Author Archive

Automated Ontology Building in Ecology

Automated Ontology Building in Ecology

One of the more difficult aspects of trying to apply “big data” thinking in ecology is the massive heterogeneity of terms. I stumble over this issue every time I work on a data set for the Encyclopedia of Life. The many different ways to describe the same habitat (among other things) and the varying granularity…

Keystone Predators and Centrality: Ecosystem as Social Network Part 2

Keystone Predators and Centrality: Ecosystem as Social Network Part 2

My last post looked at a very small, but well studied rocky intertidal ecosystem and was able to identify a keystone predator (Pisaster) in a network using centrality measures. I was worried, though, that this method would not work on a larger, more complicated system. Let’s try these same calculations on a slightly larger kelp…

Keystone Predators and Centrality: Ecosystem as Social Network Part 1

Keystone Predators and Centrality: Ecosystem as Social Network Part 1

A few weeks ago I announced a project that would train an algorithm to recognize important taxa in an ecosystem using the characteristics of species interactions within that ecosystem. This post documents the first bit of work I’ve done. I’ve made a github repo with data and code. I’m using Python 2.7 with NetworkX. First I…

EarthCube in Denver

EarthCube in Denver

I was invited to give a keynote presentation at the EarthCube All-Hands Meeting in Denver last week. EarthCube is a project funded by the US National Science Foundation to build data infrastructure for geoscience. Every year they have an “all-hands meeting” for all of the people working on EarthCube projects to get together and discuss…

Ecosystem as Social Network

Ecosystem as Social Network

Lately, I’ve been thinking about how interactions between organisms in an ecosystem can be represented as a graph, with nodes and edges, similar to a social network. The nodes represent an organism or group of organisms while the edges represent the relationship between them. For example, a graph representation of an African savanna ecosystem would…

Trickle Down Attribution

Trickle Down Attribution

Last week I was in Portland, Oregon attending the annual meeting of Force11, a community interested in the future of research communications. There were many great speakers and panel discussions, but what interested me the most was the unveiling of OpenVIVO. Anyone with an ORCiD can “claim” their OpenVIVO profile. I logged in using my…

Data Rescue in Tokyo

Data Rescue in Tokyo

Two weeks ago I attended the 7th Plenary of the Research Data Alliance (RDA) in Tokyo. I enjoy attending RDA Plenaries not only because of the interesting topics but also because of all my wonderful RDA colleagues. I was recently appointed the RDA US Data Share Ambassador, so I work with the RDA US Data…

Citizen Science Data Integration

Citizen Science Data Integration

One of the projects I’m working on now is integrating data about North American butterfly observations collected by about a dozen different citizen science butterfly monitoring programs. The people who collect the data are volunteers who are assigned a specific route and keep track of all the butterflies they observe while walking along the route….

Semantic Linking of Phenotypes and Environments

Semantic Linking of Phenotypes and Environments

One of the fundamental goals of biology is understanding the interactions of environment and phenotype, but this is a surprisingly difficult topic to study – not because of the concepts, but because of the data. Observations about environment and phenotype occur in separate data sets and the terms used are far too idiosyncratic for automated…

Molecules and Metadata

GenBank is a repository for genetic sequences sponsored by the National Institutes of Health. It holds over 100 million different sequences from organisms across the tree of life, from humans to mushrooms to amoebae. Studying genetic sequences and how similar or different they are from one species to the next can reveal a lot about…

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