Re: [Obo-format] superfluous synonyms in PRO

[Erick A. <eri...@gm...>]

thanks for taking into account the changes.

w.r.t. the alphabetical ordering, I see your point in having the EXACT
synonyms at the top specially when you (and/or PRO users) are going to
inspect the OBO file directly, which I don't think would be the case
most of the time (I believe that OE or other applications will be a
most common interface)...moreover, there might be some cases, in which
users inspect the OBO file directly, and would find much more
"natural" to have the a synonym appearing next to a very "similarly
written" synonym, for instance:

synonym: "succinic dehydrogenase activity" BROAD [EC:1.3.99.1]
synonym: "succinyl dehydrogenase activity" EXACT [EC:1.3.99.1]

so that they could compare both term synonyms or simply note that
there exist another synonym which is written in very similarily... but
again, I think that would be interesting for the people manipulating
the OBO file directly...

maybe good compromise would be to have such alphabetical ordering by
type of synomyn so that all the EXACT synomyns would be alphabetically
sorted (and appearing at the top)...I think we agree that having an
ordering is advantegeous (while comparing two different releases of an
ontology file for instance)...  I am CC-ing the obo-format list to see
how to tackle that "minor" issue...

cheers,
Erick

On 19 August 2011 21:36, Darren Natale <da...@ge...> wrote:
> Done. The changes will appear in the next release. I think they came from a
> change to the UniProtKB name, where what was once a synonym became the
> preferred name. The switch was accounted for on the name line but not
> deleted from the synonym line.
>
> PRO OBO files are edited both manually and using OE, depending on the nature
> of the change and the ability of the curator to withstand the frustrations
> of OE ;)
>
> As for the alphabetical ordering, it can be done, but I wonder if it is best
> to do within the scope of each synonym type. That is, it makes sense to me
> to have all EXACT synonyms at the top...
>
> On 8/18/2011 9:45 AM, Erick Antezana wrote:
>>
>> Hi,
>>
>> the following synonyms should be deleted:
>>
>> <  synonym: "FK506-binding protein 10" EXACT []
>> <  synonym: "FK506-binding protein 11" EXACT []
>> <  synonym: "FK506-binding protein 14" EXACT []
>> <  synonym: "FK506-binding protein 2" EXACT []
>> <  synonym: "FK506-binding protein 3" EXACT []
>> <  synonym: "FK506-binding protein 4" EXACT []
>> <  synonym: "FK506-binding protein 5" EXACT []
>> <  synonym: "FK506-binding protein 6" EXACT []
>> <  synonym: "FK506-binding protein 7" EXACT []
>> <  synonym: "FK506-binding protein 8" EXACT []
>> <  synonym: "FK506-binding protein 9" EXACT []
>>
>> <  synonym: "cytochrome P450 17A1" EXACT []
>> <  synonym: "cytochrome P450 39A1" EXACT []
>> <  synonym: "cytochrome P450 46A1" EXACT []
>> <  synonym: "cytochrome P450 4F2" EXACT []
>> <  synonym: "cytochrome P450 4F3" EXACT []
>> <  synonym: "cytochrome P450 51A1" EXACT []
>> <  synonym: "cytochrome P450 7A1" EXACT []
>> <  synonym: "cytochrome P450 7B1" EXACT []
>> <  synonym: "cytochrome P450 8B1" EXACT []
>>
>> <  synonym: "chloride channel protein, skeletal muscle" EXACT []
>> <  synonym: "chloride channel protein 3" EXACT []
>> <  synonym: "chloride channel protein 4" EXACT []
>> <  synonym: "chloride channel protein 5" EXACT []
>> <  synonym: "chloride channel protein 6" EXACT []
>> <  synonym: "chloride channel protein 7" EXACT []
>>
>> <  synonym: "smad4" EXACT []
>> <  synonym: "smad1" EXACT []
>> <  synonym: "smad2" EXACT []
>> <  synonym: "smad3" EXACT []
>> <  synonym: "smad5" EXACT []
>> <  synonym: "smad6" EXACT []
>> <  synonym: "smad7" EXACT []
>> <  synonym: "smad9" EXACT []
>>
>> <  synonym: "tripartite motif-containing protein 11" EXACT []
>> <  synonym: "tripartite motif-containing protein 25" EXACT []
>> <  synonym: "tripartite motif-containing protein 32" EXACT []
>> <  synonym: "tripartite motif-containing protein 36" EXACT []
>>
>> Is the pro.obo file edited manually? with OBO-Edit? It would be great
>> if the term synonyms are sorted alphabetically...
>>
>> thanks,
>> Erick
>