Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Conceptual graph-based knowledge representation for supporting reasoning in African traditional medicine

Although African patients use both conventional or modern and traditional healthcare simultaneously, it has been proven that 80% of people rely on African traditional medicine (ATM). ATM includes medical activities stemming from practices, customs and traditions which were integral to the distinctive African cultures. It is based mainly on the oral transfer of knowledge, with the risk of losing critical knowledge. Moreover, practices differ according to the regions and the availability of medicinal plants. Therefore, it is necessary to compile tacit, disseminated and complex knowledge from various Tradi-Practitioners (TP) in order to determine interesting patterns for treating a given disease. Knowledge engineering methods for traditional medicine are useful to model suitably complex information needs, formalize knowledge of domain experts and highlight the effective practices for their integration to conventional medicine. The work described in this paper presents an approach which addresses two issues. First it aims at proposing a formal representation model of ATM knowledge and practices to facilitate their sharing and reusing. Then, it aims at providing a visual reasoning mechanism for selecting best available procedures and medicinal plants to treat diseases. The approach is based on the use of the Delphi method for capturing knowledge from various experts which necessitate reaching a consensus. Conceptual graph formalism is used to model ATM knowledge with visual reasoning capabilities and processes. The nested conceptual graphs are used to visually express the semantic meaning of Computational Tree Logic (CTL) constructs that are useful for formal specification of temporal properties of ATM domain knowledge. Our approach presents the advantage of mitigating knowledge loss with conceptual development assistance to improve the quality of ATM care (medical diagnosis and therapeutics), but also patient safety (drug monitoring)

HILT : High-Level Thesaurus Project. Phase IV and Embedding Project Extension : Final Report

Ensuring that Higher Education (HE) and Further Education (FE) users of the JISC IE can find appropriate learning, research and information resources by subject search and browse in an environment where most national and institutional service providers - usually for very good local reasons - use different subject schemes to describe their resources is a major challenge facing the JISC domain (and, indeed, other domains beyond JISC). Encouraging the use of standard terminologies in some services (institutional repositories, for example) is a related challenge. Under the auspices of the HILT project, JISC has been investigating mechanisms to assist the community with this problem through a JISC Shared Infrastructure Service that would help optimise the value obtained from expenditure on content and services by facilitating subject-search-based resource sharing to benefit users in the learning and research communities. The project has been through a number of phases, with work from earlier phases reported, both in published work elsewhere, and in project reports (see the project website: http://hilt.cdlr.strath.ac.uk/). HILT Phase IV had two elements - the core project, whose focus was 'to research, investigate and develop pilot solutions for problems pertaining to cross-searching multi-subject scheme information environments, as well as providing a variety of other terminological searching aids', and a short extension to encompass the pilot embedding of routines to interact with HILT M2M services in the user interfaces of various information services serving the JISC community. Both elements contributed to the developments summarised in this report

Integrated Framework for Discovering Digital Library Collections, An

Information seekers are generally on their own to discover and use a research library's growing array of digital collections, and coordination of these collections' development and maintenance is often not optimal. The frequent lack of a conscious design for how collections fit together is of equal concern because it means that research libraries are not making the most of the substantial investments they are making in digital initiatives. This paper proposes a framework for a research library's digital collections that offers integrated discovery and a set of best practices to underpin collection building, federated access, and sustainability. The framework's purpose is to give information seekers a powerful and easy way to search across existing and future collections and to retrieve integrated sets of results. The paper and its recommendations are based upon research undertaken by the author and a team of librarians and technologists at Cornell University Library. The team conducted structured interviews of forty-five library staff members involved in digital collection building at Cornell, studied an inventory of the library's more than fifty digital collections, and evaluated seven existing OAI and federated search production or prototype systems. Discusses the author's team's research and the rationale for their recommendations to: present a cohesive view of the library's digital collections for both browsing and searching at the object level; take a programmatic (rather than project-based) approach to digital collection building; require that all new digital collections conform to library-developed and agreed-upon OAI best practices for data providers; and implement organizational structures to sustain the library's digital collections over the long term

Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science

Data hosting infrastructure for primary biodiversity data

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 12 Suppl. 15 (2011): S5, doi:10.1186/1471-2105-12-S15-S5.Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized

Newly available technologies present expanding opportunities for scientific and technical information exchange

The potential for expanded communication among researchers, scholars, and students is supported by growth in the capabilities for electronic communication as well as expanding access to various forms of electronic interchange and computing capabilities. Research supported by the National Aeronautics and Space Administration points to a future where workstations with audio and video monitors and screen-sharing protocols are used to support collaborations with colleagues located throughout the world. Instruments and sensors all over the world will produce data streams that will be brought together and analyzed to produce new findings, which in turn can be distributed electronically. New forms of electronic journals will emerge and provide opportunities for researchers and scientists to electronically and interactively exchange information in a wide range of structures and formats. Ultimately, the wide-scale use of these technologies in the dissemination of research results and the stimulation of collegial dialogue will change the way we represent and express our knowledge of the world. A new paradigm will evolve-perhaps a truly worldwide 'invisible college'