Daniel Himmelstein
Head of Data Integration at Related Sciences. Digital craftsman of the biodata revolution.
The hetnet awakens: understanding disease through data integration & open science
2:00–3:00 PM, April 26, 2016
Genentech Hall Auditorium
University of California, San Francisco
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dipper.ucsf.edu
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Created on deepart.io using deep neural networks
Sandler Neurosciences Center
Sergio
What can I tell about my Facebook Friends, just knowing their mutual friendships?
Disease network from GWAS
Khankhanian et al. (2016) Int J Epidemiol. DOI: bfmj
Hetio Disease Genes
Himmelstein & Baranzini (2015) PLOS Comp Bio. DOI: 98q
network of pathogenesis:
- integrates diverse data
- 40,343 nodes of 18 types
- 1,608,168 edges of 19 types
type is essential when operating on hetnets
metapath-based approach
feature extraction: the DWPC
mechanisms of pathogenesis:
comparing gene set collections
Project Rephetio
Himmelstein, Lizee, Khankhanian, Brueggeman, Chen, Hessler, Green Hadley & Baranzini (2015–201?) Thinklab. DOI: 993
Metagraph in 2013
Metagraph in 2016
Compounds
Diseases
Pharmacologic Classes
Side Effects
Symptoms
Anatomies
Genes
Pathways
Molecular Functions
Biological Processes
Cellular Components
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1,552 small molecule compounds
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137 complex diseases
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755 treatments
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47,031 nodes of 11 types
- 2,250,197 edges of 24 types
- 29 resources
- millions of studies from last half century
- 1,206 types of paths
- 209,168 potential treatments
(1,538 compounds × 136 complex diseases) - 6 hetnets (5 permuted)
- ~60 million database queries
- predictive model of efficacy
Machine Learning Paradigm
Greene & Himmelstein (2016) Circ Cardiovasc Genet. DOI: bffr
SNPlentiful Effect
Lung Cancer Rates, 2007–2011
Simeonov & Himmelstein (2015) PeerJ. DOI: 98p
Trouble at the Town Hall
1908 in Silverton, CO
San Juan Historical Society
San Juan County, Colorado
3,473 m
−35% O₂
−65,496
⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛⌛
Time from submission to acceptance for 3,330,333 articles since 1965
- 40 contributors
(see leaderboard) - 71 discussions
- 424 comments
- 83,546 words
- 694,254 characters
- ~14 publications
- https://thinklab.com/p/rephetio
Visualization by Antoine Lizee
I am a lawyer, but not your lawyer (or UC’s lawyer), and this isn’t legal advice.
Others, like myself, try to remember to rate everything that I've read.
It took me a while to figure out.
I would like to enter into the discussion the cases where there was a tough decision to be made
117 Ratings
1504 Word Post
2776 Word Post
Project
Rephetio
All-Stars
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.
- Hetionet integrates data from 29 resources
- 12 had an open license
- 9 had no license
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Incompatibilities - Share Alike vs Non-Commercial
- Requested permission for 11 resources
- Median time to first reponse was 16 days
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2 affirmative responses
- Removed MSigDB
- "LICENSEE agrees not to put … the DATABASE on a … server … that may be accessed by any individual other than the LICENSEE."
- LICENSEE agrees to provide … a written evaluation of the PROGRAM and the DATABASE, including a description of its functionality or problems and areas for further improvement
Legal barriers to data reuse
Recommendation:
release data under an open license
agnitiōnum
This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. 1144247. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation.
Jesse Spaulding
Creator of Thinklab
Kristin Sainani
?
George Johnson
Kendall Powell
Simon Oxenham
DNA from my maternal grandmother & susceptibility genes for educational attainment
Nina Gonzaludo
Cyrus Maher
Mason Louie
María Chavez
Leo Brueggeman
Sabrina Chen
Presentation online at:
- https://slides.com/dhimmel/thesis-seminar
- https://youtu.be/H8DfXop8K7g
Reception & Exhibit to Follow:
- Sandler Neurosciences Center, 2nd Floor
- http://blog.dhimmel.com/phd-exhibit/
Questions?
Thesis Seminar · Daniel Himmelstein · Biological & Medical Informatics · UCSF
By Daniel Himmelstein
Thesis Seminar · Daniel Himmelstein · Biological & Medical Informatics · UCSF
Daniel Himmelstein's Thesis Seminar covering his PhD studies. See the accompanying recording on YouTube (https://youtu.be/H8DfXop8K7g). This presentation is released under a CC BY 4.0 license.
