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[go-helpdesk] Gene Ontology's Amigo software

Rebecca Foulger rfoulger at ebi.ac.uk
Tue Jun 14 01:53:57 PDT 2011


Dear Edge,

What query are you putting into GOOSE to try and return 
'metallochaperone activity ; GO:0016530'?

GO:0016530 is a direct child of 'molecular_function', and the term can 
be retrieved with a simple SQL search:

SELECT * FROM term WHERE name='metallochaperone activity';


Best,
Rebecca



On 14/06/2011 02:36, Edge Edge wrote:
> Dear Dr Rebecca,
>
> I found one problem between GO Online SQL Environment, the 
> http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003674_!_molecular_function 
> <http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003674_%21_molecular_function> 
> and 
> http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003674&session_id=1001amigo1307696671 
> <http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003674&session_id=1001amigo1307696671>
> At the link 
> http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003674_!_molecular_function 
> <http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003674_%21_molecular_function> 
> and 
> http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003674&session_id=1001amigo1307696671 
> <http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003674&session_id=1001amigo1307696671> , 
> it shown that "metallochaperone activity 
> <http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016530_%21_metallochaperone_activity>" 
> got produce some gene product.
> However, I can't find any GO IDs that corresponding to 
> "metallochaperone activity" by using GO Online SQL Environment :(
>
> Thanks for advice to solve my doubt about this issue.
> Thanks.
>
> best regards
> Edge
> Research Student
>
> ------------------------------------------------------------------------
> *From:* Rebecca Foulger <rfoulger at ebi.ac.uk>
> *To:* Edge Edge <edge_diners at yahoo.com>
> *Cc:* go-helpdesk at lists.stanford.edu
> *Sent:* Mon, June 13, 2011 8:41:11 PM
> *Subject:* Re: Gene Ontology's Amigo software
>
>
> Dear Edge,
>
> The ontologies contain terms that can be used to describe the 
> function, process, and component of a gene product from any organism.  
> The ontologies exist independent of any species, so you can not add a 
> species name to this SQL search.
>
> The association of an ontology term to a gene product (along with a 
> reference and evidence code) is known as an annotation. You can 
> download the annotations from different species here:
>
> http://www.geneontology.org/GO.downloads.annotations.shtml
>
> Thanks,
> Rebecca
>
>
>
> On 13/06/2011 12:05, Edge Edge wrote:
>> Dear Dr Rebecca,
>>
>> Really thanks a lot for your advice and explanation in detail :)
>> The links that you share with me are very useful and meaningful for 
>> my research.
>>
>> At the following link, http://www.berkeleybop.org/goose
>> I try the following info in order to extract out only the cell part 
>> that inside human by using the following content:
>>
>> SELECT DISTINCT descendant.acc, descendant.name 
>> <http://descendant.name>, descendant.term_type
>> FROM
>>  term
>>  INNER JOIN graph_path ON (term.id=graph_path.term1_id)
>>  INNER JOIN term AS descendant ON (descendant.id=graph_path.term2_id)
>> WHERE
>> species.common_name='human'      AND
>> term.name='cell part' AND distance <> 0 ;
>>
>> Unfortunately, it gives me the following error message:
>> Couldn't run, possibly bad SQL syntax.
>>
>> Is it I no need to specific the "species common_name" to human in 
>> order to filter out only human's cell part's GO ID?
>> Thanks again.
>>
>> best regards
>> Edge
>> Research Student
>> ------------------------------------------------------------------------
>> *From:* Rebecca Foulger <rfoulger at ebi.ac.uk>
>> *To:* Edge Edge <edge_diners at yahoo.com>; go-helpdesk at lists.stanford.edu
>> *Sent:* Mon, June 13, 2011 6:56:25 PM
>> *Subject:* Re: Gene Ontology's Amigo software
>>
>>
>> Dear Edge,
>>
>> GO is arranged as a directed acyclic graph. This means that a GO term 
>> may have more than one parent, and can therefore appear as a 
>> descendant of multiple parent GO terms.
>>
>> There is more information (and a diagram) on the structure of GO 
>> terms on the Gene Ontology website, that you may find helpful:
>> http://www.geneontology.org/GO.ontology.structure.shtml
>>
>> On the AmiGO page for 'synaptic vesicle lumen ; GO:0034592' 
>> (http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0034592), 
>> scroll down and click on the 'Graph View' tab. This will show you the 
>> parent and ancestor terms for GO:0034592, and you should be able to 
>> see why it appears as a descendant in your multiple searches.
>>
>> There is an introduction to GO, and more detail on GO content and 
>> structure in the 'Documentation' section of the GO webpage, that you 
>> may wish to read:
>> http://www.geneontology.org/GO.contents.doc.shtml
>>
>> Best wishes,
>> Rebecca
>>
>>
>>
>> On 13/06/2011 11:33, Edge Edge wrote:
>>> Dear Dr Rebecca,
>>>
>>> Is it normal that some of the GO ID appear more than one times in 
>>> different descendent?
>>> eg.
>>> GO:0034592 was found to be in:
>>> cell
>>> cell part
>>> membrane-enclosed lumen
>>> organelle
>>> organelle part
>>> synapse
>>> synapse part
>>>
>>> Thanks again for your advice.
>>>
>>> best regard
>>> Edge
>>> Research Student
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *From:* Rebecca Foulger <rfoulger at ebi.ac.uk>
>>> *To:* Edge Edge <edge_diners at yahoo.com>; 
>>> go-helpdesk at mailman.stanford.edu
>>> *Sent:* Mon, June 13, 2011 6:22:56 PM
>>> *Subject:* Gene Ontology's Amigo software
>>>
>>>
>>> Dear Edge,
>>>
>>> You could use the default Berkeley database: you get the same result 
>>> from all options (24 descendants of synapse) since they are database 
>>> mirrors (i.e are a second copy of a single database), and are all 
>>> updated.
>>>
>>> Best of luck in your studies,
>>> Rebecca
>>>
>>>
>>>
>>> On 13/06/2011 10:46, Edge Edge wrote:
>>>> Dear Dr Rebecca,
>>>>
>>>> Thanks a lot for your advice.
>>>> I'm trying it now :)
>>>> Regarding the following database:
>>>>
>>>>     * *Berkeley BOP *: Use the database mirror in Berkeley, CA Last
>>>>       updated on 2011-03 (assocdb
>>>>       <http://geneontology.org/GO.database.shtml#dbtypes>).
>>>>     * *EBI *: Use the database mirror in Cambridge, UK Last updated
>>>>       on 2011-06 (assocdb
>>>>       <http://geneontology.org/GO.database.shtml#dbtypes>).
>>>>     * *Princeton (lite) *: Use the database mirror in Princeton, NJ
>>>>       Last updated on 2011-06-04 (seqdb
>>>>       <http://geneontology.org/GO.database.shtml#dbtypes>).
>>>>     * *Princeton *: Use the database mirror in Princeton, NJ Last
>>>>       updated on 2011-06 (assocdb
>>>>       <http://geneontology.org/GO.database.shtml#dbtypes>).
>>>>     * *Berkeley BOP (lite) *: Use the database mirror in Berkeley,
>>>>       CA Last updated on 2011-06-04 (seqdb
>>>>       <http://geneontology.org/GO.database.shtml#dbtypes>).
>>>>
>>>>
>>>> Which db will you recommend in order to extract out all the GO IDs 
>>>> related to its 'parents'?
>>>> Which database is more comprehensive?
>>>> Thanks.
>>>>
>>>> best regards
>>>> Edge
>>>> Research Student
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* Rebecca Foulger <rfoulger at ebi.ac.uk>
>>>> *To:* Edge Edge <edge_diners at yahoo.com>
>>>> *Cc:* goa at ebi.ac.uk; go-helpdesk at mailman.stanford.edu
>>>> *Sent:* Mon, June 13, 2011 5:39:12 PM
>>>> *Subject:* Gene Ontology's Amigo software
>>>>
>>>>
>>>> Dear Edge,
>>>>
>>>> If you wish to know all descendants of a specific GO term (rather 
>>>> than just the immediate children), you could perform an SQL query 
>>>> using the GOOSE tool: http://www.berkeleybop.org/goose
>>>>
>>>> There are a number of template queries you can use here: 
>>>> http://wiki.geneontology.org/index.php/Example_Queries
>>>>
>>>> For example, if you wish to find all the descendants of the GO term 
>>>> 'synapse ; GO:0045202', you can use the query:
>>>>
>>>> SELECT DISTINCT descendant.acc, descendant.name 
>>>> <http://descendant.name>, descendant.term_type
>>>> FROM
>>>>  term
>>>>  INNER JOIN graph_path ON (term.id=graph_path.term1_id)
>>>>  INNER JOIN term AS descendant ON (descendant.id=graph_path.term2_id)
>>>> WHERE term.name='synapse' AND distance <> 0 ;
>>>>
>>>> I hope this is the information you are after. Please let us know if 
>>>> you require further help.
>>>>
>>>> With best wishes,
>>>> Rebecca
>>>>
>>>>
>>>>
>>>> On 13/06/2011 09:59, Edge Edge wrote:
>>>>> Dear Dr Rebecca,
>>>>>
>>>>> Thanks a lot for your reply and sharing :)
>>>>> I would like to know that what GO IDs is involved in each children 
>>>>> of Molucular Function, Cellular Component, and biological process.
>>>>> eg.
>>>>> At the following link for cellular compenent, 
>>>>> http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005575#term=children
>>>>> It shown that
>>>>>  All direct descendants (child terms) available for this GO term:
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0045202> 
>>>>> GO:0045202 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045202> synapse
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0019012> 
>>>>> GO:0019012 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0019012> virion
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0005623> 
>>>>> GO:0005623 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005623> cell
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0031974> 
>>>>> GO:0031974 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031974> 
>>>>> membrane-enclosed lumen
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0005576> 
>>>>> GO:0005576 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005576> 
>>>>> extracellular region
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0043226> 
>>>>> GO:0043226 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0043226> 
>>>>> organelle
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0055044> 
>>>>> GO:0055044 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0055044> 
>>>>> symplast
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0032991> 
>>>>> GO:0032991 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0032991> 
>>>>> macromolecular complex
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0044421> 
>>>>> GO:0044421 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044421> 
>>>>> extracellular region part
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0044422> 
>>>>> GO:0044422 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044422> 
>>>>> organelle part
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0044423> 
>>>>> GO:0044423 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044423> 
>>>>> virion part
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0044456> 
>>>>> GO:0044456 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044456> 
>>>>> synapse part
>>>>> Is a 	// <http://www.ebi.ac.uk/QuickGO/Selection?id=GO:0044464> 
>>>>> GO:0044464 <http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044464> cell 
>>>>> part
>>>>>
>>>>>
>>>>> I would like to know that what GO IDs are in the synapse, virion, 
>>>>> cell, membrane-enclosed lumen, etc
>>>>>
>>>>> I wanna to know the GO IDs that corresponding to the descendants 
>>>>> of Molecular Function, Cellular Component, and Biological Process.
>>>>>
>>>>> Really appreciate for your help and advice.
>>>>>
>>>>> best regards
>>>>> Edge
>>>>> Research Student
>>>>> ------------------------------------------------------------------------
>>>>> *From:* Rebecca Foulger <rfoulger at ebi.ac.uk>
>>>>> *To:* edge_diners at yahoo.com
>>>>> *Cc:* go-helpdesk at mailman.stanford.edu
>>>>> *Sent:* Mon, June 13, 2011 4:49:06 PM
>>>>> *Subject:* Gene Ontology's Amigo software
>>>>>
>>>>>
>>>>> Dear Edge,
>>>>>
>>>>> Thank you for contacting GO help.
>>>>>
>>>>> A tab delimited file that contains the term ID, term name, and 
>>>>> term aspect (molecular function (F), biological process (P), 
>>>>> cellular component (C)) can be found here:
>>>>> http://www.geneontology.org/doc/GO.terms_alt_ids
>>>>>
>>>>> Additionally, The QuickGO tool provides a list of all current 
>>>>> (non-obsolete) GO IDs and term names in each of biological 
>>>>> process, molecular function, and cellular component:
>>>>> http://www.ebi.ac.uk/QuickGO/GSearch?format=termlist&what=Process 
>>>>> <http://www.ebi.ac.uk/QuickGO/GSearch?format=termlist&what=Process>
>>>>> http://www.ebi.ac.uk/QuickGO/GSearch?format=termlist&what=Function 
>>>>> <http://www.ebi.ac.uk/QuickGO/GSearch?format=termlist&what=Function>
>>>>> http://www.ebi.ac.uk/QuickGO/GSearch?format=termlist&what=Component <http://www.ebi.ac.uk/QuickGO/GSearch?format=termlist&what=Component>
>>>>>
>>>>> Please let us know if you need further clarification.
>>>>>
>>>>> With best wishes,
>>>>> Rebecca (GO help desk).
>>>>>
>>>>>>
>>>>>> Subject:
>>>>>> Gene Ontology's Amigo software
>>>>>> From:
>>>>>> Edge Edge <edge_diners at yahoo.com>
>>>>>> Date:
>>>>>> Sat, 11 Jun 2011 15:18:17 -0700 (PDT)
>>>>>>
>>>>>> To:
>>>>>> go-helpdesk at lists.stanford.edu
>>>>>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Can I know that how to get the GO that involved in each children 
>>>>>> of biological process, molecular function, cellular component?
>>>>>>
>>>>>> Biological Process:
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008150&session_id=1001amigo1307696671 
>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008150&session_id=1001amigo1307696671>
>>>>>> Molecular Function:
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0005575&session_id=1001amigo1307696671 
>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0005575&session_id=1001amigo1307696671>
>>>>>> Cellular Component:
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003674&session_id=1001amigo1307696671 
>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003674&session_id=1001amigo1307696671>
>>>>>>
>>>>>> eg.
>>>>>> I plan to know the "children" of Biological Process, Molecular 
>>>>>> Function, Cellular Component.
>>>>>> From the following link, 
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008150&session_id=1001amigo1307696671 
>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008150&session_id=1001amigo1307696671>
>>>>>> Biological process corresponding to 383420 gene product.
>>>>>> 5059 gene product corresponding to biological adhesion, 80092 
>>>>>> gene product corresponding to biological regulation, etc.
>>>>>> I wanna to know the GO ID that involved in biological adhesion, 
>>>>>> biological regulation, etc.
>>>>>>
>>>>>> I just wanna to know what GO ID is involved in each 'children' of 
>>>>>> Biological Process, Molecular Function, Cellular Component.
>>>>>>
>>>>>> Thanks for advice and sharing.
>>>>>>
>>>>>> best regards
>>>>>> Edge
>>>>>> Research Student
>>>>>
>>>>>
>>>>> -- 
>>>>> Dr Rebecca Foulger
>>>>> GO Editorial Office
>>>>> EMBL-EBI
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridgeshire, UK
>>>>> CB10 1SD
>>>>>
>>>>> p: +44 1223 492523
>>>>> f: +44 1223 494468
>>>>
>>>>
>>>> -- 
>>>> Dr Rebecca Foulger
>>>> GO Editorial Office
>>>> EMBL-EBI
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridgeshire, UK
>>>> CB10 1SD
>>>>
>>>> p: +44 1223 492523
>>>> f: +44 1223 494468
>>>
>>>
>>> -- 
>>> Dr Rebecca Foulger
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492523
>>> f: +44 1223 494468
>>
>>
>> -- 
>> Dr Rebecca Foulger
>> GO Editorial Office
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridgeshire, UK
>> CB10 1SD
>>
>> p: +44 1223 492523
>> f: +44 1223 494468
>
>
> -- 
> Dr Rebecca Foulger
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492523
> f: +44 1223 494468


-- 
Dr Rebecca Foulger
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492523
f: +44 1223 494468

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