[BioMart Users] Quick thoughts on 0.8

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[BioMart Users] Quick thoughts on 0.8

Bob MacCallum
Hi BioMarters,  (BioMartyrs?)

I looked at the cancer genome biomart and it looks really great and
the text field/menu completion stuff works great.  The three levels of
interface complexity are very nice.  Overall, it's great to see things
like "dataset" and "database" eliminated from the end user's
experience.

The martreport pages are a useful addition but I wondered why on the
icgc site the gene reports don't have any links to Ensembl, for
example.  Are such link-outs still configurable in 0.8+?  A site (like
us) with its own genome browser would want to be careful not to
confuse the user with two subtly different gene report pages
(hopefully showing the same information though!).  Maybe a reasonably
prominent "View this information in the source database
(Database_name)" link/button or similar would work?

I also feel with the advanced interface that a "count" button is
lacking, but that is not dampening my enthusiasm about having this on
VectorBase sometime this year I hope.  Congratulations on a great job,
and sorry if I missed any formal feedback questionnaires or focus
groups.

cheers,
Bob.
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] Quick thoughts on 0.8

Arek Kasprzyk-2

Hi Bob,
great to know you like the new version :)


The gene report page on dcc.icgc.org is a compilation of several databases federated on the fly. However ensembl provides a backbone of data integration.
The links are configurable and it is a good point that we should provide a link to the source somewhere.

The 'count' button is definitely planned but this time it is a little bit more tricky with the advanced federation features so we may need more time to implement it properly.


a




Arek Kasprzyk
Director, Bioinformatics Operations and Principal Investigator

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:       416-673-8559
Toll-free:           1-866-678-6427
www.oicr.on.ca



Administrative Assistant: [hidden email]



This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Bob MacCallum [[hidden email]]
Sent: Monday, January 31, 2011 8:01 AM
To: [hidden email]
Subject: [BioMart Users] Quick thoughts on 0.8

Hi BioMarters,  (BioMartyrs?)

I looked at the cancer genome biomart and it looks really great and
the text field/menu completion stuff works great.  The three levels of
interface complexity are very nice.  Overall, it's great to see things
like "dataset" and "database" eliminated from the end user's
experience.

The martreport pages are a useful addition but I wondered why on the
icgc site the gene reports don't have any links to Ensembl, for
example.  Are such link-outs still configurable in 0.8+?  A site (like
us) with its own genome browser would want to be careful not to
confuse the user with two subtly different gene report pages
(hopefully showing the same information though!).  Maybe a reasonably
prominent "View this information in the source database
(Database_name)" link/button or similar would work?

I also feel with the advanced interface that a "count" button is
lacking, but that is not dampening my enthusiasm about having this on
VectorBase sometime this year I hope.  Congratulations on a great job,
and sorry if I missed any formal feedback questionnaires or focus
groups.

cheers,
Bob.
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] Quick thoughts on 0.8

Bob MacCallum
Hi Arek,

Thanks for the info. 'Count' is not a dealbreaker!

Assuming that DAS support (location and (gene) symbol based?) will be
coming at some point, 0.8 with its martreport pages will be a likely
successor our home-brewed GDAV annotation server and DAS source, and
maybe some other ad-hoc things we host at VectorBase.

cheers,
Bob.

On Mon, Jan 31, 2011 at 2:26 PM, Arek Kasprzyk <[hidden email]> wrote:

>
> Hi Bob,
> great to know you like the new version :)
>
>
> The gene report page on dcc.icgc.org is a compilation of several databases federated on the fly. However ensembl provides a backbone of data integration.
> The links are configurable and it is a good point that we should provide a link to the source somewhere.
>
> The 'count' button is definitely planned but this time it is a little bit more tricky with the advanced federation features so we may need more time to implement it properly.
>
>
> a
>
>
>
>
> Arek Kasprzyk
> Director, Bioinformatics Operations and Principal Investigator
>
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
>
> Tel:       416-673-8559
> Toll-free:           1-866-678-6427
> www.oicr.on.ca
>
>
>
> Administrative Assistant: [hidden email]
>
>
>
> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
>
> ________________________________________
> From: [hidden email] [[hidden email]] On Behalf Of Bob MacCallum [[hidden email]]
> Sent: Monday, January 31, 2011 8:01 AM
> To: [hidden email]
> Subject: [BioMart Users] Quick thoughts on 0.8
>
> Hi BioMarters,  (BioMartyrs?)
>
> I looked at the cancer genome biomart and it looks really great and
> the text field/menu completion stuff works great.  The three levels of
> interface complexity are very nice.  Overall, it's great to see things
> like "dataset" and "database" eliminated from the end user's
> experience.
>
> The martreport pages are a useful addition but I wondered why on the
> icgc site the gene reports don't have any links to Ensembl, for
> example.  Are such link-outs still configurable in 0.8+?  A site (like
> us) with its own genome browser would want to be careful not to
> confuse the user with two subtly different gene report pages
> (hopefully showing the same information though!).  Maybe a reasonably
> prominent "View this information in the source database
> (Database_name)" link/button or similar would work?
>
> I also feel with the advanced interface that a "count" button is
> lacking, but that is not dampening my enthusiasm about having this on
> VectorBase sometime this year I hope.  Congratulations on a great job,
> and sorry if I missed any formal feedback questionnaires or focus
> groups.
>
> cheers,
> Bob.
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users