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![Amanuens.is
ContentMine
IAnnotate!, Berlin, DE, 2016-
05-18
Peter Murray-Rust
[1]University of Cambridge [2]TheContentMine
ContentMine + Hypothesis annotate the scientific literature!
100, 000 + per day.
Live demos!](https://image.slidesharecdn.com/amanuens-160519120633-160519122648/75/Amanuens-is-HUmans-and-machines-annotating-scholarly-literature-1-2048.jpg)
![Scholarly publishing
• 10, 000 articles per day
• 20 Billion USD / year [1]
• Totally and scandalously broken. Primary revenue
comes from throttling the flow of knowledge
• Massive disruption likely (Sci-Hub)
• Mining and annotation liberation tools.
[1] (2x digital music industry!)](https://image.slidesharecdn.com/amanuens-160519120633-160519122648/75/Amanuens-is-HUmans-and-machines-annotating-scholarly-literature-2-2048.jpg)
![I am a statistician interested in detecting potentially problematic research such as data fabrication,
which results in unreliable findings and can harm policy-making, confound funding decisions, and
hampers research progress.
To this end, I am content mining results reported in the psychology literature. Content mining the
literature is a valuable avenue of investigating research questions with innovative methods. For
example, our research group has written an automated program to mine research papers for errors in
the reported results and found that 1/8 papers (of 30,000) contains at least one result that could
directly influence the substantive conclusion [1].
In new research, I am trying to extract test results, figures, tables, and other information reported in
papers throughout the majority of the psychology literature. As such, I need the research papers
published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research
papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account
potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention
to redistribute the downloaded materials, had legal access to them because my university pays a
subscription, and I only wanted to extract facts from these papers.
Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days.
This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day.
Approximately two weeks after I started downloading psychology research papers, Elsevier notified my
university that this was a violation of the access contract, that this could be considered stealing of
content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading
(which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university.
I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly
hampering me in my research.
[1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The
prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22.
doi: 10.3758/s13428-015-0664-2
Chris Hartgerink’s blog post](https://image.slidesharecdn.com/amanuens-160519120633-160519122648/75/Amanuens-is-HUmans-and-machines-annotating-scholarly-literature-18-2048.jpg)
Uploaded byTheContentMine
Amanuens.is HUmans and machines annotating scholarly literature
Peter Murray-Rust discusses the need for content mining and annotation tools in scholarly publishing, highlighting issues with current practices that restrict knowledge flow. He illustrates the importance of mining scientific literature for data and error detection, citing examples like the challenges faced by researchers when accessing articles due to copyright restrictions. The document also emphasizes the potential of automated tools to enhance research through data extraction and analysis.
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- 1. Amanuens.is ContentMine IAnnotate!, Berlin, DE,2016- 05-18 Peter Murray-Rust [1]University of Cambridge [2]TheContentMine ContentMine + Hypothesis annotate the scientific literature! 100, 000 + per day. Live demos!
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- 10. Mining for phytochemicals •getpapers –q carvone –o carvone –x –k 100 Search “carvone”, output to carvone/, fmt XML, limit 100 hits • cmine carvone Normalize papers; search locally for species, sequences, diseases, drugs Results in dataTables.html and results/…/results.xml (includes W3C annotation) • python cmhypy.py carvone/ -u petermr <key> send annotations -> hypothes.is
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- 14. Mining for phytochemicals •getpapers –q carvone –o carvone –x –k 100 Search “carvone”, output to carvone/, fmt XML, limit 100 hits • cmine carvone Normalize papers; search locally for species, sequences, diseases, drugs Results in dataTables.html and results/…/results.xml (includes W3C annotation) • python cmhypy.py carvone/ -u petermr <key> send annotations -> hypothes.is
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- 17. @Senficon (Julia Reda):Text & Data mining in times of #copyright maximalism: "Elsevier stopped me doing my research" http://onsnetwork.org/chartgerink/2015/11/16/elsevi er-stopped-me-doing-my-research/ … #opencon #TDM Elsevier stopped me doing my research Chris Hartgerink
- 18. I am astatistician interested in detecting potentially problematic research such as data fabrication, which results in unreliable findings and can harm policy-making, confound funding decisions, and hampers research progress. To this end, I am content mining results reported in the psychology literature. Content mining the literature is a valuable avenue of investigating research questions with innovative methods. For example, our research group has written an automated program to mine research papers for errors in the reported results and found that 1/8 papers (of 30,000) contains at least one result that could directly influence the substantive conclusion [1]. In new research, I am trying to extract test results, figures, tables, and other information reported in papers throughout the majority of the psychology literature. As such, I need the research papers published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention to redistribute the downloaded materials, had legal access to them because my university pays a subscription, and I only wanted to extract facts from these papers. Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days. This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day. Approximately two weeks after I started downloading psychology research papers, Elsevier notified my university that this was a violation of the access contract, that this could be considered stealing of content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading (which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university. I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly hampering me in my research. [1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22. doi: 10.3758/s13428-015-0664-2 Chris Hartgerink’s blog post