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standardizing nanopublications

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Tobias Kuhn

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Dec 6, 2024, 2:58:25 AM12/6/24
to Nanopublications
Hi all,

I am currently exploring how we could properly standardize the
nanopublication format.

The obvious standardization body would be the W3C, and I am checking
their documentation on the requirements and processes.

But at the same time I also want to ask around here. Specifically:

- Do you think standardizing nanopublications is a good idea / important
/ urgent?

- Do you think W3C is a good place for that, or do you have other
suggestions?

- Have you been involved in earlier/ongoing standardization efforts, and
could you share your experience?

- Would you be interested in joining such a standardization effort,
including the participation in discussions, calls, and document drafting?

I am curious to hear your thoughts on this! :)

Regards,
Tobias

Erik Schultes

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Dec 6, 2024, 7:51:03 AM12/6/24
to Tobias Kuhn, Nanopublications
Hi Tobias -

> - Do you think standardizing nanopublications is a good idea / important / urgent?
I would not say urgent, but it is a good time to initiate the process. It is likely to be a process with a life of its own in any case.
It is certainly a good idea: I think there is no down side, and may be a lot of up sides.
It is important as it signals a growing maturity around the concept.

> - Do you think W3C is a good place for that, or do you have other suggestions?
W3C is a great choice, as I like to think of nanopubs as “nothing but” WWW.

However, we have also been exploring the idea that an appropriately constructed nanopub is conformant to the emerging FDO spec. How cool to have 2 standards (one in W3C and the other FDO) that can be aligned.

> - Have you been involved in earlier/ongoing standardization efforts, and could you share your experience?
I have limited experience in technical standardization (I helped in the original design of nanopubs early on), but do have experience using nanopub templates as standards themselves:
- Using nanopubs for FIPs and FERs
- Driving the nanopub-as-FDO idea

> - Would you be interested in joining such a standardization effort, including the participation in discussions, calls, and document drafting?

Count me in !

- E

Erik Schultes
schu...@hedgehogresearch.info
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Andrew George

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Dec 6, 2024, 9:25:47 AM12/6/24
to Erik Schultes, Tobias Kuhn, Nanopublications
Hello Tobias,

I’ve been following nanopublications for some time, though I haven’t used them directly in my work. From what I understand, they hold significant potential as a foundational tool for evidence use across various domains.

I agree that standardizing the format is both important and timely, as it could greatly enhance interoperability and adoption. I’d be happy to contribute to the standardization process in any way that would be helpful, whether through discussions, calls, or document drafting.

Looking forward to hearing more about how this initiative develops!

Best,
Andrew

--
Andrew George, Ph.D.
STEM Innovation and Engagement Director
Institute for Methods Innovation



For more options, visit https://groups.google.com/d/optout.


--
Andrew George, Ph.D.

George Patrinos

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Dec 6, 2024, 10:20:03 AM12/6/24
to Andrew George, Erik Schultes, Tobias Kuhn, Nanopublications
Hi all, 
Couldn’t agree moron the potential of nanopubs, as our group first demonstrated the value of microattribution and nano pubs back in 2011 (Giardine et al., Nat Genet 2011).

Looking forward to working with you all towards this end.

Cheers
George 

Andrew George

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Dec 6, 2024, 10:46:26 AM12/6/24
to George Patrinos, Erik Schultes, Tobias Kuhn, Nanopublications

Hello all,

This discussion inspired me to create a practical tool to demonstrate the potential of having standardization of the format. I’ve developed a custom GPT-based assistant that integrates the NanoPub Guidelines outlined in the working draft. This assistant is designed to streamline understanding and application of the guidelines, making it easier for users to engage with nanopublications effectively.

You can access the assistant here: NanoPub Assistant.

To give you a sense of its functionality, here’s an example chat interaction: Example Chat Thread.

I’d love to hear your feedback on the assistant, including thoughts on its potential utility.

Looking forward to your thoughts

Best
Andrew

--
Andrew George, Ph.D.
STEM Innovation and Engagement Director
Institute for Methods Innovation
and...@methodsinnovation.org

Tuan Amith

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Dec 6, 2024, 1:56:50 PM12/6/24
to Nanopublications
- Do you think standardizing nanopublications is a good idea / important
/ urgent?

>- A good idea 


- Do you think W3C is a good place for that, or do you have other
suggestions?

>- W3C is a natural choice


- Have you been involved in earlier/ongoing standardization efforts, and
could you share your experience?

>- not specific to nanopublications


- Would you be interested in joining such a standardization effort,
including the participation in discussions, calls, and document drafting?

>- Absolutely. I would like to contribute in this effort

Piotr Sowiński

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Dec 7, 2024, 11:30:10 AM12/7/24
to nanopu...@googlegroups.com

Hi,

> Do you think standardizing nanopublications is a good idea / important / urgent

It may make nanopubs more convincing to adopters that care about this. I personally do not, but I'm the smallest of adopters. In any case, standardization takes a lot of effort, so it's some sort of a cost/benefit analysis.

An alternative is a different form of "stewardship". Something like becoming an Apache project. Or setting up a non-profit kind of thing.

Anyway, the definition of a "standard" is very loose. For example, I've heard some IEEE-affiliated people say that W3C is not a real SDO. What matters in the end is whether people believe the tech is stable, has good stewardship, and that nobody is going to ruin this unilaterally overnight. Do you always need an SDO for that?

> Do you think W3C is a good place for that, or do you have other suggestions?

Like others said, W3C is the natural choice. I am however slightly concerned about one issue.

Solid. It has some overlap with Nanopubs regarding the objectives. It is backed by none other than Tim Berners-Lee himself, but nonetheless it's been stuck in standardization hell since 2018, with no W3C Recommendation in sight. I think it would be tremendously important to first research this topic very, very well, for two reasons. First, why are they stuck and is the root cause applicable also to the Nanopub effort? Second, would the existence of Solid make W3C reluctant to give us a charter for a Working Group? I recall one similar situation with the HDT binary format. The HDT team submitted a W3C Member Submission to which the reply was (in my very loose interpretation) "oh that's a lovely idea, now go and use EXI instead". I have zero idea about how the actual HDT team-W3C interaction played out, though.

Setting up a Community Group (CG) should not be too hard. The question is whether this CG will result in a WG down the line. Many CGs go nowhere.

> Have you been involved in earlier/ongoing standardization efforts, and could you share your experience?

I have only observed some efforts in IEEE and W3C, without active participation.

> Would you be interested in joining such a standardization effort, including the participation in discussions, calls, and document drafting?

Yes, definitely, whatever the form of this effort is going to be.

-- 
Piotr Sowiński
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