Daniel Himmelstein
Head of Data Integration at Related Sciences. Digital craftsman of the biodata revolution.
Dartmouth Libraries Research Facilitation Lightning Talks
2025-11-20
Daniel Himmelstein
Trang Le
https://slides.com/dhimmel/dartlib
slides released under CC BY 4.0
Sci-Hub versus Penn Libraries
- Penn Libraries spent $13.13 million on electronic resources in 2017
- Average per-download cost of $1.61
- 326 toll access articles (manually checked)
- Penn's access: 80.7%
- Sci-Hub's database: 94.2%
https://github.com/greenelab/library-access
https://manubot.org
deep review contribution history
citation by persistent identifier
This is a sentence with 5 citations [ @doi:10.1038/nbt.3780; @pmid:29424689; @pmcid:PMC5938574; @arxiv:1407.3561; @url:https://greenelab.github.io/meta-review/ ].
References
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Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones, Casey S Greene
Nature Biotechnology (2017-03-13) https://doi.org/f9ttx6
DOI: 10.1038/nbt.3780 · PMID: 28288103 · PMCID: PMC6103790
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Sci-Hub provides access to nearly all scholarly literature.
Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
eLife (2018-03-01) https://www.ncbi.nlm.nih.gov/pubmed/29424689
DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410
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Opportunities and obstacles for deep learning in biology and medicine
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman, … Casey S. Greene
Journal of the Royal Society Interface (2018-04) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574/
DOI: 10.1098/rsif.2017.0387 · PMID: 29618526 · PMCID: PMC5938574
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IPFS - Content Addressed, Versioned, P2P File System
Juan Benet
arXiv (2014-07-14) https://arxiv.org/abs/1407.3561v1
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Open collaborative writing with Manubot
Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
(2018-08-03) https://greenelab.github.io/meta-review/
This is a sentence with 5 citations [1,2,3,4,5].
https://manubot.org/catalog/
- knowledge graph for drug repurposing
- integrates 29 public resources
knowledge from millions of studies
- ~50 thousand nodes
11 types (labels)
- ~2.25 million relationships
24 types
Hetionet v1.0
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Daniel S Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
eLife (2017) https://doi.org/cdfk
Nice of you to share this big network with everyone; however, I think you need to take care not to get yourself into legal trouble here. …
I am not trying to cause trouble here — just the contrary. When making a meta-resource, licenses and copyright law are not something you can afford to ignore. I regularly leave out certain data sources from my resources for legal reasons.
One network to rule them all
We have completed an initial version of our network. …
Network existence (SHA256 checksum for graph.json.gz) is proven in Bitcoin block 369,898.
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Hetionet (≤ v1.0) integrated data from 31 resources:
- 5 United States Government works
- 12 openly licensed
- 4 non-commercial use only
- 9 were all rights reserved
- 1 explicitly & contractually forbid reuse
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Requested permission for 11 resources:
- median time to first response was 16 days
- 2 affirmative responses
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Other considerations:
- who owns data
- incompatibilities: share alike vs non-commercial
- copyright status of data & fair use
- Solution: license attribute per node/relationship
Legal barriers to data reuse
by default, scientific outputs subject to copyright
sometimes universities place additional legal barriers to reuse
Recommendations:
- release data under an open license
- University researchers: commit to open in your resource sharing plan
OpenAlex
a fully open catalog of the global research system
oa_fetch(
entity = "works",
institutions.ror = "049s0rh22", # Dartmouth college
type = "article",
group_by = "primary_topic.field.id",
publication_year = 2020,
is_oa = TRUE,
) 
- Which journals publish Dartmouth research most frequently—and what are their OA policies?
- Which Dartmouth departments are gaining the fastest citation momentum in the last 5 years?
- Can we auto-generate a list of NSF-funded publications for a PI's annual report?
- How quickly Dartmouth work is entering “planetary health” or “computational social science”?
- How does Dartmouth’s OA percentage compare to peer institutions?
This is an excellent story on all counts but two things stood out to me. 1) the “ski-rose” is an example of a complex visualization that is so well-served by scrollytelling. 2) this scrolly at openskistats.org sits alongside a technical manuscript and beautiful interactive data table, showing how different formats can serve complementary roles in communicating insights about data.
Andrew Bray:
Parambulations
Dartmouth Libraries Research Facilitation Lightning Talks on 2025-11-20
By Daniel Himmelstein
