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Workshop Working Groups: Difference between revisions
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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 | * Group Page: [[Computable Graphs]] | ||
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 # | * Project Pages: | ||
** [[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?) | |||
* [[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research | |||
* [[Jodi Schneider]]? | |||
[[Jodi Schneider]]? | |||
=== Progress so far === | === Progress so far === | ||
Some resources: | |||
https:// | * 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" == | ||
* | * 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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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!) === | ||
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 === | ||
Resources | Resources | ||
BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/ | * BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/ | ||
* [[Fediverse]] | |||
* [[Mastodon]] | |||
* [[ActivityPub]] | |||
[[ | [[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) === | === 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 | * 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 == | ||
* | * 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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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- | 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 | * [[Kyle MacLaury]] | ||
* [[Peter Murray-Rust]] | |||
[[Peter- | * [[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]] | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
= Latent/forming = | = Latent/forming = | ||
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== Information models for (collaborative) interdisciplinary synthesis == | == Information models for (collaborative) interdisciplinary synthesis == | ||
* | * Group page: [[Interdisciplinary Models]] | ||
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #interdisciplinary-models] | * Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #interdisciplinary-models] | ||
=== What === | === 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). | |||
* see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973 | |||
* and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853 | |||
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!) === | |||
[[Peter- | * [[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 === | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
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== Synthesis-oriented search/discovery/exploration user interfaces == | == Synthesis-oriented search/discovery/exploration user 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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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 === | ||
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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 | ||
* [[Eirini Malliaraki]] | |||
* [[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 === | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
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== Surfacing/managing/resolving disagreements in ontologies/terms/federation == | == Surfacing/managing/resolving disagreements in ontologies/terms/federation == | ||
* | * 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] | ||
=== 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 === | ||
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== 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 | 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!) === | |||
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) === | ||