Proposal

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link to pre-proposal requirements
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Ecostations Data Access Monitor (EDAM) Proposal

Problem Statement

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Existing Solutions

Information on species distribution in space is essential for effective management of biodiversity and ecosystems and in addressing ecological and evolutionary questions. There currently exists several databases of species biodiversity information. However, these are disjointed and inconsistent, and do not provide a definitive information base. Recent studies have shown that gaps in digital accessible information (DAI) on species distributions hinders the efforts of ecosystem and biodiversity services to protect and conserve endangered species [1]. Outside of a few regions, DAI on point occurrences provide a very limited and biased inventory of species. Achieving international targets on biodiversity knowledge requires that information gaps be identified. Multi-model inference shows that completeness is limited by distance to researchers, locally available research funding and the ability and willingness to participate in data sharing networks. The EDAM project aims to build a platform that compresses data, enabling data sharing to enable a wholesome, side-by-side data comparison of ecosystems. These aims would be achieved by automating data processing algorithms to compile species lists and associated food webs for participating ecostations, estimating the completeness of the lists and webs, calculating similarity of the lists and webs and creating a web accessible visualization tool that allows comparison.

Proposed Innovation

As large biodiversity collections and environmental data are accessible online, global research communities have an unprecedented access to datasets. Now that methods are within reach to combine and process biodiversity data at global scales, institutions can start to re-examine existing data to coordinate data collection efforts, evolve data sharing strategies and discover methods to efficiently sustain ecosystems. A first step toward integrating the data is to provide a side-by-side comparison of existing data associated with active ecostation communities to stimulate knowledge sharing and collaboration.

--- please contact Jorrit ---

Ecostation biodiversity data summaries are derived from openly available biodiversity data repositories (e.g. GBIF, iDigBio, GloBI). Initially only species lists and associated food webs are compiled for participating ecostations using automated data processing algorithms. For each ecostation, the completeness of the lists and webs are estimated. Also, the similarity of the lists and webs are calculated across the spatially separated island ecosystems to highlight ecological likeness. With EDAM, spatially and institutionally disjointed projects now have a data-driven method to see how much ecological data is available for specific spatio-taxonomic spaces. We hope that comparing available ecological data across ecostations will help stimulate collaboration between scientists, technologists, educators, local governments and research foundations to help better understand and sustain ecosystems around us.

Current and Past Contributors

• Jonathan Wang - Jonathan is a graduate student studying computer science and statistics. He has experience with data analysis and developing web apps. In the scope of this project, Jonathan is helping to clean and model the data as well as integrating our research into a web app to present our findings.

• Brian Lin - Brian Lin is a senior undergraduate student studying Computer Science and Statistics with an interest in Economics. He is mainly interested in applying machine learning and data science to solving real life problems.

• Lavanya Harinarayan - Lavanya Harinarayan is a senior undergraduate student studying Computer Science. She is interested in exploring the various applications of machine learning and artificial intelligence, especially in the field of security.

• Jack Ye - Jack Ye is a senior undergraduate student studying Computer Science and Statistics. Apart from BIDS, he is currently working in the Berkeley ICSI multimedia team for research about music information retrieval.

• Caleb Siu - Caleb Siu is a junior undergraduate student studying Computer Science and Economics. In addition, he is the Director of Finance for Society of Asian Americans and Engineers at Berkeley and part of a college ministry.

• Jusitn Mi - Justin Mi is a sophomore undergraduate student studying Electrical Engineering and Computer Sciences. Outside of BIDS, Justin is involved in Berkeley’s AUTOLAB.

• Nisreen Hejab - Nisreen is a graduate student at the Comparative Biochemistry program. She focuses on 3D atomic modeling of proteins and pharmaceutical ligands. She has experience with data collection, processing, and modeling.

• Carlo Liquido - Carlo is a graduate student at the School of Information focusing on data science and information visualization. He is focusing his efforts on the UI/UX and front-end side of the project.

• Vedant Saran - Vedant is a freshman undergraduate student studying electrical engineering and computer science. He has experience with data science and visualization, and is working on the data collection part of the project.

• Jong-kai Yang - Jong-kai is a graduate student at the School of Information focusing on biosensors and data science. He contributes to the project his experience in web-based SaaS business development and business analysis.

• Tong Zhang - Tong is a junior undergraduate student studying industrial engineering and operations research. She has experience with data visualization and analysis in optimization area. She is also helping to design the UI/UX of the project.

• Jorrit Poelen - Jorrit is a freelance software engineer based in Oakland, California with 15+ years of experience in academia, industry and startup environments. He was awarded an Encyclopedia of Life Rubenstein Fellowship, created Global Biotic Interactions, published a paper in Ecological Informatics, and has ongoing collaborations spanning many non-profit and academic organizations (e.g. Manylabs, Encyclopedia of Life, rOpenSci, iNaturalist, Texas A&M). Jorrit is a mentor/advisor for the EDAM project.

References

1. National Research Council: Convergence : Facilitating Transdisciplinary Integration of Life Sciences,Physical Sciences , Engineering , and Beyond. 2014.
2. Mace G: Ecology must evolve. Nature 2013, 503:191–2.
3. Karr JR, Sanghvi JC, Macklin DN, Gutschow M V, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW: A whole-cell computational model predicts phenotype from genotype. Cell 2012, 150:389–401.
4. Meyer, C. et al., 2015. Global priorities for an effective information basis of biodiversity distributions. Nat Comms, 6, p.8221
5. Butchart, S. H. M.et al.Global biodiversity: indicators of recent declines.Science328,1164–1168(2010).
6. Boitani, L.et al.What spatial data do we need to develop global mammal conservation strategies?Philos. Trans. R. Soc. Lond. B. Biol. Sci366, 2623–2632(2011).
7. Global Biodiversity Information Facility (http://gbif.org)
8. Matthews, T.J. et al., 2014. Thresholds and the species-area relationship: a synthetic analysis of habitat island datasets K. C. Burns, ed. J. Biogeogr., 41(5), pp.1018–1028.
9. The Theory of Island Biogeography by Robert H. MacArthur & Edward O. Wilson