@proceedings {4575, title = {Change in Pictures: Creating best practices in archiving ecological imagery for reuse}, journal = {Biodiversity Information Science and Standards}, volume = {4}, year = {2020}, month = {09/2020}, abstract = {

The research data repository of the Environmental Data Initiative (EDI) is building on over 30 years of data curation research and experience in the National Science Foundation-funded US Long-Term Ecological Research (LTER) Network. It provides mature functionalities, well established workflows, and now publishes all \‘long-tail\’ environmental data. High quality scientific metadata are enforced through automatic checks against community developed rules and the Ecological Metadata Language (EML) standard. Although the EDI repository is far along in making its data findable, accessible, interoperable, and reusable (FAIR), representatives from EDI and the LTER are developing best practices for the edge cases in environmental data publishing. One of these is the vast amount of imagery taken in the context of ecological research, ranging from wildlife camera traps to plankton imaging systems to aerial photography. Many images are used in biodiversity research for community analyses (e.g., individual counts, species cover, biovolume, productivity), while others are taken to study animal behavior and landscape-level change.

Some examples from the LTER Network include: using photos of a heron colony to measure provisioning rates for chicks (Clarkson and Erwin 2018) or identifying changes in plant cover and functional type through time (Peters et al. 2020). Multi-spectral images are employed to identify prairie species. Underwater photo quads are used to monitor changes in benthic biodiversity (Edmunds 2015). Sosik et al. (2020) used a continuous Imaging FlowCytobot to identify and measure phyto- and microzooplankton. Cameras at McMurdo Dry Valleys assess snow and ice cover on Antarctic lakes allowing estimation of primary production (Myers 2019).

It has been standard practice to publish numerical data extracted from images in EDI; however, the supporting imagery generally has not been made publicly available. Our goal in developing best practices for documenting and archiving these images is for them to be discovered and re-used. Our examples demonstrate several issues. The research questions, and hence, the image subjects are variable. Images frequently come in logical sets of time series. The size of such sets can be large and only some images may be contributed to a dedicated specialized repository. Finally, these images are taken in a larger monitoring context where many other environmental data are collected at the same time and location.

Currently, a typical approach to publishing image data in EDI are packages containing compressed (ZIP or tar) files with the images, a directory manifest with additional image-specific metadata, and a package-level EML metadata file. Images in the compressed archive may be organized within directories with filenames corresponding to treatments, locations, time periods, individuals, or other grouping attributes. Additionally, the directory manifest table has columns for each attribute. Package-level metadata include standard coverage elements (e.g., date, time, location) and sampling methods. This approach of archiving logical \‘sets\’ of images reduces the effort of providing metadata for each image when most information would be repeated, but at the expense of not making every image individually searchable. The latter may be overcome if the provided manifest contains standard metadata that would allow searching and automatic integration with other images.

}, keywords = {LTER-MCM, data repository, ecological data, metadata}, doi = {10.3897/biss.4.59082}, url = {https://biss.pensoft.net/article/59082/}, author = {Gries, Corinna and Beaulieu, Stace and Brown, Ren{\'e}e F. and Gastil-Buhl, Gastil and Elmendorf, Sarah C. and Hsieh, Hsun-Yi and Kui, Li and Maurer, Greg and Porter, John H.} } @article {4159, title = {BioTIME: A database of biodiversity time series for the Anthropocene}, journal = {Global Ecology and Biogeography}, volume = {27}, year = {2018}, month = {07/2018}, pages = {760-786}, abstract = {

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). Time period and grain BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

Major taxa and level of measurement:\ BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software format: .csv and .SQL.

}, keywords = {LTER-MCM, biodiversity, global, spatial, species richness, temporal, turnover}, doi = {10.1111/geb.12729}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.12729}, author = {Dornelas, Maria and Ant{\~a}o, Laura H. and Moyes, Faye and Bates, Amanda E. and Magurran, Anne E. and Adam, Du{\v s}an and Akhmetzhanova, Asem A. and Appeltans, Ward and Arcos, Jos{\'e} Manuel and Arnold, Haley and Ayyappan, Narayanan and Badihi, Gal and Baird, Andrew H. and Barbosa, Miguel and Barreto, Tiago Egydio and B{\"a}ssler, Claus and Bellgrove, Alecia and Belmaker, Jonathan and Benedetti-Cecchi, Lisandro and Bett, Brian J. and Bjorkman, Anne D. and B{\l}a{\.z}ewicz, Magdalena and Blowes, Shane A. and Bloch, Christopher P. and Bonebrake, Timothy C. and Boyd, Susan and Bradford, Matt and Brooks, Andrew J. and Brown, James H. and Bruelheide, Helge and Budy, Phaedra and Carvalho, Fernando and Casta{\~n}eda-Moya, Edward and Chen, Chaolun Allen and Chamblee, John F. and Chase, Tory J. and Siegwart Collier, Laura and Collinge, Sharon K. and Condit, Richard and Cooper, Elisabeth J. and Cornelissen, J. Hans C. and Cotano, Unai and Kyle Crow, Shannan and Damasceno, Gabriella and Davies, Claire H. and Davis, Robert A. and Day, Frank P. and Degraer, Steven and Doherty, Tim S. and Dunn, Timothy E. and Durigan, Giselda and Duffy, J. Emmett and Edelist, Dor and Edgar, Graham J. and Elahi, Robin and Elmendorf, Sarah C. and Enemar, Anders and Ernest, S. K. Morgan and Escribano, Rub{\'e}n and Estiarte, Marc and Evans, Brian S. and Fan, Tung-Yung and Turini Farah, Fabiano and Loureiro Fernandes, Luiz and Farneda, F{\'a}bio Z. and Fidelis, Alessandra and Fitt, Robert and Fosaa, Anna Maria and Daher Correa Franco, Geraldo Antonio and Frank, Grace E. and Fraser, William R. and Garc{\'\i}a, Hernando and Cazzolla Gatti, Roberto and Givan, Or and Gorgone-Barbosa, Elizabeth and Gould, William A. and Gries, Corinna and Grossman, Gary D. and Gutierr{\'e}z, Julio R. and Hale, Stephen and Harmon, Mark E. and Harte, John and Haskins, Gary and Henshaw, Donald L. and Hermanutz, Luise and Hidalgo, Pamela and Higuchi, Pedro and Hoey, Andrew and Van Hoey, Gert and Hofgaard, Annika and Holeck, Kristen and Hollister, Robert D. and Holmes, Richard and Hoogenboom, Mia and Hsieh, Chih-hao and Hubbell, Stephen P. and Huettmann, Falk and Huffard, Christine L. and Hurlbert, Allen H. and Macedo Ivanauskas, Nat{\'a}lia and Jan{\'\i}k, David and Jandt, Ute and Ja{\.z}d{\.z}ewska, Anna and Johannessen, Tore and Johnstone, Jill and Jones, Julia and Jones, Faith A. M. and Kang, Jungwon and Kartawijaya, Tasrif and Keeley, Erin C. and Kelt, Douglas A. and Kinnear, Rebecca and Klanderud, Kari and Knutsen, Halvor and Koenig, Christopher C. and Kortz, Alessandra R. and Kr{\'a}l, Kamil and Kuhnz, Linda A. and Kuo, Chao-Yang and Kushner, David J. and Laguionie-Marchais, Claire and Lancaster, Lesley T. and Min Lee, Cheol and Lefcheck, Jonathan S. and L{\'e}vesque, Esther and Lightfoot, David and Lloret, Francisco and Lloyd, John D. and L{\'o}pez-Baucells, Adri{\`a} and Louzao, Maite and Madin, Joshua S. and Magn{\'u}sson, Borg{\th}{\'o}r and Malamud, Shahar and Matthews, Iain and McFarland, Kent P. and McGill, Brian and Diane M. McKnight and McLarney, William O. and Meador, Jason and Meserve, Peter L. and Metcalfe, Daniel J. and Meyer, Christoph F. J. and Michelsen, Anders and Milchakova, Nataliya and Moens, Tom and Moland, Even and Moore, Jon and Mathias Moreira, Carolina and M{\"u}ller, J{\"o}rg and Murphy, Grace and Myers-Smith, Isla H. and Myster, Randall W. and Naumov, Andrew and Neat, Francis and Nelson, James A. and Paul Nelson, Michael and Newton, Stephen F. and Norden, Natalia and Oliver, Jeffrey C. and Olsen, Esben M. and Onipchenko, Vladimir G. and Pabis, Krzysztof and Pabst, Robert J. and Paquette, Alain and Pardede, Sinta and Paterson, David M. and P{\'e}lissier, Rapha{\"e}l and Pe{\~n}uelas, Josep and P{\'e}rez-Matus, Alejandro and Pizarro, Oscar and Pomati, Francesco and Post, Eric and Prins, Herbert H. T. and John C. Priscu and Provoost, Pieter and Prudic, Kathleen L. and Pulliainen, Erkki and Ramesh, B. R. and Mendivil Ramos, Olivia and Rassweiler, Andrew and Rebelo, Jose Eduardo and Reed, Daniel C. and Reich, Peter B. and Remillard, Suzanne M. and Richardson, Anthony J. and Richardson, J. Paul and van Rijn, Itai and Rocha, Ricardo and Rivera-Monroy, Victor H. and Rixen, Christian and Robinson, Kevin P. and Ribeiro Rodrigues, Ricardo and de Cerqueira Rossa-Feres, Denise and Rudstam, Lars and Ruhl, Henry and Ruz, Catalina S. and Sampaio, Erica M. and Rybicki, Nancy and Rypel, Andrew and Sal, Sofia and Salgado, Beatriz and Santos, Flavio A. M. and Savassi-Coutinho, Ana Paula and Scanga, Sara and Schmidt, Jochen and Schooley, Robert and Setiawan, Fakhrizal and Shao, Kwang-Tsao and Shaver, Gaius R. and Sherman, Sally and Sherry, Thomas W. and Sici{\'n}ski, Jacek and Sievers, Caya and da Silva, Ana Carolina and Rodrigues da Silva, Fernando and Silveira, Fabio L. and Slingsby, Jasper and Smart, Tracey and Snell, Sara J. and Soudzilovskaia, Nadejda A. and Souza, Gabriel B. G. and Maluf Souza, Flaviana and Castro Souza, Vin{\'\i}cius and Stallings, Christopher D. and Stanforth, Rowan and Stanley, Emily H. and Mauro Sterza, Jos{\'e} and Stevens, Maarten and Stuart-Smith, Rick and Rondon Suarez, Yzel and Supp, Sarah} }