Exploring historical trends using taxonomic name metadata

© 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 8 (2008): 144, doi:10.1186/1471-2148-8-144.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. From the over 10.7 million taxonomic names that are part of the uBio system, 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. 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.The work presented here was funded in part by the MBLWHOI Library and the DAB Lindberg Research Fellowship from the Medical Library Association to INS

Taxonomic informatics tools for the electronic nomenclator zoologicus

Author Posting. © Marine Biological Laboratory , 2006. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 210 (2006): 18-24.Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.This work was supported with funding from the Andrew W. Mellon Foundation and GBIF

LigerCat : using “MeSH clouds” from journal, article, or gene citations to facilitate the identification of relevant biomedical literature

© AMIA, 2009. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose. The definitive version was published in AMIA Annual Symposium Proceedings 2009: 563-567.The identification of relevant literature from within large collections is often a challenging endeavor. In the context of indexed resources, such as MEDLINE, it has been shown that keywords from a controlled vocabulary (e.g., MeSH) can be used in combination to retrieve relevant search results. One effective strategy for identifying potential search terms is to examine a collection of documents for frequently occurring terms. In this way, “Tag clouds” are a popular mechanism for ascertaining terms associated with a collection of documents. Here, we present the Literature and Genomic Electronic Resource Catalogue (LigerCat) system for exploring biomedical literature through the selection of terms within a “MeSH cloud” that is generated based on an initial query using journal, article, or gene data. The resultant interface is encapsulated within a Web interface: http://ligercat.ubio.org. The system is also available for installation under an MIT license.This work is funded in part thanks to grants from the Ellison Medical Foundation and the National Institutes of Health (R01LM009725-01A1)

SCOR/IODE/MBLWHOI Library collaboration on data publication [poster] 

Author Posting. © The Author(s), 2011. This is the author's version of the work. Accepted by the ACM/IEEE Joint Conference on Digital Libraries, June 13-17, 2011, Ottawa, CanadaThis poster describes the development of international standards to publish oceanographic datasets. Research areas include the assignment of persistent identifiers, tracking provenance, linking datasets to publications, attributing credit to data providers, and best practices for the physical composition and semantic description of the content.Funding provided by the George Frederick Jewett Foundation

Lessons learned from 104 years of mobile observatories [poster]

Poster session IN13B-1211 presented 10 December 2007 at the AGU Fall Meeting, 10–14 December 2007, San Francisco, CA, USAAs the oceanographic community ventures into a new era of integrated observatories, it may be helpful to look back on the era of "mobile observatories" to see what Cyberinfrastructure lessons might be learned. For example, SIO has been operating research vessels for 104 years, supporting a wide range of disciplines: marine geology and geophysics, physical oceanography, geochemistry, biology, seismology, ecology, fisheries, and acoustics. In the last 6 years progress has been made with diverse data types, formats and media, resulting in a fully-searchable online SIOExplorer Digital Library of more than 800 cruises (http://SIOExplorer.ucsd.edu). Public access to SIOExplorer is considerable, with 795,351 files (206 GB) downloaded last year. During the last 3 years the efforts have been extended to WHOI, with a "Multi-Institution Testbed for Scalable Digital Archiving" funded by the Library of Congress and NSF (IIS 0455998). The project has created a prototype digital library of data from both institutions, including cruises, Alvin submersible dives, and ROVs. In the process, the team encountered technical and cultural issues that will be facing the observatory community in the near future. Technological Lessons Learned: Shipboard data from multiple institutions are extraordinarily diverse, and provide a good training ground for observatories. Data are gathered from a wide range of authorities, laboratories, servers and media, with little documentation. Conflicting versions exist, generated by alternative processes. Domain- and institution-specific issues were addressed during initial staging. Data files were categorized and metadata harvested with automated procedures. With our second-generation approach to staging, we achieve higher levels of automation with greater use of controlled vocabularies. Database and XML- based procedures deal with the diversity of raw metadata values and map them to agreed-upon standard values, in collaboration with the Marine Metadata Interoperability (MMI) community. All objects are tagged with an expert level, thus serving an educational audience, as well as research users. After staging, publication into the digital library is completely automated. The technical challenges have been largely overcome, thanks to a scalable, federated digital library architecture from the San Diego Supercomputer Center, implemented at SIO, WHOI and other sites. The metadata design is flexible, supporting modular blocks of metadata tailored to the needs of instruments, samples, documents, derived products, cruises or dives, as appropriate. Controlled metadata vocabularies, with content and definitions negotiated by all parties, are critical. Metadata may be mapped to required external standards and formats, as needed. Cultural Lessons Learned: The cultural challenges have been more formidable than expected. They became most apparent during attempts to categorize and stage digital data objects across two institutions, each with their own naming conventions and practices, generally undocumented, and evolving across decades. Whether the questions concerned data ownership, collection techniques, data diversity or institutional practices, the solution involved a joint discussion with scientists, data managers, technicians and archivists, working together. Because metadata discussions go on endlessly, significant benefit comes from dictionaries with definitions of all community-authorized metadata values.Funding provided by the Library of Congress and NSF (IIS 0455998

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points