Blog Archives

Scholarly metadata in R

March 16, 2013
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Scholarly metadata in R

Scholarly metadata - the meta-information surrounding articles - can be super useful. Although metadata does not contain the full content of articles, it contains a lot of useful information, including title, authors, abstract, URL to the article, etc.One of the largest sources of metadata is provided via the Open Archives Initiative Protocol for Metadata Harvesting or OAI-PMH....

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Visualizing rOpenSci collaboration

March 8, 2013
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Visualizing rOpenSci collaboration

We (rOpenSci) have been writing code for R packages for a couple years, so it is time to take a look back at the data. What data you ask? The commits data from GitHub ~ data that records who did what and when.Using the Github commits API we can gather data on who commited code to a...

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Visualizing rOpenSci collaboration

March 8, 2013
By
Visualizing rOpenSci collaboration

We (rOpenSci) have been writing code for R packages for a couple years, so it is time to take a look back at the data. What data you ask? The commits data from GitHub ~ data that records who did what and when.Using the Github commits API we can gather data on who commited code to a...

Read more »

Visualizing rOpenSci collaboration

March 8, 2013
By
Visualizing rOpenSci collaboration

We (rOpenSci) have been writing code for R packages for a couple years, so it is time to take a look back at the data. What data you ask? The commits data from GitHub ~ data that records who did what and when.Using the Github commits API we can gather data on who commited code to a...

Read more »

Getting a simple tree via NCBI

February 14, 2013
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Getting a simple tree via NCBI

I was just at the Phylotastic hackathon in Tucson, AZ at the iPlant facilities at the UofA.A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant phylogenies (at least 250 or so papers...

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Getting a simple tree via NCBI

February 14, 2013
By
Getting a simple tree via NCBI

I was just at the Phylotastic hackathon in Tucson, AZ at the iPlant facilities at the UofA.A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant phylogenies (at least 250 or so papers...

Read more »

Waiting for an API request to complete

January 26, 2013
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Dealing with API tokens in RIn my previous post I showed an example of calling the Phylotastic taxonomic name resolution API Taxosaurus here. When you query their API they give you a token which you use later to retrieve the result (see examples on their page above). However, you don't know when the query will be...

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Waiting for an API request to complete

January 26, 2013
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Dealing with API tokens in RIn my previous post I showed an example of calling the Phylotastic taxonomic name resolution API Taxosaurus here. When you query their API they give you a token which you use later to retrieve the result (see examples on their page above). However, you don't know when the query will be...

Read more »

Resolving species names when you have a lot of them

January 25, 2013
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taxize use case: Resolving species names when you have a lot of themSpecies names can be a pain in the ass, especially if you are an ecologist. We ecologists aren't trained in taxonomy, yet we often end up with huge species lists. Of course we want to correct any spelling errors in the names, and get the newest...

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Resolving species names when you have a lot of them

January 25, 2013
By

taxize use case: Resolving species names when you have a lot of themSpecies names can be a pain in the ass, especially if you are an ecologist. We ecologists aren't trained in taxonomy, yet we often end up with huge species lists. Of course we want to correct any spelling errors in the names, and get the newest...

Read more »