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  • Keyword Search
    • Familiar simple search that can be used to find names, symbols, identifiers.
  • Template Searches
    • Pre-defined searches.
  • Query Builder
    • Alter pre-defined searches or build searches of your own.

Templates are pre-defined searches. A subset of templates can be found in the middle section of the ZebrafishMine home page, divided into categories (see previous page). You can get a complete list of templates by clicking the "Templates" tab.
Do a template search:

  1. Click on the "Templates" tab at the top of the home page


  1. Go to the full list of templates by clicking on the "Templates" tab on the home page.
  2. Find and open the "Gene  Morpholino + MO sequence" template.
  3. Select the checkbox next to "constrain to be IN" saved Gene list and select "Hedgehog Signaling Pathway" from the menu of lists.
  4. Click on "Show Results" to run the search.


  • You can exclude a list of genes by selecting "constrain to be NOT IN".
  • To find all expression, replace "heart" with "*".

2. Template: Find antibodies that detect subcellular structures
How many antibodies in ZFIN detect protein expression the ciliary basal body?
(Hints: Enter the term "ciliary basal body" into the "Ontology Term > Name (E)" box. Make sure that the antibody symbol is "*").
Additional exploration tips for this template:

  • To get a list of all ZFIN antibodies that detect subcellular structures, change the "Antibody > Symbol" field from cc2d2a to the wildcard *.

3. Template: Find a gene annotated to a GO term and expressed in structure
How many genes involved in kidney development are expressed in the pronephros?
(Hints: The default template returns genes annotated with the "fibroblast growth factor receptor binding" GO term and expressed in the "anterior macula". Alter the defaults to find genes that are involved in "kidney development" and expressed in the "pronephros".)
Additional exploration tips for this template:

  • Since this query returns all the "children" of each term, the query will be very slow for higher level ontology terms. The use of a very general term like "protein kinase" is not recommended.