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

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/

A Survey of e-Biodiversity: Concepts, Practices, and Challenges

The unprecedented size of the human population, along with its associated economic activities, have an ever increasing impact on global environments. Across the world, countries are concerned about the growing resource consumption and the capacity of ecosystems to provide them. To effectively conserve biodiversity, it is essential to make indicators and knowledge openly available to decision-makers in ways that they can effectively use them. The development and deployment of mechanisms to produce these indicators depend on having access to trustworthy data from field surveys and automated sensors, biological collections, molecular data, and historic academic literature. The transformation of this raw data into synthesized information that is fit for use requires going through many refinement steps. The methodologies and techniques used to manage and analyze this data comprise an area often called biodiversity informatics (or e-Biodiversity). Biodiversity data follows a life cycle consisting of planning, collection, certification, description, preservation, discovery, integration, and analysis. Researchers, whether producers or consumers of biodiversity data, will likely perform activities related to at least one of these steps. This article explores each stage of the life cycle of biodiversity data, discussing its methodologies, tools, and challenges

Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers

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

Ocean Biodiversity Informatics - an emerging field of science

‘Ocean Biodiversity Informatics’ (OBI) heralds a new era in biological research and management that is revolutionising the way we approach marine biodiversity research. OBI uses computer technology to manage marine biodiversity information (capturing, storing, searching for, retrieving, visualising, mapping, modelling, analysing and publishing data). This allows more users better and faster access to biodiversity information than ever before. The global nature of phenomena such as climate change, over-fishing, and other changes in ecosystems, would not have been recognised had it not been for informatics-aided analyses.The prospect of data mining and exploration on a global scale is enough to gladden the hearts of marine scientists across the world, as marine biology embraces the computer age. Access to global data through OBI will allow for worldwide gap analysis resulting in new perspectives on current research, the promotion of collaborations between research groups and real data sets for teaching purposes, to mention just a few of the potential benefits. OBI is an initiative of the 21st century and will make conventional marine biodiversity research more dynamic and comprehensive, with a range of constantly evolving online tools

Bridging the biodiversity data gaps: Recommendations to meet users’ data needs

A strong case has been made for freely available, high quality data on species occurrence, in order to track changes in biodiversity. However, one of the main issues surrounding the provision of such data is that sources vary in quality, scope, and accuracy. Therefore publishers of such data must face the challenge of maximizing quality, utility and breadth of data coverage, in order to make such data useful to users. Here, we report a number of recommendations that stem from a content need assessment survey conducted by the Global Biodiversity Information Facility (GBIF). Through this survey, we aimed to distil the main user needs regarding biodiversity data. We find a broad range of recommendations from the survey respondents, principally concerning issues such as data quality, bias, and coverage, and extending ease of access. We recommend a candidate set of actions for the GBIF that fall into three classes: 1) addressing data gaps, data volume, and data quality, 2) aggregating new kinds of data for new applications, and 3) promoting ease-of-use and providing incentives for wider use. Addressing the challenge of providing high quality primary biodiversity data can potentially serve the needs of many international biodiversity initiatives, including the new 2020 biodiversity targets of the Convention on Biological Diversity, the emerging global biodiversity observation network (GEO BON), and the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES)

An open-access platform for camera-trapping data

In southern Mexico, local communities have been playing important roles in the design and collection of wildlife data through camera-trapping in community-based monitoring of biodiversity projects. However, the methods used to store the data have limited their use in matters of decision-making and research. Thus, we present the Platform for Community-based Monitoring of Biodiversity (PCMB), a repository, which allows storage, visualization, and downloading of photographs captured by community-based monitoring of biodiversity projects in protected areas of southern Mexico. The platform was developed using agile software development with extensive interaction between computer scientists and biologists. System development included gathering data, design, built, database and attributes creation, and quality control. The PCMB currently contains 28,180 images of 6478 animals (69.4% mammals and 30.3% birds). Of the 32 species of mammals recorded in 18 PA since 2012, approximately a quarter of all photographs were of white-tailed deer (Odocoileus virginianus). Platforms permitting access to camera-trapping data are a valuable step in opening access to data of biodiversity; the PCMB is a practical new tool for wildlife management and research with data generated through local participation. Thus, this work encourages research on the data generated through the community-based monitoring of biodiversity projects in protected areas, to provide an important information infrastructure for effective management and conservation of wildlife