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Triple-store for nanopublication

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saurav kumar

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Nov 1, 2024, 4:37:57 PM11/1/24
to Nanopublications
Hello everyone,

Does the nanopub-server come with a built-in triple-store database, or does it require separate configuration? If a separate setup is needed, which triple-store would be best suited for handling nanopublications?

Regards,
Saurav

Tobias Kuhn

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Nov 4, 2024, 2:12:48 AM11/4/24
to saurav kumar, Nanopublications
Hi Saurav,

Nanopub-server itself doesn't come with a triple store, because it is
only responsible for publishing / ID-based retrieval and not querying.
Querying happens on the layer above. There is now a new generation of
such query services, called Nanopub Query:
https://github.com/knowledgepixels/nanopub-query

Nanopub Query uses the RDF4J triple store (I think the same one that
GraphDB uses under the hood). Virtuoso is a good choice too. (The
deprecated first-generation nanopub query services are using it.)

You can also just use the publicly available instances, if they are
performant enough for you, e.g. here:
https://query.knowledgepixels.com/page/full

If you only want to query the nanopubs of a particular pubkey or
particular type, you can choose a more specific triple store from this
list: https://query.knowledgepixels.com/

There are 3 more instances of Nanopub Query available, btw:
https://monitor.knowledgepixels.com/

All this is unfortunately not yet well documented. I will work on
this... And happy to answer any further questions you might have!

Regards,
Tobias
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Tobias Kuhn

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Nov 11, 2024, 2:11:53 AM11/11/24
to saurav kumar, Nanopublications
Hi Saurav,

Yes, Nanodash at petapico.org was having problems over the weekend. Now
it's up again. The disk ran full at some point, but I am not sure
whether that was the cause or a symptom. So, I am not sure it's fully
resolved or not...

In any case, petapico.org keeps making troubles, so you might better be
using one of the other Nanodash instances such as
https://nanodash.knowledgepixels.com/

You can currently not supersede a nanopublication from a different
instance, but you can create a new one on a different instance with
"edit as derived nanopublication" and later retract the old one.

I hope that helps!

Regards,
Tobias


On 10.11.24 13:25, saurav kumar wrote:
> Hi everyone,
>
> I'm encountering a server error when trying to update a NanoHub template
> on the NanoDash platform. Here is the template I'm working on:
> https://nanodash.petapico.org/explore?id=https://w3id.org/np/
> RAZQ3zsjF-8p0GsCMVBdfRmH21PKWyl3Q0axl5Lfn_u1w <https://
> nanodash.petapico.org/explore?id=https://w3id.org/np/
> RAZQ3zsjF-8p0GsCMVBdfRmH21PKWyl3Q0axl5Lfn_u1w>
>
> I've tried updating it multiple times, making extensive changes to many
> fields, but I keep encountering errors. Is there an alternative way to
> update this template on NanoDash?
>
> image.png
>
> Regards,
> Saurav
>
>
> On Fri, 8 Nov 2024 at 19:47, saurav kumar <sauravbi...@gmail.com
> <mailto:sauravbi...@gmail.com>> wrote:
>
> Thank you for sharing these resources.
>
> At the moment, I’m using a local Blazegraph instance to store
> nanopub triples and conduct searches. From the resources you
> provided, it appears that once a nanopublication is published to a
> Nanodash instance, similar searches could be performed using the
> public SPARQL endpoint. Since the public triple store hosts all
> published nanopubs, I’m wondering if this might affect response times.
>
> Additionally, I’m curious whether frequent querying on the public
> endpoint could place too much load on the server and potentially
> impact other functionalities on Nanodash.
>
> Regards,
> Saurav
>
> On Mon, 4 Nov 2024 at 08:12, Tobias Kuhn <kuhnt...@gmail.com
> <mailto:kuhnt...@gmail.com>> wrote:
>
> Hi Saurav,
>
> Nanopub-server itself doesn't come with a triple store, because
> it is
> only responsible for publishing / ID-based retrieval and not
> querying.
> Querying happens on the layer above. There is now a new
> generation of
> such query services, called Nanopub Query:
> https://github.com/knowledgepixels/nanopub-query <https://
> github.com/knowledgepixels/nanopub-query>
>
> Nanopub Query uses the RDF4J triple store (I think the same one
> that
> GraphDB uses under the hood). Virtuoso is a good choice too. (The
> deprecated first-generation nanopub query services are using it.)
>
> You can also just use the publicly available instances, if they are
> performant enough for you, e.g. here:
> https://query.knowledgepixels.com/page/full <https://
> query.knowledgepixels.com/page/full>
>
> If you only want to query the nanopubs of a particular pubkey or
> particular type, you can choose a more specific triple store
> from this
> list: https://query.knowledgepixels.com/ <https://
> query.knowledgepixels.com/>
>
> There are 3 more instances of Nanopub Query available, btw:
> https://monitor.knowledgepixels.com/ <https://
> monitor.knowledgepixels.com/>
>
> All this is unfortunately not yet well documented. I will work on
> this... And happy to answer any further questions you might have!
>
> Regards,
> Tobias
>
> On 01.11.24 21:37, saurav kumar wrote:
> > Hello everyone,
> >
> > Does the nanopub-server come with a built-in triple-store
> database, or
> > does it require separate configuration? If a separate setup
> is needed,
> > which triple-store would be best suited for handling
> nanopublications?
> >
> > Regards,
> > Saurav
> >
> > --
> > You received this message because you are subscribed to the
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> <mailto:nanopub-users%2Bunsu...@googlegroups.com>
> <mailto:nanopub- <mailto:nanopub->
> > users+un...@googlegroups.com
> <mailto:users%2Bunsu...@googlegroups.com>>.
> > To view this discussion visit https://groups.google.com/d/
> msgid/nanopub- <https://groups.google.com/d/msgid/nanopub->
> > users/09392559-36d8-48a6-9ec2-
> c8bddc092027n%40googlegroups.com <http://40googlegroups.com>
> <https://
> > groups.google.com/d/msgid/nanopub-
> users/09392559-36d8-48a6-9ec2- <http://groups.google.com/d/
> msgid/nanopub-users/09392559-36d8-48a6-9ec2->
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> <https://groups.google.com/d/optout> <https://
> > groups.google.com/d/optout <http://groups.google.com/d/optout>>.
>

Tobias Kuhn

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Nov 11, 2024, 2:33:18 AM11/11/24
to saurav kumar, Nanopublications
Hi Saurav,

Replying to your other message:

> At the moment, I’m using a local Blazegraph instance to store nanopub
> triples and conduct searches. From the resources you provided, it
> appears that once a nanopublication is published to a Nanodash instance,
> similar searches could be performed using the public SPARQL endpoint.

Yes!

> Since the public triple store hosts all published nanopubs, I’m
> wondering if this might affect response times.

It depends. To make this whole thing scalable, you can restrict yourself
to a given type or pubkey by chosing the respective endpoint. We might
have to add some more restrictions in the future (# of queries etc.),
but you can of course always load the data locally, as you do, for more
complex querying.

> Additionally, I’m curious whether frequent querying on the public
> endpoint could place too much load on the server and potentially impact
> other functionalities on Nanodash.

The querying service is provided by Nanopub Query which is separate from
Nanodash. And going forward, the plan is to have more service instances
(including both, Nanodash and Nanopub Query) available to distribute the
load. Overall the whole architecture is designed to be scalable in the
long term, but we will still need to gather some practical experience of
how to get there.

I hope that makes sense, and happy to discuss more :)

Regards,
Tobias

saurav kumar

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Nov 12, 2024, 7:16:38 AM11/12/24
to Tobias Kuhn, Nanopublications

Thank you for sharing these resources.

At the moment, I’m using a local Blazegraph instance to store nanopub triples and conduct searches. From the resources you provided, it appears that once a nanopublication is published to a Nanodash instance, similar searches could be performed using the public SPARQL endpoint. Since the public triple store hosts all published nanopubs, I’m wondering if this might affect response times.

Additionally, I’m curious whether frequent querying on the public endpoint could place too much load on the server and potentially impact other functionalities on Nanodash.

Regards,
Saurav

saurav kumar

unread,
Nov 12, 2024, 7:16:43 AM11/12/24
to Tobias Kuhn, Nanopublications
Hi everyone,

I'm encountering a server error when trying to update a NanoHub template on the NanoDash platform. Here is the template I'm working on:
I've tried updating it multiple times, making extensive changes to many fields, but I keep encountering errors. Is there an alternative way to update this template on NanoDash?

image.png

Regards,
Saurav

saurav kumar

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Nov 14, 2024, 8:30:09 AM11/14/24
to Tobias Kuhn, Nanopublications
Thanks Tobias,
I will look into the NanoPub query and try it for my use-case.
Thanks again for your detailed response.

Regards,
Saurav
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