Thinking programmatically


Scott Chamberlain (@recology_/@ropensci)

UC Berkeley / rOpenSci

ORCID: 0000-0003-1444-9135


Supported by:
sloan

LICENSE: CC-BY 4.0

Infrastructure!!!

Let's talk about






INFRASTRUCTURE


&


SCIENCE

Infrastructure -


necessary building blocks for awesome science

Huge opportunity




to make science better

  • Stories
  • What infrastructure enables
  • Things that could be better




 Stories/Use Cases

Use cases: Author inflation (rplos)

author_inflation
From: Benjamin Moore's blog

Use cases: Open science papers (rentrez)

papers published about open science open_science_papers
From: The Tao of open science for ecology, DOI:10.1890/ES14-00402.1

Use cases: Statistical reporting errors (rplos)

stats_reporting
From: The prevalence of statistical reporting errors in psychology (1985–2013), DOI:10.3758/s13428-015-0664-2
Via EBSCOhost we manually downloaded all articles in HTML from six ... journals ... Furthermore, we manually downloaded all articles ... from two journals in general psychology... Finally, we automatically downloaded all HTML articles with the subject “psychology” from the Public Library of Science (PLoS; 2000–2013), using the rplos R package.

Use cases: Do metadata predict publication lag (rplos)

publication_lag
From: Publication cycle: A study of the Public Library of Science (PLOS) https://www.authorea.com/users/2013/articles/36067

Use cases: find DOI and proper citation from text bits (rcrossref)

comadre
From: jonesor/compadreDB

Infrastructure:
the enabler

Huge amount of open data!

But...we aren't trained to use it



And few programmatic tools



What's needed?

toolset

specifically: programmatic tools



All science should be done programatically



API: Application Programming Interface





  



Reproducibly plug data from the web into research workflows








rOpenSci



ad-hoc conversation over Twitter in 2010 Now a worldwide community of developers/researchers

http://ropensci.org/community

We make:


Software


to facilitate reproducible and open science

We focus on:


R has a lot of packages
(mostly data manip./viz & statistics)


Currently: 7501

R widely used academia, industry, gov't, etc.




Data acquisition    

data manipulation/analysis/viz    

writing    

publish




Data acquisition    

data manipulation/analysis/viz    

writing    

publish




Data acquisition    

data manipulation/analysis/viz    

writing    

publish




Data acquisition    

data manipulation/analysis/viz    

writing    

publish




Data acquisition    

data manipulation/analysis/viz    

writing    

publish

rOpenSci packages

ropensci.org/packages

 Biology


       

 Literature


     

 Publishing

rOpenSci packages

ropensci.org/packages

 History


 

 Archeology


 

 Altmetrics





 Text mining



Still painful though


  • Authentication, yikes
  • Figuring out URLs to full text
  • PDF text extraction
  • making text analysis simple




 Metadata






 Altmetrics



think: DET






 Publishing

carl

EML


EML provides a common data structure, to enable scientists to document, share, and interpret ecological data




Read more about EML

Write APIs?




remember the coolness of DET push model?






Lessons / Observations

Crossref TDM:
Very few links available


5563/5772 (< 4%)


provide full text links

Crossref TDM:
few links


after removing zeros...

Crossref TDM: fragile

Manually generated links fragile software



Crossref TDM:
Some don't resolve

Publisher % That Resolve
311 0
78 100
316 100
301 100
286 100
276 80
179 100
263 100
4374 100
4443 100

Link rot / Broken links



This



Not This

Creates huge barrier to: Reproducibility

Documentation, documentation, documentation



Make developers a first class citizen on your landing page



Support client libraries to work with your web services



Auth should be easy



API keys / OAuth is plenty

Institutional access



This is still very painful

We've got to make auth easier


no idea how to do it

Outside of Crossref's API


it's kind of a mess

  • how do I know if my institution has access?
  • who do I talk to to get access?
  • if my institution doesn't know to do, what then?
  • great that licenses are provided in TDM, but what do they mean?

use proper HTTP status codes

Supplements: Use open file formats






Supplements: Use open file formats



Hard problem



easy to share - hard to reuse

Though...


A 3rd party - convert to easily machine consumable format?

Do people even know programmatic tools exist?




we need to educate

Infrastructure
programmatic tools
... fix some things ...
reproducible science

The end

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			      "name": "bootstrap",
			      "url": "http://getbootstrap.com/",
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			      "name": "font awesome",
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