Workshop Working Groups
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
Progress so far
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
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
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 #discourse-modeling channel
Entry point: https://discord.com/channels/1029514961782849607/1039384335423389836/1039388306208718938
Who
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
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:
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
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)
e.g., ontologies vs. dictionaries