What Do I Get?

There are 2 types of cards in GeneCards:

• Minicard - The search results are first displayed closed, showing the gene symbol, description, category, GCID and a relevance score. To open the minicard click on the plus to the left of the gene symbol on the appropriate minicard. All fields of the GeneCard in which your search term(s) were found will be displayed. All of the keywords entered in your search, including any variants found due to stemming, will be highlighted in the minicards.
  
  The minicard list is sorted by relevance (determined by the relevance scoring method).

• GeneCard - A detailed display of all the data concerning a specific gene, including relevant links to other important websites.

Superscripts indicating sources for information throughout the card link directly to the information, from a given sources site, on the specific gene you are viewing.

More on: The GeneCard

Simple Search

1. Enter an expression into the search field on the GeneCards homepage and
   choose one of these to search by:
   
   
   • Symbol only - Brings up the GeneCard for the specified symbol. This is done by selecting the Symbol only button and typing the requested gene symbol in the search box.
      
   • Symbol/Alias - Searches the database for a gene name, or its alias. This is done by selecting the Symbol/alias button and typing the requested symbol or alias for the gene in the search box.
      
   • GCid - the Id given to the gene by GeneCards (determined by the GeneLoc Algorithm).
     A gene can be searched by its GCid by selecting the GCid button and typing the requested Id in the search box.
      
   • External Id - A gene can also be searched by an External Id (accessions from HGNC, EntrezGene, UniProt, and Ensembl). This is done by selecting the External Id button and typing the requested Id in the search box.
      
   • Keywords - Searches the database in a full free text search. This is done by selecting the (default) keywords button and typing any kind of text relevant to the search in the search box.

   * A use of space in the search string automatically results in a Keywords Search
     (see Search Examples for more on multiword searches).
   * The GeneCards search is case insensitive.
   * All variants of your search terms that are found due to stemming will be highlighted in the search results.
   * The * character serves as a wildcard, which matches all possible character strings,
      Note that this is different from stemming, which matches strings that are considered to be related to the specified keyword.
   * When search terms are encapsulated with double quotes, exact match is made. Exact match enables you to determine the distance between two or more terms. The exact match ignores trivial words, like "a","and","then" etc. For example, searching "heart brain" would also retrieve the string "heart and a brain".
   You can also use Tilde (~) to determine the distance between the terms (excluding trivial words), i.e. :
   "heart brain"~50, would search for heart brain in the distance of maximum 50 words, excluding trivial words.

Advanced Search

Advanced search enables you to browse GeneCards for more specific results. A broader variety of search options is offered in order to focus the search.

There are two ways to use the Advanced search:

1. Click the Advanced Search link next to the search box at the GeneCards homepage - a new page with more search options appears.
   
   First choose which type of search you wish to perform:

   • Keywords - only genes that contain the search term in the specified sections will be displayed.

   • Symbol/Alias - only genes with the symbols/aliases typed in this box will be displayed.

   • Symbol Only - only genes with the symbols typed in this box will be displayed.

   If you are performing a keywords search you will need to choose which section of the GeneCard you would like to search in (e.g. location, summaries, pathways). This option is located in the menu between the type of search dropdown and the search box.
   
   Now type the search string in the search field. If you wish to search in more than one field Click on the + button next to the search box to get another field to add more terms to your search, or to search in multiple fields within a GeneCard for your search terms. Having more than one term in separate fields will search for your first term AND your second term and so on.

2. Perform a simple search, and improve the search after getting the results - click on the Show Advanced Search link in the top left corner above the search results. The advanced search will appear on the top of the page containing your search results.
   
   To further refine your results, you can choose a specific category of genes to look for (e.g. protein-coding, genetic loci, RNA genes), the source of the gene symbol (HGNC, EntrezGene and/or RNA genes) and to only return genes within a specific range of GIFtS values (all, high, medium or low).

   Try it! Refine this simple search example

See Search Examples for more on advanced searches.

Search Examples:

I.   Simple Search:

Search String:	Matching Words:	Search Description:
brca1	brca1, BRCA1	Exact word match (case insensitive).*
x84746	x84746	GenBank accession number

* A Keyword Search would result in a list of MiniCards if there is more than on gene that matches your search. If there is only one gene that matches your search the GeneCard will be displayed.
  A Symbol Only Search would result in the GeneCard itself right away!

II.   Wild Card Search (*):

This type of search will usually give out a large number of results.

Search String:	Matching Words:	Search Description:
live	live, lives, liver, lively, lived, living	Any object that begins with the string "live" or some derivative of "live" determined by the search engines stemming algorithm. A search for live* will return the same results.

* In version 3.0 the search string "live" is equivalent to "live*".
* Please note that wild card searches using preceding asterisks, for example *gammaglob*, are not supported in version 3.0 searches.

III.   Multiword Search:

Search String:	Matching Words:	Search Description:
obesity diabetes	diabetes,with hyperproinsulinemia... for obesity in association with Ig action profile in obese non-diabetic subjects.	Search behaves as if an AND was used(see the AND search below!)
obesity AND diabetes	preponderance of insulin resistance, diabetes mellitus ... genetic predisposition to obesity action profile in obese non-diabetic subjects.	All strings or variants of strings must exist in the GeneCard.
obesity OR diabetes	obesity, obese, diabetes, diabetic	At least one of the strings or its variants must exist in the GeneCard (notice the difference from the AND search!)
(neurodegenerative OR senile) AND Alzheimer	...senile dementia of the Alzheimer type: relation with the cognitive state and with quantitative studies of senile plaques...	Finds all instances of either neurodegenerative AND alzheimer or senile AND alzheimer.
"macular degeneration"	associated with age-related macular degeneration type 4...	Exact phrase search. All words in the order that they are entered must be in the GeneCard.

* In the search (neurodegenerative or senile) and Alzheimer the use of parentheses is important. Without parentheses the AND takes precedence in this search so that the results returned are for the neurodegenerative or senile AND alzheimer.

IV.   Advanced Search:

Example 1: Search by section. Finds all instances where the word angiogenesis is found in summaries and the word cancer is found anywhere in the entry.
Example 2: Search within the disorders section for alzheimers or dementia or within the literature section for those same keywords. Also, choose to view only those genes with a high GIFtS score.

Relevance Scores

The search platform used is SOLR, based on Apache's Lucene text search API.
When a term is searched Lucene returns a set of scored hits.
A "hit" represents a document (in our case a GeneCard), whose fields (actual annotations) were previously indexed by Lucene.
The scoring is calculated by a Lucene defined algorithm: (see Lucene's Similarity class)

score(q,d)   =   coord(q,d)  ·  queryNorm(q)  ·	∑	( tf(t in d)  ·  idf(t)  ·  t.getBoost() ·  norm(t,d) )
	t in q

the factors in this formula are : (see Solr Relevancy FAQ)

• tf stands for term frequency - the more times a search term appears in a document, the higher the score
• idf stands for inverse document frequency - matches on rarer terms count more than matches on common terms
• coord is the coordination factor - if there are multiple terms in a query, the more terms that match, the higher the score
• lengthNorm - matches on a smaller field score higher than matches on a larger field
• index-time boost - if a boost was specified for a document at index time, scores for searches that match that document will be boosted.
• query clause boost - a user may explicitly boost the contribution of one part of a query over another.

Each field can be "boosted" - this means increase the weight of a specific field at search time.
In GeneCards, we "boost" a few fields:

• The Symbol
• Aliases and Descriptions
• Accessions for the major bioinformatics databases (NCBI, Ensembl, SwissProt)
• Gene Summaries
• Disorders

You can read more about Lucene's scoring mechanism here: Apache Lucene - Scoring