From ea59e5b6c5edec416b683cafc1fc16079bef0fe2 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 16:45:52 -0500 Subject: [PATCH 01/10] Fix broken DOI --- content/20.pharmaceuticals.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/20.pharmaceuticals.md b/content/20.pharmaceuticals.md index a20629fbc..418b566b5 100644 --- a/content/20.pharmaceuticals.md +++ b/content/20.pharmaceuticals.md @@ -117,7 +117,7 @@ Similarly, this medication was pursued for COVID-19, but a retrospective cohort Therefore, experience with prior severe threats from HCoV provided some ideas of how to approach the treatment of COVID-19, but it was not clear how effective these measures would be. However, one treatment adapted from prior HCoV outbreaks is currently the best-known treatment for severe cases of COVID-19. -Corticosteroids are a well-known, widely available treatment for pneumonia [@doi:10.1002/14651858.CD007720.pub3; @doi:10.1002/14651858.CD007720.pub2; @doi: 10.1183/09031936.00154107; @doi:10.1007/s00408-007-9020-3; @doi:10.1371/journal.pone.0047926; @doi:10.1186/cc10103] that have also been debated as a possible treatment for ARDS [@doi:10/ggpxzc; @doi:10/gcv2; @doi:10.1378/chest.06-1743; @doi:10.1378/chest.07-0714; @doi:10.1056/NEJMoa051693; @doi:10.1136/bmj.39537.939039.BE]. +Corticosteroids are a well-known, widely available treatment for pneumonia [@doi:10.1002/14651858.CD007720.pub3; @doi:10.1002/14651858.CD007720.pub2; @doi:10.1183/09031936.00154107; @doi:10.1007/s00408-007-9020-3; @doi:10.1371/journal.pone.0047926; @doi:10.1186/cc10103] that have also been debated as a possible treatment for ARDS [@doi:10/ggpxzc; @doi:10/gcv2; @doi:10.1378/chest.06-1743; @doi:10.1378/chest.07-0714; @doi:10.1056/NEJMoa051693; @doi:10.1136/bmj.39537.939039.BE]. Corticosteroids were also used and subsequently evaluated as possible supportive care for SARS and MERS. In general, studies and meta-analyses have not found strong support for efficacy of corticosteroids against mortality in these HCoV infections [@doi:10.1136/thx.2003.017665; @doi:10.1016/j.jinf.2006.01.005; @doi:10.1136/thx.2003.017665; @doi:10.1038/s41375-020-0848-3]; however, others did find that the treatments showed some potential and suggested that greater effects might be revealed by refining treatment protocols, such as dosage and timing [@doi:10.1007/s10156-003-0296-9]. While much of the information available about the corticosteroid treatment of SARS focuses on methylprednisolone and hydrocortisone, availability issues for these drugs at the time led to dexamethasone also being used in North America [@doi:10.1056/NEJMp030072]. From 340c63fd370607e4e506f48ce655e568c9570767 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 16:56:30 -0500 Subject: [PATCH 02/10] Automate consortium members --- content/60.methods.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/content/60.methods.md b/content/60.methods.md index 6242089f6..883c95407 100644 --- a/content/60.methods.md +++ b/content/60.methods.md @@ -214,7 +214,7 @@ This approach allows for a version of record to be maintained alongside the most Currently, three manuscripts have been submitted, with one accepted for publication [@individual-nutraceuticals] and two under revision [@individual-pathogenesis; @individual-pharmaceuticals]. The remaining four manuscripts are in preparation. These manuscripts cover a wide range of topics including the fundamental biology of SARS-CoV-2 (pathogenesis [@individual-pathogenesis] and evolution [@individual-evolution]), biomedical advances in responding to the virus and COVID-19 (pharmaceutical therapeutics [@individual-pharmaceuticals], nutraceutical therapeutics [@individual-nutraceuticals], vaccines [@individual-vaccines], and diagnostic technologies [@individual-diagnostics]), and biological and social factors influencing disease transmission and outcomes [@individual-inequality]. -To date, 50 authors are associated with the consortium (Figure @fig:projectstats). +To date, {{ consortiummembers|length }} authors are associated with the consortium (Figure @fig:projectstats). Efforts to integrate with existing projects providing support for undergraduate students during COVID-19 were also successful. We collaborated with the Immunology Institute at the Mount Sinai School of Medicine to incorporate summaries written by their students, post-docs, and faculty [@url:https://github.com/ismms-himc/covid-19_sinai_reviews; @doi:10.1038/s41577-020-0319-0]. Additionally, two of the consortium authors were undergraduate students recruited through the American Physician Scientist Association's Virtual Summer Research Program. @@ -281,7 +281,8 @@ By facilitating the versioning of text, such platforms also allow for documentat This application of version control holds the potential to improve scientific publishing in a range of disciplines, including those outside of traditional computational fields. While Manubot is a technologically complex tool, this project demonstrates that it can be broadly appealing even outside of technical and/or computational areas of research. -{% if individual is defined and individual == "methods" and format is defined and format == "tex"-%} +{% if individual is defined and individual == "methods" and format is defined and format == "tex" and consortiummembers is defined-%} #### Consortium Members -The COVID-19 Review Consortium is made up of: Vikas Bansal, John P. Barton, Simina M. Boca, Joel D. Boerckel, Christian Brueffer, James Brian Byrd, Stephen Capone, Shikta Das, Anna Ada Dattoli, John J. Dziak, Jeffrey M. Field, Soumita Ghosh, Anthony Gitter, Rishi Raj Goel, Casey S. Greene, Marouen Ben Guebila, Daniel S. Himmelstein, Fengling Hu, Nafisa M. Jadavji, Jeremy P. Kamil, Sergey Knyazev, Likhitha Kolla, Alexandra J. Lee, Ronan Lordan, Tiago Lubiana, Temitayo Lukan, Adam L. MacLean, David Mai, Serghei Mangul, David Manheim, Lucy D'Agostino McGowan, Amruta Naik, YoSon Park, Dimitri Perrin, Yanjun Qi, Diane N. Rafizadeh, Bharath Ramsundar, Halie M. Rando, Sandipan Ray, Michael P. Robson, Vincent Rubinetti, Elizabeth Sell, Lamonica Shinholster, Ashwin N. Skelly, Yuchen Sun, Yusha Sun, Gregory L Szeto, Ryan Velazquez, Jinhui Wang, and Nils Wellhausen +The COVID-19 Review Consortium is made of: +{% for member in consortiummembers %}{{ member }}{% if not loop.last %}, {% endif %}{% endfor %} {%- endif %} From 3f66db62766e9757993dcb70818fe7451bce4c52 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 17:07:07 -0500 Subject: [PATCH 03/10] Combine methods content files and remove problematic URL citations --- content/60.methods.md | 14 ++++++++++---- content/61.methods-ack.md | 5 ----- 2 files changed, 10 insertions(+), 9 deletions(-) delete mode 100644 content/61.methods-ack.md diff --git a/content/60.methods.md b/content/60.methods.md index 883c95407..2f41ed844 100644 --- a/content/60.methods.md +++ b/content/60.methods.md @@ -196,9 +196,9 @@ Additionally, new contributors have continued to join even as the project begins A dot indicates the number of words added or edited by each author each month since March 2020. In order to make the project accessible to individuals from a range of backgrounds, we developed resources explaining how to use GitHub's web interface to develop and edit text and interact with Manubot for individuals with no prior experience working with git or other version control platforms. -We developed tutorials containing visuals to explain how to open an issue, open a pull request, and review a pull request [@url:https://github.com/greenelab/covid19-review/blob/master/CONTRIBUTING.md; @url:https://github.com/greenelab/covid19-review/blob/master/INSTRUCTIONS.md]. +We developed tutorials containing visuals to explain how to open an issue, open a pull request, and review a pull request ( and ). Additionally, the framework for evaluating literature was converted into issue templates to simplify the review of new articles. -Articles were classified as _diagnostic_, _therapeutic_, or _other_, with an associated template developed to guide the review of papers and preprints in each category [@url:https://github.com/greenelab/covid19-review/blob/master]. +Articles were classified as _diagnostic_, _therapeutic_, or _other_, with an associated template developed to guide the review of papers and preprints in each category. A total of 273 new paper issues had been opened as of April 30, 2021. ![ @@ -281,8 +281,14 @@ By facilitating the versioning of text, such platforms also allow for documentat This application of version control holds the potential to improve scientific publishing in a range of disciplines, including those outside of traditional computational fields. While Manubot is a technologically complex tool, this project demonstrates that it can be broadly appealing even outside of technical and/or computational areas of research. -{% if individual is defined and individual == "methods" and format is defined and format == "tex" and consortiummembers is defined-%} -#### Consortium Members +{% if individual is defined and individual == "methods" and format is defined and format == "tex" -%} +{% if consortiummembers is defined-%} +#### Consortium Members {.unnumbered} The COVID-19 Review Consortium is made of: {% for member in consortiummembers %}{{ member }}{% if not loop.last %}, {% endif %}{% endfor %} {%- endif %} + +### Acknowledgements {.unnumbered} +We are grateful to Josh Nicholson and Milo Mordaunt for their support with the scite plugin, and to David Nicholson for the suggestion and feedback to enable the reporting of the locations of spelling errors in the spell-checker tool. +We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data. +{%- endif %} diff --git a/content/61.methods-ack.md b/content/61.methods-ack.md deleted file mode 100644 index c62a9bdb4..000000000 --- a/content/61.methods-ack.md +++ /dev/null @@ -1,5 +0,0 @@ -{% if individual is defined and individual == "methods" and format is defined and format == "tex"-%} -### Acknowledgements {.unnumbered} -We are grateful to Josh Nicholson and Milo Mordaunt for their support with the scite plugin, and to David Nicholson for the suggestion and feedback to enable the reporting of the locations of spelling errors in the spell-checker tool. -We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data. -{%- endif %} From f665c01b26b703d1402d4fad29e08fec910fd1db Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 17:10:36 -0500 Subject: [PATCH 04/10] Cite Our World in Data --- content/60.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/60.methods.md b/content/60.methods.md index 2f41ed844..28dd30127 100644 --- a/content/60.methods.md +++ b/content/60.methods.md @@ -226,7 +226,7 @@ We integrated data into the manuscripts from several sources. Data about worldwide cases and deaths came from the COVID-19 Data Repository by the Center for Systems Science and Engineering at Johns Hopkins University [@https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series]. Similarly, the clinical trials statistics and figure were generated based on data from the University of Oxford Evidence-Based Medicine Data Lab's COVID-19 TrialsTracker [@doi:10.5281/zenodo.3732709]. The evolution of this figure over time is shown in Figure @fig:ebm-trials. -Information about vaccine distribution was extracted from Our World In Data (). +Information about vaccine distribution was extracted from Our World In Data () [@owidcoronavirus]. Figure 1 dynamically integrates data directly from the CORD-19 dataset [@arxiv:2004.10706]. Manubot's bibliographic management capabilities were critical because the amount of relevant literature published far outstripped what we had anticipated at the beginning of the project. From 8c3a0dbc68b8a36f1f1e905c9f3da55ff2f16e98 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 17:16:30 -0500 Subject: [PATCH 05/10] Attribute original template source --- build/assets/acm-pandoc-conf.tex | 3 +++ 1 file changed, 3 insertions(+) diff --git a/build/assets/acm-pandoc-conf.tex b/build/assets/acm-pandoc-conf.tex index 80734e772..5c84c4b06 100644 --- a/build/assets/acm-pandoc-conf.tex +++ b/build/assets/acm-pandoc-conf.tex @@ -1,3 +1,6 @@ +% Adaptation of the template by Wouter Groeneveld +% https://brainbaking.com/post/2021/02/writing-academic-papers-in-markdown/ + \documentclass[sigconf]{acmart} \usepackage{balance} % balancing bibstyles as per request in accepted submission From 6e7593c982c840b91fe2446ff79b4a8f01268fce Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 17:18:14 -0500 Subject: [PATCH 06/10] Remove acknowledgement of contributors who are now authors --- content/70.coi-contribs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/70.coi-contribs.md b/content/70.coi-contribs.md index 8a5b729bd..55afb2615 100644 --- a/content/70.coi-contribs.md +++ b/content/70.coi-contribs.md @@ -14,7 +14,7 @@ ### Acknowledgements -We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data and Vincent Rubinetti and Daniel Himmelstein for feedback on and support with Manubot. +We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data. We thank Yael Evelyn Marshall who contributed writing (original draft) as well as reviewing and editing of pieces of the text but who did not formally approve the manuscript, as well as Ronnie Russell, who contributed text to and helped develop the structure of the manuscript early in the writing process and Matthias Fax who helped with writing and editing text related to diagnostics. We are grateful to the following contributors for reviewing pieces of the text: Nadia Danilova, James Eberwine and Ipsita Krishnan. From 6c98cfbb9d16f01c1731d519a5c0d8d6a2c78ba6 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 21 May 2021 17:33:33 -0500 Subject: [PATCH 07/10] Address cbrueffer review comments Original review https://github.com/greenelab/covid19-review/pull/947#pullrequestreview-649782471 Co-authored-by: Christian Brueffer --- content/60.methods.md | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/content/60.methods.md b/content/60.methods.md index 28dd30127..bd69e50f2 100644 --- a/content/60.methods.md +++ b/content/60.methods.md @@ -6,7 +6,7 @@ The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures presents unique challenges to collaborative science. We sought to apply a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators contributed summaries and critiques of literature via issue templates and contributed literature summaries to a review manuscript as pull requests. -Manubot rendered the manuscript content into pdf, HTML, and docx outputs, and an up-to-date version was always available online. +Manubot rendered the manuscript content into PDF, HTML, and DOCX outputs, and an up-to-date version was always available online. This particular project presented unique challenges that necessitated additions to Manubot. Some challenges related to the technical barrier to entry, as most contributors were from biomedical backgrounds and had limited experience with git. @@ -38,7 +38,7 @@ The result has been the rapid release of data, results, and publications related Over 20,000 articles about COVID-19 were released in the first four months of the pandemic [@doi:10.1053/j.ackd.2020.08.003], and the velocity and volume of information being released led to the pandemic being termed an "infodemic" as well [@doi:10.1053/j.ackd.2020.08.003; @doi:10/ggpx67]. While this influx of information is likely evidence of important work towards understanding the virus and the disease, there are also downsides to the availability of too much information. The downsides of "excessive publication" have been recognized for over forty years, as it was raised as a major concern about the move towards electronic, rather than print, publishing at the turn of the millennium [@doi:10/d3bmnv]. -The contents of the COVID-19 Open Research Dataset (CORD-19) [@arxiv:2004.10706], which was developed in part to assist in efforts to train machine learning algorithms on COVID-19-related text, illustrates the volume of publication relevant to understanding this virus (Figure @fig:cord19-growth). +The contents of the COVID-19 Open Research Dataset (CORD-19) [@arxiv:2004.10706], which was developed in part to assist in efforts to train machine learning algorithms on COVID-19-related text, illustrates the volume of scholarly literature relevant to understanding this virus (Figure @fig:cord19-growth). This resource was developed by querying several sources for terms related to SARS-CoV-2 and COVID-19, as well as the coronaviruses SARS-CoV-1 and MERS-CoV and their associated viruses [@arxiv:2004.10706]. CORD-19 contained {{cord19_total_pubs}} manuscripts as of {{cord19_date_pretty}}. Additional curation by CoronaCentral [@doi:10.1101/2020.12.21.423860] has produced, at present, a set of over 150,000 publications particularly relevant to COVID-19 and these closely related viruses. @@ -56,7 +56,7 @@ With information being produced rapidly through both traditional publishing venu Concerns have been raised that the number of COVID-19 papers being retracted may be higher, or potentially much higher, than is typical, although a thorough investigation of this question will not be possible until more time has elapsed [@doi:10.1080/08989621.2020.1782203; @doi:10.1080/08989621.2020.1793675]. Other papers are updated with corrections or expressions of concern [@doi:10.1080/08989621.2020.1793675;url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers]. These include both preprints and papers published in more traditional venues [@url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers; @url:https://asapbio.org/preprints-and-covid-19]. -Preprints provide a venue for scientists to release findings rapidly but have both the advantage and disadvantage of making research available before it has undergone the peer-review process. +Preprints provide a venue for scientists to release findings rapidly but have both the advantage and disadvantage of making research available before it has undergone the peer review process. However, some traditional publishing venues have also fast-tracked COVID-19 through peer review, leading to questions about whether this research is being held to the usual standards for publication [@doi:10.1111/bioe.12772]. Therefore, monitoring the COVID-19 literature requires not only digesting the high volume of information released but also critically evaluating it and monitoring for subsequent adjustments. @@ -77,7 +77,7 @@ Collaboration via massively open online papers has been identified as a strategy Manubot is an ideal platform for analyzing COVID-19 literature because it facilitates the automatic integration of new data through continuous integration (CI). However, the Manubot workflow can appear intimidating to contributors who are not well-versed in git [@doi:10.5334/kula.63]. The synthesis and discussion of the emerging literature by biomedical scientists and clinicians is imperative to a robust interpretation of COVID-19 research, but in biology, such efforts often rely on What You See Is What You Get tools such as Google Docs, despite the significant limitations of these platforms in the face of excessive publication. -Therefore, we recognized that the problem of synthesizing the COVID-19 literature lent itself well to the Manubot platform, but that the potential technical expertise required to work with Manubot present a significant technical barrier to domain experts. +Therefore, we recognized that the problem of synthesizing the COVID-19 literature lent itself well to the Manubot platform, but that the potential technical expertise required to work with Manubot presented a significant technical barrier to domain experts. Here, we describe efforts to adapt Manubot to handle the extreme case of the COVID-19 infodemic, with the objective of extending manuscript reviewing to develop a centralized platform for summarizing and synthesizing a massive amount of preprints, news stories, journal publications, and data. Unlike prior collaborations built on Manubot, here most contributors came from a biological or medical background. @@ -105,7 +105,7 @@ These contributions were not strictly defined and could range from minor correct Each pull request was reviewed and approved by at least one other contributor before being merged into the main branch. We tagged potential reviewers based on the introductions they had contributed in order to encourage participation. Emphasizing the use of issues and pull requests was designed to encourage authors with and without git experience to discuss papers and provide feedback (both formal and informal) on proposed text additions or changes. -We also used gitter () to promote informal questions and sharing of information among collaborators. +We also used the Gitter chat platform () to promote informal questions and sharing of information among collaborators. #### Utilization and Expansion of Manubot @@ -141,12 +141,12 @@ In order to enable Manubot to pull metadata associated with clinical trials base Other researchers identified the same need [@url:https://forums.zotero.org/discussion/74933/import-from-clinical-trials-registry; @url:https://forums.zotero.org/discussion/77721/add-reference-from-clinical-trials-org]. To implement this feature, we query clinicaltrials.gov to retrieve XML metadata associated with each identifier using JavaScript [@url:https://github.com/zotero/translators/pull/2153]. Then, when Manubot requests clinical trial metadata from the Zotero translation server, it receives a more informative response that includes the trial sponsors, responsible investigators, title, and summary. -We extended Manubot to support directly citing any of the hundreds of Compact Uniform Resource Identifier registered with , including the `clinicaltrials` identifier. +We extended Manubot to support directly citing any of the hundreds of Compact Uniform Resource Identifiers registered with , including the `clinicaltrials` identifier. This extension enables citing a trial as `@clinicaltrials:NCT04280705` instead of `@https://clinicaltrials.gov/ct2/show/NCT04280705`. Another challenge that emerged was that, because of the large number of citations used in this manuscript and the fast-moving nature of COVID-19 research, keeping track of retractions, corrections, and notices of concern became a priority. We implemented a new Manubot plugin to support "smart citations" in the HTML build of manuscripts. -The plugin uses the [Scite](https://scite.ai/) [@doi:10.1101/2021.03.15.435418] service to display a badge below any citation with a DOI. +The plugin uses the [scite](https://scite.ai/) [@doi:10.1101/2021.03.15.435418] service to display a badge below any citation with a DOI. The badge contains a set of icons and numbers that indicate how many times that source has been mentioned, supported, or disputed and whether there have been any important editorial notices, such as retractions or corrections. Using this, we were able to identify references that needed to be reevaluated by an expert. This addition was invaluable given the nature of the project, where we were disseminating rapidly evolving information of great consequence from over a thousand different sources. @@ -162,16 +162,16 @@ The filter enables checking only the manuscript text, ignoring URLs and formatti Manubot can render a manuscript in several formats that serve different purposes. -Prior to this project, Manubot was able to convert the markdown-formatted manuscript to HTML, pdf, and docx formats. -We expanded this functionality to allow individual sections of the manuscript to be exported as separate docx files while still rendering the complete manuscript in HTML and pdf formats. +Prior to this project, Manubot was able to convert the markdown-formatted manuscript to HTML, PDF, and DOCX formats. +We expanded this functionality to allow individual sections of the manuscript to be exported as separate DOCX files while still rendering the complete manuscript in HTML and PDF formats. This development was necessary because the manuscript grew so large that it needed to be split into seven separate papers for journal submission. When exporting an individual section, Manubot customizes the manuscript title, authors, and author contributions to pertain to that specific section. In addition, we expanded the export formats to include partial LaTeX support via Pandoc. -Pandoc converts the markdown content for an individual section to tex and the Citation Style Language JSON, which contains reference metadata generated by Manubot, to BibTeX. +Pandoc converts the markdown content for an individual section to TeX and the Citation Style Language JSON, which contains reference metadata generated by Manubot, to BibTeX. We customized a LaTeX template and reformat the Manubot metadata, such as authors and their affiliations, for the LaTeX template. -The exported tex file requires manual refinement but contains all manuscript content and most of the formatting. +The exported TeX file requires manual refinement but contains all manuscript content and most of the formatting. Because LaTeX is required for manuscript submission in many fields, automating most of the process of converting markdown to a submission-friendly format expands Manubot's potential user base. -Manubot users can write in the simple markdown format, render the manuscript in continuously-updated pdf or interactive HTML formats, and export the manuscript in docx or tex and BibTeX for submission to traditional publishers, taking full advantage of Pandoc's powerful document conversion capabilities and Manubot's automation. +Manubot users can write in the simple markdown format, render the manuscript in continuously-updated PDF or interactive HTML formats, and export the manuscript in DOCX or TeX and BibTeX for submission to traditional publishers, taking full advantage of Pandoc's powerful document conversion capabilities and Manubot's automation. ### RESULTS @@ -186,7 +186,7 @@ For a period of time in summer 2020, a large appendix was erroneously duplicated We received a large amount of interest from the broad community, beginning with coverage of the project by _Nature Toolbox_ [@doi:10.1038/d41586-020-00916-6] and an associated tweet about the project on April 1, 2020 [@url:https://twitter.com/j_perkel/status/1245454628235309057] (Figure @fig:projectstats). Because the GitHub issues and comment systems are relatively similar to other common web activities, we found that authors were able to learn these tools fairly quickly. -Similarly, the gitter chat also presented a low barrier to entry. +Similarly, the Gitter chat also presented a low barrier to entry. The manuscript has continued to grow throughout the first year of the project in both word count and the number of references (Figure @fig:projectstats). Though only a fraction of potential contributors ended up contributing to the text included in the manuscripts (Figure @fig:projectstats), many of these contributors remained engaged over the course of a full year (Figure with dots). Additionally, new contributors have continued to join even as the project begins its second year. @@ -221,6 +221,7 @@ Additionally, two of the consortium authors were undergraduate students recruite Thus, the consortium was successful in providing a venue for researchers across all career stages to continue investigating and publishing at a time when many biomedical researchers were unable to access their laboratory facilities. #### Using Manubot to Investigate COVID-19 + We integrated data into the manuscripts from several sources. Data about worldwide cases and deaths came from the COVID-19 Data Repository by the Center for Systems Science and Engineering at Johns Hopkins University [@https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series]. @@ -246,13 +247,13 @@ This project demonstrates that Manubot can be applied to projects where not all Through the development of cyberinfrastructure both for training novice users to interact with GitHub and simplifying the workflows to allow them to receive many of the benefits of What You See Is What You Get platforms such as Google Docs, we were able to adapt a powerful open publishing tool to harness the domain expertise of a large group of non-technical users and to respond to the flood of COVID-19 publications. While Manubot manuscripts are written in markdown, they can be rendered in several formats that provide different advantages. -For example, beyond building just a PDF, Manubot also renders the manuscript in HTML, docx, and now, LaTeX (in a more limited capacity). +For example, beyond building just a PDF, Manubot also renders the manuscript in HTML, DOCX, and now, LaTeX (in a more limited capacity). The interactive HTML manuscript format offers several advantages over a static PDF to harmonize available resources that we were able to apply to specific problems of COVID-19. The integration of scite into the HTML build makes references more manageable by visually representing whether their results are contested or whether they have been corrected or retracted. Cross-referencing different pieces of the manuscript, such as cited preprints with reviews stored in an appendix, is another interactive option presented by HTML. -Additionally, because of the heavy emphasis on Word processing in biology, Manubot's ability to generate docx outputs was expanded to allow users to generate docx files containing only a section of the manuscript. +Additionally, because of the heavy emphasis on Word processing in biology, Manubot's ability to generate DOCX outputs was expanded to allow users to generate DOCX files containing only a section of the manuscript. In our case, where the full project is nearly 100,000 words, this allows individual pieces to be shared widely. -Finally, the preliminary addition of LaTeX output is useful for researchers from computational fields who submit papers in tex format and removes the step of reformatting markdown prior to submission. +Finally, the preliminary addition of LaTeX output is useful for researchers from computational fields who submit papers in TeX format and removes the step of reformatting markdown prior to submission. Working with biomedical scientists not only addressed the immediate goal of applying Manubot to the challenges of COVID-19, but also provided a second but equally important outcome. Interested participants came from a wide range of backgrounds and many of the responses to the introductory issue emphasized a willingness to learn about a new topic, as well as an interest in COVID-19 and SARS-CoV-2 (Figure @fig:wordcloud). From 3a8d41b7dd15d7bfe317eadb38e61f1681d1826b Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Sat, 22 May 2021 09:16:45 -0500 Subject: [PATCH 08/10] Add funding statement and semi-automated funding updates --- .gitignore | 1 + build/assets/acm-pandoc-conf.tex | 6 ++++-- build/update-latex-metadata.py | 15 +++++++++++++++ content/60.methods.md | 2 ++ 4 files changed, 22 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 9f7973c22..1fdc31c7b 100644 --- a/.gitignore +++ b/.gitignore @@ -41,6 +41,7 @@ Thumbs.db ## Text Editors .vscode +.idea ## Spellcheck script spellcheck.lua diff --git a/build/assets/acm-pandoc-conf.tex b/build/assets/acm-pandoc-conf.tex index 5c84c4b06..5eb8a845e 100644 --- a/build/assets/acm-pandoc-conf.tex +++ b/build/assets/acm-pandoc-conf.tex @@ -93,6 +93,10 @@ $body$ +% Add funding statement as a comment so it can be manually reviewed and condensed +$if(funding)$ + %{$funding$} +$endif$ $if(bibfile)$ \balance @@ -101,5 +105,3 @@ \end{document} \endinput -%% -%% End of file `sample-authordraft.tex'. diff --git a/build/update-latex-metadata.py b/build/update-latex-metadata.py index 282048f88..01ccadfe2 100644 --- a/build/update-latex-metadata.py +++ b/build/update-latex-metadata.py @@ -77,6 +77,7 @@ def update_latex(keyword, manubot_file, pandoc_file): keep_fields = {"name", "email", "orcid"} # do not keep the old affiliations latex_authors = [] conflicts = [] + funding = [] for author in individual_authors: latex_author = {field: author[field] for field in keep_fields if field in author} @@ -94,6 +95,17 @@ def update_latex(keyword, manubot_file, pandoc_file): if conflict != "None": conflicts.append(f"{author['name']}: {conflict}.") + # Check whether the author has funding + # This text will not be used directly but will help write a funding statement manually + if "funders" in author: + # Less robust handling of funders field than Manubot + # https://github.com/manubot/manubot/blob/3ff3000f76dcf82a30694d076a4da95326e3f6ae/manubot/process/util.py#L78 + funders = author["funders"] + if isinstance(funders, list): + funders = "; ".join(funders) + # Assumes initials are always provided + funding.append(f"{author['initials']}: {funders}.") + sys.stderr.write(f"Found {len(latex_authors)} authors for {keyword} manuscript\n") # Do not retain the other metadata fields and add the .bib file references @@ -102,6 +114,9 @@ def update_latex(keyword, manubot_file, pandoc_file): # Add conflicts if any exist if len(conflicts) > 0: metadata["conflicts"] = "Conflicts of interest. " + " ".join(conflicts) + # Add funding comment if funders were listed + if len(funding) > 0: + metadata["funding"] = "Author funding. " + " ".join(funding) dump_yaml(metadata, pandoc_file) diff --git a/content/60.methods.md b/content/60.methods.md index bd69e50f2..13dfcbf7a 100644 --- a/content/60.methods.md +++ b/content/60.methods.md @@ -292,4 +292,6 @@ The COVID-19 Review Consortium is made of: ### Acknowledgements {.unnumbered} We are grateful to Josh Nicholson and Milo Mordaunt for their support with the scite plugin, and to David Nicholson for the suggestion and feedback to enable the reporting of the locations of spelling errors in the spell-checker tool. We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data. +This research was supported by the Gordon and Betty Moore Foundation award GBMF 4552 (HMR, DSH, CSG), the National Institutes of Health award R01HG010067 (CSG), and the John W. and Jeanne M. Rowe Center for Research in Virology (AG). + {%- endif %} From d57a84d75906c9f4beaad69b0e0610193fb93d71 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Sat, 22 May 2021 09:19:20 -0500 Subject: [PATCH 09/10] Remove unused GitHub field --- content/metadata.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/content/metadata.yaml b/content/metadata.yaml index a13c05b08..8cc66e3f3 100644 --- a/content/metadata.yaml +++ b/content/metadata.yaml @@ -1336,7 +1336,6 @@ authors: contributions: - Software - - github: None name: Jeremy P. Kamil affiliations: - Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA From 4c9e2ed35ed186828097593b72c34826548dcf95 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Sun, 23 May 2021 15:22:03 -0500 Subject: [PATCH 10/10] Support additional affiliations Restructure metadata to match Use empty affiliation as default instead of None --- build/assets/acm-pandoc-conf.tex | 19 +++++++++++ build/update-latex-metadata.py | 9 ++++-- content/metadata.yaml | 55 ++++++++++++++++++++++---------- 3 files changed, 64 insertions(+), 19 deletions(-) diff --git a/build/assets/acm-pandoc-conf.tex b/build/assets/acm-pandoc-conf.tex index 5eb8a845e..73c3a220b 100644 --- a/build/assets/acm-pandoc-conf.tex +++ b/build/assets/acm-pandoc-conf.tex @@ -47,6 +47,25 @@ $endif$ } $endfor$ + $for(author.additionalaffiliations)$ + \additionalaffiliation{ + $if(author.additionalaffiliations.institution)$ + \institution{$author.additionalaffiliations.institution$} + $endif$ + $if(author.additionalaffiliations.department)$ + \department{$author.additionalaffiliations.department$} + $endif$ + $if(author.additionalaffiliations.city)$ + \city{$author.additionalaffiliations.city$} + $endif$ + $if(author.additionalaffiliations.state)$ + \state{$author.additionalaffiliations.state$} + $endif$ + $if(author.additionalaffiliations.country)$ + \country{$author.additionalaffiliations.country$} + $endif$ + } + $endfor$ $if(author.email)$ \email{$author.email$} $endif$ diff --git a/build/update-latex-metadata.py b/build/update-latex-metadata.py index 01ccadfe2..7a2041e0c 100644 --- a/build/update-latex-metadata.py +++ b/build/update-latex-metadata.py @@ -8,7 +8,7 @@ import yaml from manubot.util import read_serialized_data -MISSING_AFFILIATIONS = [{"institution": "None"}] +MISSING_AFFILIATIONS = [{"institution": " "}] MISSING_COI = "None" ACM_BCB_2021 = {"acm": [{"copyrightyear": "2021", "copyright": "acmcopyright", @@ -82,11 +82,16 @@ def update_latex(keyword, manubot_file, pandoc_file): latex_author = {field: author[field] for field in keep_fields if field in author} # A list of the author's affiliations formatted for the template + # The first affiliation is stored in the "affiliations" field + # Any additional affiliations are stored in the "additionalaffiliations" field affiliations = author["manuscripts"][keyword].get("affiliations", MISSING_AFFILIATIONS) if affiliations == MISSING_AFFILIATIONS: sys.stderr.write(f"Missing {keyword} affiliations for {author['name']}\n") - latex_author["affiliations"] = affiliations + if len(affiliations) > 0: + latex_author["affiliations"] = affiliations[0] + if len(affiliations) > 1: + latex_author["additionalaffiliations"] = affiliations[1:] latex_authors.append(latex_author) # Check whether the author has declared conflicts of interest diff --git a/content/metadata.yaml b/content/metadata.yaml index 8cc66e3f3..d1458cb14 100644 --- a/content/metadata.yaml +++ b/content/metadata.yaml @@ -67,17 +67,21 @@ authors: - Writing - Review & Editing - Writing - Original Draft affiliations: - - institution: University of Pennsylvania - department: Department of Systems Pharmacology and Translational Therapeutics - city: Philadelphia - state: PA + - institution: University of Colorado School of Medicine + department: Center for Health AI + city: Aurora + state: CO country: USA - institution: University of Colorado School of Medicine department: Department of Biochemistry and Molecular Genetics - - department: Center for Health AI city: Aurora state: CO country: USA + - institution: University of Pennsylvania + department: Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics + city: Philadelphia + state: PA + country: USA - github: cgreene name: Casey S. Greene @@ -125,19 +129,26 @@ authors: - Software - Conceptualization affiliations: - - institution: University of Pennsylvania - department: Department of Systems Pharmacology and Translational Therapeutics - - institution: Alex's Lemonade Stand Foundation - department: Childhood Cancer Data Lab - city: Philadelphia - state: PA + - institution: University of Colorado School of Medicine + department: Center for Health AI + city: Aurora + state: CO country: USA - institution: University of Colorado School of Medicine department: Department of Biochemistry and Molecular Genetics - - department: Center for Health AI city: Aurora state: CO country: USA + - institution: University of Pennsylvania + department: Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics + city: Philadelphia + state: PA + country: USA + - institution: Alex's Lemonade Stand Foundation + department: Childhood Cancer Data Lab + city: Philadelphia + state: PA + country: USA - github: mprobson name: Michael P. Robson @@ -404,6 +415,9 @@ authors: affiliations: - institution: University of Wisconsin-Madison department: Department of Biostatistics and Medical Informatics + city: Madison + state: WI + country: USA - institution: Morgridge Institute for Research city: Madison state: WI @@ -689,16 +703,16 @@ authors: - Writing - Original Draft - Software affiliations: - - institution: University of Pennsylvania - department: Perelman School of Medicine - city: Philadelphia - state: PA - country: USA - institution: University of Colorado School of Medicine department: Center for Health AI city: Aurora state: CO country: USA + - institution: University of Pennsylvania + department: Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics + city: Philadelphia + state: PA + country: USA - github: jinhui2 name: Jinhui Wang @@ -1335,6 +1349,13 @@ authors: order: 4 contributions: - Software + affiliations: + - institution: Related Sciences + - institution: University of Pennsylvania + department: Perelman School of Medicine, Department of Systems Pharmacology and Translational Therapeutics + city: Philadelphia + state: PA + country: USA - name: Jeremy P. Kamil affiliations: