Synthesis Infrastructures - User contributions [en]

Interfaces

2022-11-13T17:25:05Z

ArthurPerret: /* Miro board */

{{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
|Facilitator=Jodi Schneider
|Members=Elianna DeSota, Jay Patel, Jodi Schneider, Jordan Wick, Joseph Chee Chang, Konrad Hinsen, Pao Siangliulue, Pooja Upadhyay, Arthur Perret
}}
[[Category:Group]]

== What ==

How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?

Jordan Wick: We need to improve the UX of reading papers (not PDFs) in "single-player" mode.

Jodi: We really need narratives. Should we have databases instead of papers? I don't think that databases can take the place of papers.

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

== Who ==
First breakout group session: Jodi, Joseph, Pao, Jay, Jordan, Arthur, Pooja

== Workshop goals ==

* '''Organization'''
** Jodi: what can we map (discourse) of this workshop?
** Jay: we could find a common problem to work on, engaging in cycles of collaboration and competition
*** Similar to how early cognitive science pioneers proposed studying the mind/brain
**** Focus on one thing as a discipline and reach a “thorough” description of it
* '''Questions for workshop'''
** What is needed to build …[missed this part]
** What is missing from current set of tools
** Incentivizing more people to get involved in collaborations - social systems

* '''Projected outcomes'''
** Diagram processes/ types
** Needs and solutions for collaboration, first principles

== Second day outcomes ==

=== Researchers’ needs and options for collaborative synthesis (essay) ===

[https://www.arthurperret.fr/articles/2022-11-13-researchers-needs-and-options-for-collaborative-synthesis.html Published on Arthur’s website]. This essay examines the needs of researchers in relation to collaborative research synthesis, compares them to some the software solutions that exist at the time of writing, and discusses potential ways to progress forward.

=== User's processes and the tools that support them (diagram) ===

Miro board: https://miro.com/app/board/uXjVO7IFHEQ=/

== First day discussions ==

=== What could a tool do for synthesis (wiki style topic page) ===

* '''Processes within tool'''
** - move towards stabilization, but could be never ending - always more things could be added

* Process (joseph)
** '''Individual level:'''
** Discovery - finding right set of papers for literature review
** Sharing papers, notes on how papers were relevant
** '''Collaborative:'''
** Shared document - shuffle around -organizing - Documents relevant!
*** Wiki
*** Shared document Google doc - - commenting/open topics/prioritization topics to go check out
**** Hyperlinks (may have scaling issue)
*** Writing: related work section
*** Synchronized Chat Room is used for syncing on ideas , coordination - works for small groups with similar background knowledge / shared understanding of concepts that may be implicit
**** Might break down for larger groups
**** More diversity of thought & backgrounds
** Identify gaps - subtopics
** Pick out things central to paper
** '''Iteration''', slack communication - converge

* Process (Jodi)
** '''Individual level'''
** Asynchronous: Send people an email about papers to look at.
*** Linear process - share title first, doi, then abstract. Maybe add ideas about it.
*** Copying and pasting a bunch of info is cumbersome
** Early on - overview of the information landscape
*** “Keyword searching” inside Zotero -> Use of terms related to concept
** '''Collaborative:''' Lab Zotero collection
*** Literature at the field level
*** Folders of different subtopics to make sure good coverage
*** [triaging] Manual auditing process when you are looking at 30+ things
** '''Individual level:''' Later - citation chasing (can sometimes become a rabbit hole)
*** Citation context are very useful for this because they point to interesting aspects of a paper
** Writing - one level of synthesis, identifying gaps
*** Sometimes help realize missing area that needs further exploration
** Formal scoping review (similar to medical systematic reviews / meta-analysis)
*** Current tool “EPPI-Reviewer”
*** Comparable concepts, non-comparable but related, develop an '''evolving taxonomy (collaborative)'''
*** One person developing taxonomy, another commenting - linear - putting papers with concept types into categories
*** Ontology collaboration - shared vocabulary
*** Becomes a shared mental model about topic at hand
** '''Highly iterative, not same across projects'''
** Sometimes use multi-modal formats (e.g. diagrams) for synthesis
** Concerns: diffuse topics, discussed differently across subdomains
*** Topics that are under-explored
*** Empirical research (including case studies) Philosophical research would be out of scope

=== Discussion about tools for synthesis ===

* '''Maybe PDFs are not evil?'''
** MVP: moving beyond PDFs is hard, so using them as a starting point to gather insights may help (Jay).
** E.g. claim extraction that users may do from scientific papers, may vary in different paper types (e..g theory)
** Augmenting PDFs?
* '''People consume linearly'''
** PDFs/pages/documents provide narratives that are easier to digest than graph
** Sometimes with evidence maps/databases, it’s nonlinear (practitioner/policy maker searching for interventions)
** Users may have diverse strategies of sensemaking of narrative formats, bringing in background knowledge
** What is the right granular level?
*** Tradeoffs: clear & succinct claims + readability
** Is the “best” way to write the “best” way to read?
* '''The limitation of Wikipedia / large scale collaboration'''
** How do you deal with conflicts and disagreements?
*** [https://arxiv.org/pdf/1712.06414.pdf The Wisdom of Polarized Crowds] (Wikipedia)
*** Argumentation frameworks (Computational Logic, Rhetoric)
*** Conflict resolution literature
** How do you deal with higher coordination costs?
* '''How much support can we provide to scholarly and non-scholarly readers beyond PDFs?'''
** Distill.pub offers some example explorable essays for inspiration
*** Excellent guide: https://distill.pub/2020/communicating-with-interactive-articles/
** Jay did some prototyping of explorable essays for scholars with embedded interactive simulations and received (anecdotal) feedback (old software startup).
** Thomas is working on this issue (Jay would love to collaborate and chat long-term) with his educational psychology/tech background.
*** What are the low-hanging fruits?
*** How can we speed up the process (because it’s time-consuming!)
**** Motivation to contribute? → Consider awarding credits/tokens with Rescognito (https://rescognito.com/) to brag about.
***** Consider beginning in classrooms and interdisciplinary journal clubs (in-person and virtual)
**** UI/UX process
**** Scaffolding
***** Definitions
***** Metaphors-analogies
***** Math annotations
***** Reillustrating figures and annotating them for clarity
***** Multi-modal formats of information for sensemaking
***** Linking to videos, simulations, extra resources for curation purposes
***** Human-generated summaries
****** Could be gone in a wiki tool like Roam Research or Obsidian or even Notion.
****** Metadata for information

== Bibliography ==

=== Useful links ===

* https://zettlr.com
** (a little about it)
* http://www.kialo.com
** (a little about it)
* Polymath (link????)
** Collaborative problem-solving in mathematics.
* Rescognito (https://rescognito.com/)
** (a little about it)
* https://distill.pub/2020/communicating-with-interactive-articles/
** Excellent guide to Distill.pub

=== Collaborative writing systems ===

* Manubot: https://manubot.org (see also related papers below)

=== Problems/solutions ===

* Citing often requires page numbers, especially in fields with long documents. HTML does not natively have page numbers or paragraph numbers.
** Project MUSE papers often have page numbers in the HTML: https://muse.jhu.edu For example: [End Page 316] here: https://muse.jhu.edu/pub/50/article/781390

=== Papers and research ===
'''Beyond the PDF'''

Utopia Docs: [https://doi.org/10.1371/journal.pcbi.0010034 https://doi.org/10.1093/bioinformatics/btq383]

Bourne P (2005) Will a Biological Database Be Different from a Biological Journal? PLoS Comput Biol 1(3): e34. https://doi.org/10.1371/journal.pcbi.0010034

'''Collaborative writing'''

Perkel, Jeffrey M. "Synchronized editing: the future of collaborative writing." Nature 580, no. 7801 (2020): 154-156. https://doi.org/10.1038/d41586-020-00916-6

'''Collaborative writing using Manubot'''

Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, et al. (2019) Open collaborative writing with Manubot. PLOS Computational Biology 15(6): e1007128. https://doi.org/10.1371/journal.pcbi.1007128

Rando, Halie M., Simina M. Boca, Lucy D’Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, and Anthony Gitter. "An open-publishing response to the COVID-19 infodemic." In DISCO2021 at JCDL 2021. CEUR workshop proceedings, vol. 2976. https://ceur-ws.org/Vol-2976/paper-2.pdf

'''Collaborative writing using other systems'''

Ei Pa Pa Pe-Than, Laura Dabbish, and James D. Herbsleb. 2018. Collaborative Writing on GitHub: A Case Study of a Book Project. In Companion of the 2018 ACM Conference on Computer Supported Cooperative Work and Social Computing (CSCW '18). Association for Computing Machinery, New York, NY, USA, 305–308. https://doi.org/10.1145/3272973.3274083

'''Textbook written:'''

https://github.com/HoTT/book/

=== Citation ===
Trigg on hypertext - typing

Bluebook citation

=== Provenance ===
(sometimes using provenance vocabularies/ontologies)

On including different points of view: Europeana 1914-1918: http://www.europeana1914-1918.eu/en/explore

[http://www.europeana1914-1918.eu/en/explore Polarization]

Shi, Feng, Misha Teplitskiy, Eamon Duede, and James A. Evans. "The wisdom of polarized crowds." Nature human behaviour 3, no. 4 (2019): 329-336. https://doi.org/10.1038/s41562-019-0541-6

== Original notes ==

* https://docs.google.com/document/d/1icpvCsKiPkpxaWNRa9eOQ0j2zV1xPPRVl7G8ealRSXc/edit#

== External Documents ==

* [[Arthur Perret]] - https://www.arthurperret.fr/articles/2022-11-13-researchers-needs-and-options-for-collaborative-synthesis.html
* [[Pooja Upadhyay]] - https://miro.com/app/board/uXjVO7IFHEQ=/

Interfaces

2022-11-13T17:11:07Z

ArthurPerret:

{{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
|Facilitator=Jodi Schneider
|Members=Elianna DeSota, Jay Patel, Jodi Schneider, Jordan Wick, Joseph Chee Chang, Konrad Hinsen, Pao Siangliulue, Pooja Upadhyay, Arthur Perret
}}
[[Category:Group]]

== What ==

How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?

Jordan Wick: We need to improve the UX of reading papers (not PDFs) in "single-player" mode.

Jodi: We really need narratives. Should we have databases instead of papers? I don't think that databases can take the place of papers.

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

== Who ==
First breakout group session: Jodi, Joseph, Pao, Jay, Jordan, Arthur, Pooja

== Workshop goals ==

* '''Organization'''
** Jodi: what can we map (discourse) of this workshop?
** Jay: we could find a common problem to work on, engaging in cycles of collaboration and competition
*** Similar to how early cognitive science pioneers proposed studying the mind/brain
**** Focus on one thing as a discipline and reach a “thorough” description of it
* '''Questions for workshop'''
** What is needed to build …[missed this part]
** What is missing from current set of tools
** Incentivizing more people to get involved in collaborations - social systems

* '''Projected outcomes'''
** Diagram processes/ types
** Needs and solutions for collaboration, first principles

== Second day outcomes ==

=== Researchers’ needs and options for collaborative synthesis (essay) ===

[https://www.arthurperret.fr/articles/2022-11-13-researchers-needs-and-options-for-collaborative-synthesis.html Published on Arthur’s website]. This essay examines the needs of researchers in relation to collaborative research synthesis, compares them to some the software solutions that exist at the time of writing, and discusses potential ways to progress forward.

=== Miro board ===

https://miro.com/app/board/uXjVO7IFHEQ=/

== First day discussions ==

=== What could a tool do for synthesis (wiki style topic page) ===

* '''Processes within tool'''
** - move towards stabilization, but could be never ending - always more things could be added

* Process (joseph)
** '''Individual level:'''
** Discovery - finding right set of papers for literature review
** Sharing papers, notes on how papers were relevant
** '''Collaborative:'''
** Shared document - shuffle around -organizing - Documents relevant!
*** Wiki
*** Shared document Google doc - - commenting/open topics/prioritization topics to go check out
**** Hyperlinks (may have scaling issue)
*** Writing: related work section
*** Synchronized Chat Room is used for syncing on ideas , coordination - works for small groups with similar background knowledge / shared understanding of concepts that may be implicit
**** Might break down for larger groups
**** More diversity of thought & backgrounds
** Identify gaps - subtopics
** Pick out things central to paper
** '''Iteration''', slack communication - converge

* Process (Jodi)
** '''Individual level'''
** Asynchronous: Send people an email about papers to look at.
*** Linear process - share title first, doi, then abstract. Maybe add ideas about it.
*** Copying and pasting a bunch of info is cumbersome
** Early on - overview of the information landscape
*** “Keyword searching” inside Zotero -> Use of terms related to concept
** '''Collaborative:''' Lab Zotero collection
*** Literature at the field level
*** Folders of different subtopics to make sure good coverage
*** [triaging] Manual auditing process when you are looking at 30+ things
** '''Individual level:''' Later - citation chasing (can sometimes become a rabbit hole)
*** Citation context are very useful for this because they point to interesting aspects of a paper
** Writing - one level of synthesis, identifying gaps
*** Sometimes help realize missing area that needs further exploration
** Formal scoping review (similar to medical systematic reviews / meta-analysis)
*** Current tool “EPPI-Reviewer”
*** Comparable concepts, non-comparable but related, develop an '''evolving taxonomy (collaborative)'''
*** One person developing taxonomy, another commenting - linear - putting papers with concept types into categories
*** Ontology collaboration - shared vocabulary
*** Becomes a shared mental model about topic at hand
** '''Highly iterative, not same across projects'''
** Sometimes use multi-modal formats (e.g. diagrams) for synthesis
** Concerns: diffuse topics, discussed differently across subdomains
*** Topics that are under-explored
*** Empirical research (including case studies) Philosophical research would be out of scope

=== Discussion about tools for synthesis ===

* '''Maybe PDFs are not evil?'''
** MVP: moving beyond PDFs is hard, so using them as a starting point to gather insights may help (Jay).
** E.g. claim extraction that users may do from scientific papers, may vary in different paper types (e..g theory)
** Augmenting PDFs?
* '''People consume linearly'''
** PDFs/pages/documents provide narratives that are easier to digest than graph
** Sometimes with evidence maps/databases, it’s nonlinear (practitioner/policy maker searching for interventions)
** Users may have diverse strategies of sensemaking of narrative formats, bringing in background knowledge
** What is the right granular level?
*** Tradeoffs: clear & succinct claims + readability
** Is the “best” way to write the “best” way to read?
* '''The limitation of Wikipedia / large scale collaboration'''
** How do you deal with conflicts and disagreements?
*** [https://arxiv.org/pdf/1712.06414.pdf The Wisdom of Polarized Crowds] (Wikipedia)
*** Argumentation frameworks (Computational Logic, Rhetoric)
*** Conflict resolution literature
** How do you deal with higher coordination costs?
* '''How much support can we provide to scholarly and non-scholarly readers beyond PDFs?'''
** Distill.pub offers some example explorable essays for inspiration
*** Excellent guide: https://distill.pub/2020/communicating-with-interactive-articles/
** Jay did some prototyping of explorable essays for scholars with embedded interactive simulations and received (anecdotal) feedback (old software startup).
** Thomas is working on this issue (Jay would love to collaborate and chat long-term) with his educational psychology/tech background.
*** What are the low-hanging fruits?
*** How can we speed up the process (because it’s time-consuming!)
**** Motivation to contribute? → Consider awarding credits/tokens with Rescognito (https://rescognito.com/) to brag about.
***** Consider beginning in classrooms and interdisciplinary journal clubs (in-person and virtual)
**** UI/UX process
**** Scaffolding
***** Definitions
***** Metaphors-analogies
***** Math annotations
***** Reillustrating figures and annotating them for clarity
***** Multi-modal formats of information for sensemaking
***** Linking to videos, simulations, extra resources for curation purposes
***** Human-generated summaries
****** Could be gone in a wiki tool like Roam Research or Obsidian or even Notion.
****** Metadata for information

== Bibliography ==

=== Useful links ===

* https://zettlr.com
** (a little about it)
* http://www.kialo.com
** (a little about it)
* Polymath (link????)
** Collaborative problem-solving in mathematics.
* Rescognito (https://rescognito.com/)
** (a little about it)
* https://distill.pub/2020/communicating-with-interactive-articles/
** Excellent guide to Distill.pub

=== Collaborative writing systems ===

* Manubot: https://manubot.org (see also related papers below)

=== Problems/solutions ===

* Citing often requires page numbers, especially in fields with long documents. HTML does not natively have page numbers or paragraph numbers.
** Project MUSE papers often have page numbers in the HTML: https://muse.jhu.edu For example: [End Page 316] here: https://muse.jhu.edu/pub/50/article/781390

=== Papers and research ===
'''Beyond the PDF'''

Utopia Docs: [https://doi.org/10.1371/journal.pcbi.0010034 https://doi.org/10.1093/bioinformatics/btq383]

Bourne P (2005) Will a Biological Database Be Different from a Biological Journal? PLoS Comput Biol 1(3): e34. https://doi.org/10.1371/journal.pcbi.0010034

'''Collaborative writing'''

Perkel, Jeffrey M. "Synchronized editing: the future of collaborative writing." Nature 580, no. 7801 (2020): 154-156. https://doi.org/10.1038/d41586-020-00916-6

'''Collaborative writing using Manubot'''

Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, et al. (2019) Open collaborative writing with Manubot. PLOS Computational Biology 15(6): e1007128. https://doi.org/10.1371/journal.pcbi.1007128

Rando, Halie M., Simina M. Boca, Lucy D’Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, and Anthony Gitter. "An open-publishing response to the COVID-19 infodemic." In DISCO2021 at JCDL 2021. CEUR workshop proceedings, vol. 2976. https://ceur-ws.org/Vol-2976/paper-2.pdf

'''Collaborative writing using other systems'''

Ei Pa Pa Pe-Than, Laura Dabbish, and James D. Herbsleb. 2018. Collaborative Writing on GitHub: A Case Study of a Book Project. In Companion of the 2018 ACM Conference on Computer Supported Cooperative Work and Social Computing (CSCW '18). Association for Computing Machinery, New York, NY, USA, 305–308. https://doi.org/10.1145/3272973.3274083

'''Textbook written:'''

https://github.com/HoTT/book/

=== Citation ===
Trigg on hypertext - typing

Bluebook citation

=== Provenance ===
(sometimes using provenance vocabularies/ontologies)

On including different points of view: Europeana 1914-1918: http://www.europeana1914-1918.eu/en/explore

[http://www.europeana1914-1918.eu/en/explore Polarization]

Shi, Feng, Misha Teplitskiy, Eamon Duede, and James A. Evans. "The wisdom of polarized crowds." Nature human behaviour 3, no. 4 (2019): 329-336. https://doi.org/10.1038/s41562-019-0541-6

== Original notes ==

* https://docs.google.com/document/d/1icpvCsKiPkpxaWNRa9eOQ0j2zV1xPPRVl7G8ealRSXc/edit#

== External Documents ==

* [[Arthur Perret]] - https://www.arthurperret.fr/articles/2022-11-13-researchers-needs-and-options-for-collaborative-synthesis.html
* [[Pooja Upadhyay]] - https://miro.com/app/board/uXjVO7IFHEQ=/

Interfaces

2022-11-13T17:08:09Z

ArthurPerret:

{{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
|Facilitator=Jodi Schneider
|Members=Elianna DeSota, Jay Patel, Jodi Schneider, Jordan Wick, Joseph Chee Chang, Konrad Hinsen, Pao Siangliulue, Pooja Upadhyay, Arthur Perret
}}
[[Category:Group]]

== What ==

How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?

Jordan Wick: We need to improve the UX of reading papers (not PDFs) in "single-player" mode.

Jodi: We really need narratives. Should we have databases instead of papers? I don't think that databases can take the place of papers.

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

== Who ==
First breakout group session: Jodi, Joseph, Pao, Jay, Jordan, Arthur, Pooja

== Workshop goals ==

* '''Organization'''
** Jodi: what can we map (discourse) of this workshop?
** Jay: we could find a common problem to work on, engaging in cycles of collaboration and competition
*** Similar to how early cognitive science pioneers proposed studying the mind/brain
**** Focus on one thing as a discipline and reach a “thorough” description of it
* '''Questions for workshop'''
** What is needed to build …[missed this part]
** What is missing from current set of tools
** Incentivizing more people to get involved in collaborations - social systems

* '''Projected outcomes'''
** Diagram processes/ types
** Needs and solutions for collaboration, first principles

== Outcomes ==

=== Researchers’ needs and options for collaborative synthesis (essay) ===

[https://www.arthurperret.fr/articles/2022-11-13-researchers-needs-and-options-for-collaborative-synthesis.html Published on Arthur’s website]. This essay examines the needs of researchers in relation to collaborative research synthesis, compares them to some the software solutions that exist at the time of writing, and discusses potential ways to progress forward.

=== Miro board ===

== What could a tool do for synthesis (wiki style topic page) ==

* '''Processes within tool'''
** - move towards stabilization, but could be never ending - always more things could be added

* Process (joseph)
** '''Individual level:'''
** Discovery - finding right set of papers for literature review
** Sharing papers, notes on how papers were relevant
** '''Collaborative:'''
** Shared document - shuffle around -organizing - Documents relevant!
*** Wiki
*** Shared document Google doc - - commenting/open topics/prioritization topics to go check out
**** Hyperlinks (may have scaling issue)
*** Writing: related work section
*** Synchronized Chat Room is used for syncing on ideas , coordination - works for small groups with similar background knowledge / shared understanding of concepts that may be implicit
**** Might break down for larger groups
**** More diversity of thought & backgrounds
** Identify gaps - subtopics
** Pick out things central to paper
** '''Iteration''', slack communication - converge

* Process (Jodi)
** '''Individual level'''
** Asynchronous: Send people an email about papers to look at.
*** Linear process - share title first, doi, then abstract. Maybe add ideas about it.
*** Copying and pasting a bunch of info is cumbersome
** Early on - overview of the information landscape
*** “Keyword searching” inside Zotero -> Use of terms related to concept
** '''Collaborative:''' Lab Zotero collection
*** Literature at the field level
*** Folders of different subtopics to make sure good coverage
*** [triaging] Manual auditing process when you are looking at 30+ things
** '''Individual level:''' Later - citation chasing (can sometimes become a rabbit hole)
*** Citation context are very useful for this because they point to interesting aspects of a paper
** Writing - one level of synthesis, identifying gaps
*** Sometimes help realize missing area that needs further exploration
** Formal scoping review (similar to medical systematic reviews / meta-analysis)
*** Current tool “EPPI-Reviewer”
*** Comparable concepts, non-comparable but related, develop an '''evolving taxonomy (collaborative)'''
*** One person developing taxonomy, another commenting - linear - putting papers with concept types into categories
*** Ontology collaboration - shared vocabulary
*** Becomes a shared mental model about topic at hand
** '''Highly iterative, not same across projects'''
** Sometimes use multi-modal formats (e.g. diagrams) for synthesis
** Concerns: diffuse topics, discussed differently across subdomains
*** Topics that are under-explored
*** Empirical research (including case studies) Philosophical research would be out of scope

== Discussion about tools for synthesis ==

* '''Maybe PDFs are not evil?'''
** MVP: moving beyond PDFs is hard, so using them as a starting point to gather insights may help (Jay).
** E.g. claim extraction that users may do from scientific papers, may vary in different paper types (e..g theory)
** Augmenting PDFs?
* '''People consume linearly'''
** PDFs/pages/documents provide narratives that are easier to digest than graph
** Sometimes with evidence maps/databases, it’s nonlinear (practitioner/policy maker searching for interventions)
** Users may have diverse strategies of sensemaking of narrative formats, bringing in background knowledge
** What is the right granular level?
*** Tradeoffs: clear & succinct claims + readability
** Is the “best” way to write the “best” way to read?
* '''The limitation of Wikipedia / large scale collaboration'''
** How do you deal with conflicts and disagreements?
*** [https://arxiv.org/pdf/1712.06414.pdf The Wisdom of Polarized Crowds] (Wikipedia)
*** Argumentation frameworks (Computational Logic, Rhetoric)
*** Conflict resolution literature
** How do you deal with higher coordination costs?
* '''How much support can we provide to scholarly and non-scholarly readers beyond PDFs?'''
** Distill.pub offers some example explorable essays for inspiration
*** Excellent guide: https://distill.pub/2020/communicating-with-interactive-articles/
** Jay did some prototyping of explorable essays for scholars with embedded interactive simulations and received (anecdotal) feedback (old software startup).
** Thomas is working on this issue (Jay would love to collaborate and chat long-term) with his educational psychology/tech background.
*** What are the low-hanging fruits?
*** How can we speed up the process (because it’s time-consuming!)
**** Motivation to contribute? → Consider awarding credits/tokens with Rescognito (https://rescognito.com/) to brag about.
***** Consider beginning in classrooms and interdisciplinary journal clubs (in-person and virtual)
**** UI/UX process
**** Scaffolding
***** Definitions
***** Metaphors-analogies
***** Math annotations
***** Reillustrating figures and annotating them for clarity
***** Multi-modal formats of information for sensemaking
***** Linking to videos, simulations, extra resources for curation purposes
***** Human-generated summaries
****** Could be gone in a wiki tool like Roam Research or Obsidian or even Notion.
****** Metadata for information

== Bibliography ==

=== Useful links ===

* https://zettlr.com
** (a little about it)
* http://www.kialo.com
** (a little about it)
* Polymath (link????)
** Collaborative problem-solving in mathematics.
* Rescognito (https://rescognito.com/)
** (a little about it)
* https://distill.pub/2020/communicating-with-interactive-articles/
** Excellent guide to Distill.pub

=== Collaborative writing systems ===

* Manubot: https://manubot.org (see also related papers below)

=== Problems/solutions ===

* Citing often requires page numbers, especially in fields with long documents. HTML does not natively have page numbers or paragraph numbers.
** Project MUSE papers often have page numbers in the HTML: https://muse.jhu.edu For example: [End Page 316] here: https://muse.jhu.edu/pub/50/article/781390

=== Papers and research ===
'''Beyond the PDF'''

Utopia Docs: [https://doi.org/10.1371/journal.pcbi.0010034 https://doi.org/10.1093/bioinformatics/btq383]

Bourne P (2005) Will a Biological Database Be Different from a Biological Journal? PLoS Comput Biol 1(3): e34. https://doi.org/10.1371/journal.pcbi.0010034

'''Collaborative writing'''

Perkel, Jeffrey M. "Synchronized editing: the future of collaborative writing." Nature 580, no. 7801 (2020): 154-156. https://doi.org/10.1038/d41586-020-00916-6

'''Collaborative writing using Manubot'''

Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, et al. (2019) Open collaborative writing with Manubot. PLOS Computational Biology 15(6): e1007128. https://doi.org/10.1371/journal.pcbi.1007128

Rando, Halie M., Simina M. Boca, Lucy D’Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, and Anthony Gitter. "An open-publishing response to the COVID-19 infodemic." In DISCO2021 at JCDL 2021. CEUR workshop proceedings, vol. 2976. https://ceur-ws.org/Vol-2976/paper-2.pdf

'''Collaborative writing using other systems'''

Ei Pa Pa Pe-Than, Laura Dabbish, and James D. Herbsleb. 2018. Collaborative Writing on GitHub: A Case Study of a Book Project. In Companion of the 2018 ACM Conference on Computer Supported Cooperative Work and Social Computing (CSCW '18). Association for Computing Machinery, New York, NY, USA, 305–308. https://doi.org/10.1145/3272973.3274083

'''Textbook written:'''

https://github.com/HoTT/book/

=== Citation ===
Trigg on hypertext - typing

Bluebook citation

=== Provenance ===
(sometimes using provenance vocabularies/ontologies)

On including different points of view: Europeana 1914-1918: http://www.europeana1914-1918.eu/en/explore

[http://www.europeana1914-1918.eu/en/explore Polarization]

Shi, Feng, Misha Teplitskiy, Eamon Duede, and James A. Evans. "The wisdom of polarized crowds." Nature human behaviour 3, no. 4 (2019): 329-336. https://doi.org/10.1038/s41562-019-0541-6

== Original notes ==

* https://docs.google.com/document/d/1icpvCsKiPkpxaWNRa9eOQ0j2zV1xPPRVl7G8ealRSXc/edit#

== External Documents ==

* [[Arthur Perret]] - https://www.arthurperret.fr/articles/2022-11-13-researchers-needs-and-options-for-collaborative-synthesis.html
* [[Pooja Upadhyay]] - https://miro.com/app/board/uXjVO7IFHEQ=/

Discourse Modeling

2022-11-12T17:13:24Z

ArthurPerret:

{{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=Federated knowledge synthesis, Making Discourse Graphs Indexable & Discoverable
|Discord Channel Name=#discourse-modeling
|Discord Channel URL=https://discord.com/channels/1029514961782849607/1038988750677606432
|Facilitator=Karola Kirsanow
|Members=Karola Kirsanow, Konrad Hinsen, 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.
}}
== 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 the semantic climate setting that [[Peter Murray-Rust]] is working on

== Now you're playing with templates ==
* <tt>{{</tt><tt> [[:template:source|Source]]}} </tt> template : URL, publisher, publisher-url, date, author, title

{{source
| url = https://synthesis-infrastructures.wiki/Discourse_Modeling
| publisher = Synthesis Infrastructures wiki
| publisher-url = https://synthesis-infrastructures.wiki/index.php?title=Discourse_Modeling
| date = 2022-11-12
| author = Sj
| title = Discourse modeling templates}}

* Evidence :
* Claim :
* Axiom (?) :

== 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

2022-11-12T14:23:34Z

ArthurPerret:

Workshop Working Groups

2022-11-11T17:34:53Z

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

= 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
* [[Arthur Perret]] (can assist with write-up & tests)

=== 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) ===

Arthur Perret

2022-10-29T12:53:03Z

ArthurPerret:

{{Participant
|Timezone=CET (GMT+01:00/GMT+02:00)
|Affiliation=Université Bordeaux Montaigne
|Projects=Cosma
|Table Assignment=Table 5
}}
{{Workshop Submission
|Interest=I am a doctoral student in information science, I will be defending my thesis in December. I have spent the past few years studying personal documentation, document graphs and the use of hypertext for synthesizing individual knowledge. My findings relate to linking as a knowledge organization process; the epistemology of visualization; the importance of link semantics; and the usefulness of interfaces (e.g. contextualized backlinks). Now, I would like to expand my focus from individual work to collaboration, public infrastructures and open science. This would bring me back to an area of expertise, which is digital publishing tools and platforms. I hope to contribute as an early career researcher/rookie tool designer/reflective practitioner, and to contextualize my findings with other people's inquiries. I will bring attention to visualization, ownership of data, folksonomies, and the specific challenges associated with humanities/social sciences research.
|Frame=Practitioner
|Materials=As part of my doctoral research, I designed and oversaw the development of a visualization tool called Cosma. It reads text files written in Markdown with wiki links and generates a standalone HTML file with an interactive graph and a few other tools. More information: https://cosma.graphlab.fr/en/

My peer-reviewed publications are about other topics and I cannot share my dissertation yet, but there are relevant entries from my research blog (in chronological order):

Cosma, from record to graph https://www.arthurperret.fr/blog/2022-01-30-cosma-from-record-to-graph.html

What is the point of a graph view? https://www.arthurperret.fr/blog/2022-02-13-what-is-the-point-of-a-graph-view.html

Analyze, synthesize, visualize: about cards, links & graphs https://www.arthurperret.fr/blog/2022-02-17-analyze-synthesize-visualize.html
|Organizer Topics=Graphs, Documents, Social Systems, Interfaces
}}

Cosma

2022-10-29T12:47:22Z

ArthurPerret: Created page with "Cosma is a document graph visualization tool. It modelizes interlinked Markdown files and renders them as an interactive network in a web interface. More information at https://cosma.graphlab.fr/en/."

Cosma is a document graph visualization tool. It modelizes interlinked Markdown files and renders them as an interactive network in a web interface. More information at https://cosma.graphlab.fr/en/.