Dataset Information

Exploring historical trends using taxonomic name metadata.

ABSTRACT: BACKGROUND: Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. RESULTS: From the over 10.7 million taxonomic names that are part of the uBio system 4, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs) and societal importance (e.g., world wars). The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. CONCLUSION: Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.

SUBMITTER: Sarkar IN

PROVIDER: S-EPMC2408592 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Exploring historical trends using taxonomic name metadata.

Sarkar Indra Neil IN Schenk Ryan R Norton Catherine N CN

BMC evolutionary biology 20080513

<h4>Background</h4>Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy.<h4>Results</h4>From the over 10.7 million taxonomic names that are part of the uBio system 4, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pip ...[more]

PMID: 18477399

Similar Datasets

Project description:The efficacy and safety of herbal supplements suffer from challenges due to non-uniform representation of ingredient terms within biomedical and observational health data sources. The nature of how supplement data are reported within Spontaneous Reporting Systems (SRS) can limit analyses of supplement-associated adverse events due to the use of incorrect nomenclature or failing to identify herbs. This study aimed to extract, standardize, and summarize supplement-relevant reports from two SRSs: (1) Food and Drug Administration Adverse Event Reporting System (FAERS) and (2) Canada Vigilance Adverse Reaction (CVAR) database. A thesaurus of plant names was developed and integrated with a mapping and normalization approach that accommodated misspellings and variants. The reports gathered from FAERS between the years 2004 and 2016 show 185,915 herbal and 7,235,330 non-herbal accounting for 2.51%. The data from CVAR found 36,940 reports of herbal and 503,580 non-herbal reports between the years 1965 and 2017 for a total of 6.83%. Although not all cases were actual adverse events due to numerous variables and incomplete reporting, it is interesting to note that the herbs most frequently reported and significantly associated with adverse events were as follows: Avena sativa (Oats), Cannabis sativa (marijuana), Digitalis purpurea (foxglove), Humulus lupulus (hops), Hypericum perforatum (St John's Wort), Paullinia cupana (guarana), Phleum pretense (timothy-grass), Silybum marianum (milk thistle), Taraxacum officinale (Dandelion), and Valeriana officinalis (valerian). Using a scalable approach for mapping and resolution of herb names allowed data-driven exploration of potential adverse events from sources that have remained isolated in this specific area of research. The results from this study highlight several herb-associated safety issues providing motivation for subsequent in-depth analyses, including those that focus on the scope and severity of potential safety issues with supplement use.

Project description:BackgroundThe digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this 'names problem' has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.ResultsThe TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.ConclusionsWe show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.

Project description:Background: The evolution of names, from "medical informatics" to "connected health", implies that the evolvement of technology in health care has been shifted from technology-oriented to healthcare-oriented implementation. Connected healthcare, a healthcare platform of remote monitoring and self-management through technological measures, is suggested to contribute to the efficiency, cost-effectiveness, and satisfaction of healthcare recipient enhancement. However, limited understanding of related connected health (CH) terminology may constrain its implementation. Whether CH is a buzzword only or a practice that can contribute to an aging society is controversial. Objective: This study aims to distinguish CH-related terminology and to identify the trend of CH through reviewing its definition, initiation, development, and evolvement, in order to offer management insights and implications. The objective is to understand what is connected and who is cared about in the connected health model so that better applications can be addressed for the benefit of society. Method: This study reviews the evolution of names, from "medical informatics" in the 1970s to "connected health" after 2000, as well as relevant literature of CH, including e-health, telemedicine, telehealth, telecare, and m-health, to discover the trend of technology-related healthcare innovations. Results: The current status and issues facing accessibility, quality, and cost were presented. Its future trends will be explored through reviewing how changes in healthcare are managed, in addition to its operation and practice. Pre-conditions and requirements for implementing CH are identified to select a typical case to study. Findings suggest that areas with a complete business ecosystem-isolated locations, advanced information technology, aging in population, integrated health, and social care system-are prevalent for designing friendly CH environments. Conclusion: The evidence and tendency of technological convergence create a demand for innovation and partnering with start-up companies that offer a competitive advantage in innovation.

Dataset Information

Exploring historical trends using taxonomic name metadata.

Publications

Exploring historical trends using taxonomic name metadata.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets