Biological Informatics Resources
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A Review of Approach and Applications in Ecological Research
Review Article Proceedings of NIE 2020;1(1):9-21 https://doi.org/10.22920/PNIE.2020.1.1.9 pISSN 2733-7243, eISSN 2734-1372 Ecoinformatics: A Review of Approach and Applications in Ecological Research Chau Chin Lin* Society of Subtropical Ecology, Taipei, Taiwan ABSTRACT Ecological communities adapt the concept of informatics in the late 20 century and develop rapidly in the early 21 century to form Ecoinformatics as the new approach of ecological research. The new approach takes into account the data-intensive nature of ecology, the precious information content of ecological data, and the growing capacity of computational technology to leverage complex data as well as the critical need for informing sustainable management of complex ecosystems. It comprehends techniques for data management, data analysis, synthesis, and forecasting on ecological research. The present paper attempts to review the development history, studies and application cases of ecoinformatics in ecological research especially on Long Term Ecological Research (LTER). From the applications show that the ecoinformatics approach and management system have formed a new paradigm in ecological research Keywords: Ecology, EML, Informatics, Information management system, LTER, Metadata Introduction takes into account the data-intensive nature of ecology, the precious information content of ecological data, and Informatics is a distinct scientific discipline, character- the growing capacity of computational technology to ized by its own concepts, methods, body of knowledge, leverage complex data as well as the critical need for in- and open issues. It covers the foundations of computa- forming sustainable management of complex ecosystems. tional structures, processes, artifacts and systems; and It comprehends techniques for data management, data their software designs, their applications, and their im- analysis, synthesis, and forecasting on ecological research pact on society (CECE, 2017). -
January, 1999
FINAL REPORT OF THE OECD MEGASCIENCE FORUM WORKING GROUP ON BIOLOGICAL INFORMATICS January, 1999 Contents Executive Summary.......................................................................................................................................................2 Background....................................................................................................................................................................5 What is Informatics?...............................................................................................................................................5 Why is Biological Informatics Important and Needed?..........................................................................................6 Rationale for Focus on Biodiversity Informatics and Neuroinformatics.................................................................6 Opportunities in Biological Informatics for OECD Countries................................................................................7 Scientific and Infrastructural Challenges and Issues...............................................................................................8 Intellectual Property Rights ..................................................................................................................................11 Support and Funding.............................................................................................................................................12 Report of the Biodiversity Informatics Subgroup ........................................................................................................14 -
A New Era for Specimen Databases and Biodiversity Information Management in South Africa
Biodiversity Informatics, 8, 2012, pp.1-11. A NEW ERA FOR SPECIMEN DATABASES AND BIODIVERSITY INFORMATION MANAGEMENT IN SOUTH AFRICA WILLEM COETZER, OFER GON South African Institute for Aquatic Biodiversity, Somerset Street, Grahamstown, South Africa. Email for correspondence: [email protected]. MICHELLE HAMER South African National Biodiversity Institute, Cussonia Ave, Pretoria, South Africa FATIMA PARKER-ALLIE South African National Biodiversity Institute, Rhodes Drive, Cape Town, South Africa Abstract. ‒ We present observations and a commentary on the inherited legacy and current state of biodiversity information management in South African natural history museums, and make recommendations for the future. We emphasize the importance of using a recognized database application, and training and capacity development to improve the quality and integration of biodiversity information for research. In the last decade, biodiversity information in approximately 26% (Hamer 2011) of vouchered specimen databases of natural history museums specimens in South African zoological collections has seen renewed interest and much innovation could be queried through the SABIF Data Portal and development (Bisby 2000, Soberón and or the GBIF Data Portal. Peterson 2004, Johnson 2007, Peterson et al. The vast majority of information about South 2010). Biodiversity Informatics has been defined African biodiversity, which is relatively well as ‘application of informatics to recorded and yet- sampled (Figure 1), originates from South African to-be discovered -
Biodiversity Informatics Vs
MOHD. SAJID IDRISI & MOMD. IMRAN KHAN le ic rt Biodiversity networks and databases will play a crucial role in managing the vast and A Biodiversity increasing information on biodiversity re components all around the world. India u t with its emerging strength in Information a e Technology is in an excellent position to F Informatics take up the challenge of developing robust Digitizing the Web of Life information networks and databases. N the wake of increased threats from population genetics, philosophy, microorganism repositories in various Ideforestation, alteration in land use, anthropology, sociology, information universities, natural history museums, species invasion, soil degradation, technology, economics etc. For research institutions and organizations pollution and climate change, the global conservation biologists or biodiversity concentrated mainly in developed community felt an urgent need to address experts it is a challenge to preserve the countries. Experts are often asked for quick biodiversity as an important perspective evolutionary potential and ecological advice or input by government and private of our lives. Global concerns for the viability of a vast array of biodiversity, and agencies regarding issues such as status conservation of biodiversity led to the preserve the complex nature, dynamics of a species population in a particular Convention on Biological Diversity. At the and interrelationships of natural systems. region or area, potential effects of moment, 188 countries including India are This calls for high connectivity between introduced species, forest fire impacts in party to the convention. experts and their available work in various a protected area, ecological effects of The Convention on Biological Diversity research institutions and organizations. -
Biological Informatics 2021
Biological Informatics 2021 By Marcus P. Zillman, M.S., A.M.H.A. Executive Director – Virtual Private Library [email protected] Biological Informatics 2021 is a comprehensive listing of biological informatics resources currently available on the Internet. The below list of sources is taken from my Subject Tracer™ Information Blog titled Biological Informatics and is constantly updated with Subject Tracer™ bots at the following URL: http://www.BiologicalInformatics.info/ These resources will help you to discover the many pathways available to you through the Internet to find the latest health informatics, neuroinformatics, biodiversity informatics and biomolecular informatics sources and sites. Figure 1: Biological Informatics 2021 Subject Tracer™ Information Blog 1 [Updated: June 1, 2021] Biological Informatics 2021 White Paper Link Compilation http://www.BiologicalInformatics.info/ [email protected] eVoice: 239-206-3450 © 2008 - 2021 Marcus P. Zillman, M.S., A.M.H.A. Note: This Biological Informatics Subject Tracer Information Blog is divided into the following categories: BIOLOGICAL INFORMATICS HEALTH INFORMATICS (Medical Informatics) NEUROINFORMATICS (NI) BIODIVERSITY INFORMATICS (BDI) BIOMOLECULAR INFORMATICS (BioInformatics) Current Subject Tracer™ Information Blogs Biological Informatics: 1000 Genomes Project http://www.1000genomes.org/ About Bioscience http://www.aboutbioscience.org/ Academic and Scholar Search Engines and Sources 2021 http://www.ScholarSearchEngines.com/ A Genetic Atlas of Human -
The Biodiversity Informatics Landscape: Elements, Connections and Opportunities
Research Ideas and Outcomes 3: e14059 doi: 10.3897/rio.3.e14059 Research Article The Biodiversity Informatics Landscape: Elements, Connections and Opportunities Heather C Bingham‡‡, Michel Doudin , Lauren V Weatherdon‡, Katherine Despot-Belmonte‡, Florian Tobias Wetzel§, Quentin Groom |, Edward Lewis‡¶, Eugenie Regan , Ward Appeltans#, Anton Güntsch ¤, Patricia Mergen|,«, Donat Agosti », Lyubomir Penev˄, Anke Hoffmann ˅, Hannu Saarenmaa¦, Gary Gellerˀ, Kidong Kim ˁ, HyeJin Kimˁ, Anne-Sophie Archambeau₵, Christoph Häuserℓ, Dirk S Schmeller₰, Ilse Geijzendorffer₱, Antonio García Camacho₳, Carlos Guerra ₴, Tim Robertson₣, Veljo Runnel ₮, Nils Valland₦, Corinne S Martin‡ ‡ UN Environment World Conservation Monitoring Centre, Cambridge, United Kingdom § Museum fuer Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany | Botanic Garden Meise, Meise, Belgium ¶ The Biodiversity Consultancy, Cambridge, United Kingdom # Ocean Biogeographic Information System (OBIS), Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium ¤ Freie Universität Berlin, Berlin, Germany « Royal Museum for Central Africa, Tervuren, Belgium » Plazi, Bern, Switzerland ˄ Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria ˅ Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany ¦ University of Eastern Finland, Joensuu, Finland ˀ Group on Earth Observations, Geneva, Switzerland ˁ National Institute of Ecology, Seocheon, Korea, South ₵ Global Biodiversity Information Facility France, Paris, -
Biodiversity Informatics: Managing Knowledge Beyond Humans and Model Organisms
Pacific Symposium on Biocomputing 12:340-342(2007) BIODIVERSITY INFORMATICS: MANAGING KNOWLEDGE BEYOND HUMANS AND MODEL ORGANISMS INDRA NEIL SARKAR† Marine Biological Laboratory, 7 MBL Street Woods Hole, MA 02543, USA E-mail: [email protected] In the biomedical domain, researchers strive to organize and describe organisms within the context of health and epidemiology. In the biodiversity domain, researchers seek to understand how organisms relate to one another, either historically through evolution or spatially and geographically in the environment. Currently, there is limited cross-communication between these domains. As a result, valuable knowledge that could inform studies in either domain often goes unnoticed. Biodiversity knowledge has long been a valuable source for many biomedical advances [1]. Before the creation of synthetic compounds, medicinal compounds originated from solely natural plant and animal extracts. Although there are upward estimates of between 10-100 million organisms on Earth [2], biomedical research primarily focuses on only a fraction of these as “model” organisms [3]. Furthermore, much knowledge may be lost from the biomedical community because many organisms are only described within biodiversity resources. These studies can form the basis for research on evolution, speciation, and distribution, and also provide an important baseline for studies of not only conservation but also the study of emerging diseases. The integration of biodiversity knowledge from museum collections, for example, has provided significant insights into the etiology and distribution of diseases such as hantavirus [4]. Understanding the etiology of diseases and their host epidemiology may also further the development of vaccinations and treatments that can help prevent epidemics or pandemics, such as the looming threat of the avian flu [5]. -
Taxonomy and Systematics in Biodiversity Informatics: Lessons Learned from Ichthyology and General Perspectives
Biodiversity Information Science and Standards 3: e37657 doi: 10.3897/biss.3.37657 Conference Abstract Taxonomy and Systematics in Biodiversity Informatics: Lessons learned from ichthyology and general perspectives Nicolas Bailly ‡ ‡ University of British Columbia / Beaty Biodiversity Museum, Vancouver, Canada Corresponding author: Nicolas Bailly ([email protected]) Received: 24 Jun 2019 | Published: 02 Jul 2019 Citation: Bailly N (2019) Taxonomy and Systematics in Biodiversity Informatics: Lessons learned from ichthyology and general perspectives . Biodiversity Information Science and Standards 3: e37657. https://doi.org/10.3897/biss.3.37657 Abstract Although still strongly intertwined, taxonomy and systematics are diverging more and more in their paradigms, methods, and agendas: it is not possible to consider them as synonyms anymore. While taxonomy remains an analytical science based on abductive reasoning (trying to find the historical pathways leading to present species delineations), systematics diverged as an information science since the rise of computers: summarizing, organising, and exposing taxonomical, biological, and ecological data, information, and knowledge in the most efficient ways, with respect to various targeted audiences. One could even consider synonymising biodiversity informatics with systematics instead! Schematically, this led to two different types of information systems: one dedicated to pure taxonomic and nomenclatural data; one oriented to record life-traits. Obviously, the latter must be built along reliable taxonomic backbones, therefore the former should have been built before the latter. It did not happen as exemplified in fishes by the Food and Agriculture Organisation (FAO) Fisheries Global Information System (FIGIS) and related, Catalog of Fishes, and FishBase, and later the databases of the International Union for Conservation of Nature (IUCN) and World Register of Marine Species (WoRMS), or for aggregators with Catalogue of Life and e.g., GBIF, Encyclopedia of Life. -
Data and Information Management and Communication - Walter G
BIODIVERSITY: STRUCTURE AND FUNCTION – Vol. I - Data and Information Management and Communication - Walter G. Berendsohn DATA AND INFORMATION MANAGEMENT AND COMMUNICATION Walter G. Berendsohn Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem, Germany Keywords: Biodiversity informatics, biological informatics, bioinformatics, taxonomic databases, systematics, taxonomy, biological collections, natural history collections, herbaria, botanical gardens, zoological gardens, culture collections. Contents 1. Introduction 2. Scope of the information domain in biodiversity informatics 2.1. Primary biodiversity records: biological collection data 2.2. Collection-level data 2.3. Nomenclatural data 2.4. Taxa and concepts 2.5. Descriptive data 2.6. Auxiliary data and information services 2.7. The molecular and the ecosystem level 3. State of the art 3.1. Data input and management tools 3.2. The common access system 3.2.1. History 3.2.2. Protocol and data specification 3.2.3. Linking biodiversity databases 3.3. Tools for display and analysis 4. Some perspectives 5. Conclusion Acknowledgements Glossary Bibliography Biographical Sketch UNESCO – EOLSS Summary Developments SAMPLEin data and information CHAPTERSmanagement and communications for biodiversity research are exemplified by an account of progress and perspectives in biodiversity informatics. The information domain, its networking techniques and applications are described and an attempt is made to deduce perspectives from current developments in this fast moving field. 1. Introduction The topic of data and information management and communication for biodiversity research is here exemplified by a description of the emergence, current state and ©Encyclopedia of Life Support Systems (EOLSS) BIODIVERSITY: STRUCTURE AND FUNCTION – Vol. I - Data and Information Management and Communication - Walter G. -
A Decadal View of Biodiversity Informatics: Challenges and Priorities
UvA-DARE (Digital Academic Repository) A decadal view of biodiversity informatics: challenges and priorities Hardisty, A.; Roberts, D.; The Biodiversity Informatics Community; Addink, W.; Aelterman, B.; Agosti, D.; Amaral-Zettler, L.; Ariño, A.H.; Arvanitidis, C.; Backeljau, T.; Bailly, N.; Belbin, L.; Berendsohn, W.; Bertrand, N.; Caithness, N.; Campbell, D.; Cochrane, G.; Conruyt, N.; Culham, A.; Damgaard, C.; Davies, N.; Fady, B.; Faulwetter, S.; Feest, A.; Field, D.; Garnier, E.; Geser, G.; Gilbert, J.; Grosche, B.; Grosser, D.; Herbinet, B.; Hobern, D.; Jones, A.; de Jong, Y.; King, D.; Knapp, S.; Koivula, H.; Los, W.; Meyer, C.; Morris, R.A.; Morrison, N.; Morse, D.; Obst, M.; Pafilis, E.; Page, L.M.; Page, R.; Pape, T.; Parr, C.; Paton, A.; Patterson, D.; van Tienderen, P. DOI 10.1186/1472-6785-13-16 Publication date 2013 Document Version Final published version Published in BMC Ecology Link to publication Citation for published version (APA): Hardisty, A., Roberts, D., The Biodiversity Informatics Community, Addink, W., Aelterman, B., Agosti, D., Amaral-Zettler, L., Ariño, A. H., Arvanitidis, C., Backeljau, T., Bailly, N., Belbin, L., Berendsohn, W., Bertrand, N., Caithness, N., Campbell, D., Cochrane, G., Conruyt, N., Culham, A., ... van Tienderen, P. (2013). A decadal view of biodiversity informatics: challenges and priorities. BMC Ecology, 13, 16. https://doi.org/10.1186/1472-6785-13-16 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). -
Biodiversity Informatics Infrastructure: an Information Commons for the Biodiversity Community
Biodiversity Informatics Infrastructure: An Information Commons for the Biodiversity Community Gladys A. Cotter Barbara T. Bauldock U.S. Geological Survey U.S. Geological Survey 300 National Center 300 National Center Reston, VA 20192 Reston, VA 20192 USA USA [email protected] [email protected] Abstract and scientists and are maintained in natural history museums. Journal articles exist in libraries throughout This paper provides an overview of efforts to the world, often in paper format. Other information such create an informatics infrastructure for the as numeric and visual representations are maintained at biodiversity community. A vast amount of high performance computer facilities and are fully biodiversity information exists, but no compre- digitized. A significant portion of the information re- hensive infrastructure is in place to provide easy mains in the hands of the scientists who originated it. The assess and effective use of this information. The fact that biodiversity information is collected and stored advent of modern information technologies in diverse forms, formats and locations has proved a provides a foundation for a remedy. Biodiversity serious obstacle to our ability to correlate and synthesize informatics infrastructures are being called for at the information to create new knowledge. national, regional, and global levels, and plans The biodiversity information which exists today has are in place to coordinate these efforts to ensure economic value and represents an investment of billions interoperability. The paper reviews some essen- of dollars worldwide. Unfortunately, a comprehensive tial requirements and some challenges related to infrastructure that would allow this information to be building this infrastructure. easily accessed and effectively used so that society can reap a return on its investment does not yet exist. -
Getting Past the Prototype in Biological Informatics
A Graduate Program for Scientific Communication Specialists: Getting Past the Prototype in Biological Informatics Carole L. Palmer and Bryan Heidorn Graduate School of Library and Information Science University of Illinois at Urbana-Champaign National Science Foundation/IIS/CISE Education Research and Curriculum Development January 2006-January 2009 Project Summary We propose to develop a comprehensive masters level training program in scientific communication. The program will build on our long-standing, top-rated masters of science in library and information science (MSLIS), our new digital library certificate of advanced studies program (DL-CAS), and our ongoing information technology research initiatives in biodiversity, neuroscience, and genomics. Intellectual merit: The nature of science communication is changing to include new forms of information collection, management, use, and dissemination, and biologists are generating new information at a staggering rate. Methods of information management, such as globally federated data sets in ecology and neuroscience not only alter the quantity of information that is available but also cause a qualitative shift in the nature of the scientific questions that can be asked and answered. For example, when information on the historic global distribution of species is combined with historic climatic data we can begin to answer questions about the future distribution of species under the pressure of climate change. This data transformation however is not free. It requires the collaborative effort of scientists with information specialists who both understand some aspects of the science and who are skilled in the associated computational and information management tasks. This new breed of information specialist must know how to collect, organize, access, use, and preserve information, freeing biological scientists to focus on biology.