AmiGO help Gene Product Search Results: Difference between revisions

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The "Gene Product Search Results" page provides a list of gene products matching a 'gene symbols or names'  search.
==Page contents==
This search is matching (where assigned) the database identifier, the primary gene product name, systematic identifier or any synonyms used to refer to the gene product (I think what I have written here is wrong see comments below).
<P>The "Gene Product Search Results" page provides a list of 'gene products names' matching a 'gene symbols or names'  search.
This search is matching the primary gene product name, systematic identifier or any synonyms used to refer to the gene product (I think what I have written here is wrong see comments below).  
</P>


The result is a list of the 'gene product names', and the 'organism'.
==Page navigation==
<P>


Clicking on a 'gene product name' takes you to the "Gene Product Details" page. This page provides further information about the individual search hits including:
Clicking on a 'gene product name' takes you to the "Gene Product Details" page. This page provides further information about the individual search results. This includes:
#Gene product information with database cross-references
#Access to the protein sequence
#All of the associations for the gene product


If you would like to filter your "Gene Product Search Results" results on 'organism' or 'data source (database)' use the 'Filter' option on the menu bar.
*Gene product information with database cross-references
*Access to the protein sequence
*All of the gene ontology associations (annotations) for the gene product


If you would like to search other fields (i.e. ***??? I'm not sure exactly what is being searched by default? see below) use the 'Advanced Query' option on the menu bar.
==Filtering the results==


Notes:
*1. This documentation will need to be updated when the search results relevence is implemented


Gene product searches can be filtered by the species and the database from which the gene product comes.  You can also filter gene products by their association data, using the ontology and evidence code filters. These will limit your results to those gene products associated to terms in the selected ontology (or ontologies) that are annotated with the chosen evidence code(s). All the filters allow you to pick one or more of the options, and will default to 'all' if no options are selected.


# explain how to filter the search results, and what the filters are acting on (i.e. species and db filters are based on info about the gene products, but ontology and ev code filters are based on the terms associated with the gene product). Also say that you can select multiple options in each set
The 'Filter' option is avaiable from the menu bar


comment from Val I can't think of any reason why you would want to filter the products based on evidence code or ontology. I would only use these options when looking at annotations to a terms.  
==Searching additional fields==
 
By default the fieds ***** are searched. To search additional fields (list *****)  use the 'Advanced Query' option on the menu bar.
</P>
 
==Notes (to be removed)==
<P>
#This documentation will need to be updated when the search results relevence is implemented
 
 
# comment from Val I can't think of any reason why you would want to filter the products based on evidence code or ontology. I would only use these options when looking at annotations to a terms.  
I don't really use the product search anyway, as if I know the gene name I would come via the organism database, but this is really only a way to locate (usually) a single gene of interest (you can't use it to identify related genes because names are so inconsitent). The organism/database filters are useful here if you get 100's of results and you are only interested in one organism but I don't think the other filters aren't very menaingful in this context.
I don't really use the product search anyway, as if I know the gene name I would come via the organism database, but this is really only a way to locate (usually) a single gene of interest (you can't use it to identify related genes because names are so inconsitent). The organism/database filters are useful here if you get 100's of results and you are only interested in one organism but I don't think the other filters aren't very menaingful in this context.


comment from Val/ inconsistency
#comment from Val/ inconsistency
gene symbols or names are bing searched (from front page)
gene symbols or names are bing searched (from front page)
for advanced search "Name and symbol" is checked already (which field is this?)...but, gene symbol isn't checked?
for advanced search "Name and symbol" is checked already (which field is this?)...but, gene symbol isn't checked?
# I'm still not sure why you would want to batch download protein fasta sequences from this query....they generally won 't be related results...any comments?
[[Category:AmiGO working group]]

Latest revision as of 13:26, 5 December 2006

Page contents

The "Gene Product Search Results" page provides a list of 'gene products names' matching a 'gene symbols or names' search. This search is matching the primary gene product name, systematic identifier or any synonyms used to refer to the gene product (I think what I have written here is wrong see comments below).

Page navigation

Clicking on a 'gene product name' takes you to the "Gene Product Details" page. This page provides further information about the individual search results. This includes:

  • Gene product information with database cross-references
  • Access to the protein sequence
  • All of the gene ontology associations (annotations) for the gene product

Filtering the results

Gene product searches can be filtered by the species and the database from which the gene product comes. You can also filter gene products by their association data, using the ontology and evidence code filters. These will limit your results to those gene products associated to terms in the selected ontology (or ontologies) that are annotated with the chosen evidence code(s). All the filters allow you to pick one or more of the options, and will default to 'all' if no options are selected.

The 'Filter' option is avaiable from the menu bar

Searching additional fields

By default the fieds ***** are searched. To search additional fields (list *****) use the 'Advanced Query' option on the menu bar.

Notes (to be removed)

  1. This documentation will need to be updated when the search results relevence is implemented
  1. comment from Val I can't think of any reason why you would want to filter the products based on evidence code or ontology. I would only use these options when looking at annotations to a terms.

I don't really use the product search anyway, as if I know the gene name I would come via the organism database, but this is really only a way to locate (usually) a single gene of interest (you can't use it to identify related genes because names are so inconsitent). The organism/database filters are useful here if you get 100's of results and you are only interested in one organism but I don't think the other filters aren't very menaingful in this context.

  1. comment from Val/ inconsistency

gene symbols or names are bing searched (from front page) for advanced search "Name and symbol" is checked already (which field is this?)...but, gene symbol isn't checked?

  1. I'm still not sure why you would want to batch download protein fasta sequences from this query....they generally won 't be related results...any comments?