searches

BiOGRID Gene/Identifier searches can be performed by clicking on the “gene” tab from the main search page. To perform a gene/identifier search, you simply enter your term (such as STE11 or KSS1) and our engine will search for matching identifiers. For a list of our currently supported identifiers, you can check out our supported identifiers for searches listing.

  • Wildcard Searches - The BioGRID supports wildcard searching (ie. searching where the search is not exact but rather a range of possible matches) on the TAIL end of any keyword entered in our search field. To perform a wildcard search, simply enter your prefix (must be 3 letters or more) followed by a star (*).
    • Examples: STE*, CDC*, YAL01*, CLN*
    • These will not work: ST*E, *L01, CC* (too short)

Publication Searches (By Pubmed ID)

If you click on the “Publication” tab from the main page, you can search by pubmed id. Simply enter a list of valid pubmed ids separated by spaces, commas, or newlines and our search will pull up as many as it can find as long as they contain interactions within our database. Here are some examples:

  • 9006895
  • 10391924,12361954,11923305,9050991,12624098

Be sure that you don't mix pubmed ID searches with full text searches (described below) if for example you search for “10391924 DIABETES” (combining a pubmed and a full text term) our search will simply ignore the full text term and search exclusively for the pubmed id, potentially returning a result you were not interested in. Also, pubmed IDs can contain only numbers 0-9, so any alpha characters will result in an invalid pubmed id.

Note: BioGRID does not archive the entire pubmed database. When searching by Pubmed ID you are searching only those publications that have been curated by our curation team. If a publication is not available that you think contains interactions, please contact us at biogridadmin@gmail.com and let us know the pubmed ID so we can ensure its availability in a future update.

Publication Searches (By Full Text)

BioGRID supports searching publications by full text terms which can be performed using boolean operators for greater flexibility and customization of search results. To search a publication by full text terms, simply click on the “publication” tab and enter your terms into the text field. Full text searches are performed on 4 fields simultaneously: Title, Authors, Abstract, and NCBI Mesh Terms. Results will be returned if your keywords are found in any of these 4 fields. As with identifier searching, wildcard matches can be performed by appending a * to the TAIL end of any term.

Here are some of the options available to modify your full text search using boolean operators:

  1. OR Searching
    • If you search for keywords simply separated by spaces, you are performing an OR search. For example, if you search for SH2 Domain this is the equivalent of saying return papers containing SH2 OR Domain OR both. This is most useful for searching multiple relevant terms for a specific project such as Kinase Phosphatase Cyclin where any one of them is relevant enough to return the publication.
  2. AND Searching
    • If you search for keywords prefixed with a plus sign +, you are performing an AND search. For example if you search for +protein +kinase +adapter this is the equivalent of saying return papers containing protein AND kinase AND adapter. This is useful when attempting to find papers containing a longer list of relevant keywords.
  3. NEGATIVE Searching
    • If you search for keywords prefixed with a minus sign -, you are performing a NEGATIVE search. For example, if you search for +protein +kinase -yeast this is the equivalent of saying return papers containing protein AND kinase but only if those papers DO NOT contain the keyword yeast. You cannot perform an all negative search so a search like -yeast -human is invalid.
  4. EXACT PHRASE Searching
    • If you search for keywords encased in double quotations ”, you are performing an EXACT PHRASE search. For example, if you search for “protein kinase domain” this is the equivalent of saying return papers containing the EXACT PHRASE protein kinase domain. You can use exact phrase searching in combination with the above options such as +“protein kinase domain” -“SH2 Domain” which will return papers containing protein kinase domain but not if they also contain SH2 domain. You should use exact phrase searching anytime you want to find a specifically worded phrase including looking for authors “Smith AC” or exact titles “Analysis of murine HOXA-2 activity in Drosophila melanogaster”. When search for a title of a publication make sure you put quotes around it, otherwise you'll get back every paper containing any of those words in the title. Also, make sure to remove invalid characters from the title if it contains any…
  5. GROUPED Searching
    • If you search for keywords encased in round brackets ( ), you are performing a grouped search. This option is useful for more complicated queries where you want to string together many keywords. For example, +(protein kinase domain) +(sh2 domain) is the equivalent of saying search for any one of protein, kinase, OR domain (but one must be there because of the + sign) and also any one of sh2 and domain (also, one of the 2 must be there because of the second + sign). So, in this case grouping has allowed for the combination of both OR and AND searches into a single query.

Here are some practical examples of how to use Full Text searching to retrieve publications of interest:

  • Search for papers by a specific author, “Marti A”, or several authors +“Marti A” +“Avruch J”.
  • Search for papers on Breast Cancer but not if they contain Human or Fruit Fly terms, +“Breast Cancer” -(Human* “homo sapiens” “fruit fly” “Drosophila melanogaster”)
  • Search for papers on breast cancer or colon cancer, “breast cancer” “colon cancer”
  • Search for publications mentioning specific genes with regards to cell cycle, +(kss1 cln1 cln2) +“cell cycle”
  • Search for papers mentioning any of the STE family member of genes in Saccharomyces cerevisiae, +STE* +“Saccharomyces cerevisiae”
  • Search for publications discussing the sh2 domain but not discussing the ring domain, +“SH2 Domain” -“Ring Domain”
  • Search for papers on Chromatin Remodelling in Human, +“Chromatin Remodelling” +Human*

Coming Soon

  • Multiple Gene/Publications Searches - Coming Soon
 
advanced_search.txt · Last modified: 2012/01/23 18:48 (external edit)