Synthesis Infrastructures

Interfaces

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Property "Has Member" (as page type) with input value "The query result could not be obtained from the SPARQL database. This error might be temporary or indicate a bug in the database software." contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.{| style="width: 30em; font-size: 90%; border: 1px solid #aaaaaa; background-color: #f9f9f9; color: black; margin-bottom: 0.5em; margin-left: 1em; padding: 0.2em; float: right; clear: right; text-align:left;" ! style="text-align: center; background-color:#ccccff;" colspan="2" |Interfaces |- ! Description | How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit? |- ! Related Topics | Documents, HCI

|- ! Discord Channel | #interfaces |- ! Facilitator | Jodi Schneider |- ! Members | Jay Patel, Elianna DeSota, Joseph Chee Chang, Pao Siangliulue, Jordan Wick, Jodi Schneider, Konrad Hinsen, Arthur Perret, Pooja Upadhyay

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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:

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?
    • 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
    • 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

Collaborative writing systems

Problems/solutions

Papers and research

Beyond the PDF

Utopia Docs: 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

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

Writing

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