Workshop Working Groups: Difference between revisions

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


=== What ===
=== What ===
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Discussion entry points:
Discussion entry points:


[[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!) ===


[[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research
* [[Akila Wijerathna-Yapa]]
 
* [[Matthew Akamatsu]] (lead?)
[[Akila Wijerathna-Yapa]]
* [[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research
 
* [[Jodi Schneider]]?
[[Matthew Akamatsu]]
 
[[Jodi Schneider]]?


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


https://synthesis-infrastructures.wiki/Translate_Logseq_Knowledge_Graph_to_Systems_Biology_Network_Diagrams
Some resources:


https://synthesis-infrastructures.wiki/Synthesis_center_for_cell_biology
* Simularium https://simularium.allencell.org/


Simularium https://simularium.allencell.org/
* Vivarium Collective https://vivarium-collective.github.io/
 
Vivarium Collective https://vivarium-collective.github.io/


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


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


could use:
could use:


someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies
* 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" ==
== Synthesis-oriented social media aka "from the stream to the garden" ==
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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!) ===
 
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
* [[Ronen Tamari]] (lead?), probably also [[Daniel Friedman]]?
* [[Konrad Hinsen]]
* [[Jonny Saunders]]
* [[Benjamin Goering]]
* 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 ===
=== Progress so far ===
https://synthesis-infrastructures.wiki/Linked_Data_Publishing_On_Activitypub#Linked_Attention_Data_Publishing


Resources
Resources


BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/
* BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/
* [[Fediverse]]
* [[Mastodon]]
* [[ActivityPub]]


[[Fediverse]]
[[Benjamin Goering]] 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
 
[[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) ===
=== Next (ideas for next steps, open problems) ===
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could use:
could use:


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


== Extending semantic mediawiki to cover discourse graph modeling ==
== Extending semantic mediawiki to cover discourse graph modeling ==
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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.
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
Could have applications to thesemantic climate setting that [[Peter Murray-Rust]] is working on


See discussion in <code>#discourse-modeling</code> channel
See discussion in <code>#discourse-modeling</code> channel
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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 McLaury]]
* [[Kyle MacLaury]]
 
* [[Peter Murray-Rust]]
[[Peter-Murray Rust]]
* [[Karola Kirsanow]]?
 
* [[Joel Chan]] also interested in assisting
[[Karola Kirsanow]]?
* [[Arthur Perret]] (can assist with write-up & tests)
 
[[Joel Chan]] also interested in assisting


=== Progress so far ===
=== Progress so far ===
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* [[Discourse Modeling]]
* [[Discourse Modeling]]
* [[Making Discourse Graphs Indexable & Discoverable]]
* [[Making Discourse Graphs Indexable & Discoverable]]
Resources


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===
A bit unformed at the moment.
Might be best to start off by just talking!


= Latent/forming =
= Latent/forming =
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=== What ===
=== What ===


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."


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)
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


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


and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853
This connects also with [[Peter-Murray Rust]]'s work on semantic climate (semantifying the IPCC report).  


but also to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation
* see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973
* and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853


=== Who ===
And also connects to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation


[[Joel Chan]] is definitely interested in this, happy to lead this
=== Who (add/edit/remove your name as desired!) ===


[[Peter-Murray Rust]]
* [[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
* 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
And [[Paul Itoi]] based on interest in multiplayer zettelkastens


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


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


[[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli
* [[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."
* [[Joseph Chee Chang]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1040001880002154546
* [[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli


=== Progress so far ===
=== Progress so far ===
Line 204: Line 182:
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!) ===
 
possibly interested:
 
[[Eirini Maliaraki]]


[[Pao Siangliulue]], based on past work on integrated crowdsourcing
* [[Matt Clancy]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1037560902800658514
* [[Eirini Malliaraki]]


Maybe also and [[Nouran Soliman]] based on LiTweeture project
* [[Martin Karlsson]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1039238852721770556
* [[Karola Kirsanow]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1039228139366268938
* [[Matthew Evans]]: https://discord.com/channels/1029514961782849607/1033091597635694694/1036658723596279868


And [[Angelina Lesnikova]] and [[Valerii Kremnev]] based on the sci2sci approach of integrating publishing into lab notebooks
* [[Pao Siangliulue]], based on past work on integrated crowdsourcing
 
* Maybe also and [[Nouran Soliman]] based on LiTweeture project
[[Jay Patel]], based on expressed interests in reimagining peer review processes
* 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]]?
* [[Wayne Lutters]]?


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


=== Next (ideas for next steps, open problems) ===
=== Next (ideas for next steps, open problems) ===
Line 233: Line 208:
=== 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


=== Progress so far ===
=== Progress so far ===
Line 242: Line 217:


== Hidden value / mental model mismatches in transitions between workflows / tools ==
== Hidden value / mental model mismatches in transitions between workflows / tools ==
* Group page: [[Mental Models]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040470706271555706 #mental-models]


=== What ===
=== 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?
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 ===
 
 
[[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346
 
twitter (centralized platform) to mastodon (decentralization, federation)


[[Peter-Murray Rust]]
=== Who (add/edit/remove your name as desired!) ===


e.g., ontologies vs. dictionaries
* [[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 ===
=== Progress so far ===


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

Latest revision as of 17:34, 11 November 2022

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:

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

Progress so far

Some resources:

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

Progress so far

Resources

Benjamin Goering 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 Upadhyay?

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 #discourse-modeling channel

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

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

Progress so far

Next (ideas for next steps, open problems)

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 also with Peter-Murray Rust's work on semantic climate (semantifying the IPCC report).

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

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

  • 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

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

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

Progress so far

Next (ideas for next steps, open problems)

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

What

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

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

Progress so far

Next (ideas for next steps, open problems)

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