2. Getting started
3. Genome Browser
4. Sequence Viewer
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3-5. Filter by Keywords

If there are too many genes or candidates in the specified interval of area 6, you can utilize the "filter by keyword" function to reduce their number.

 

3-5-1. Filter by a word or phrase

  1. Enter the query words in the text box on the bottom of area 3.
    How to create a query for OmicBrowse is the same as PosMed and explained here.

  2. Hit to execute the search.



  3. Only the entries including your keywords will be shown in area 6.




  4. The keywords filter remains unless you intentionally execute another filtering. To clear the filter, do another filtering with no words. ( erases all the words typed in the text box. )




3-5-2. Filter by an ontology term

Ontology filtering allows you to see the entries related to a certain ontology term. A specialized ontology filter browser is available to choose ontology term(s) since it is necessary to enter their IDs.

  1. Select "MP" from the keyword pull-down menu on area 3 to open the ontology filter display in Main zone.
    *MP;Mammalian Phenotype for mouse genes, GO;Gene Ontology for human and mouse genes,
    PO; Plant Ontology (Plant Structure) for Arabidopsis genes



  2. The Ontology hierarchy is displayed. Click on a tree node to explore the tree. The "+" on the right or the circle on the left of a term indicates that it has subclasses.

  3. You can do a keyword search from the "Find" text box to find a term of interest. Click the execute button to display the ontologies including the keyword. ( e.g. cardiovascular )

  4. The details of an ontology term can be checked by pressing "Details" button. The corresponding ontology page opens in another browser window.

  5. To choose an ontology term for the ontology filter, click on the ontology term, then press the "Add ontology" button. The ontology id of the selected term will be displayed in the lower box. Click the "Remove" button to cancel your selections in the lower box, or the "OK" button to finish ontology term selection. To cancel and close the ontology filter display , click the "Cancel" button.

  6. The chosen ontology terms are automatically transferred to the "Filter by keyword" box, and the filtering is executed. The entries associated with one of the selected ontology terms are displayed in area 6.







  7. The ontology filter works the same way as the "Filter by keyword" function; it remains even after you change the coordinates on the chromosome. To clear the filter, do another keyword search with no words. ( erases all the words typed in the text box. )

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