press release about collaboration involving nanopublications

[Tobias Kuhn]

Dear all,

We would like to share the news we are employing nanopublication
technology in a pilot project we launched earlier this week, as a
collaboration of our company Knowledge Pixels with our partners IOS
Press and Pensoft. Researchers can now publish nanopublications together
with their articles. You can find out more in these press releases:

- Via Pensoft: https://www.eurekalert.org/news-releases/988615
- Via IOS Press:
https://www.iospress.com/news/introducing-fair-findings-innovators-and-publishers-join-forces-to-make-scientific-articles

We hope you find it iteresting.

Regards,
Tobias

[Tobias Kuhn]

Hi Jorrit,

Sure, you can find examples for each of the nanopub types as listed on
the connector pages:

- Connector page for RIO journal:
https://nanodash.petapico.org/connector/pensoft/rio
- Connector page for Data Science journal:
https://nanodash.petapico.org/connector/ios/ds

An example of a simple kind of nanopub assertion is shown here:
https://nanodash.petapico.org/connector/ios/ds/type?type=biorel

An example of a more complex one here:
https://nanodash.petapico.org/connector/ios/ds/type?type=superpattern

We hope that we can soon replace these with examples that were actually
submitted (and accepted) at one of these journals, but I hope they are
helpful to understand the types and the approach overall.

We will also soon have templates for biodiversity-related statements in
our upcoming pilot at Biodiversity Data Journal.

Regards,
Tobias


On 12.05.23 17:29, Jorrit Poelen wrote:
> Thanks for sharing!
>
> Can you point to some specific examples?
>
> -jorrit

[Tobias Kuhn]

Hi Jorrit,

> Excellent - perhaps a good reason to revisit the GloBI - Nanopub
> publications integrations . . .

Yes, indeed!

> Hope to find one or two good examples and create issues for them with
> expected results on
> https://github.com/globalbioticinteractions/globalbioticinteractions/issues . In my experience, integrating early and often helps to keep our discussion flowing and improvements coming.
>
> I would very much appreciate if you could help express your ideas on how
> you'd expect your published nanopublications with biotic interactions to
> appear on GloBI and associated data products.

I think this template ("Expressing an association between two organism
taxons") in Nanodash that we just created a few weeks ago is the best
starting point on our side:
https://nanodash.petapico.org/publish?template=http://purl.org/np/RAfkBEHGmvTphfKcesMTreOcXTekxZmf3iO50SXoRBX48

This is part of the Biodiversity Data Journal pilot.

It creates nanopublications like this one ("cats prey on mice"):
http://purl.org/np/RAmlZqUxZndYaflGLxhspiGCdN6UNi4G2W7JQEiSApmFc Or the
same a bit nicer to look at in Nanodash:
https://nanodash.petapico.org/explore?id=http://purl.org/np/RAmlZqUxZndYaflGLxhspiGCdN6UNi4G2W7JQEiSApmFc

I can easily set up an API that will collect these in a table like this:

subj,pred,obj
https://www.checklistbank.org/dataset/2169/taxon/9685,http://purl.obolibrary.org/obo/RO_0002439,https://www.checklistbank.org/dataset/9880/taxon/7VW9H
...

How much closer would that get us to an integration into GloBI?

> I'd like to be able to say: yes, these nanopublications work very well,
> and help increase the mobility of our biodiversity knowledge.

Yes, absolutely, let's work towards that! :)

Regards,
Tobias

[Tobias Kuhn]

Hi Jorrit,

> Apologies for missing Nanosessions #4 today - I am currently with family
> to prepare for the departure of my partner's father from this earthly
> realm. This is why my schedule is a little challenging and I am distracted.

I am very sorry to hear that. I wish your partner, yourself, and your
families strength in what must be a very difficult time.

> Thank you for sharing the specific cat and mouse example: I was able to
> see the rendering in nanodash at
> https://nanodash.petapico.org/explore?1&id=http://purl.org/np/RAmlZqUxZndYaflGLxhspiGCdN6UNi4G2W7JQEiSApmFc . But for some reason, I was unable to find any references that support your claim that cats prey on mice. Is that expected?

Yes, in this example I just attributed it to myself without any reference.

I made some more examples that link to a DOI in the provenance part:

- http://purl.org/np/RAoxoYhxKUgNOUw98746A_K72iSJBJ-VLF3XpSTcqJ3cs
- http://purl.org/np/RAYIq_uMC4oHHLfKaAMn5rvfHstAANj9PYaEcfPbIZ0uo

> Yes, having a hardcoded query producing interaction claims would be a
> great first step towards integrating/indexing your work. I'd hope to see
> the following fields:
>
> subj,pred,obj,nanopubId, nanopubUrl, referenceCitation, referenceDoi,
> referenceUrl
>
> Ideally, we'd also include things like location, time, etc, and the
> above would be a great first step.

OK, this should be a first step to that:
https://grlc.petapico.org/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs

Request 'text/csv' in the HTTP header or append '.csv' to the URL to get
it in CSV format.

It's part of the API for the Biodiversity Data Journal pilot. I just
added the "source" column.

"nanopubId" is the same as "nanopubUrl" in our system (both in column
"np"). "source" is mostly supposed to be a DOI URL (starting with
https://doi.org/) but could be any other URL, or empty. We don't have
"referenceCitation" at this point (I suppose you mean something like
"Doe et al. Journal X, 2023"), as we don't have that data in nanopubs at
the moment. This could should be included in one way or another at some
point, but we can also just make a request to doi.org to get that info.

> Curious to hear your thoughts,

Curious to hear yours. But no hurry.

Regards,
Tobias