The Phylogeny of a Dataset

<p>The field of evolutionary biology offers many approaches to study the changes that occur between and within generations of species; these methods have recently been adopted by cultural anthropologists, linguists and archaeologists to study the evolution of physical artifacts. In this paper, we further extend these approaches by using phylogenetic methods to model and visualize the evolution of a long-standing, widely used digital dataset in climate science.</p> <p>Our case study shows that clustering algorithms developed specifically for phylogenetic studies in evolutionary biology can be successfully adapted to the study of digital objects, and their known offspring. Although we note a number of limitations with our initial effort, we argue that a quantitative approach to studying how digital objects evolve, are reused, and spawn new digital objects represents an important direction for the future of Information Science. [Presentation from ASIST 2014, Seattle]</p

Supplemental materials for "Documenting provenance in non-computational workflows: research process models based on geobiology fieldwork in Yellowstone National Park"

This fileset contains supplementary materials to "Documenting provenance in non-computational workflows: research process models based on geobiology fieldwork in Yellowstone National Park", forthcoming from JASIST<br

ESIP Semantic Web Technologies Committee Poster, Summer 2017

ESIPfed Semantic Web Technology Committee poster for Summer 2017 meeting<br

iSamples user stories: common themes and areas for future work

<div> <div> <div> <div><br></div> </div> </div> </div>Paper presented at Physical Samples, Digital Collections workshop at ASIST 2016. Full citation:<div><br></div><div>Thomer, AK, Ramdeen, S, Adrian, B, Hosford-Scheirer, A (2016). <i>iSamples user stories: Common themes and areas for future work.</i>Physical Samples, Digital Collections Workshop, Annual Meeting of the Association of Information Science and Technology. Copenhagen. doi: <a target="_blank">10.6084/m9.figshare.4272164</a></div

Mobilizing taxonomic data: the importance of user-centered design

<p>Through the NSF-Funded "Transforming Taxonomic Interfaces" project, we are working to understand the user interaction and experience needs of taxonomists -- the biologists that organize, describe, classify and name life on earth. With an estimated 8.7 million (rapidly disappearing) species on earth, this is no small task, and no small data. Publishing and mobilizing this semantically rich data is critically important for modern biology, and thus, a key challenge for modern academic publishing. <br></p><p></p> <p> </p> <p>Traditionally, taxonomists describe their species through semi-structured prose narratives. These descriptions have been traditionally published as <i>paper </i>journal articles or in books (only very recently have the governing nomenclatural bodies begun to accept electronically published papers as “acceptable” species descriptions). This publishing process can take years – sometimes decades. Worse, this data is bound in natural language text, and cannot be easily parsed computationally. A growing number of taxonomists have argued for the use of formal ontologies for species descriptions, thereby making the descriptions machine readable; others have proposed forms of “nanopublications” or “quantum publications”, through which taxonomists could publish small data packages as they are finished, in lieu of entire tomes. However, there are considerable infrastructural and practical barriers to this – notably that formal ontologies can be quite difficult to use.</p> <p> </p> <p>We believe that much of the labor of using formal ontologies can be reduced through the design of robust, user-centered software interfaces, thereby streamlining the pipeline from data collection to publication. In this poster, we describe our efforts to rapidly prototype user interfaces for working taxonomists, to support efficient and fit-for-use publication of species descriptions and their supporting data. We further argue that user-centered interface design is fundamental to the creation and publication of open data. We present several prototype interfaces, and describe how they would reduce the burden on taxonomists in publishing their data.</p

SWEET Synthesis: ESIP FUNding Friday results

A poster describing interim results of a 2017 FUNding Friday project sponsored by ESIP<br

A Scientific Author Guide for Publishing Open Research Using Physical Samples

Material samples are foundational for research across a wide range of biological, environmental, and other interdisciplinary sciences. Their value and the value of the data derived from them depend to a large extent on the way we describe, identify, and reference them in publications and datasets. Use of globally unique and persistent sample identifiers and availability of rich and consistent information (metadata and data) about a sample on the web are critical for making samples and sample data findable, accessible, interoperable, and reusable (FAIR). This guide presents best practices for supporting open science for samples, developed by the Physical Sample Curation Cluster of the Earth Science Information Partners (ESIP) organization. Following this guidance will help ensure that we are able to track use of samples over time, which enables reproducible research, future data integration, reuse, and credit. The ESIP Physical Sample Curation Cluster is a forum for the community supporting physical samples in the earth, space, and environmental sciences. The working group consists of individual researchers who collect and work with physical samples, curators and collections managers, and cyberinfrastructure providers and developers.</p