org.bridgedb.bio.Organism improvement

[Igor Rodchenkov]

I suggest to extend the org.bridgedb.bio.Organism as follows:

1. add a new member and the constructor argument int taxonomyID and define values, e.g., mouse as MusMusculus("Mus musculus", "Mm", "Mouse", 10090);

2. add the method: public static Organism fromTaxonomyId(int taxid);

3. add the corresponding getter: public int taxonomyId();

Cheers,
--
Igor Rodchenkov

[Martijn van Iersel]

Hi Igor

That is an excellent suggestion, but what would you say of this
modification: instead of returning the taxonomyID as an int, we would
return it as an Xref with a suitable DataSource (for example
BioDataSource.TAXONOMY_ID, this still needs to be created of course).

Although Xref is a bit more complicated than just int, it would be
consistent with the rest of the API and would give us an option to go to
map to other classification systems in the future.

Anyhow, I think this is a good idea and I'd like to add it to the list
for BridgeDb 1.1.

Martijn

Igor Rodchenkov wrote:
> I suggest to extend the org.bridgedb.bio.Organism as follows:
>
>

> 1. add a new member and the constructor argument /int taxonomyID/ and

> define values, e.g., mouse as MusMusculus("Mus musculus", "Mm",
> "Mouse", 10090);
> 2. add the method: public static Organism fromTaxonomyId(int taxid);

> 3. add the corresponding getter: public /int taxonomyId();/
>
> Cheers,
> --
> Igor Rodchenkov
> --
> You received this message because you are subscribed to the Google
> Groups "bridgedb-discuss" group.
> To post to this group, send email to bridgedb...@googlegroups.com.
> To unsubscribe from this group, send email to
> bridgedb-discu...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/bridgedb-discuss?hl=en.

[IgorRodchenkov]

Great, you're absolutely right! Being in rush, I missed that taxonomy
is actually official data source :)

<datatype id="MIR:00000006" pattern="^\d+$">
<name>Taxonomy</name>
...

On Mar 25, 12:11 pm, Martijn van Iersel <mvanier...@gmail.com> wrote:
> Hi Igor
>
> That is an excellent suggestion, but what would you say of this
> modification: instead of returning the taxonomyID as an int, we would
> return it as an Xref with a suitable DataSource (for example
> BioDataSource.TAXONOMY_ID, this still needs to be created of course).
>
> Although Xref is a bit more complicated than just int, it would be
> consistent with the rest of the API and would give us an option to go to
> map to other classification systems in the future.
>
> Anyhow, I think this is a good idea and I'd like to add it to the list
> for BridgeDb 1.1.
>

[Egon Willighagen]

Igor, Martijn,

On Wednesday, 24 March 2010 13:55:45 UTC+1, Igor Rodchenkov wrote:

I suggest to extend the org.bridgedb.bio.Organism as follows:

 this is now implemented and will be part of the BridgeDb 1.2.2 release (being an API extension).

Egon