jodischneider.com/blog

While I’m in Cambridge, today members of my Information Quality Lab present a talk and 9 posters as part of the iSchool Research Showcase 2024, noon to 4:30 PM in the Illini Union. View posters from 12 to 1; during the break between presentation sessions 2-2:45; and 4-4:30 PM.

TALK by Dr. Heng Zheng, based on our forthcoming JCDL 2024 paper:
Addressing Unreliability Propagation in Scientific Digital Libraries
Heng Zheng, Yuanxi Fu, M. Janina Sarol, Ishita Sarraf, Jodi Schneider

POSTERS
Addressing Biomedical Information Overload: Identifying Missing Study Designs to Design Multi-Tagger 2.0
Puranjani Das, Jodi Schneider

Assessing the Quality of Pathotic Arguments
Dexter Williams

Cognitive and Behavioral Approaches to Disinformation Inoculation through a Hidden Object Game
Emily Wegrzyn

Distinguishing Retracted Publications from Retraction Notices in Crossref Data
Luyang Si, Malik Oyewale Salami, Jodi Schneider

Harmonizing Data: Discovering “The Girl From Ipanema”
John Rutherford, Liliana Giusti Serra, Jodi Schneider

“I Lost My Job to AI” — Social Movement Emergence?
Ted Ledford, Jodi Schneider

Recognizing People, Organizations, and Locations Mentioned in the News
Xioran Zhou, Heng Zheng, Jodi Schneider

Representation of Socio-technical Elements in Non-English Audio-visual Media
Puranjani Das, Travis Wagner

What People Say Versus What People Do: Developing a Methodology to Assess Conceptual Heterogeneity in a Scientific Corpus
Yuanxi Fu, Jodi Schneider

Check my latest piece, Retract Now: Negating Flawed Research Must Be Quicker — Incentives and streamlined processes can prevent the spread of incorrect science in “Second Opinions”, the editorial section of MedPage Today.

I argue that

“It is urgent to be faster and more responsive in retracting publications.”

Retract Now: Negating Flawed Research Must Be Quicker Jodi Schneider in MedPage Today

Thanks to The OpEd Project, the Illinois’ Public Voices Fellowship, and my coach Michele Weldon (whose newest book is out in July). Editorial writing is part of my NSF CAREER: Using Network Analysis to Assess Confidence in Research Synthesis. The Alfred P. Sloan Foundation funds my retraction research in Reducing the Inadvertent Spread of Retracted Science including the NISO Communication of Retractions, Removals, and Expressions of Concern (CREC) Working Group.

Prof. Jodi Schneider’s Information Quality Lab <https://infoqualitylab.org> seeks a paid graduate hourly researcher ($25/hour) to be a chemistry expert for a computer information system design project. Your work will help us understand a computational chemistry protocol by Willoughby, Jansma, and Hoye (2014 Nature Protocols), and the papers citing this protocol. A code glitch impacted part of the Python script for the protocol; our computer information system aims to determine which citing papers might have been impacted by the code glitch, based on reading the papers.

The project can start as soon as possible and needs to be completed in July or early August 2024. We expect your work to take 15 to 20 hours, paid at $25/hour for University of Illinois Urbana-Champaign graduate students. 

Tasks

• Read and understand a computational chemistry protocol (Willoughby et al. 2014)
• Read Bhandari Neupane et al. (2019) to understand the nature of the code glitch
• Make decisions about whether the main findings are at risk for citing publications. You’ll read sentences around citations to ~80 citing publications.
• Work with an information scientist to design a decision tree to capture the decision-making process.

Required Qualifications

• Enrolled in a graduate program (Master’s or PhD) in chemistry at University of Illinois Urbana-Champaign and/or background in chemistry sufficient to understand Willoughby et al. (2014) and Bhandari Neupane et al. (2019)
• Good verbal and written communication skills
• Interest and/or experience in collaboration

Preferred Qualifications

• Experience in computational chemistry (quantum chemistry or molecular dynamics) preferred
• Interest in informatics or computer systems preferred

How to apply

Please email your CV and a few sentences about your interest in the project to Prof. Jodi Schneider (jodi@illinois.edu). Application review will start June 10, 2024 and continue until the position is filled.

Sample citation sentence for Willoughby et al. 2014

“Perhaps one of the most well-known and almost mandatory “to-read” papers for those initial practitioners of the discipline is a 2014 Nature Protocols report by Willoughby, Jansma, and Hoye (WJH).¹⁰ In this magnificent piece of work, a detailed 26-step protocol was described, showing how to make the overall NMR calculation procedure up to the final decision on the structure elucidation.”

from: Marcarino, M. O., Zanardi, M. M., & Sarotti, A. M. (2020). The risks of automation: A study on DFT energy miscalculations and its consequences in NMR-based structural elucidation. Organic Letters, 22(9), 3561–3565. https://doi.org/10.1021/acs.orglett.0c01001

Bibliography

Bhandari Neupane, J., Neupane, R. P., Luo, Y., Yoshida, W. Y., Sun, R., & Williams, P. G. (2019). Characterization of Leptazolines A–D, polar oxazolines from the cyanobacterium Leptolyngbya sp., reveals a glitch with the “Willoughby–Hoye” scripts for calculating NMR chemical shifts. Organic Letters, 21(20), 8449–8453. https://doi.org/10.1021/acs.orglett.9b03216

Willoughby, P. H., Jansma, M. J., & Hoye, T. R. (2014). A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts. Nature Protocols, 9(3), Article 3. https://doi.org/10.1038/nprot.2014.042

Part 2 of an occasional series on the Empirical Retraction Lit bibliography

Our systematic search for the Empirical Retraction Lit bibliography EXCLUDES retraction notices or retracted publications using database filters. Still, some turn up. (Isn’t there always a metadata mess?)

While most retraction notices and retracted publications can be excluded at the title screening stage, a few make it through to the abstract screening, and, for items with no abstracts, to the full-text screening. Today’s example is “Retraction of unreliable publication“. Kept at the title-screening stage**; no abstract; so it’s part of the full-text screening. PubMed metadata would have told us it’s a “Retraction of Publication” – but this particular record came from Scopus.

The Zotero-provisioned article, “Clinical guidelines: too much of a good thing“, had nothing to do with retraction so I went back to the record (which had this link with the Scopus EID). To see what went wrong, I searched Scopus for EID(2-s2.0-84897800625) which finds the Scopus record, complete with an incorrect DOI: 10.1308/xxx which today takes me to a third article with another DOI.***

Scopus Preview is even more interesting because it shows the EMTREE terms “note” and “retracted article” (which are not so accurate in my opinion):

In my 2020 Scientometrics article, I cataloged challenges in getting to the full-text retraction notice for a single article. It’s not clear how common such errors are, nor how to systematically check for errors.

I’m continuing to think about this, since, for RISRS II, I’m on the lookout for metadata disasters (in research-ese: What are the implications of specific instances of successes and failures in the metadata pipeline, for designing consensus practices?)

This particular retrieval error is due to the wrong DOI – which could affect any article (not just retraction notices). I’ve reported the DOI error to the Scopus document correction team.

It’s helpful that working on the Empirical Retraction Lit bibliography surfaces anomalous situations.

**Keeping “Retraction of unreliable publication” for abstract screening may seem overgenerous. But consider the title “Retractions”. Surely “Retractions” is the title of a bulk retraction notice! Nope, it’s a research article in the Review of Economics and Statistics by Azoulay, Furman, Krieger, and Murray. Thanks, folks. While plurals are more likely than singulars to signal research articles and editorials I try to keep vague/ambiguous titles for a closer look.

***For 10.1308/xxx Crossref just lists this latest article. Same with Scopus.

But my university library system has multiple results – a mystery!

My newest piece is in The Hill today: Science is littered with zombie studies. Here’s how to stop their spread.

Many people think of science as complete and objective. But the truth is, science continues to evolve and is full of mistakes. Since 1980, more than 40,000 scientific publications have been retracted. They either contained errors, were based on outdated knowledge or were outright frauds. 

Identifying these inaccuracies is how science is supposed to work. …Yet these zombie publications continue to be cited and used, unwittingly, to support new arguments. 

Why? Almost always it’s because nobody noticed they had been retracted. 

Science is littered with zombie studies. Here’s how to stop their spread. Jodi Schneider in The Hill

Thanks to The OpEd Project, the Illinois’ Public Voices Fellowship, and my coach Luis Carrasco. Editorial writing is part of my NSF CAREER: Using Network Analysis to Assess Confidence in Research Synthesis. The Alfred P. Sloan Foundation funds my retraction research in Reducing the Inadvertent Spread of Retracted Science including the NISO Communication of Retractions, Removals, and Expressions of Concern (CREC) Working Group.

I’m pleased that the draft Recommended Practice, NISO RP-45-202X, Communication of Retractions, Removals, and Expressions of Concern (CREC) is open for public comment through December 2, 2023. I’m a member of the NISO Working Group which is funded in part by the Alfred P. Sloan Foundation in collaboration with my Reducing the Inadvertent Spread of Retracted Science project.

The NISO CREC Recommended Practice will address the dissemination of retraction information (metadata & display) to support a consistent, timely transmission of that information to the reader (machine or human), directly or through citing publications, addressing requirements both of the retracted publication and of the retraction notice or expression of concern. It will not address the questions of what a retraction is or why an object is retracted.

NISO CREC

Part 1 of an occasional series on the Empirical Retraction Lit bibliography

In 2020, my team released the first version of the Empirical Retraction Lit bibliography, updated a number of times. The last updates are July 2021 (content); September 2021 (taxonomy); December 2022 (JSON/web design giving access to the taxonomy).

The bibliography is part of my Alfred P. Sloan-funded project, Reducing the Inadvertent Spread of Retracted Science, and it has also been an avenue for me to experiment with literature review automation and bibliography web tools. Since August members of my lab have been writing up a review on post-retraction citation, building on work a number of people have done on the review over the past several years. To update the content, we’re also working on a systematic search and screening process.

I expect a substantial number of new items. In July 2021 we had 385 items. After that I’d been estimating perhaps 7 new papers a month, which would mean ~175 new items July 2021-August 2023 (since our systematic search was September 5, 2023). That ballpark number seems plausible now that I’m in the middle of full-text screening. 2+ years is a very long time in retraction research, especially with the attention retraction has been receiving in the past few years!

A number of questions arise in trying to optimize a scoping review update process. Here are just a few:

• Is the search I used last time adequate? Should it be updated or changed in any way?
  • Is date-based truncation appropriate for my search?
  • Is it appropriate to exclude certain items from the initial search (e.g., data, preprints)?
  • Is there a high-precision way to exclude retraction notices and retracted publications when the database indexing is insufficient?
  • Could citation-based searching in one or several sources replace multi-database searching on this topic? What are its precision and recall?
  • Are there additional databases that should be added to the search?
  • Is additional author-based searching relevant?
• What is the most painless and effective way to deduplicate items? (Complicated in my case by retraction notices; retracted publications; and non-English language items that have multiple translations.)
• Which items without abstracts may be relevant in this topic?
• What is the shortest item that can make a research contribution in this topic?
• Is original, “empirical” research a clear and appropriate scope?

Ideally the Empirical Retraction Lit bibliography will become a living systematic review that relies on as much automation and as little human effort as appropriate, with an eye towards monthly updates. My experimentation with existing automation tools makes this plausible. Routinely looking at a few papers a month seems feasible as well, especially since I could repurpose the time I spend in ad-hoc tracking of the literature, which has missed a number of items compared to systematic searching (even some high-profile items in English!).

Automation is also becoming more palatable now that I’ve found errors from the laborious human-led review: at least 2 older, in-scope items that were not included in the July 2021 version of the review, presumably because they were poorly indexed at the time of previous searches; and an informally published item that appears to have been erroneously excluded, presumably due to confusion that we were only excluding data and preprints when the bibliography included a related item.

Of course, for the website, there are a number of open questions:

• How can the bibliography website be made useful for authors, reviewers, and editors? Awareness of related publications becomes even more important because the retraction literature is very scattered and diffuse!
• How can the complex taxonomy of topics be made clear?
• Would “suggest a publication” be a useful addition?

My aims in writing are:

• To share my experience about the tools and processes I’m using.
• To documenting the errors I make and the problems I have. This:
  • will remind me in the future (so I make different mistakes or try different tools).
  • can inform tool development.
  • can inspire systematic analysis of pragmatic information retrieval.
• To identify possible collaborators for the Empirical Retraction Lit bibliography scoping review and website; for finalizing the post-retraction citation review; and for writing other reviews from the scoping review.
• To solicit feedback from various communities working on pragmatic information retrieval, systematic review automation, retraction, library technology, scholarly publishing metadata workflows, literature review methodology, publication ethics, science of science,… more generally.

My Information Quality Lab presents 14 posters as part of the iSchool Research Showcase 2023, Wednesday noon to 4:30 PM in the Illini Union. View posters from 12 to 1; during the break between presentation sessions 2:15-2:45; and 3:30-4:30 PM.

Visualizing Race in Medicine
Chris Wiley

Three-Dimensional Archiving of Native American Artifacts at the Spurlock Museum
David Eby

Harold Baron Digital Archival Research and Publication Project
Divya Pathak

Disinformation Tactics and Designing to Deceive
Emily Wegrzyn

Who Needs a Main Entry, Anyway?
Liliana Giusti Serra, José Fernando Modesto da Silva

Epistemological Responsibility in Law and Science: Sharing the burden
Ted Ledford

How Computable is Scientific Knowledge?
Yuanxi Fu

Unified Framework for Evaluating Confidence in Research Synthesis
Hannah Smith, Yuanxi Fu, Jodi Schneider

Using argument graphs to audit reasoning in empirical scientific publications
Heng Zheng, Yuanxi Fu, Jodi Schneider

Activist Organizations and Their Strategies to Influence the Legalization of Medical Cannabis in Brazil
Janaynne Carvalho do Amaral, Jodi Schneider

Assessing Citation Integrity in Biomedical Publications: Annotation and NLP Models
Janina Sarol, Shufan Ming, Jodi Schneider, Halil Kilicoglu

Can ChatGPT Augment PDF-to-Text Conversion Errors in Scientific Publications?
Janina Sarol, Xuhan Zhang, Tanisha Roman, Jodi Schneider

Analyzing Retraction Indexing Quality in Subject-Specific and Multidisciplinary Databases
Malik Salami, Jodi Schneider

How Knowledge Intermediaries Gather and Make Sense of COVID-19 Information: An Interview Study
Togzhan Seilkhanova, Jodi Schneider

[Updated: 14!]

The Washington Post quoted NIH researcher Paul Hwang: “Amazing findings in medicine are sometimes based on one patient”.

The findings here are a breakthrough discovery in a disease called ME/CFS – commonly known as chronic fatigue syndrome or myalgic encephalomyelitis – which led to a recent PNAS paper. This is an amazing moment: Without biomarkers, it’s been a contested disease “you have to fight to get”.

What really strikes me, though, is the individual interactions that created a space for knowledge production: an email from one citizen (Amanda Twinam) to one scientist (Paul Hwang); “serendipitous correspondence” from another scientist (Brian Walitt) with access to “an entire population” (9 of the 14 tested for the PNAS paper were similar to Amanda). Reading the literature, writing well-timed correspondence, and “hearing about” synergistic work going on in another lab all seem to have contributed.

Mady Hornig, a researcher not involved in the project, told the reporter: “It’s not very common that we do all of these … steps, having doctors who are really persistent about what is happening with one individual and applying a scientific lens.”

But what if we did?

Dumit, Joseph (2006). Illnesses you have to fight to get: Facts as forces in uncertain, emergent illnesses. Social Science & Medicine, 62(3), 577–590. https://doi.org/10.1016/j.socscimed.2005.06.018

Wang, Ping-yuan, Ma, Jin, Kim, Young-Chae, Son, Annie Y., Syed, Abu Mohammad, Liu, Chengyu, Mori, Mateus P., Huffstutler, Rebecca D., Stolinski, JoEllyn L., Talagala, S. Lalith, Kang, Ju-Gyeong, Walitt, Brian T., Nath, Avindra, & Hwang, Paul M. (2023). WASF3 disrupts mitochondrial respiration and may mediate exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome. Proceedings of the National Academy of Sciences, 120(34), e2302738120. https://doi.org/10.1073/pnas.2302738120

Vastag, Brian (2023, September 19). She wrote to a scientist about her fatigue. It inspired a breakthrough. Washington Post. https://www.washingtonpost.com/health/2023/09/17/fatigue-cfs-longcovid-mitochondria/ Temporarily open to read via this gift link.