[Geneontology-gowebsite] [ geneontology-GO website-901210 ] document dbxrefs

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GO website item #901210, was opened at 2004-02-20 17:17
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Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Jennifer I Clark (jenclark)
Assigned to: Jennifer I Clark (jenclark)
Summary: document dbxrefs

Initial Comment:
I am writing documentation for the dbxrefs. Here are midori's 
comments on the first draft and the drafts are below.


Hi,

I've finally got round to looking at these; good start.

First, a couple of things to clarify:

- 'Dbxref' isn't an acronym; it's an abbreviation for 'database
cross-reference'. Also, strictly speaking, the reference needn't be to 
an
external database (the 'x' is for cross, not external), though most of
them are.

- We don't usually use 'general dbxref' to mean 'analog dbxref'. It's
probably closest in meaning to plain 'dbxref', which is generic and 
can be
thought of as a superclass (parent) of the other types:

 dbxref
  %definition dbxref
  %analog dbxref
  %anatomy dbxref (not used yet, but built into the mySQL db and 
DAG-Edit)
  ... etc.

It would be OK to say that the 'definition_reference' field in the old
flat file is equivalent to 'definition dbxref'.



>> I have just been tying my brain in knots trying to explain 
>> dbxrefs in the faq-o-matic. I came up with these two entries:
>> 
>> http://www.ebi.ac.uk/faq/cgi-bin/go?
auth=ck4f8613bb238ce7fac7b05983a8b58302&editCmds=hide&file=
122&keywords=login&showAttributions=hide&showLastModified=hid
e&showModerator=hide
>> GO Faq-O-Matic : GO content : What is the difference between 
>> a dbxref and a general dbxref?


For this one, more than two kinds of dbxref are allowed in GO, even 
though
only two are really used at present.

It would be nice to explain more what we mean by 'analogous' in 
the
context of analog dbxrefs. there might be some useful material in 
the
external2go directory README.



>> http://www.ebi.ac.uk/faq/cgi-bin/go?
auth=ck4f8613bb238ce7fac7b05983a8b58302&editCmds=hide&file=
123&keywords=login&showAttributions=hide&showLastModified=hid
e&showModerator=hide
>> GO Faq-O-Matic : GO content : Can a general dbxref be 
>> inferred from a dbxref and vice versa?


A better overall approach might be to have a FAQ entry on dbxrefs
generally, such as 'what kinds of dbxrefs does GO use, and what do 
they
mean?' The answer could include a paragraph on the distinction 
between
analog and definition dbxrefs.

At the moment I don't think we need an FAQ entry on inferring 
dbxrefs,
especially if it's worded exactly the same thing as Chris' email -- it's
literally not a frequently asked question, as it's only come up once. 
What
might be more useful is a specific FAQ entry like 'Why are the 
definition
and analog dbxrefs sometimes the same? Isn't that redundant?' 
along with
an answer explaining what the two different dbxref types mean and 
why
they're not redundant.

cheers,
m










What is the difference between a 'dbxref' and a 'general dbxref'?
The acronym 'dbxref' stands for a REFerence to an eXternal 
DataBase.

GO uses two different kinds of dbxref:
     1) 'dbxref' or 'definition dbxref'
          - cites a source that was used in writing the definition of a 
GO term.
     2) 'general dbxref' or 'analog dbxref'
          - indicates that an entry in an external database is analogous 
to the GO term.

For more information about dbxrefs please see the GO Editorial 
Style Guide








Can a general dbxref be inferred from a dbxref and vice versa?

dbxrefs and general dbxrefs can be the same, but cannot be 
inferred from one another.

     1) 'dbxref' or 'definition dbxref'
          - cites a source that was used in writing the definition of a 
GO term.
     2) 'general dbxref' or 'analog dbxref'
          - indicates that an entry in an external database is analogous 
to the GO term.

For example:
pectin lyase activity ; GO:0047490
definition: Catalysis of the eliminative cleavage of (14)-a-D-
galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-
O-methyl-a-D-galact-4-enuronosyl groups at their nonreducing ends.
dbxref = EC:4.2.2.10
general dbxref = EC:4.2.2.10

'pectin lyase activity ; GO:0047490' is the GO term that represents 
the catalysis of the pectin lyase reaction, and 'EC:4.2.2.10' is the 
Enzyme Commission database entry for the enzyme pectin lyase. In 
the case of this term both the dbxref and the general dbxref are 
EC:4.2.2.10.

The 'dbxref' or 'definition dbxref' is EC:4.2.2.10 and this shows that 
the definition of the GO term was written with the help of 
information in the EC:4.2.2.10 entry in the Enzyme Commission 
database. In addition to this, the 'general dbxref' or 'analog dbxref' 
is also EC:4.2.2.10 and this shows that the concept represented by 
the GO term 'pectin lyase activity ; GO:0047490' is analogous to the 
concept represented by the 'pectin lyase ; EC:4.2.2.10' entry in the 
enzyme commission database.

This term has the same items as dbxref and general dbxref, but the 
presence of one does not automatically imply the other since they 
are there for different reasons.

For more information about dbxrefs please see the GO Editorial 
Style Guide


Jen

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