Feedback Submission from the Live Site

[Pankaj Jaiswal]

Dear Jeff,

These definitions come from the Gene Ontology Consortium's database. I 
communicated with them following your feedback. For the moment the problems have 
been fixed, by including the full name of the molecule in addition to the symbol 
(e.g. Co2). In future, we hope to establish some kind of equivalency tables in 
the database, so that depending on the query, either by symbol/name, it should 
return the same results, despite the differences in synonyms/definitions. 
Following is the discussion on the Gene Ontology's curator request tracker. Your 
inputs are greatly appreciated.

As far as fixing the problems on Gramene, the new updates in our Ontology 
Database will be available in our next database release in December/January.

We are sorry for the inconveniences at this moment, and look forward to your 
help in improving the information provided by Gramene.

Sincerely,

Pankaj
gramene at gramene.org



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Curator requests item #827547, was opened at 2003-10-21 14:35
Message generated for change (Comment added) made by girlwithglasses
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=827547&group_id=36855

Category: Other term-related request
Group: GO
Status: Open
Resolution: None
Priority: 5
Submitted By: Pankaj Jaiswal (pj37)
Assigned to: Amelia Ireland (girlwithglasses)
Summary: Use of CO2 Vs carbon dioxide

Initial Comment:
Hi,

We just got a feedback on Gramene site from Jeff
Blanchard concerning use of molecule name/symbol. I
think his point is a genuine one. We should use both
the full name and the symbol for every molecule.
Otherwise users will continue to face the problems
cited by him. Recently, I asked the same for terms
using ACP (acyl carrier protein) in term name.

Suggestion: We should use both the full name and the
symbol for every molecule mentioned in ontology &
definition files. Atleast in the synonyms and definitions.

Pankaj

Jeff's feedback is as follows:

Feedback:
refer_to_url:
http://www.gramene.org/perl/ontology/search?query=co2

comments: In some enzyme reactions you use the CO2 and
others you use carbon dioxide.  Searching does not pick
up both

name: Jeff Blanchard

email: blanchard at microbio.umass.edu

organization: University of Massachusetts

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 >>Comment By: Amelia Ireland (girlwithglasses)

Date: 2003-10-22 10:09

Message:
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I have added synonyms for the terms with carbon dioxide in the
name. I think it would be better to have some rules like "if it's an
enzyme reaction, use the chemical symbol; if not, use the full
name in the def". For the time being, I've changed all the
chemical reactions to say "CO2" and the other instances say
"carbon dioxide (CO2)".

A better long term solution would be to have intelligent search
engines which had a table of equivalencies and would search for
both "CO2" and "carbon dioxide" if either of those terms were
entered as a search string.

I thought of a few other common chemicals that should be
checked: dioxygen vs O2; water vs H2O; H2O2; diphosphate vs
pyrophosphate. Any others?

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Comment By: Pankaj Jaiswal (pj37)
Date: 2003-10-21 15:32

Message:
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I agree with you that this excise will be quite extensive,
and there should be a better way of dealing with it. May be
something in the db, where, all such mappings are stored for
providing efficiency. This may help in retrieving the same
results, whether we use symbol or full name/synonym. This
structure will not put a strain on our existing term
names/definitions/synonyms.

Pankaj

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Comment By: Amelia Ireland (girlwithglasses)
Date: 2003-10-21 14:52

Message:
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Hi Pankaj,

I think that using the full name and the symbol for *every*
chemical that appears in the ontologies is going a bit far - it
would be silly to put in the chemical formula for compounds like
chondroitin sulfate or even some of the saccharides. I'm happy to
add chemical formulae as synonyms but in the defs file, I would
prefer to have a standard way of referring to a chemical, either
always using a specific name or the chemical formula. With well
known compounds like carbon dioxide, I would have thought that
"CO2" would be fine.

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feedback_submission at www.gramene.org wrote:
>     *** Feedback from the Live Site ***
> 
> refer_to_url: http://www.gramene.org/perl/ontology/search?query=co2
> 
> comments: In some enzyme reactions you use the CO2 and others you use carbon dioxide.  Searching does not pick up both
> 
> name: Jeff Blanchard
> 
> email: blanchard at microbio.umass.edu
> 
> organization: University of Massachusetts
> 
> send_feedback: Send your feedback
> 
>