Grand challenges in biodiversity informatics

Author Posting. © The Author, 2007. This is the author's version of the work. It is posted here by permission of KH Biotech Services Pte for personal use, not for redistribution. The definitive version was published in Asia-Pacific Biotech News 11(1): 15-18.The exponentially growing array of biological data has necessitated the development of a new information management domain, biodiversity informatics. It is one of the newest members of the ‘informatics’ sub-disciplines, which all generally focus on the management of information through the application of advanced technologies. Like other informatics sub-disciplines, biodiversity informatics depends on fundamental computer science and information science principles to facilitate the management of heterogeneous data. Biodiversity informatics distinguishes itself as being the most focused on biological knowledge dating back to the earliest dates of recorded history – while most biological or biomedical informatics studies focus on organizing and studying information spanning less than 100 years, the scope of biodiversity informatics spans the age of the Earth. Biodiversity informatics is also concerned with the widest range of disparate data types – including climatology, epidemiology, geography, and taxonomy. To this end, many informatics principles can readily be incorporated into biodiversity informatics; however, there are equally as many challenges that will require creative solutions. Here, several such challenges are presented in an effort to lay a framework for the types of issues that will define the future of biodiversity informatics and, in turn, the future of biology and biomedicine

Bringing Together Species Observations: A Case Story of Sweden's Biodiversity Informatics Infrastructures

Biodiversity informatics produces global biodiversity knowledge through the collection and analysis of biodiversity data using informatics techniques. To do so, biodiversity informatics relies upon data accrual, standardization, transferability, openness, and "invisible" infrastructure. What biodiversity informatics mean to society, however, cannot be adequately understood without recognizing what organizes biodiversity data. Using insights from science and technology studies, we story the organizing "visions" behind the growth of biodiversity informatics infrastructures in Sweden-an early adopter of digital technologies and significant contributor to global biodiversity data-through interviews, scientific literature, governmental reports and popular publications. This case story discloses the organizational formation of Swedish biodiversity informatics infrastructures from the 1970s to the present day, illustrating how situated perspectives or "visions" shaped the philosophies, directions and infrastructures of its biodiversity informatics communities. Specifically, visions related to scientific progress and species loss, their institutionalization, and the need to negotiate external interests from governmental organizations led to unequal development across multiple infrastructures that contribute differently to biodiversity knowledge. We argue that such difference highlights that the social and organizational hurdles for combining biodiversity data are just as significant as the technological challenges and that the seemingly inconsequential organizational aspects of its infrastructure shape what biodiversity data can be brought together, modelled and visualised

Ipb Biodiversity Informatics (Ipbiotics) Untuk Pembangunan Berkelanjutan

Indonesia is the country with the second highest biodiversity in the world. It is not only the diversity of biodiversity, but also diversity of indigenous knowledge such as functional foods and other traditional ingredients. IPB as one of the leading university in Indonesia has important role in the management of natural resources of biodiversity. Currently, management of biodiversity resource require an integrated and holistic system using computer science and technology which develop rapidly at this time. This study developed a system of biodiversity informatics IPB (IPBiotics) for biodiversity information management of Indonesia's natural resources in order to improve the knowledge management (knowledge management), exploration, analysis, synthesis and interpretation of data ranging from the level of genomic biodiversity, species level to the ecosystem level. Activities undertaken in this research include exploration of organism, biodiversity database development and biodiversity informatics infrastructure using model Resources Descriptions framework RDF with biodiversity data standards. Taxonomic Databases Working Group (TDWG). IPBiotics participatory and integrated. Some of the features of the application that was developed in organism such as IPBiotics system, location mapping and exploration missions. IPBiotics also uses computer vision technology in application development. By IPBiotics we hope that the data information and knowledge of Indonesian natural wealth can be utilized appropriately and optimally, so that the preservation of natural resources can be properly maintained

A global perspective on decadal challenges and priorities in biodiversity informatics

Biodiversity informatics is a field that is growing rapidly in data infrastructure, tools, and participation by researchers worldwide from diverse disciplines and with diverse, innovative approaches. A recent ‘decadal view’ of the field laid out a vision that was nonetheless restricted and constrained by its European focus. Our alternative decadal view is global, i.e., it sees the worldwide scope and importance of biodiversity informatics as addressing five major, global goals: (1) mobilize existing knowledge; (2) share this knowledge and the experience of its myriad deployments globally; (3) avoid ‘siloing’ and reinventing the tools of knowledge deployment; (4) tackle biodiversity informatics challenges at appropriate scales; and (5) seek solutions to difficult challenges that are strategic

BioGUID: resolving, discovering, and minting identifiers for biodiversity informatics

Background: Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). Results: BioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. Conclusion: BioGUID is available at http://bioguid.info/. Source code is available from http://code.google.com/p/bioguid/

Towards a biodiversity knowledge graph

One way to think about "core" biodiversity data is as a network of connected entities, such as taxa, taxonomic names, publications, people, species, sequences, images, and collections that form the "biodiversity knowledge graph". Many questions in biodiversity informatics can be framed as paths in this graph. This article explores this futher, and sketches a set of services and tools we would need in order to construct the graph

Wikipedia as an encyclopaedia of life

In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision

Unifying European Biodiversity Informatics (BioUnify)

In order to preserve the variety of life on Earth, we must understand it better. Biodiversity research is at a pivotal point with research projects generating data at an ever increasing rate. Structuring, aggregating, linking and processing these data in a meaningful way is a major challenge. The systematic application of information management and engineering technologies in the study of biodiversity (biodiversity informatics) help transform data to knowledge. However, concerted action is required to be taken by existing e-infrastructures to develop and adopt common standards, provisions for interoperability and avoid overlapping in functionality. This would result in the unification of the currently fragmented landscape that restricts European biodiversity research from reaching its full potential. The overarching goal of this COST Action is to coordinate existing research and capacity building efforts, through a bottom-up trans-disciplinary approach, by unifying biodiversity informatics communities across Europe in order to support the long-term vision of modelling biodiversity on earth. BioUnify will: 1. specify technical requirements, evaluate and improve models for efficient data and workflow storage, sharing and re-use, within and between different biodiversity communities; 2. mobilise taxonomic, ecological, genomic and biomonitoring data generated and curated by natural history collections, research networks and remote sensing sources in Europe; 3. leverage results of ongoing biodiversity informatics projects by identifying and developing functional synergies on individual, group and project level; 4. raise technical awareness and transfer skills between biodiversity researchers and information technologists; 5. formulate a viable roadmap for achieving the long-term goals for European biodiversity informatics, which ensures alignment with global activities and translates into efficient biodiversity policy