Workshop Working Groups

Coalesced

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

• Project Page: Translate Logseq Knowledge Graph to Systems Biology Network Diagrams
• Discord Channel: #logseq-systems-bio

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"

• Wiki Page: Linked Data Publishing On Activitypub
• Discord Channel: #linked-data-activitypub

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

• Project page: Discourse Modeling
• Discord Channel: #discourse-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

Kyle McLaury

Peter-Murray Rust

Karola Kirsanow?

Joel Chan also interested in assisting

Progress so far

• Discourse Modeling
• Making Discourse Graphs Indexable & Discoverable

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

• Wiki page: Interdisciplinary Models
• Discord Channel: #interdisciplinary-models

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

Synthesis-oriented search/discovery/exploration user interfaces

• Wiki Page: Interfaces
• Discord Channel: #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

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

• Wiki Page: Social Systems
• Discord Channel: #social-systems

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

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

• Wiki page: Forking and Federating
• Discord Channel: #forking-and-federating

Who

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

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