Workshop Working Groups - Revision history

ArthurPerret: /* Who (add/edit/remove your name as desired!) */

2022-11-11T17:34:53Z

Who (add/edit/remove your name as desired!)

← Older revision		Revision as of 17:34, 11 November 2022
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	* [[Karola Kirsanow]]?		* [[Karola Kirsanow]]?
	* [[Joel Chan]] also interested in assisting		* [[Joel Chan]] also interested in assisting
			* [[Arthur Perret]] (can assist with write-up & tests)

	=== Progress so far ===		=== Progress so far ===

Joelchan: /* Who */

2022-11-11T04:02:52Z

Who

← Older revision		Revision as of 04:02, 11 November 2022
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	* [[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822		* [[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Akila Wijerathna-Yapa]]		* [[Akila Wijerathna-Yapa]]
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	SEPIO + ActivitySteams via JSON-LD: https://discord.com/channels/1029514961782849607/1040042059916120094/1040042094363942932		SEPIO + ActivitySteams via JSON-LD: https://discord.com/channels/1029514961782849607/1040042059916120094/1040042094363942932

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Ronen Tamari]] (lead?)		* [[Ronen Tamari]] (lead?), probably also [[Daniel Friedman]]?
	* [[Konrad Hinsen]]		* [[Konrad Hinsen]]
	* [[Jonny Saunders]]		* [[Jonny Saunders]]
			* [[Benjamin Goering]]
	* this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde		* this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde
	* and [[Nouran Soliman]] based on LiTweeture project		* and [[Nouran Soliman]] based on LiTweeture project
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	Entry point: https://discord.com/channels/1029514961782849607/1039384335423389836/1039388306208718938		Entry point: https://discord.com/channels/1029514961782849607/1039384335423389836/1039388306208718938

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Kyle MacLaury]]		* [[Kyle MacLaury]]
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	How do we define minimal information models tuned for synthesis that can interoperate across various disciplines?		How do we define minimal information models tuned for synthesis that can interoperate across various disciplines?


	Concrete problem expressed by [[Peter-Murray Rust]] here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it."		Concrete problem expressed by [[Peter-Murray Rust]] here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it."
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	And also connects to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation		And also connects to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Joel Chan]] is definitely interested in this, happy to lead this		* [[Joel Chan]] is definitely interested in this, happy to lead this
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	How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?		How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Elianna DeSota]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1036629378567770223 - "I would love to explore how we might better navigate the increasing 'bits' of knowledge and research that we are publishing and sharing among our communities, and new + better ways of thinking about how to synthesize and evaluate the relationships between different fields of research."		* [[Elianna DeSota]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1036629378567770223 - "I would love to explore how we might better navigate the increasing 'bits' of knowledge and research that we are publishing and sharing among our communities, and new + better ways of thinking about how to synthesize and evaluate the relationships between different fields of research."
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	How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?		How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Matt Clancy]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1037560902800658514		* [[Matt Clancy]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1037560902800658514
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	=== What ===		=== What ===

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	* [[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956		* [[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956
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	What hidden value / mental (mis)matches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists?		What hidden value / mental (mis)matches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists?

	=== Who ===		=== Who (add/edit/remove your name as desired!) ===

	[[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346		* [[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346
			** twitter (centralized platform) to mastodon (decentralization, federation)
	twitter (centralized platform) to mastodon (decentralization, federation)		* [[Peter Murray-Rust]]
			** e.g., ontologies vs. dictionaries
	[[Peter Murray-Rust]]

	e.g., ontologies vs. dictionaries

	=== Progress so far ===		=== Progress so far ===

	=== Next (ideas for next steps, open problems) ===		=== Next (ideas for next steps, open problems) ===

Joelchan: cleaned up text, added group pages/channel links

2022-11-11T03:56:15Z

cleaned up text, added group pages/channel links

Show changes

Jonny at 22:12, 10 November 2022

2022-11-10T22:12:37Z

← Older revision		Revision as of 22:12, 10 November 2022
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	== Integrating/bridging narrative/discourse with computable knowledge graphs (and back) ==		== Integrating/bridging narrative/discourse with computable knowledge graphs (and back) ==

	* Project ~~Page~~: [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]]		* Group Page: [[Computable Graphs]]
			* Project Pages: [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]]
	* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 #logseq-systems-bio]		* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 #logseq-systems-bio]

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	== Synthesis-oriented social media aka "from the stream to the garden" ==		== Synthesis-oriented social media aka "from the stream to the garden" ==

	* ~~Wiki~~ Page: [[Linked Data Publishing On Activitypub]]		* Group Page: [[Synthesizing Social Media]]
			* Project Pages: [[Linked Data Publishing On Activitypub]]
	* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983225348993184 #linked-data-activitypub]		* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983225348993184 #linked-data-activitypub]

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	== Extending semantic mediawiki to cover discourse graph modeling ==		== Extending semantic mediawiki to cover discourse graph modeling ==

	* ~~Project~~ page: [[Discourse Modeling]]		* Group page: [[Discourse Modeling]]
	* Discord Channel: [https://discord.com/channels/1029514961782849607/1038988750677606432 #discourse-modeling]		* Discord Channel: [https://discord.com/channels/1029514961782849607/1038988750677606432 #discourse-modeling]

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	== Information models for (collaborative) interdisciplinary synthesis ==		== Information models for (collaborative) interdisciplinary synthesis ==

	* ~~Wiki~~ page: [[Interdisciplinary Models]]		* Group page: [[Interdisciplinary Models]]
	* Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #interdisciplinary-models]		* Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #interdisciplinary-models]

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	== Synthesis-oriented search/discovery/exploration user interfaces ==		== Synthesis-oriented search/discovery/exploration user interfaces ==

	* ~~Wiki~~ Page: [[Interfaces]]		* Group Page: [[Interfaces]]
	* Discord Channel: [https://discord.com/channels/1029514961782849607/1040386439575240704 #interfaces]		* Discord Channel: [https://discord.com/channels/1029514961782849607/1040386439575240704 #interfaces]

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	== Surfacing/managing/resolving disagreements in ontologies/terms/federation ==		== Surfacing/managing/resolving disagreements in ontologies/terms/federation ==

	* ~~Wiki~~ page: [[Forking and Federating]]		* Group page: [[Forking and Federating]]
	* Discord Channel: [https://discord.com/channels/1029514961782849607/1040387015545454632 #forking-and-federating]		* Discord Channel: [https://discord.com/channels/1029514961782849607/1040387015545454632 #forking-and-federating]

Jonny at 22:05, 10 November 2022

2022-11-10T22:05:58Z

← Older revision		Revision as of 22:05, 10 November 2022
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	== Integrating/bridging narrative/discourse with computable knowledge graphs (and back) ==		== Integrating/bridging narrative/discourse with computable knowledge graphs (and back) ==

			* Project Page: [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 #logseq-systems-bio]

	=== What ===		=== What ===
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	== Synthesis-oriented social media aka "from the stream to the garden" ==		== Synthesis-oriented social media aka "from the stream to the garden" ==

			* Wiki Page: [[Linked Data Publishing On Activitypub]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983225348993184 #linked-data-activitypub]

	=== What ===		=== What ===
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	BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/		BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/

	Fediverse		[[Fediverse]]

	Mastodon		[[Mastodon]]

	ActivityPub		[[ActivityPub]]

	[[bengo]] started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094		[[bengo]] started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094
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	== Extending semantic mediawiki to cover discourse graph modeling ==		== Extending semantic mediawiki to cover discourse graph modeling ==

			* Project page: [[Discourse Modeling]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1038988750677606432 #discourse-modeling]

	=== What ===		=== What ===
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	=== Progress so far ===		=== Progress so far ===

	~~https://synthesis-infrastructures.wiki/Discourse_Modeling~~		* [[Discourse Modeling]]
			* [[Making Discourse Graphs Indexable & Discoverable]]

	Resources		Resources
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	== Information models for (collaborative) interdisciplinary synthesis ==		== Information models for (collaborative) interdisciplinary synthesis ==

			* Wiki page: [[Interdisciplinary Models]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #interdisciplinary-models]

	=== What ===		=== What ===
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	== Synthesis-oriented search/discovery/exploration user interfaces ==		== Synthesis-oriented search/discovery/exploration user interfaces ==

			* Wiki Page: [[Interfaces]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1040386439575240704 #interfaces]

	=== What ===		=== What ===
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	== Social infrastructures for synthesis (e.g., incentives, funding) ==		== Social infrastructures for synthesis (e.g., incentives, funding) ==

			* Wiki Page: [[Social Systems]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1040386737836412928 #social-systems]

	=== What ===		=== What ===
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	== Surfacing/managing/resolving disagreements in ontologies/terms/federation ==		== Surfacing/managing/resolving disagreements in ontologies/terms/federation ==

			* Wiki page: [[Forking and Federating]]
			* Discord Channel: [https://discord.com/channels/1029514961782849607/1040387015545454632 #forking-and-federating]

	=== What ===		=== What ===

Joelchan: initial attempt at synthesis of pre-workshop themes/projects/discussions

2022-11-10T19:18:29Z

initial attempt at synthesis of pre-workshop themes/projects/discussions

New page

= Coalesced =

== Integrating/bridging narrative/discourse with computable knowledge graphs (and back) ==

=== What ===

How to ground knowledge graphs (that can be used for prediction or computational simulation experiments and models) in the discourse of evidence in scientific literature? How to transition from unstructured literature to knowledge graphs and keep things updated with appropriate provenance for (un)certainty?

Discussion entry points:

[[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822

=== Who ===

[[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research

[[Akila Wijerathna-Yapa]]

[[Matthew Akamatsu]]

[[Jodi Schneider]]?

=== Progress so far ===

https://synthesis-infrastructures.wiki/Translate_Logseq_Knowledge_Graph_to_Systems_Biology_Network_Diagrams

https://synthesis-infrastructures.wiki/Synthesis_center_for_cell_biology

Simularium https://simularium.allencell.org/

Vivarium Collective https://vivarium-collective.github.io/

=== Next (ideas for next steps, open problems) ===

don't know if a joint project makes sense, but perhaps coordinated first prototypes of a bridge

could use:

someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies

== Synthesis-oriented social media aka "from the stream to the garden" ==

=== What ===

How to enable sharing/direction of scholarly attention in a synthesis-oriented manner (e.g., not just popularity, but relevance to questions/hypotheses/methods, etc.)?

context in discussions on Discord:

https://discord.com/channels/1029514961782849607/1033091723389317160/1037771875012591616

concrete example: https://discord.com/channels/1029514961782849607/1037786518800039978/1037791239908622466

SEPIO + ActivitySteams via JSON-LD: https://discord.com/channels/1029514961782849607/1040042059916120094/1040042094363942932

=== Who ===

lead: [[Ronen Tamari]]

[[Konrad Hinsen]]

[[Jonny Saunders]]

this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde

and [[Nouran Soliman]] based on LiTweeture project

and [[Michael Toomim]] and team based on their work on peeryview

=== Progress so far ===

https://synthesis-infrastructures.wiki/Linked_Data_Publishing_On_Activitypub#Linked_Attention_Data_Publishing

Resources

BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/

Fediverse

Mastodon

ActivityPub

[[bengo]] started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094

=== Next (ideas for next steps, open problems) ===

there seems to be some energy behind producing a prototype/spec, perhaps to implement in an ActivityPub base

could use:

a "user" (preferably non-technical) to give feedback on mental models here. maybe pooja?

== Extending semantic mediawiki to cover discourse graph modeling ==

=== What ===

It could be really valuable to try to prototype a "computable" synthesis of the knowledge in this workshop here in the wiki. One test of the "computability" would be to make it visualizable.

Could have applications to thesemantic climate setting that [[Peter-Murray Rust]] is working on

See discussion in <code>#discourse-modeling</code> channel

Entry point: https://discord.com/channels/1029514961782849607/1039384335423389836/1039388306208718938

=== Who ===

[[Kyle McLaury]]

[[Peter-Murray Rust]]

[[Karola Kirsanow]]?

[[Joel Chan]] also interested in assisting

=== Progress so far ===

https://synthesis-infrastructures.wiki/Discourse_Modeling

Resources

=== Next (ideas for next steps, open problems) ===

A bit unformed at the moment.

Might be best to start off by just talking!

= Latent/forming =

== Information models for (collaborative) interdisciplinary synthesis ==

=== What ===

how do we define minimal information models tuned for synthesis that can interoperate across various disciplines?

concrete problem expressed by [[Peter-Murray Rust]] here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it."

and to a certain extent, the issue of representing/discussing the discourse of computational research (e.g., model parameters), discussed by [[Konrad Hinsen]] here: https://discord.com/channels/1029514961782849607/1038988750677606432/1039576903838859326

this connects with [[Peter-Murray Rust]]'s work on semantic climate (semantifying the IPCC report)

see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973

and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853

but also to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation

=== Who ===

[[Joel Chan]] is definitely interested in this, happy to lead this

[[Peter-Murray Rust]]

Possibly also [[James Howison]], based on emphasis in workshop submission on software artifacts as a locus of synthesis

And [[Paul Itoi]] based on interest in multiplayer zettelkastens

=== Progress so far ===

Resources

=== Next (ideas for next steps, open problems) ===

== Synthesis-oriented search/discovery/exploration user interfaces ==

=== What ===

How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?

=== Who ===

[[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli

=== Progress so far ===

Resources

=== Next (ideas for next steps, open problems) ===

== Social infrastructures for synthesis (e.g., incentives, funding) ==

=== What ===

How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?

=== Who ===

possibly interested:

[[Eirini Maliaraki]]

[[Pao Siangliulue]], based on past work on integrated crowdsourcing

Maybe also and [[Nouran Soliman]] based on LiTweeture project

And [[Angelina Lesnikova]] and [[Valerii Kremnev]] based on the sci2sci approach of integrating publishing into lab notebooks

[[Jay Patel]], based on expressed interests in reimagining peer review processes

[[Wayne Lutters]]?

=== Progress so far ===

Resources

=== Next (ideas for next steps, open problems) ===

== Surfacing/managing/resolving disagreements in ontologies/terms/federation ==

=== What ===

=== Who ===

[[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956

=== Progress so far ===

=== Next (ideas for next steps, open problems) ===

== Hidden value / mental model mismatches in transitions between workflows / tools ==

=== What ===

What hidden value / mental mismatches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists?

=== Who ===

[[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346

twitter (centralized platform) to mastodon (decentralization, federation)

[[Peter-Murray Rust]]

e.g., ontologies vs. dictionaries

=== Progress so far ===

=== Next (ideas for next steps, open problems) ===