Daniel Himmelstein dhimmel

## autobib.py
"""
This file contains python functions for automatically retreiving DOI metadata
and creating bibtex references. `get_bibtex_entry(doi)` creates a bibtex entry
for a DOI. It fixes a Data Cite author name parsing issue. Short DOIs are used
for bibtex citation keys.

Created by Daniel Himmelstein and released under CC0 1.0.
"""

import urllib.request

## README.md

      
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                MeSH topical descriptor network for cosmograph
              
          
    MeSH in Cosmograph

This gist includes the topical descriptor ontology from MeSH (Medical Subject Headings).
Here is a link that loads the data from this gist and prepopulates the cosmograph configuration
Screenshot

The visualization will look something like:
![cosmograph of mesh topical descriptors with radial

  
## weighted-r2.R
# Compare four methods for computing the R-squared (R2, coefficient of determination)
# with wieghted observations for a linear regression model in R.
# This work was written by Daniel Himmelstein (@dhimmel) with guidance
# from Alex Pankov (@a-pankov). It is released as CC0 (public domain).

get_r2_cor <- function(y, y_pred, w) {
  # Calculate R2 using the correlation coefficient method
  xy = cbind(y, y_pred)
  return(boot::corr(d=xy, w=w) ^ 2)
}

## benevolent-ai-metagraph-data-sources.drawio
<mxfile host="app.diagrams.net" modified="2021-06-08T17:05:33.560Z" agent="5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/90.0.4430.85 Safari/537.36" etag="oN2ExXKtZoTKyfjxyag6" version="14.7.6" type="device"><diagram id="CpBVq6cUYyMfxSufbEmF" name="Page-1">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

## openalex-metagraph.drawio
<mxfile host="Electron" modified="2022-01-11T22:24:44.620Z" agent="5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) draw.io/16.1.2 Chrome/96.0.4664.55 Electron/16.0.5 Safari/537.36" etag="3d_x8ajHgV-OkkuHk2Cl" version="16.1.2" type="device"><diagram id="CRBQrBPZslJF9kaArlf7" name="Page-1">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

## ubuntu-quarter-screen-issue.md

      
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                dhimmel
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              Created
              May 4, 2022 01:38
            
              
                Diagnosing the Ubuntu top left quarter display issue
              
          
    Information for comment at Ubuntu uses only the top left quarter of the screen
Output from lsb_release -a:
No LSB modules are available.
Distributor ID:	Pop
Description:	Pop!_OS 22.04 LTS
Release:	22.04
Codename:	jammy


## disease-v2-review.md

      
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                DISEASES v2 Review by Daniel Himmelstein
              
          
    DISEASES 2.0 Review

Reference

DISEASES 2.0: a weekly updated database of disease–gene associations from text mining and data integration

Dhouha Grissa, Alexander Junge, Tudor I Oprea, Lars Juhl Jensen

bioRxiv (2021-12-09) https://doi.org/gn3fj4

DOI: 10.1101/2021.12.07.471296
The webapp and latest downloads are available at . Version 1 is described in the 2015 publication.

  
## tiga-review.md

      
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                dhimmel
                / tiga-review.md
            
            
              Created
              December 1, 2020 17:53
            
              
                Review of TIGA (Target illumination GWAS analytics) preprint v1
              
          
    Review of TIGA Preprint v1 by Daniel Himmelstein on 2020-12-01

Resources

TIGA: Target illumination GWAS analytics

Jeremy J. Yang, Dhouha Grissa, Christophe G. Lambert, Cristian G. Bologa, Stephen L. Mathias, Anna Waller, David J. Wild, Lars Juhl Jensen, Tudor I. Oprea

bioRxiv (2020-11-12) https://www.biorxiv.org/content/10.1101/2020.11.11.378596v1

DOI: 10.1101/2020.11.11.378596
Related links:

  
## sciscore-manuscript-review.md

      
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                Review of the "Rigor and Transparency Index" manuscript (https://doi.org/dkg6)
              
          
    Daniel Himmelstein's review of preprint v2

Review of version 2 of the following preprint:

Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods

Joe Menke, Martijn Roelandse, Burak Ozyurt, Maryann Martone, Anita Bandrowski

bioRxiv (2020-01-18) https://doi.org/dkg6

DOI: 10.1101/2020.01.15.908111

The study introduces an automated method called SciScore to detect whether an article's methods section mentions any of 15 categories, such as a consent statement or an organism. These metrics are combined to create a single score for each article called the "Rigor and Transparency Index". The authors applied the method to the PubMed Central Open Access subset with over 1 million articles to identify trends in the level of details provided by method sections.

  
## cypher-edge-swap.adoc

      
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                Randomized edge swaps in cypher
              
          
    Degree-Preserving Edge-Swap


Background


We designed a hetnet for drug repurposing that contains 50 thousand nodes (of 10 labels) and 3 million relationships (of 27 types). And we’ve chosen neo4j for handling network storage and interaction.
	"""
	This file contains python functions for automatically retreiving DOI metadata
	and creating bibtex references. `get_bibtex_entry(doi)` creates a bibtex entry
	for a DOI. It fixes a Data Cite author name parsing issue. Short DOIs are used
	for bibtex citation keys.

	Created by Daniel Himmelstein and released under CC0 1.0.
	"""

	import urllib.request
	# Compare four methods for computing the R-squared (R2, coefficient of determination)
	# with wieghted observations for a linear regression model in R.
	# This work was written by Daniel Himmelstein (@dhimmel) with guidance
	# from Alex Pankov (@a-pankov). It is released as CC0 (public domain).

	get_r2_cor <- function(y, y_pred, w) {
	# Calculate R2 using the correlation coefficient method
	xy = cbind(y, y_pred)
	return(boot::corr(d=xy, w=w) ^ 2)
	}