Synthesis Infrastructures - User contributions [en]

Interfaces

2022-11-12T18:37:23Z

Paopow: Add the people section

{{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

== 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

* '''Collaborative synthesis: what interfaces do we need? What solutions exist today?''' (written from the researcher’s perspective, focusing on digital tools)
** '''What interfaces do we need for collaborative synthesis?'''
*** We need ways to work with materials.
**** This includes:
***** Gathering things (collecting)
***** Breaking them down ('''analyzing''')
***** Organizing them (classifying, tagging, linking)
***** Combining them to create new things ('''synthesizing''')
***** … ?
**** This can be done with:
***** Specialized software (e.g. reference management software for references)
***** Relational databases, '''graph databases'''
***** Outlining, mind mapping
***** '''Hypertext''' (e.g. wikis, plain text files with wikilinks…)
***** … ?
*** We need collaborative writing interfaces that meet our scientific writing needs, which are:
**** Writing citations, math, footnotes, figures, code, mixing different languages/scripts…
**** Producing structured output
**** Automation (e.g. processing citations and generating bibliographies, cross-referencing figure labels, indexes…)
**** Choice of synchronous/asynchronous editing
**** Editorial workflow management
**** … ?
*** We need ways to navigate and share what we're creating
**** Lists
**** Tables
**** Document views
**** Graph views
**** Backlinks
**** … ?
** '''What are our options if we want to do this right now?'''
*** Multiple interoperable tools. This can be:
**** Web applications exchanging data via API?
***** Any examples?
**** Decentralized plain text-based solutions, with collaboration enabled by version control software (e.g. Git). Like Manubot but not document/publication centric.
***** Any examples?
**** …?
*** All-in-one solution
**** Are there existing examples?
***** Semantic software:
****** Semantic MediaWiki
****** Omeka-S
****** …?
**** Are there solutions that could be adapted or expanded to meet our needs?
***** …?

== 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#

Interfaces

2022-11-12T18:26:27Z

Paopow: Update formatting

{{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]]

== 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

== 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

* '''Collaborative synthesis: what interfaces do we need? What solutions exist today?''' (written from the researcher’s perspective, focusing on digital tools)
** '''What interfaces do we need for collaborative synthesis?'''
*** We need ways to work with materials.
**** This includes:
***** Gathering things (collecting)
***** Breaking them down ('''analyzing''')
***** Organizing them (classifying, tagging, linking)
***** Combining them to create new things ('''synthesizing''')
***** … ?
**** This can be done with:
***** Specialized software (e.g. reference management software for references)
***** Relational databases, '''graph databases'''
***** Outlining, mind mapping
***** '''Hypertext''' (e.g. wikis, plain text files with wikilinks…)
***** … ?
*** We need collaborative writing interfaces that meet our scientific writing needs, which are:
**** Writing citations, math, footnotes, figures, code, mixing different languages/scripts…
**** Producing structured output
**** Automation (e.g. processing citations and generating bibliographies, cross-referencing figure labels, indexes…)
**** Choice of synchronous/asynchronous editing
**** Editorial workflow management
**** … ?
*** We need ways to navigate and share what we're creating
**** Lists
**** Tables
**** Document views
**** Graph views
**** Backlinks
**** … ?
** '''What are our options if we want to do this right now?'''
*** Multiple interoperable tools. This can be:
**** Web applications exchanging data via API?
***** Any examples?
**** Decentralized plain text-based solutions, with collaboration enabled by version control software (e.g. Git). Like Manubot but not document/publication centric.
***** Any examples?
**** …?
*** All-in-one solution
**** Are there existing examples?
***** Semantic software:
****** Semantic MediaWiki
****** Omeka-S
****** …?
**** Are there solutions that could be adapted or expanded to meet our needs?
***** …?

== 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#

Interfaces

2022-11-12T17:58:41Z

Paopow: Port the note from Google Doc

{{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]]

== 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

== 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?
*** 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: <nowiki>https://distill.pub/2020/communicating-with-interactive-articles/</nowiki>
** 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 (<nowiki>https://rescognito.com/</nowiki>) 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

* Collaborative synthesis: what interfaces do we need? What solutions exist today? (written from the researcher’s perspective, focusing on digital tools)
** What interfaces do we need for collaborative synthesis?
*** We need ways to work with materials.
**** This includes:
***** Gathering things (collecting)
***** Breaking them down (analyzing)
***** Organizing them (classifying, tagging, linking)
***** Combining them to create new things (synthesizing)
***** … ?
**** This can be done with:
***** Specialized software (e.g. reference management software for references)
***** Relational databases, graph databases
***** Outlining, mind mapping
***** Hypertext (e.g. wikis, plain text files with wikilinks…)
***** … ?
*** We need collaborative writing interfaces that meet our scientific writing needs, which are:
**** Writing citations, math, footnotes, figures, code, mixing different languages/scripts…
**** Producing structured output
**** Automation (e.g. processing citations and generating bibliographies, cross-referencing figure labels, indexes…)
**** Choice of synchronous/asynchronous editing
**** Editorial workflow management
**** … ?
*** We need ways to navigate and share what we're creating
**** Lists
**** Tables
**** Document views
**** Graph views
**** Backlinks
**** … ?
** What are our options if we want to do this right now?
*** Multiple interoperable tools. This can be:
**** Web applications exchanging data via API?
***** Any examples?
**** Decentralized plain text-based solutions, with collaboration enabled by version control software (e.g. Git). Like Manubot but not document/publication centric.
***** Any examples?
**** …?
*** All-in-one solution
**** Are there existing examples?
***** Semantic software:
****** Semantic MediaWiki
****** Omeka-S
****** …?
**** Are there solutions that could be adapted or expanded to meet our needs?
***** …?

== Bibliography ==

=== Useful links ===

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

=== Collaborative writing systems ===

* Manubot: <nowiki>https://manubot.org</nowiki> (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: <nowiki>https://muse.jhu.edu</nowiki> For example: [End Page 316] here: <nowiki>https://muse.jhu.edu/pub/50/article/781390</nowiki>

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

Utopia Docs: <nowiki>https://doi.org/10.1093/bioinformatics/btq383</nowiki>

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

Collaborative writing

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

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. <nowiki>https://doi.org/10.1371/journal.pcbi.1007128</nowiki>

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. <nowiki>https://ceur-ws.org/Vol-2976/paper-2.pdf</nowiki>

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. <nowiki>https://doi.org/10.1145/3272973.3274083</nowiki>

Textbook written:

<nowiki>https://github.com/HoTT/book/</nowiki>

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

Bluebook citation

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

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

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. <nowiki>https://doi.org/10.1038/s41562-019-0541-6</nowiki>

== Original notes ==

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

Interfaces

2022-11-12T07:17:02Z

Paopow: