Synthesis Infrastructures - User contributions [en]

Computable Graphs

2022-11-18T14:18:29Z

Joelchan: /* question What additional context beyond provenance could be useful? */

{{Group
|Decription=How to ground knowledge graphs (that can be used for prediction or computational simulation experiments and models) in the discourse and quantitative evidence in scientific literature?
|Topics=Knowledge Graphs
|Projects=Synthesis center for cell biology, Translate Logseq Knowledge Graph to Systems Biology Network Diagrams
|Discord Channel Name=#computable-graphs
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1038983137222467604
|Facilitator=Joel Chan
|Members=Aakanksha Naik, Akila Wijerathna-Yapa, Joel Chan, Matthew Akamatsu, Michael Gartner, Dafna Shahaf, Belinda Mo
}}
Facilitator/Point of Contact: [[Has Facilitator::Joel Chan]]

== 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

== Resources ==

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

=== First breakout group session ===
who was present: Joel, Matt, Michael, Sid, Aakanksha, Belinda
* anchoring on [[Synthesis center for cell biology]]
* challenge: students wrapping their heads around the model; get really excited once they do

* Dafna: very much like the old issue-based argument maps!

* Belinda: what is scope of the project in terms of users?
** Matt: hoping this accessible all the way to high school students also!
* AICS is making platform for running simulations, make it easy to run and share with others - [[Simularium]]
* Dafna: are there pain points on the input side? (seems painful!)
* Dafna: how similar are the things that people pull out from the same paper?
** Matt: for our field, pretty similar, esp. for well-written papers
** Belinda: compare what each person is highlighting and extract summary that is representative of all the annotations
* Dafna: how useful are these (bits of) knowledge graphs for others?
** Works well within lab; better than unstructured text, motivating to try to create micropublications to summarize outcome 10-week rotation
* Dafna: "compiling" discourse graph to manuscript seems much easier, esp. if have consistent structure and human-in-the-loop
** Similar to brainstorming discussion/ethics statements for a paper given abstract (via GPT-3
* Belinda: how much variation in paper structure within your field?
** some variations by journal
** some authors (think more highly of themselves), more declarative/general, less clear distinction between claims and evidence
* Aakanksha:
** hypothes.is experiment
** need infra changes
*** help make the case for these changes
**** maybe how much $$ each person would pay for this!!)
**** demonstration of value
**** brainstorming what research projects would be part of this
**

emerging themes/problems:

* idea around changing the reading process somehow (with high hopes for somehting like semantic scholar PD reader that has beginning annotations tuned to what matt is trying to extract, maybe also on the abstract level) --> these could also feed back / forward to other users
** can probably start from this: Scim: Intelligent Faceted Highlights for Interactive, Multi-Pass Skimming of Scientific Papers <nowiki>https://arxiv.org/pdf/2205.04561.pdf</nowiki>
** cross connections to what

* idea of compiling from discourse graph to manuscript seems feasible?
** Belinda could mock something up in OpenAI playground really quickly for a few papers
*** need examples or access to repo
** Could also integrate into Matt's lab via GPT-3 extension
* question: understanding different levels of value of having a knowledge graph for someone else who didn't create it
** --> Joel can add links to ongoing lit review on this question - not resolved yet
* theme/idea: "compiling" from discourse to knowledge graphs
** Aakanksha: often see ontologies in isolation
*** Aakanksha: can look into NLP around adding context to knowledge graphs
** Michael: interesting to think about the user experience on this - how do they interact?
** Grounding abstractions: https://www.susielu.com/data-viz/abstractions

== Contextualizing knowledge graphs ==

=== Key Question: Research connections between knowledge base provenance and NLP ===

==== Background ====
Knowledge bases or graphs are typically stored in the form of subject-predicate-object triples, often using formats like RDF (Resource Description Format) and OWL (Web Ontology Language). These triple-based formats don’t include provenance data, which covers information such as the source from which a triple was extracted, time of extraction, modification history, evidence for the triple, etc., or any other additional context by default. But contextual information can improve overall utility of a KG/KB, and is particularly helpful to capture when scholars are synthesizing literature into such structures (either individually or collectively).

==== What can additional context help with? ====

* Authority or trustworthiness of information
* Transparency of the process leading to the conclusion
* Validation and review of experiments conducted to attain a result

Property graphs/attribute graphs in which entities and relations can have attributes

==== Ways to insert additional context into a KG ====
Broadly can be distilled into the following strategies: Increasing number of nodes in a triple, allowing “nodes” to be triples themselves, adding attributes or descriptions to nodes, adding attributes to triples (attributes may or may not be treated the same as predicates)

RDF reification: Add additional RDF triples that link a subject, predicate or object entity with its source (or any other provenance attribute of interest). Leads to bloating - 4x the number of triples if you want to store information about subject, predicate, object and overall triple.

N-ary relations: Instead of binary relations, allow more entities (aside from subject and object) to be included in the same relation. This can complicate traversal of the knowledge graph.

Adding metadata property-value pairs to RDF triples

Forming RDF molecules, where subjects/objects/predicates are RDF triples (allowing recursion)

Two named graphs, default graph and assertion graph, store data and another graph details provenance data

Nanopublications, which seem very similar in structure to the discourse graph format

Most of these representations are text-only, what about multimodal provenance (images, toy datasets, audio and video recordings)?

==== At what levels can we have additional context? ====
[[/link.springer.com/content/pdf/10.1007/s41019-020-00118-0.pdf|[1]]] provides a review (slight focus on cybersecurity domain) and suggests the following granularities at which provenance/context information can be recorded:

Element-level provenance (how were certain entity or predicate types defined)

Triple-level provenance (most common level of provenance)

Molecule-level and graph-level provenance (having provenance information for composites or collections of RDF triples, but not individual triples)

Document-level provenance and corpus-level provenance (only having provenance information for documents or corpora from which triples are identified)

Scalability is a concern when deciding the level and extent to which provenance data can be retained

==== What kinds of information does provenance cover? ====
Domain-agnostic information types:

* Creation of the data
* Publication of the data
* Distribution of the data
* Copyright information
* Modification and revision history
* Current validity

Domain-specific provenance ontologies: defined for BBC, US Government, scientific experiments

DeFacto tool for deep fact validation on the web: [[/github.com/DeFacto/DeFacto|https://github.com/DeFacto/DeFacto]]

==== [[question]] What additional context beyond provenance could be useful for scholarly knowledge graphs specifically? ====

* Concept drift over time (in general entity/relation evolution over time)
* Seems like discourse links across papers don’t neatly fit the provenance definition, but are an aspect we want to capture?
* Are there other aspects that provenance doesn’t cover?
* Some key pointers in Bowker (2000): https://joelchan.me/INST801-FA22%20Readings/Bowker_2000_Biodiversity%20Datadiversity.pdf

==== Links to NLP research ====
Seems like there's a bit of a gap between NLP research

[[question]] What are the points of overlap between subproblems around scholarly knowledge graph provenance and existing NLP research?

(probably a rich opportunity for a position paper - could bei nteresting to NLP venues; e.g., [[NeuRIPS AI for science workshop]]: possible contact: Kexin Huang

* Biggest open questions seem to be:
** scalability vs expressivity, multiple modalities, updation
** Interpretability or transparency: Provenance information can be used to make KGs more transparent, because we have sources that provide evidence for why this fact/relation holds true.
** Commonsense angle: Another broader application where storing context might be helpful could be for commonsense knowledge graphs?
*** Might have an analog in terms of "scholarly" (un)common sense, esp. across disciplinary boundaries (but this also has analogs in cross-cultural barriers to communication)
* Maps to things with some existing body of work
** Scoring functions in KRL: In representation learning for KGs, models are trained to embed entities and relations in a common space and then score (subject, predicate, object) triples according to likelihood - can these scores be use as additional “plausibility” or “validity” metadata from a provenance perspective? However, these scores are usually produced by models that are learning to replicate the structure of the knowledge graph, so they can’t link back to any textual evidence to support the judgements.
** Auxiliary knowledge in graphs: [https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9416312 <nowiki>[2]</nowiki>] lists some work that stores textual descriptions alongside entities, entity images (image-embodied IKRL) and uncertainty score information (ProBase, NELL and ConceptNet).
** Temporal knowledge graphs: [2] is a survey of knowledge graphs from an NLP perspective and highlights temporal knowledge graphs as a key area of research. Temporality is one kind of provenance information. Current directions being explored include
*** Temporal embeddings: extending existing KRL methods for quadruples instead of triples, where time is the fourth entity
*** Entity dynamics: changes in entity states over time
*** Temporal relational dependence (e.g., a person must be born before dying)
*** Temporal logic reasoning: graphs in which temporal information is uncertain.
** Knowledge acquisition: Some work has tried to explore jointly extracting entities/relations from unstructured text and performing knowledge graph completion. This can be a useful way to jointly model unstructured text from previous papers that do not have associated graphs and papers for which discourse graphs have been annotated. In general, joint graph+text embedding techniques seem useful. Additionally, a technique often used to train models to extract relations from text, distant supervision, can probably be leveraged to detect and add provenance information post-hoc. The idea behind distant supervision is to scan text and find sentences that mention both entities involved in the relation, considering such sentences to be potential evidence sentences. But this is a noisy heuristic - a sentence mentioning two connected entities may not be mentioning the relation between them - and will likely require some curation.

[[/link.springer.com/chapter/10.1007/978-3-642-13818-8 32|Application to finding evidence for clinical KBs]]

==== Important contexts to be captured for synthesis of scientific literature ====
[[/dl.acm.org/doi/pdf/10.1145/3227609.3227689|[3]]] proposes a framework to construct a knowledge graph for science. Problems, methods and results are key semantic resources, in addition to people, publications, institutions, grants, and datasets. Four modes of input:

# Bridge existing KGs, ontologies, metadata and information models
# Enable scientists to add their research possibly with some intelligent interface support
# Use automated methods for information extraction and linking
# Support curation and quality assurance by domain experts and librarians

The underlying data model that supports this endeavor can adopt RDF or Linked Data as a scaffold but must add comprehensive provenance, evolution and discourse information. Other requirements include ability to store and query graphs at scale, UI widgets that support collaborative authoring and curation and integration with semi-automated ways of extraction, search and recommendation.

Top-level ontology: research contribution, communicates one or more results in an attempt to address a problem using a set of methods. Top-down design of more specific elements is needed from domain experts across a set of domains.

Infrastructure: KG can be queried and explored by anyone, but registration is required to contribute to the KG (a way to ensure proper authorization and domain expertise?)

KGs need to capture fuzziness: competing evidence, differing definitions and conceptualizations

Interesting question around score for contributions to the scientific KG instead of document-centric metrics like h-indices (potentially more accurate assessment of contributions)

[https://www.researchgate.net/profile/Soeren-Auer/publication/330751750_Open_Research_Knowledge_Graph_Towards_Machine_Actionability_in_Scholarly_Communication/links/5c5e9bc7a6fdccb608b28f6f/Open-Research-Knowledge-Graph-Towards-Machine-Actionability-in-Scholarly-Communication.pdf <nowiki>[4]</nowiki>] has a really nice analogy: when we moved from phone books and maps were digitally transformed, we didn’t just created PDF books with this information, instead we developed new means to organize and access information. Why not push for such a re-organization in scholarly communication too? Building on [3], their ontology also contains: problem statement, approach, evaluation and conclusions. They use RDF with a minor difference: everything can be modeled as an entity with a unique ID. Limited subset of OWL (subclass inference) is supported. Small user study with this tool, but it doesn’t seem like Dafna’s question about utility of KG constructed by someone else or consensus across people were measured. But they do speak to Dafna's question about how painful it is to construct KGs.

so possible good open [[question]]: how might KGs constructed by one set of scientists actually be useful or not for other scientists, and what factors influence whether this is the case?

* [[experiment]] idea: even just starting by compiling any successful instances of adoption of KGs taht span multiple groups would be a good thing to do; [[Peter Murray-Rust]]. maybe [https://www.nlm.nih.gov/research/umls/index.html UMLS] also

Note: Both papers actually reference a fair number of other works in this direction, which could be good follow-up reading

=== Papers I didn’t get to ===
(numbering here does *not* map to numbering in sections above)

[1] [https://pdfs.semanticscholar.org/713b/b398b85b034f2139e08b4ca0f7791fd545bc.pdf?_ga=2.19474043.2123037593.1668226180-648530244.1660769576 Empirical study of RDF reification]

[2] [[/dl.acm.org/doi/pdf/10.1145/3459637.3482330|Maintaining provenance in uncertain KGs]], [[/arxiv.org/pdf/2007.14864.pdf|maintaining provenance in dynamic KGs]]

[3] [[/kaixu.files.wordpress.com/2011/09/provtrack-ickde-submission.pdf|System for provenance exploration]]

[4] [[/www.semanticscholar.org/paper/iKNOW:-A-platform-for-knowledge-graph-construction-Babalou-Costa/3a492a7b2d04221941919f80ca259506866490b3|iKNOW: KG construction for biodiversity]]

[5] [[/eprints.soton.ac.uk/412923/1/WD sources iswc 7 .pdf|Provenance information in a collaborative environment: evaluation of Wikipedia external references]]

[6] [[/arxiv.org/pdf/2210.14846.pdf|ProVe: Automated provenance verification of KGs against text]]

== Understanding knowledge graph transfer ==
I was able to track down my main notes/sources from before and clean them up a little (not *that* much effort :)):

Last version (not most updated, bc export is slooowwwwww from Roam rn) here: https://publish.obsidian.md/joelchan-notes/discourse-graph/questions/QUE+-+How+can+we+best+bridge+private+vs.+public+knowledge

Will clean up based on this: https://roamresearch.com/#/app/megacoglab/page/XHvRRSi_0

TL;DR (can clean up here based on [[Discourse Modeling]] conventions :):

* distributed sensemaking (Kittur, Goyal, etc.; some promise of yes helpful to share)
* sensemaking handoff (limited, but a major focus in intelligence analysis, there are tools and processes for doing this)
* reuse of records/data/stuff in general in CSCW across a bunch of work domains/settings, like aircraft safety, healthcare, etc. (generally talks about why it's hard to reuse stuff from others, need context)
* annotations / social reading (generally negative/mixed)
MG: can we search the literature based on what tool they studied things with?

NO. not right now.

lack of good tools to "refactor" the literature to match those queries

maybe like Elicit? https://elicit.org/search?q=What+is+the+impact+of+creatine+on+cognition%3F&token=01GHRSBKG6P1R9343NBP2ZWZ5B&c-ps=intervention&c-ps=outcome-measured&c-s=What+tool+did+they+study but for everything??

== Compiling graphs to manuscripts ==

=== Overview ===

We'd like to build a prototype of a tool that starts with discourse units (phrases with the category Question/motivation, Method, Evidence, Claim) and uses NLP to generate a draft of a manuscript paragraph.
[[File:Discourse graph to manuscript draft via NLP.png|900x900px]]

=== Purpose ===

Such a tool would speed up a really time consuming aspect of the academic job: drafting grant proposals and manuscripts from content. It would also encourage researchers to generate structured content (questions/claims/evidence) which will get incorporated into a discourse graph.

The benefit to the user is a structured approach to writing papers and grant proposals. Using the tool will introduce researchers to the concept of discourse units, and generate a repository of discourse units that can be turned into discourse graphs.

=== Ideal outcomes ===

(more to add here)

This tool could also enable the micropublication of mini discourse graphs (one question/method/evidence/claim) by generating a draft of the explanatory text.
* Could also integrate into Roam Research graphs, e.g. in Matt's lab, via the Roam GPT-3 extension

=== What we're doing next ===

* Belinda could mock something up in OpenAI playground really quickly for a few papers
** need examples or access to repo
* Matt and Michael will share some examples of papers or content from the discourse graph to use as source data
* Sid can check out [https://github.com/LayBacc/roam-ai Roam AI extension] for incorporation into our roam graph workflow (fork, make modifications etc)
** ([https://www.reddit.com/r/RoamResearch/comments/yigf6q/im_genuinely_fascinated_with_the_roam_ai/ discussion on its usage])
** [https://www.loom.com/share/d152e7a184f94080b8777f595821f43e usage video]

=== Related conversation ===
* Dafna: "compiling" discourse graph to manuscript seems much easier, esp. if have consistent structure and human-in-the-loop
** Similar to brainstorming discussion/ethics statements for a paper given abstract (via GPT-3
* Belinda: how much variation in paper structure within your field?
** some variations by journal

=== Claims in the conversation that need evidence ===
* the majority of empirical research papers in biology have a similar structure (question/ motivation/ evidence (fig.1a)/ claim for each paragraph & figure panel)
* multiple researchers (or students) asked to highlight the questions/claims/evidence text from a paper will highlight similar/consensus text (part of the NLP-to-highlights project)
notes/questions

* may need more than just the sentences, but also mapping to intra-project/paper elements, like figures and tables to

[[File:Screenshot example of GPT-3 task for extracting components from narrative.png|none|thumb]]

== Next Steps ==

* 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

Workshop Agenda

2022-11-13T20:53:05Z

Joelchan: add day 2 recording

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

A concrete example of that co-evolution: participants could volunteer as guinea pigs for tools being built by other participants. Or provide early feedback on preprints.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 convert to your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff --> [[Kickoff "Slides"]]
Recording [https://umd.zoom.us/rec/share/X3l4732OANMOB4f7Og3anVy4cOJLaPcAkt6x9TAgRcTknYwY6dQRz0rIWabavM4K.ykSOL6NR1lydtQVl?startTime=1668263915000 Passcode: Qrd?2c@y HERE].
|-
|09:45 - 10:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Jodi to facilitate welcome / why are we here hellos from everyone.
Joel to summarize TL;DR of people/projects/themes from [[Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:15 - 12:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:15 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. With 6 groups, this gives us up to ~5 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
Recording [https://umd.zoom.us/rec/share/X3l4732OANMOB4f7Og3anVy4cOJLaPcAkt6x9TAgRcTknYwY6dQRz0rIWabavM4K.ykSOL6NR1lydtQVl?startTime=1668273710000 Passcode: Qrd?2c@y HERE].
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Space for any quick reminders of requests from working groups
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing + documenting progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|With 6 groups, this gives us up to ~20 mins per group for sharing/discussion
Recording [https://umd.zoom.us/rec/share/08ClhDRRaFyJARIrE0qDxZhbP_LNKrtid3KuXmchua0K_TYWyJXT4PznCf3bBC8.z1yd3gYRncUNKXd7?startTime=1668354363000 Passcode: m+u%ZSX5 HERE]
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!). To help you get up to speed, we've tried to synthesize key entry points in the Discord discussions in the [[Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* We expect that those of you who've already been coalescing into one of the workshop working groups will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!).
* We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Computable Graphs

2022-11-13T17:33:47Z

Joelchan: notes from day 2

{{Group
|Decription=How to ground knowledge graphs (that can be used for prediction or computational simulation experiments and models) in the discourse and quantitative evidence in scientific literature?
|Topics=Knowledge Graphs
|Projects=Synthesis center for cell biology, Translate Logseq Knowledge Graph to Systems Biology Network Diagrams
|Discord Channel Name=#computable-graphs
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1038983137222467604
|Facilitator=Joel Chan
|Members=Aakanksha Naik, Akila Wijerathna-Yapa, Joel Chan, Matthew Akamatsu, Michael Gartner, Dafna Shahaf, Belinda Mo
}}
Facilitator/Point of Contact: [[Has Facilitator::Joel Chan]]

== 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

== Resources ==

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

=== First breakout group session ===
who was present: Joel, Matt, Michael, Sid, Aakanksha, Belinda
* anchoring on [[Synthesis center for cell biology]]
* challenge: students wrapping their heads around the model; get really excited once they do

* Dafna: very much like the old issue-based argument maps!

* Belinda: what is scope of the project in terms of users?
** Matt: hoping this accessible all the way to high school students also!
* AICS is making platform for running simulations, make it easy to run and share with others - [[Simularium]]
* Dafna: are there pain points on the input side? (seems painful!)
* Dafna: how similar are the things that people pull out from the same paper?
** Matt: for our field, pretty similar, esp. for well-written papers
** Belinda: compare what each person is highlighting and extract summary that is representative of all the annotations
* Dafna: how useful are these (bits of) knowledge graphs for others?
** Works well within lab; better than unstructured text, motivating to try to create micropublications to summarize outcome 10-week rotation
* Dafna: "compiling" discourse graph to manuscript seems much easier, esp. if have consistent structure and human-in-the-loop
** Similar to brainstorming discussion/ethics statements for a paper given abstract (via GPT-3
* Belinda: how much variation in paper structure within your field?
** some variations by journal
** some authors (think more highly of themselves), more declarative/general, less clear distinction between claims and evidence
* Aakanksha:
** hypothes.is experiment
** need infra changes
*** help make the case for these changes
**** maybe how much $$ each person would pay for this!!)
**** demonstration of value
**** brainstorming what research projects would be part of this
**

emerging themes/problems:

* idea around changing the reading process somehow (with high hopes for somehting like semantic scholar PD reader that has beginning annotations tuned to what matt is trying to extract, maybe also on the abstract level) --> these could also feed back / forward to other users
** can probably start from this: Scim: Intelligent Faceted Highlights for Interactive, Multi-Pass Skimming of Scientific Papers <nowiki>https://arxiv.org/pdf/2205.04561.pdf</nowiki>
** cross connections to what

* idea of compiling from discourse graph to manuscript seems feasible?
** Belinda could mock something up in OpenAI playground really quickly for a few papers
*** need examples or access to repo
** Could also integrate into Matt's lab via GPT-3 extension
* question: understanding different levels of value of having a knowledge graph for someone else who didn't create it
** --> Joel can add links to ongoing lit review on this question - not resolved yet
* theme/idea: "compiling" from discourse to knowledge graphs
** Aakanksha: often see ontologies in isolation
*** Aakanksha: can look into NLP around adding context to knowledge graphs
** Michael: interesting to think about the user experience on this - how do they interact?
** Grounding abstractions: https://www.susielu.com/data-viz/abstractions

== Contextualizing knowledge graphs ==

=== Key Question: Research connections between knowledge base provenance and NLP ===

==== Background ====
Knowledge bases or graphs are typically stored in the form of subject-predicate-object triples, often using formats like RDF (Resource Description Format) and OWL (Web Ontology Language). These triple-based formats don’t include provenance data, which covers information such as the source from which a triple was extracted, time of extraction, modification history, evidence for the triple, etc., or any other additional context by default. But contextual information can improve overall utility of a KG/KB, and is particularly helpful to capture when scholars are synthesizing literature into such structures (either individually or collectively).

==== What can additional context help with? ====

* Authority or trustworthiness of information
* Transparency of the process leading to the conclusion
* Validation and review of experiments conducted to attain a result

Property graphs/attribute graphs in which entities and relations can have attributes

==== Ways to insert additional context into a KG ====
Broadly can be distilled into the following strategies: Increasing number of nodes in a triple, allowing “nodes” to be triples themselves, adding attributes or descriptions to nodes, adding attributes to triples (attributes may or may not be treated the same as predicates)

RDF reification: Add additional RDF triples that link a subject, predicate or object entity with its source (or any other provenance attribute of interest). Leads to bloating - 4x the number of triples if you want to store information about subject, predicate, object and overall triple.

N-ary relations: Instead of binary relations, allow more entities (aside from subject and object) to be included in the same relation. This can complicate traversal of the knowledge graph.

Adding metadata property-value pairs to RDF triples

Forming RDF molecules, where subjects/objects/predicates are RDF triples (allowing recursion)

Two named graphs, default graph and assertion graph, store data and another graph details provenance data

Nanopublications, which seem very similar in structure to the discourse graph format

Most of these representations are text-only, what about multimodal provenance (images, toy datasets, audio and video recordings)?

==== At what levels can we have additional context? ====
[[/link.springer.com/content/pdf/10.1007/s41019-020-00118-0.pdf|[1]]] provides a review (slight focus on cybersecurity domain) and suggests the following granularities at which provenance/context information can be recorded:

Element-level provenance (how were certain entity or predicate types defined)

Triple-level provenance (most common level of provenance)

Molecule-level and graph-level provenance (having provenance information for composites or collections of RDF triples, but not individual triples)

Document-level provenance and corpus-level provenance (only having provenance information for documents or corpora from which triples are identified)

Scalability is a concern when deciding the level and extent to which provenance data can be retained

==== What kinds of information does provenance cover? ====
Domain-agnostic information types:

* Creation of the data
* Publication of the data
* Distribution of the data
* Copyright information
* Modification and revision history
* Current validity

Domain-specific provenance ontologies: defined for BBC, US Government, scientific experiments

DeFacto tool for deep fact validation on the web: [[/github.com/DeFacto/DeFacto|https://github.com/DeFacto/DeFacto]]

==== [[question]] What additional context beyond provenance could be useful? ====

* Concept drift over time (in general entity/relation evolution over time)
* Seems like discourse links across papers don’t neatly fit the provenance definition, but are an aspect we want to capture?
* Are there other aspects that provenance doesn’t cover?

==== Links to NLP research ====
Seems like there's a bit of a gap between NLP research

[[question]] What are the points of overlap between subproblems around scholarly knowledge graph provenance and existing NLP research?

(probably a rich opportunity for a position paper - could bei nteresting to NLP venues; e.g., [[NeuRIPS AI for science workshop]]: possible contact: Kexin Huang

* Biggest open questions seem to be:
** scalability vs expressivity, multiple modalities, updation
** Interpretability or transparency: Provenance information can be used to make KGs more transparent, because we have sources that provide evidence for why this fact/relation holds true.
** Commonsense angle: Another broader application where storing context might be helpful could be for commonsense knowledge graphs?
*** Might have an analog in terms of "scholarly" (un)common sense, esp. across disciplinary boundaries (but this also has analogs in cross-cultural barriers to communication)
* Maps to things with some existing body of work
** Scoring functions in KRL: In representation learning for KGs, models are trained to embed entities and relations in a common space and then score (subject, predicate, object) triples according to likelihood - can these scores be use as additional “plausibility” or “validity” metadata from a provenance perspective? However, these scores are usually produced by models that are learning to replicate the structure of the knowledge graph, so they can’t link back to any textual evidence to support the judgements.
** Auxiliary knowledge in graphs: [https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9416312 <nowiki>[2]</nowiki>] lists some work that stores textual descriptions alongside entities, entity images (image-embodied IKRL) and uncertainty score information (ProBase, NELL and ConceptNet).
** Temporal knowledge graphs: [2] is a survey of knowledge graphs from an NLP perspective and highlights temporal knowledge graphs as a key area of research. Temporality is one kind of provenance information. Current directions being explored include
*** Temporal embeddings: extending existing KRL methods for quadruples instead of triples, where time is the fourth entity
*** Entity dynamics: changes in entity states over time
*** Temporal relational dependence (e.g., a person must be born before dying)
*** Temporal logic reasoning: graphs in which temporal information is uncertain.
** Knowledge acquisition: Some work has tried to explore jointly extracting entities/relations from unstructured text and performing knowledge graph completion. This can be a useful way to jointly model unstructured text from previous papers that do not have associated graphs and papers for which discourse graphs have been annotated. In general, joint graph+text embedding techniques seem useful. Additionally, a technique often used to train models to extract relations from text, distant supervision, can probably be leveraged to detect and add provenance information post-hoc. The idea behind distant supervision is to scan text and find sentences that mention both entities involved in the relation, considering such sentences to be potential evidence sentences. But this is a noisy heuristic - a sentence mentioning two connected entities may not be mentioning the relation between them - and will likely require some curation.

[[/link.springer.com/chapter/10.1007/978-3-642-13818-8 32|Application to finding evidence for clinical KBs]]

==== Important contexts to be captured for synthesis of scientific literature ====
[[/dl.acm.org/doi/pdf/10.1145/3227609.3227689|[3]]] proposes a framework to construct a knowledge graph for science. Problems, methods and results are key semantic resources, in addition to people, publications, institutions, grants, and datasets. Four modes of input:

# Bridge existing KGs, ontologies, metadata and information models
# Enable scientists to add their research possibly with some intelligent interface support
# Use automated methods for information extraction and linking
# Support curation and quality assurance by domain experts and librarians

The underlying data model that supports this endeavor can adopt RDF or Linked Data as a scaffold but must add comprehensive provenance, evolution and discourse information. Other requirements include ability to store and query graphs at scale, UI widgets that support collaborative authoring and curation and integration with semi-automated ways of extraction, search and recommendation.

Top-level ontology: research contribution, communicates one or more results in an attempt to address a problem using a set of methods. Top-down design of more specific elements is needed from domain experts across a set of domains.

Infrastructure: KG can be queried and explored by anyone, but registration is required to contribute to the KG (a way to ensure proper authorization and domain expertise?)

KGs need to capture fuzziness: competing evidence, differing definitions and conceptualizations

Interesting question around score for contributions to the scientific KG instead of document-centric metrics like h-indices (potentially more accurate assessment of contributions)

[https://www.researchgate.net/profile/Soeren-Auer/publication/330751750_Open_Research_Knowledge_Graph_Towards_Machine_Actionability_in_Scholarly_Communication/links/5c5e9bc7a6fdccb608b28f6f/Open-Research-Knowledge-Graph-Towards-Machine-Actionability-in-Scholarly-Communication.pdf <nowiki>[4]</nowiki>] has a really nice analogy: when we moved from phone books and maps were digitally transformed, we didn’t just created PDF books with this information, instead we developed new means to organize and access information. Why not push for such a re-organization in scholarly communication too? Building on [3], their ontology also contains: problem statement, approach, evaluation and conclusions. They use RDF with a minor difference: everything can be modeled as an entity with a unique ID. Limited subset of OWL (subclass inference) is supported. Small user study with this tool, but it doesn’t seem like Dafna’s question about utility of KG constructed by someone else or consensus across people were measured. But they do speak to Dafna's question about how painful it is to construct KGs.

so possible good open [[question]]: how might KGs constructed by one set of scientists actually be useful or not for other scientists, and what factors influence whether this is the case?

* [[experiment]] idea: even just starting by compiling any successful instances of adoption of KGs taht span multiple groups would be a good thing to do; [[Peter Murray-Rust]]. maybe [https://www.nlm.nih.gov/research/umls/index.html UMLS] also

Note: Both papers actually reference a fair number of other works in this direction, which could be good follow-up reading

=== Papers I didn’t get to ===
(numbering here does *not* map to numbering in sections above)

[1] [https://pdfs.semanticscholar.org/713b/b398b85b034f2139e08b4ca0f7791fd545bc.pdf?_ga=2.19474043.2123037593.1668226180-648530244.1660769576 Empirical study of RDF reification]

[2] [[/dl.acm.org/doi/pdf/10.1145/3459637.3482330|Maintaining provenance in uncertain KGs]], [[/arxiv.org/pdf/2007.14864.pdf|maintaining provenance in dynamic KGs]]

[3] [[/kaixu.files.wordpress.com/2011/09/provtrack-ickde-submission.pdf|System for provenance exploration]]

[4] [[/www.semanticscholar.org/paper/iKNOW:-A-platform-for-knowledge-graph-construction-Babalou-Costa/3a492a7b2d04221941919f80ca259506866490b3|iKNOW: KG construction for biodiversity]]

[5] [[/eprints.soton.ac.uk/412923/1/WD sources iswc 7 .pdf|Provenance information in a collaborative environment: evaluation of Wikipedia external references]]

[6] [[/arxiv.org/pdf/2210.14846.pdf|ProVe: Automated provenance verification of KGs against text]]

== Understanding knowledge graph transfer ==
I was able to track down my main notes/sources from before and clean them up a little (not *that* much effort :)):

Last version (not most updated, bc export is slooowwwwww from Roam rn) here: https://publish.obsidian.md/joelchan-notes/discourse-graph/questions/QUE+-+How+can+we+best+bridge+private+vs.+public+knowledge

Will clean up based on this: https://roamresearch.com/#/app/megacoglab/page/XHvRRSi_0

TL;DR (can clean up here based on [[Discourse Modeling]] conventions :):

* distributed sensemaking (Kittur, Goyal, etc.; some promise of yes helpful to share)
* sensemaking handoff (limited, but a major focus in intelligence analysis, there are tools and processes for doing this)
* reuse of records/data/stuff in general in CSCW across a bunch of work domains/settings, like aircraft safety, healthcare, etc. (generally talks about why it's hard to reuse stuff from others, need context)
* annotations / social reading (generally negative/mixed)
MG: can we search the literature based on what tool they studied things with?

NO. not right now.

lack of good tools to "refactor" the literature to match those queries

maybe like Elicit? https://elicit.org/search?q=What+is+the+impact+of+creatine+on+cognition%3F&token=01GHRSBKG6P1R9343NBP2ZWZ5B&c-ps=intervention&c-ps=outcome-measured&c-s=What+tool+did+they+study but for everything??

== Compiling graphs to manuscripts ==

=== Overview ===

We'd like to build a prototype of a tool that starts with discourse units (phrases with the category Question/motivation, Method, Evidence, Claim) and uses NLP to generate a draft of a manuscript paragraph.
[[File:Discourse graph to manuscript draft via NLP.png|900x900px]]

=== Purpose ===

Such a tool would speed up a really time consuming aspect of the academic job: drafting grant proposals and manuscripts from content. It would also encourage researchers to generate structured content (questions/claims/evidence) which will get incorporated into a discourse graph.

The benefit to the user is a structured approach to writing papers and grant proposals. Using the tool will introduce researchers to the concept of discourse units, and generate a repository of discourse units that can be turned into discourse graphs.

=== Ideal outcomes ===

(more to add here)

This tool could also enable the micropublication of mini discourse graphs (one question/method/evidence/claim) by generating a draft of the explanatory text.
* Could also integrate into Roam Research graphs, e.g. in Matt's lab, via the Roam GPT-3 extension

=== What we're doing next ===

* Belinda could mock something up in OpenAI playground really quickly for a few papers
** need examples or access to repo
* Matt and Michael will share some examples of papers or content from the discourse graph to use as source data
* Sid can check out [https://github.com/LayBacc/roam-ai Roam AI extension] for incorporation into our roam graph workflow (fork, make modifications etc)
** ([https://www.reddit.com/r/RoamResearch/comments/yigf6q/im_genuinely_fascinated_with_the_roam_ai/ discussion on its usage])
** [https://www.loom.com/share/d152e7a184f94080b8777f595821f43e usage video]

=== Related conversation ===
* Dafna: "compiling" discourse graph to manuscript seems much easier, esp. if have consistent structure and human-in-the-loop
** Similar to brainstorming discussion/ethics statements for a paper given abstract (via GPT-3
* Belinda: how much variation in paper structure within your field?
** some variations by journal

=== Claims in the conversation that need evidence ===
* the majority of empirical research papers in biology have a similar structure (question/ motivation/ evidence (fig.1a)/ claim for each paragraph & figure panel)
* multiple researchers (or students) asked to highlight the questions/claims/evidence text from a paper will highlight similar/consensus text (part of the NLP-to-highlights project)
notes/questions

* may need more than just the sentences, but also mapping to intra-project/paper elements, like figures and tables to

[[File:Screenshot example of GPT-3 task for extracting components from narrative.png|none|thumb]]

== Next Steps ==

* 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

File:Screenshot example of GPT-3 task for extracting components from narrative.png

2022-11-13T15:35:10Z

Joelchan:

screenshot example of GPT-3 task for extracting components from narrative

Workshop Agenda

2022-11-13T14:20:12Z

Joelchan: /* Day 2 (Nov 13) */

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

A concrete example of that co-evolution: participants could volunteer as guinea pigs for tools being built by other participants. Or provide early feedback on preprints.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 convert to your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff --> [[Kickoff "Slides"]]
Recording [https://umd.zoom.us/rec/share/X3l4732OANMOB4f7Og3anVy4cOJLaPcAkt6x9TAgRcTknYwY6dQRz0rIWabavM4K.ykSOL6NR1lydtQVl?startTime=1668263915000 Passcode: Qrd?2c@y HERE].
|-
|09:45 - 10:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Jodi to facilitate welcome / why are we here hellos from everyone.
Joel to summarize TL;DR of people/projects/themes from [[Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:15 - 12:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:15 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. With 6 groups, this gives us up to ~5 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
Recording [https://umd.zoom.us/rec/share/X3l4732OANMOB4f7Og3anVy4cOJLaPcAkt6x9TAgRcTknYwY6dQRz0rIWabavM4K.ykSOL6NR1lydtQVl?startTime=1668273710000 Passcode: Qrd?2c@y HERE].
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Space for any quick reminders of requests from working groups
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing + documenting progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|With 6 groups, this gives us up to ~20 mins per group for sharing/discussion
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!). To help you get up to speed, we've tried to synthesize key entry points in the Discord discussions in the [[Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* We expect that those of you who've already been coalescing into one of the workshop working groups will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!).
* We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Computable Graphs

2022-11-13T06:14:26Z

Joelchan: /* Understanding knowledge graph transfer */

Workshop Agenda

2022-11-13T04:00:52Z

Joelchan: add recording links

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

A concrete example of that co-evolution: participants could volunteer as guinea pigs for tools being built by other participants. Or provide early feedback on preprints.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 convert to your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff --> [[Kickoff "Slides"]]
Recording [https://umd.zoom.us/rec/share/X3l4732OANMOB4f7Og3anVy4cOJLaPcAkt6x9TAgRcTknYwY6dQRz0rIWabavM4K.ykSOL6NR1lydtQVl?startTime=1668263915000 Passcode: Qrd?2c@y HERE].
|-
|09:45 - 10:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Jodi to facilitate welcome / why are we here hellos from everyone.
Joel to summarize TL;DR of people/projects/themes from [[Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:15 - 12:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:15 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. With 6 groups, this gives us up to ~5 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
Recording [https://umd.zoom.us/rec/share/X3l4732OANMOB4f7Og3anVy4cOJLaPcAkt6x9TAgRcTknYwY6dQRz0rIWabavM4K.ykSOL6NR1lydtQVl?startTime=1668273710000 Passcode: Qrd?2c@y HERE].
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|With 6 groups, this gives us up to ~20 mins per group for sharing/discussion
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!). To help you get up to speed, we've tried to synthesize key entry points in the Discord discussions in the [[Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* We expect that those of you who've already been coalescing into one of the workshop working groups will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!).
* We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Computable Graphs

2022-11-12T19:40:48Z

Joelchan:

Computable Graphs

2022-11-12T17:49:19Z

Joelchan: /* First breakout group session */

Computable Graphs

2022-11-12T17:16:33Z

Joelchan:

Kickoff "Slides"

2022-11-12T14:26:56Z

Joelchan: Created page with "== Welcome! == Thank you for joining us!! A small taste of who's here (we're going to hear more throughout today and tomorrow!): * builders of semantic search engines * domain scientists across plant science, chemistry, computational sciences, materials science, cell biology, neuroscience (and more!) * hypertext tool-builders and tinkerers * fediverse/decentralized tool-builders * synthesis-writers * librarians * cognitive scientists * HCI / CSCW / information..."

== Welcome! ==
Thank you for joining us!!

A small taste of who's here (we're going to hear more throughout today and tomorrow!):

* builders of semantic search engines
* domain scientists across plant science, chemistry, computational sciences, materials science, cell biology, neuroscience (and more!)
* hypertext tool-builders and tinkerers
* fediverse/decentralized tool-builders
* synthesis-writers
* librarians
* cognitive scientists
* [[HCI]] / [[CSCW]] / information science researchers
* and more!

See [[Participants]], which includes link to profiles, and browse around the #tables channels to see more details about who's here.

Reminder of our high-level goal: build energy/momentum/resources towards projects that can advance synthesis infrastructures!

Fortuitously this is happening at the same time as [https://www.aaronswartzday.org/ Aaron Swartz day] (more notes from [[Jonny Saunders]]).

== How things are going to go ==

* Quick overview of what we'll do: [[Workshop Agenda]] (scroll down to Phase II; this should be home base today)
* Reminder of [[Code of Conduct]]
* This is your workshop! We suggest, you take or leave our suggestions (this applies to group assignments, group topics, etc.)

== What's been happening / Who's here? ==

* Let's say hello! ([[Jodi Schneider]] to facilitate)

Workshop Agenda

2022-11-12T14:11:23Z

Joelchan: /* Day 1 (Nov 12) */

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

A concrete example of that co-evolution: participants could volunteer as guinea pigs for tools being built by other participants. Or provide early feedback on preprints.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff --> [[Kickoff "Slides"]]
|-
|09:45 - 10:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Jodi to facilitate welcome / why are we here hellos from everyone.
Joel to summarize TL;DR of people/projects/themes from [[Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:15 - 12:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:15 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. With 6 groups, this gives us up to ~5 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|With 6 groups, this gives us up to ~20 mins per group for sharing/discussion
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!). To help you get up to speed, we've tried to synthesize key entry points in the Discord discussions in the [[Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* We expect that those of you who've already been coalescing into one of the workshop working groups will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!).
* We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Workshop Agenda

2022-11-12T03:46:42Z

Joelchan: /* Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 */

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

A concrete example of that co-evolution: participants could volunteer as guinea pigs for tools being built by other participants. Or provide early feedback on preprints.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff
|-
|09:45 - 10:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Jodi to facilitate welcome / why are we here hellos from everyone.
Joel to summarize TL;DR of people/projects/themes from [[Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:15 - 12:15 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:15 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. With 6 groups, this gives us up to ~5 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|With 6 groups, this gives us up to ~20 mins per group for sharing/discussion
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!). To help you get up to speed, we've tried to synthesize key entry points in the Discord discussions in the [[Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* We expect that those of you who've already been coalescing into one of the workshop working groups will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!).
* We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Computable Graphs

2022-11-12T03:45:02Z

Joelchan:

Main Page

2022-11-12T03:38:13Z

Joelchan: /* Shared Materials and Knowledge Base */

Welcome to the '''Synthesis Infrastructures Workshop''' at CSCW 2022! ([https://oasisresearchlab.github.io/synthesis-infrastructures-workshop/ Overview]) The workshop goal is to plan + develop a set of concrete projects around synthesis infrastructures, championed by workshop participants.

[[Participant Onboarding Checklist|'''Participant Onboarding''']]:
* [[Code of Conduct]]

[[Workshop Agenda|'''Workshop Agenda''']]:

* Phase I (thru Nov. 11): pre-workshop project formation
* Phase II (Nov. 12–13): synchronous working and feedback sessions

== Shared Materials and Knowledge Base ==

* [[Resources]]: docs, videos, code, ... (may link to files in our [https://drive.google.com/drive/u/0/folders/169IIfb31zur1GYeltP_s3b8kvbfpUT6iQa2UTozch7nM-1vPtSjnaoKjtEmZe3_gPBuvX89g shared drive])
* [[Technologies]]: protocols, metadata, networks, ...
* [[Concepts]]: vocabularies, ...
* [[Reading List]]

=== Groups ===

During the workshop, participants will be part of one or several [[Groups]] (See [[:Category:Group]])

=== Projects ===

Each group will have one or several projects (See [[:Category:Project]])

* [[Projects]] - within and beyond the workshop
* [[Project Ideas]]
** [[Project Ideas#Translate%20Logseq%20Knowledge%20Graph%20to%20Systems%20Biology%20Network%20Diagrams|Translate Logseq KGs to Systems-Biology Network Diagrams]]
** [[Project Ideas#Linked%20Data%20Publishing%20On%20Activitypub|Linked Data Publishing On Activitypub]]
** [[Project Ideas#Making%20Discourse%20Graphs%20Indexable%20%26%20Discoverable|Making Discourse Graphs Indexable & Discoverable]]
** [[Project Ideas#Federated knowledge synthesis|Federated knowledge synthesis]]

== Workshop Infrastructure ==

* [[Wiki]]
* [[Discord]] ([[Discord Messages]])
* [[WikiBot]] (linking the two)

== Organization ==

* [[Table Assignments]]
* [[Participants]]
* [[Organizers]]
* [[Lessons Learned]]

== Meta ==

Information about this wiki

* [[Special:Categories|Categories]], [[Special:Templates|Templates]]
* [[Semantic Wiki Guide]] : [[Special:Forms|Forms]], [[Special:Properties|Properties]]
* MediaWiki [[mediawikiwiki:Special:MyLanguage/Help:Contents|User's Guide]]

Computable Graphs

2022-11-12T03:28:40Z

Joelchan:

Interfaces

2022-11-12T03:23:42Z

Joelchan:

{{Group
|Decription=How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?
|Topics=Documents, HCI
|Discord Channel Name=#interfaces
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386439575240704
|Members=Elianna DeSota, Jodi Schneider, Jordan Wick, Joseph Chee Chang, Pooja Upadhyay, Jay Patel
}}
[[Category:Group]]

Related to:
* [[Related To::HCI]]

Social Systems

2022-11-12T03:23:34Z

Joelchan:

{{Group
|Decription=How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?
|Topics=Incentive Systems
|Discord Channel Name=#social-systems
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386737836412928
|Members=Angelina Lesnikova, Eirini Malliaraki, Martin Karlsson, Matt Clancy, Matthew Evans, Pao Siangliulue, Silvia Bessa, Valerii Kremnev
|Buddies=Peer Review
}}

Social Systems

2022-11-12T03:22:33Z

Joelchan:

{{Group
|Decription=How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?
|Topics=Incentive Systems
|Discord Channel Name=#social-systems
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386737836412928
|Members=Eirini Malliaraki, Martin Karlsson, Matt Clancy, Matthew Evans, Pao Siangliulue, Silvia Bessa, Angelina Lesnikova, Valerii Kremnev, Jay Patel
|Buddies=Peer Review
}}

Computable Graphs

2022-11-12T03:21:21Z

Joelchan:

Synthesizing Social Media

2022-11-12T03:20:41Z

Joelchan:

{{Group
|Decription=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.)?
|Topics=Discovery, Scientific Publishing, ActivityPub
|Projects=Linked Data Publishing On Activitypub
|Discord Channel Name=#linked-data-activitypub
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1038983225348993184
|Members=Benjamin Goering, Jonny Saunders, Konrad Hinsen, Ronen Tamari, Amy Zhang, Nouran Soliman, Michael Toomim
}}

Main Page

2022-11-12T03:08:55Z

Joelchan: /* Groups */

Welcome to the '''Synthesis Infrastructures Workshop''' at CSCW 2022! ([https://oasisresearchlab.github.io/synthesis-infrastructures-workshop/ Overview]) The workshop goal is to plan + develop a set of concrete projects around synthesis infrastructures, championed by workshop participants.

[[Participant Onboarding Checklist|'''Participant Onboarding''']]:
* [[Code of Conduct]]

[[Workshop Agenda|'''Workshop Agenda''']]:

* Phase I (thru Nov. 11): pre-workshop project formation
* Phase II (Nov. 12–13): synchronous working and feedback sessions

== Shared Materials and Knowledge Base ==

* [[Resources]]: docs, videos, code, ...
* [[Technologies]]: protocols, metadata, networks, ...
* [[Concepts]]: vocabularies, ...

=== Groups ===

During the workshop, participants will be part of one or several [[Groups]] (See [[:Category:Group]])

=== Projects ===

Each group will have one or several projects (See [[:Category:Project]])

* [[Projects]] - within and beyond the workshop
* [[Project Ideas]]
** [[Project Ideas#Translate%20Logseq%20Knowledge%20Graph%20to%20Systems%20Biology%20Network%20Diagrams|Translate Logseq KGs to Systems-Biology Network Diagrams]]
** [[Project Ideas#Linked%20Data%20Publishing%20On%20Activitypub|Linked Data Publishing On Activitypub]]
** [[Project Ideas#Making%20Discourse%20Graphs%20Indexable%20%26%20Discoverable|Making Discourse Graphs Indexable & Discoverable]]
** [[Project Ideas#Federated knowledge synthesis|Federated knowledge synthesis]]

== Workshop Infrastructure ==

* [[Wiki]]
* [[Discord]] ([[Discord Messages]])
* [[WikiBot]] (linking the two)

== Organization ==

* [[Table Assignments]]
* [[Participants]]
* [[Organizers]]
* [[Lessons Learned]]

== Meta ==

Information about this wiki

* [[Special:Categories|Categories]], [[Special:Templates|Templates]]
* [[Semantic Wiki Guide]] : [[Special:Forms|Forms]], [[Special:Properties|Properties]]
* MediaWiki [[mediawikiwiki:Special:MyLanguage/Help:Contents|User's Guide]]

Interfaces

2022-11-12T03:07:25Z

Joelchan:

{{Group
|Decription=How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?
|Topics=Documents, HCI
|Discord Channel Name=#interfaces
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386439575240704
|Members=Elianna DeSota, Jordan Wick, Joseph Chee Chang, Pooja Upadhyay, Jodi Schneider
}}
[[Category:Group]]

Related to:
* [[Related To::HCI]]

Interdisciplinary Models

2022-11-12T02:55:09Z

Joelchan:

{{Group
|Decription=How do we define minimal information models tuned for synthesis that can interoperate across various disciplines?
|Topics=Interoperability
|Discord Channel Name=#interdisciplinary-models
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040385502026682408
|Members=James Howison, Paul Itoi, Peter Murray-Rust, Wayne Lutters
}}

Discourse Modeling

2022-11-12T02:53:11Z

Joelchan:

{{Group
|Decription=Implement Discourse Graph schema in Semantic MediaWiki. Query Discourse Graph contents through SMW sparql endpoint. Visualize and publish Discourse Graph contents.
|Topics=Discourse Graphs, SPARQL
|Projects=Making Discourse Graphs Indexable & Discoverable
|Discord Channel Name=#discourse-modeling
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1038988750677606432
|Members=Arthur Perret, Karola Kirsanow, Kyle MacLaury, Peter Murray-Rust
|Description=Implement Discourse Graph schema in Semantic MediaWiki. Query Discourse Graph contents through SMW sparql endpoint. Visualize and publish Discourse Graph contents.
}}
=== Potential Actions ===
* Implement the Discourse Graph schema within the workshop's Semantic MediaWiki instance
** This may be duplicated by [[Making Discourse Graphs Indexable & Discoverable]]
* [[Incorporate models/algorithms into Semantic MediaWiki]]
* [[Access discourse and knowledge representations in the SMW instance]]
* Compute with the returned data
** potentially using models/algorithms from the wiki
* Visualize the results of the computation
* Publish the visualizations back to the SMW instance

=== Modules ===
There are other
* [[Semantic MediaWiki]]
** Front End
*** Embed CloudObjects from Wolfram Cloud
*** User chooses model and specifies input parameters
*** User applies model to input parameters
**** Call API that executes
** rdf database
*** [[SPARQL]] endpoint
* Wolfram Cloud
** Use [https://reference.wolfram.com/language/GraphStore/ref/SPARQLExecute.html SPARQLExecute] to call the SPARQL endpoint
** Apply Model to query results
** Publish visualizations as CloudObjects
** Publish API that executes model/algorithm

== Discord ==

{{Message
|Author=joelchan86
|Avatar=https://cdn.discordapp.com/avatars/322545403876868096/6dd171845a7a4e30603d98ae510c77b8.png?size=1024
|Date Sent=22-11-10 15:55:39
|Channel=discourse graphs
|Text=we think the problem now is user-friendly tools and workfows that can create discourse graph structures, and have seen some exciting progress across a bunch of new user-facing "personal wikis". but bridging from personal to communal is still a challenge, partially bc of tooling.

this is why i'm excited about the [[Discourse Modeling]] idea, which i sort of understand as a way to try to instantiate something like [[Discourse Graphs]] into a wiki (bc wikis have a lot more in-built affordances for collaboration, such as edit histories, talk pages, etc.), which may hopefully lead to a lower barrier to entry for collaborative discourse graphing.

a high hope is that we can develop a process that is easy enough to understand and implement that can then be applied to discourse graphing the IPCC or similarly large body of research on a focused, contentious, interdisciplinary topic.

other examples include:
- effects of masks on community transmission (can't do decisive RCTs, need to synthesize)
- effects of social media on political (dys)function: (existing crowdsourced lit review here, in traditional narrative form: https://docs.google.com/document/d/1vVAtMCQnz8WVxtSNQev_e1cGmY9rnY96ecYuAj6C548/edit#)
|Link=https://discord.com/channels/1029514961782849607/1040214388554084372/1040293673851691059
}}

Interfaces

2022-11-12T02:52:10Z

Joelchan:

{{Group
|Decription=How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?
|Topics=Documents, HCI
|Discord Channel Name=#interfaces
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386439575240704
|Members=Elianna DeSota, Jordan Wick, Joseph Chee Chang, Pooja Upadhyay, Joel Chan
}}
[[Category:Group]]

Related to:
* [[Related To::HCI]]

Sílvia Bessa

2022-11-12T02:43:13Z

Joelchan: Created page with "{{Participant}} {{Workshop Submission}}"

Social Systems

2022-11-12T02:42:24Z

Joelchan:

{{Group
|Decription=How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?
|Topics=Incentive Systems
|Discord Channel Name=#social-systems
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386737836412928
|Members=Eirini Malliaraki, Martin Karlsson, Matt Clancy, Matthew Evans, Pao Siangliulue, Silvia Bessa
|Buddies=Peer Review
}}

Interfaces

2022-11-12T02:34:38Z

Joelchan:

{{Group
|Decription=How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?
|Topics=Documents, HCI
|Discord Channel Name=#interfaces
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1040386439575240704
|Members=Elianna DeSota, Jordan Wick, Joseph Chee Chang, Pooja Upadhyay
}}
[[Category:Group]]

Related to:
* [[Related To::HCI]]

Main Page

2022-11-12T02:32:43Z

Joelchan: remove link to workshop working groups

Welcome to the '''Synthesis Infrastructures Workshop''' at CSCW 2022! ([https://oasisresearchlab.github.io/synthesis-infrastructures-workshop/ Overview]) The workshop goal is to plan + develop a set of concrete projects around synthesis infrastructures, championed by workshop participants.

[[Participant Onboarding Checklist|'''Participant Onboarding''']]:
* [[Code of Conduct]]

[[Workshop Agenda|'''Workshop Agenda''']]:

* Phase I (thru Nov. 11): pre-workshop project formation
* Phase II (Nov. 12–13): synchronous working and feedback sessions

== Shared Materials and Knowledge Base ==

* [[Resources]]: docs, videos, code, ...
* [[Technologies]]: protocols, metadata, networks, ...
* [[Concepts]]: vocabularies, ...

=== Groups ===

During the workshop, participants will be part of one or several groups (See [[:Category:Group]])

* [[Groups]]

=== Projects ===

Each group will have one or several projects (See [[:Category:Project]])

* [[Projects]] - within and beyond the workshop
* [[Project Ideas]]
** [[Project Ideas#Translate%20Logseq%20Knowledge%20Graph%20to%20Systems%20Biology%20Network%20Diagrams|Translate Logseq KGs to Systems-Biology Network Diagrams]]
** [[Project Ideas#Linked%20Data%20Publishing%20On%20Activitypub|Linked Data Publishing On Activitypub]]
** [[Project Ideas#Making%20Discourse%20Graphs%20Indexable%20%26%20Discoverable|Making Discourse Graphs Indexable & Discoverable]]
** [[Project Ideas#Federated knowledge synthesis|Federated knowledge synthesis]]

== Workshop Infrastructure ==

* [[Wiki]]
* [[Discord]] ([[Discord Messages]])
* [[WikiBot]] (linking the two)

== Organization ==

* [[Table Assignments]]
* [[Participants]]
* [[Organizers]]
* [[Lessons Learned]]

== Meta ==

Information about this wiki

* [[Special:Categories|Categories]], [[Special:Templates|Templates]]
* [[Semantic Wiki Guide]] : [[Special:Forms|Forms]], [[Special:Properties|Properties]]
* MediaWiki [[mediawikiwiki:Special:MyLanguage/Help:Contents|User's Guide]]

Workshop Agenda

2022-11-11T04:25:08Z

Joelchan: /* Detailed instructions */

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Workshop Working Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff
|-
|09:45 - 10:00 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel to summarize TL;DR of people/projects/themes from [[Workshop Working Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:00 - 12:00 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:00 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. Assuming ~6 groups, this gives us up to ~6-7 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Assuming ~6 groups, this gives us up to ~20 mins for sharing/discussion for each working group.
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!). To help you get up to speed, we've tried to synthesize key entry points in the Discord discussions in the [[Workshop Working Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* We expect that those of you who've already been coalescing into one of the workshop working groups will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!).
* We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Workshop Agenda

2022-11-11T04:23:56Z

Joelchan: edit day of instructions/schedule

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities and Schedule ====
The organizing team has synthesized (based on discussions in the pre-workshop phase, as well as workshop submissions) a number of proposed [[Workshop Working Groups]] (3 have coalesced substantially and were created by request from participants, and ~5 are latent/forming).

The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with a brief report back, and then culminating in a second/final report back with feedback/discussion from other participants on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). We're limiting synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff
|-
|09:45 - 10:00 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel to summarize TL;DR of people/projects/themes from [[Workshop Working Groups]] so far so everyone is on the same page before joining their working groups
|-
|10:00 - 12:00 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|12:00 - 12:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. Assuming ~6 groups, this gives us up to ~6-7 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Assuming ~6 groups, this gives us up to ~20 mins for sharing/discussion for each working group.
|}

==== Detailed instructions ====

* We're expecting several of you to join us for the first time on Saturday (we're glad you're joining us!!), so we've tried to synthesize key entry points in the Discord discussions in the [[Workshop Working Groups]] descriptions. We've also put down some of your names where we thought you might be interested in a working group. Feel free to vote with your feet, though! They are just suggestions.
* Those of you who've already been coalescing into one of the workshop working groups, will join that particular working group. Newcomers can feel free to self-select into any of the proposed working groups according to our suggestions or not (it's ok if some of the latent/forming ones don't gain critical mass; they're just proposals!). We'll make a Zoom breakout room available for you, but you can also choose to do things on Discord.
* Some of the projects will be concrete enough that you'll spend most of your time working on a concrete artifact and documenting progress/resources/challenges in the group page. Other projects/themes might be best approached by discussing/sharing issues/resources, and documenting learnings and questions in the group page.
* Working groups are encouraged to self-organize in the time between Day 1 and Day 2 to continue making progress on projects/discussions.
* The focus of Day 2 is on synthesizing and sharing back what has been accomplished/learned and energy for carrying forward connections/ideas/momentum past the workshop.

Workshop Working Groups

2022-11-11T04:02:52Z

Joelchan: /* Who */

= Coalesced =

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

* Group Page: [[Computable Graphs]]
* 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 ===

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

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

=== Progress so far ===

Some resources:

* 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" ==

* Group Page: [[Synthesizing Social Media]]
* Project Pages: [[Linked Data Publishing On Activitypub]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983225348993184 #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 (add/edit/remove your name as desired!) ===

* [[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 ===

Resources

* 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) ===

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 ==

* Group page: [[Discourse Modeling]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038988750677606432 #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 <code>#discourse-modeling</code> channel

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

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

* [[Kyle MacLaury]]
* [[Peter Murray-Rust]]
* [[Karola Kirsanow]]?
* [[Joel Chan]] also interested in assisting

=== Progress so far ===

* [[Discourse Modeling]]
* [[Making Discourse Graphs Indexable & Discoverable]]

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

= Latent/forming =

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

* Group page: [[Interdisciplinary Models]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #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 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!) ===

* [[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 ==

* Group Page: [[Interfaces]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040386439575240704 #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!) ===

* [[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 ===

Resources

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

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

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

* [[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 ===

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

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

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

=== What ===

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

* [[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 ==

* Group page: [[Mental Models]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040470706271555706 #mental-models]

=== 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!) ===

* [[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) ===

Workshop Working Groups

2022-11-11T03:56:15Z

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

= Coalesced =

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

* Group Page: [[Computable Graphs]]
* 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 ===

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 ===

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

=== Progress so far ===

Some resources:

* 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" ==

* Group Page: [[Synthesizing Social Media]]
* Project Pages: [[Linked Data Publishing On Activitypub]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983225348993184 #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 ===

* [[Ronen Tamari]] (lead?)
* [[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 ===

Resources

* 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) ===

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 ==

* Group page: [[Discourse Modeling]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038988750677606432 #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 <code>#discourse-modeling</code> channel

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

=== Who ===

* [[Kyle MacLaury]]
* [[Peter Murray-Rust]]
* [[Karola Kirsanow]]?
* [[Joel Chan]] also interested in assisting

=== Progress so far ===

* [[Discourse Modeling]]
* [[Making Discourse Graphs Indexable & Discoverable]]

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

= Latent/forming =

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

* Group page: [[Interdisciplinary Models]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040385502026682408 #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 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 ===

* [[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 ==

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

* [[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 ===

Resources

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

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

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

* [[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

* [[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 ===

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

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

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

=== 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 ==

* Group page: [[Mental Models]]
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040470706271555706 #mental-models]

=== 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 ===

[[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) ===

Synthesizing Social Media

2022-11-11T03:54:29Z

Joelchan: Created page with "{{Group}}"

Workshop Working Groups

2022-11-10T19:18:29Z

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

= 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) ===

Main Page

2022-11-10T19:14:37Z

Joelchan: /* Shared Material/Knowledge Base */

== Welcome! ==
* [[Participant Onboarding Checklist]]
* [[Workshop Agenda]]
* [[Code of Conduct]]

== Shared Material/Knowledge Base ==
* [[Workshop Working Groups]]
* [[Project Ideas]]
* Existing [[Projects]]
* [[Resources]]
* [[Technologies]]
* [[Concepts]]

== Workshop Infrastructure ==

* [[WikiBot]]
* [[Discord Messages]]
* [[Discord]]
* [[Wiki]]

== Organization ==

* [[Table Assignments]]
* [[Participants]]
* [[Organizers]]
* [[Lessons Learned]]

== Meta ==

Information about the wiki

* [[Special:Categories]]
* [[Special:Templates]]
* [[Special:Forms]]
* [[Special:Properties]]
* [[Semantic Wiki Guide]]
* Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

Elizabeth Vu

2022-11-10T18:48:32Z

Joelchan: Created page with "{{Participant |Timezone=America/New York (GMT−05:00/GMT−04:00) |Affiliation=Sloan Foundation }} {{Workshop Submission |Interest=We are exploring best practices for distributed collaborative scientific work. Just hoping to meet others in this space! |Frame=Researcher }}"

{{Participant
|Timezone=America/New York (GMT−05:00/GMT−04:00)
|Affiliation=Sloan Foundation
}}
{{Workshop Submission
|Interest=We are exploring best practices for distributed collaborative scientific work. Just hoping to meet others in this space!
|Frame=Researcher
}}

Nouran Soliman

2022-11-10T18:47:25Z

Joelchan: Created page with "{{Participant |Timezone=America/New York (GMT−05:00/GMT−04:00) |Projects=LiTweeture |Table Assignment=Table 4 }} {{Workshop Submission |Interest=I am very interested in scholarly communication. I have been exploring in my projects ideas around how scholars have discussions online and exchange paper recommendations, and how they present their identities online. I am building systems to navigate social issues around these ideas. I believe my work is super relevant to t..."

{{Participant
|Timezone=America/New York (GMT−05:00/GMT−04:00)
|Projects=LiTweeture
|Table Assignment=Table 4
}}
{{Workshop Submission
|Interest=I am very interested in scholarly communication. I have been exploring in my projects ideas around how scholars have discussions online and exchange paper recommendations, and how they present their identities online. I am building systems to navigate social issues around these ideas. I believe my work is super relevant to the workshop. I would love to meet others who are interested in the same area and discuss ideas there.
|Frame=Tool-builder
|Materials=I am working on a socially-sensitive research tool in collaboration with the Semantic Scholar Research Team, Allen Institute for AI to support scientists in exchanging requests and recommendations of research papers on Twitter. I am currently running a field study and would be very interested to share more about my tool and invite users to try it and discuss the ideas behind it. Learn more here https://litweeture.apps.semanticscholar.org/about
|Organizer Topics=Search
}}

Lessons Learned

2022-11-10T13:36:42Z

Joelchan:

We're gonna add to this.

Test transclusion from [[Leibniz]]:
<blockquote>
{{:Leibniz}}
</blockquote>

Workshop Agenda

2022-11-10T01:46:08Z

Joelchan: date and time

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities ====
The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with progress reports and feedback from other workshop participants, and then culminating in a second/final progress report and closing call to action on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). The intent is to limit synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 your timezone])
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff
|-
|09:45 - 10:10 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0945&p1=419&am=25 your timezone])
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel to summarize TL;DR of people/projects/themes so far so everyone is on the same page before joining their working groups
|-
|10:10 - 11:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&p1=419&ah=1&am=30 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|11:40 - 12:25 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your time zone])
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others. Assuming ~6 groups, this gives us up to ~6-7 mins for brief reporting for each working group. Report back should be mirrored/elaborated in the project/theme wiki page.
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&am=10 your time zone])
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40 ([https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0940&p1=419&ah=1&am=10 your time zone])
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T1040&p1=419&ah=2&am=10 (your timezone)]
|Working group progress reports and discussion, wrap up
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Assuming ~6 groups, this gives us up to ~20 mins for sharing/discussion for each working group.
|}

Workshop Agenda

2022-11-09T22:20:51Z

Joelchan: edit schedule, still need to update time zones

If successful, this workshop should end with a set of concrete projects (or plans for projects) around synthesis infrastructures, championed by workshop participants. We'll aim for this end goal in two phases of activities: 1) pre-workshop onboarding and project formation, and 2) synchronous "live" working and sharing/feedback sessions.

=== Phase I: Pre-Workshop Onboarding and Project/Theme Formation - Friday Oct 28 to Friday Nov 11 ===

==== Goals ====
The goal of this phase is to ''generate and converge'' on a set of ~6 [[Project Ideas|Project ideas]] or themes that participants will be excited to begin working on / discussing during the workshop and (where appropriate) complete after the workshop.

We hope that projects/themes will orient towards some tangible outcomes, which may include (but are not limited to):

* '''Resources''', such as a system map/synthesis of the problem space, synthesis/directory of tools, essential reading list, case study library, or shared synthesis benchmark dataset
* '''Proposals''', such as a study or grant proposal, or an editorial/essay
* '''Prototypes''', such as a sketch of a common synthesis protocol, proof-of-concept of synthesis interoperability, or lo-fi/mid-fi prototype iterations around a common synthesis problem
* '''Data''', such as user feedback / testing of a prototype
* '''Organization''', such as a new organization, or convening of a community

We expect some/many projects to be combinations of these outcome themes/types. We also recognize many of you are coming in with existing tools and prototypes and workflows, so it's totally ok to have "compound projects" (e.g., joint/coordinated prototypes, or joint/coordinated pilot tests of a similar question/feature across a few tools)! We want you to get the most of what you want out of this workshop, and we aim for this outcome-centric structure to facilitate that.

==== Activities ====
Your mission, should you choose to accept it, is to:

* Find a mission
* Find some fellow travelers

We will do this through facilitated conversations and engagements on the [[Discord]].

You have been [[Table Assignments|assigned to an initial "table"]] with other participants to seed initial discussions. The tables are unnamed, but they are not random! The organizers have carefully chosen a mix of people that we think will kickstart a fruitful conversation that can lead to project ideas. NOTE: these are initial seatings, that you can feel free to change! You don't have to stay in your table either! Think of this as a potluck dinner party where we give you an initial seating, but you should feel free to float around, change tables, and start new discussions - whatever brings the right group together for the conversation you want to have! For example, we split up members from teams for more cross-pollination, but please feel free to come back together if you'd rather operate as a unit.

Each table will have an assigned organizer who will moderate and scaffold the discussion to converge towards a project/theme idea associated with 1) one or more ''champions'' and fellow ''collaborators'', 2) a ''project/theme page'' here on the wiki, and 3) a ''project/theme channel'' on the Discord (with a pinned link to the wiki project page) for focused coordination and work/discussion during and after the workshop. The organizers will help you get these set up!

We estimate that participation per week should amount to (spread out across the days/weeks) ~1-2 hrs per week: one way to think about this is to divert some of the time you would spend thinking/discussing these issues on Twitter or in the lab or in your own notebooks/sketchbooks or elsewhere to the shared Discord and wiki for the ~1-2 weeks prior to the workshop.

=== Phase II: Synchronous "Live" Working and Sharing/Feedback Sessions - Saturday & Sunday Nov 12-13 ===

==== Goals ====
The goal of this phase is to iterate on and gain momentum and progress on projects and themes of interest.

There is limited time during the workshop, so priority is on achieving some escape velocity rather than "completing" a project or "closing" a topic/theme. We will consider it a success if each working group ends the workshop with 1) initial ''progress and momentum'' on the project's goals or a distillation of discussion themes, and/or 2) concrete, energized ''plans'' for next steps (e.g., "let's keep working on X and [submit it to Y, etc.])

==== Activities ====
The intent is for progress to be documented on the evolving project/theme pages, which may link to prototypes/wireframes/proposal docs/code repos, or contain reading lists, or other markers of progress to share. Progress will happen via a mix of work sprints (synchronous and asynchronous) over the course of '''Day 1''', along with progress reports and feedback from other workshop participants, and then culminating in a second/final progress report and closing call to action on '''Day 2'''.

The following is the current proposed rough schedule (in US Eastern time). The intent is to limit synchronous joint sessions to ~3 hours in the morning of US East timezone, to maximize overlap in schedules across our major time zones.

===== Day 1 (Nov 12) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:45 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0930&p1=419&am=10 your timezone]
|Welcome!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel, Jonny to kickoff
|-
|09:45 - 10:10 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T0940&am=30 your timezone]
|Launch working groups
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Joel to summarize TL;DR of people/projects/themes so far so everyone is on the same page before joining their working groups
|-
|10:10 - 11:40 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1010&am=30 your timezone]
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Participants work on and/or discuss projects/themes in their working groups
|-
|11:40 - 12:25 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221112T1140&p1=419&am=45 your timezone]
|Working groups report back
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|Working groups report back not just progress but open/new challenges that might connect to others
|-
|Various
|Work sprints / discussion in working groups
|On Discord and wiki
|Working groups continue work / discussion sync/async as they are able
|}

===== Day 2 (Nov 13) =====
{| class="wikitable"
|+
!When (US Eastern)
!What
!Where
!Notes
|-
|09:30 - 09:40
|Welcome back!
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|-
|09:40 - 10:40
|Work sprints / discussion in working groups
|In groups, on Discord voice or Zoom breakouts, as preferred, and on wiki
|Focus on summarizing/finalizing progress and next steps
|-
|10:40 - 12:50 [https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221113T0930&p1=419&ah=3 your timezone]
|Working group progress reports and discussion
|Together, on [https://umd.zoom.us/j/5993447714?pwd=VEI3eStjTERvb1ExVVluL2kxYnIxZz09 Zoom](commentary on Discord)
|
|}

Lessons Learned

2022-11-09T18:25:46Z

Joelchan: Created page with "We're gonna add to this."

We're gonna add to this.

Main Page

2022-11-09T18:25:31Z

Joelchan: /* Organization */

== Welcome! ==
* [[Participant Onboarding Checklist]]
* [[Workshop Agenda]]
* [[Code of Conduct]]

== Shared Material/Knowledge Base ==
* [[Project Ideas]]
* Existing [[Projects]]
* [[Resources]]
* [[Technologies]]
* [[Concepts]]

== Workshop Infrastructure ==

* [[WikiBot]]
* [[Discord Messages]]
* [[Discord]]
* [[Wiki]]

== Organization ==

* [[Table Assignments]]
* [[Participants]]
* [[Organizers]]
* [[Lessons Learned]]

== Meta ==

Information about the wiki

* [[Special:Categories]]
* [[Special:Templates]]
* [[Special:Forms]]
* [[Special:Properties]]
* [[Semantic Wiki Guide]]
* Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

Workshop Agenda

2022-11-08T17:40:34Z

Joelchan: /* Phase I: Pre-Workshop Onboarding and Project Formation - Friday Oct 28 to Friday Nov 11 */

Table Assignments

2022-11-04T21:50:36Z

Joelchan:

{{#ask:
[[Category:Table]]
|?Has Member=Member(s)
|format=broadtable
}}

Table Assignments

2022-11-04T21:50:24Z

Joelchan:

Force update.{{#ask:
[[Category:Table]]
|?Has Member=Member(s)
|format=broadtable
}}

Workshop Agenda

2022-11-04T03:07:58Z

Joelchan:

Workshop Agenda

2022-11-04T03:07:37Z

Joelchan:

Main Page

2022-11-04T03:07:05Z

Joelchan: /* Shared Material/Knowledge Base */

== Welcome! ==
* [[Participant Onboarding Checklist]]
* [[Workshop Agenda]]
* [[Code of Conduct]]

== Shared Material/Knowledge Base ==
* [[Project Ideas]]
* Existing [[Projects]]
* [[Resources]]
* [[Technologies]]

== Workshop Infrastructure ==

* [[WikiBot]]
* [[Discord Messages]]
* [[Discord]]
* [[Wiki]]

== Organization ==

* [[Table Assignments]]
* [[Participants]]
* [[Organizers]]

== Meta ==

Information about the wiki

* [[Semantic Wiki Guide]]
* Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.