About idea 7 - Semantic bioGPS
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Maximilian Ludvigsson
May 2, 2013, 2:33:47 PM5/2/13
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Hi Su lab,
I am glad that you want to continue developing the Semantic BioGPS and I would love to be a part of the project for one more summer.
While I've been working on my proposal some questions came up about the presentation part. You talk about a visualisation of the extracted data: so one page for one gene I suppose. I am not entirely clear on the use-case, would people use this plugin to search for information about a particular gene? What is the advantage for using something like d3 instead of listing the information in some kind of table?
Cheers,
Max
I am glad that you want to continue developing the Semantic BioGPS and I would love to be a part of the project for one more summer.
While I've been working on my proposal some questions came up about the presentation part. You talk about a visualisation of the extracted data: so one page for one gene I suppose. I am not entirely clear on the use-case, would people use this plugin to search for information about a particular gene? What is the advantage for using something like d3 instead of listing the information in some kind of table?
Cheers,
Max
Chunlei Wu
May 2, 2013, 3:11:53 PM5/2/13
to crow...@googlegroups.com, Maximilian Ludvigsson
Hi Max,
Welcome back to this group! Glad to see you are interested in
Semantic BioGPS again.
The presentation ideas about Semantic BioGPS are still quite
open for us. I can imagine a base level of it can be just a
well-formatted HTML table with extracted concepts. That will be
per-gene based. Beyond that, for a given gene list, we can imagine to
display a cloud of genes based on shared/related concepts (where D3 can
be used for visualization).
And I also want to mention that making the annotation core you
developed last year even more stable and universal for more BioGPS
plugins and genes is an equally important part of this project for this
year.
Cheers,
Chunlei
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Welcome back to this group! Glad to see you are interested in
Semantic BioGPS again.
The presentation ideas about Semantic BioGPS are still quite
open for us. I can imagine a base level of it can be just a
well-formatted HTML table with extracted concepts. That will be
per-gene based. Beyond that, for a given gene list, we can imagine to
display a cloud of genes based on shared/related concepts (where D3 can
be used for visualization).
And I also want to mention that making the annotation core you
developed last year even more stable and universal for more BioGPS
plugins and genes is an equally important part of this project for this
year.
Cheers,
Chunlei
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>
> 2012 GSoC Organization page:
> http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio
> GSoC Ideas page: http://sulab.org/gsoc/
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Maximilian Ludvigsson
May 2, 2013, 3:44:41 PM5/2/13
to crow...@googlegroups.com, Maximilian Ludvigsson, c...@scripps.edu
I see, and this would itself be a plugin in the BioGPS portal?
I understand that making everything stable is a priority and I write about it in
my proposal. I am also thinking about integrating a more robust web crawler
into the project, like scrapy in python or nutch in java. Because our XPaths
is dynamic it can be some work. Do you think it is worth putting time into or
would you rather prioritize the other aspects?
I understand that making everything stable is a priority and I write about it in
my proposal. I am also thinking about integrating a more robust web crawler
into the project, like scrapy in python or nutch in java. Because our XPaths
is dynamic it can be some work. Do you think it is worth putting time into or
would you rather prioritize the other aspects?
Chunlei Wu
May 2, 2013, 3:51:46 PM5/2/13
to crow...@googlegroups.com, Maximilian Ludvigsson
Integrating a dedicated web crawler sounds a great idea to me,
particularly when we talk about expanding a much larger gene list for
concept extraction.
Chunlei
On Thu 02 May 2013 12:44:41 PM PDT, Maximilian Ludvigsson wrote:
> I see, and this would itself be a plugin in the BioGPS portal?
>
> I understand that making everything stable is a priority and I write
> about it in
> my proposal. I am also thinking about integrating a more robust web
> crawler
> into the project, like scrapy <http://scrapy.org/> in python or nutch
> <http://nutch.apache.org> in java. Because our XPaths
> <javascript:>
> <http://groups.google.com/group/crowdbio?hl=en>.
particularly when we talk about expanding a much larger gene list for
concept extraction.
Chunlei
On Thu 02 May 2013 12:44:41 PM PDT, Maximilian Ludvigsson wrote:
> I see, and this would itself be a plugin in the BioGPS portal?
>
> I understand that making everything stable is a priority and I write
> about it in
> my proposal. I am also thinking about integrating a more robust web
> crawler
> <http://nutch.apache.org> in java. Because our XPaths
> > To unsubscribe from this group, send email to
> > crowdbio+u...@googlegroups.com <javascript:>
> > For more options, visit this group at
> > http://groups.google.com/group/crowdbio?hl=en?hl=en
> <http://groups.google.com/group/crowdbio?hl=en?hl=en>
> >
> > 2012 GSoC Organization page:
> >
> http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio
> <http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio>
>
> > GSoC Ideas page: http://sulab.org/gsoc/
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> >
> > 2012 GSoC Organization page:
> >
> http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio
> <http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio>
>
> > GSoC Ideas page: http://sulab.org/gsoc/
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Benjamin Good
May 2, 2013, 4:33:47 PM5/2/13
to crow...@googlegroups.com, Maximilian Ludvigsson
Regarding your earlier question about why D3 etc. Those are just means to the ends of a good interface. D3 is very powerful for visualization - networks, trees, charts etc. but in many cases tables are actually the best way to show data. If you look into the Exhibit project you'll see examples of interactive table-based views dynamically generated for RDF - very powerful..
Keys are: solid platform that does not fall apart when change inevitably happens to the data on the websites we pull from, views on the data that are clear and immediately useful - ideally in a way that could not be generated by any other individual plugin.
Max, welcome back to the group -look forward to seeing your application.
good luck!
-ben
For more options, visit this group at
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2012 GSoC Organization page:
http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio
GSoC Ideas page: http://sulab.org/gsoc/
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