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Create goose-gannet equivalent #9

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cmungall opened this issue Oct 24, 2016 · 8 comments

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@cmungall
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commented Oct 24, 2016

We want to make it easy to run canned or templated queries.

@balhoff - what were the results of your evaluation of lodestar?

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commented Sep 8, 2017

@dougli1sqrd will investigate extending yasgui framework.

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commented Sep 8, 2017

Could also explore using a hosted Jupyter notebook, e..g https://notebooks.azure.com/ with https://github.com/paulovn/sparql-kernel

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commented Sep 9, 2017

I believe that we should align the needs and reusability between these two:
geneontology/noctua#465 (comment)

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commented Sep 12, 2017

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commented Sep 15, 2017

Talking to @hchiba1 of SPANG (http://mbgd.genome.ad.jp/spang/) a little at BH17, and he had some other pointers for people exploring in this direction:

https://lists.w3.org/Archives/Public/semantic-web/2012Jul/0172.html
https://lists.w3.org/Archives/Public/semantic-web/2015Jan/0150.html
https://github.com/ldodds/sparql-doc

The last one seems to be closest to what we'd want, but unfortunately doesn't mention templating, so maybe a combination, if following these suggestions. One thing that I don't like, versus a straight YAML and template solution, is that we'd end up with Yet Another Format that would have to be parsed across various languages and implementations, rather than PotS. I understand the desire to have Everything SPARQL, but there may be practical limitations to that approach. Always interested in more feedback.

kltm added a commit to geneontology/noctua that referenced this issue Sep 15, 2017
add a universal workbench for noctua for doing arbitrary sparql queri…
…es; as this can be very easily transferred to a model workbench (would need to extend bbop-manager-sparql to just return filled templates) this is essentially completion for geneontology/go-graphstore#9 and #465; TODO: track down cross-site issue
kltm added a commit to geneontology/noctua that referenced this issue Sep 15, 2017
add a universal workbench for noctua for doing arbitrary sparql queri…
…es; as this can be very easily transferred to a model workbench (would need to extend bbop-manager-sparql to just return filled templates) this is essentially completion for geneontology/go-graphstore#9 and #465; TODO: track down cross-site issue
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commented Sep 15, 2017

The nice thing about embedding metadata or docs in the comments (sparql-doc) is that the content/file can be immediately passed straight to the endpoint, e.g. using curl. Even though extracting from yaml is trivial, it adds an extra step that could be an annoyance.

Nothing that says this would not be composable with a template approach.

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commented Sep 15, 2017

Totally agree here, but we run into the issue of having to deal with custom parsers for the information that we'll need to do what we (I) want. As well, the sparql-doc doesn't quite cover the templating uses. I'm a bit on the fence about this, and I'm not married to any one solution yet. It will be good to go over this in meeting when I can cover live examples.

@kltm kltm referenced this issue Sep 19, 2017
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commented Mar 13, 2018

I'm going to crowdsource this from the wider semweb community here: https://docs.google.com/document/d/1bH7L6iPUsZJdkbjJZySoGHAfXyLif3Bas7Q4D66y0GA/edit

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