Presentations and Papers

Permanent URI for this collection

https://hdl.handle.net/1912/12

This collection represents presentations made by members of the staff of the MBLWHOI Library or at the behest of the Library, and articles authored by members of the Library staff.

Browse

Browsing Presentations and Papers by Title

  • Presentation
    Advancing Open Source, Linked Data Solutions for Cross-Repository Discovery and Collaboration
    ( 2016-05) Raymond, Lisa ; Mickle, Audrey
    The MBLWHOI Library collaborated in multi-year NSF EarthCube funded projects, applying semantic technologies to enable knowledge discovery, sharing, and integration
  • Presentation
    Adventures in Minimal Marc and Bulkimport
    ( 2009-10-12T17:50:22Z) Rioux, Margaret A.
    Method for adding data, such as OCLC numbers or URLs to bibliographic records in an Ex Libris Voyager library system using minimal Marc records and Bulkimport
  • Article
    The Alvin Bibliography: from paper to on-line access
    (IAMSLIC, 1994) Berteaux, Susan S.
  • Working Paper
  • Article
    The Biodiversity Heritage Library : advancing metadata practices in a collaborative digital library
    (Taylor & Francis, 2010-04) Pilsk, Suzanne C. ; Person, Matthew A. ; deVeer, Joseph M. ; Furfey, John F. ; Kalfatovic, Martin R.
    The Biodiversity Heritage Library is an open access digital library of taxonomic literature, forming a single point of access to this collection for use by a worldwide audience of professional taxonomists, as well as “citizen scientists.” A successful mass-scanning digitization program, one that creates functional and findable digital objects, requires thoughtful metadata work flow that parallels the work flow of the physical items from shelf to scanner. This article examines the needs of users of taxonomic literature, specifically in relation to the transformation of traditional library material to digital form. It details the issues that arise in determining scanning priorities, avoiding duplication of scanning across the founding 12 natural history and botanical garden library collections, and the problems related to the complexity of serials, monographs, and series. Highlighted are the tools, procedures, and methodology for addressing the details of a mass-scanning operation. Specifically, keeping a steady flow of material, creation of page level metadata, and building services on top of data and metadata that meet the needs of the targeted communities. The replication of the BHL model across a number of related projects in China, Brazil, and Australia are documented as evidence of the success of the BHL mass-scanning project plan.
  • Presentation
    Building repositories: why DSpace?
    ( 2007-10-25) Devenish, Ann
    This presentation looked at the process of selecting a software platform for hosting the Woods Hole Open Access Server (WHOAS), an institutional repository serving the Woods Hole (MA) science community.
  • Presentation
    Building research networks to support campus programs [poster]
    ( 2012-04-04) Furfey, John F. ; Devenish, Ann ; Hurter, Colleen ; Stafford, Nancy
    This poster focuses on the methods, tools and outcomes involved in creating two targeted research networks to support large, long-running research programs in the Woods Hole scientific community.
  • Presentation
    Choosing open access licensing when publishing
    (Woods Hole Oceanographic Institution, 2020-10-21) Roth, Deborah J.
    When filling out the publication agreement forms for a manuscript to be published what license should I choose? Studies continue to show favorable impact of Open Access on the scholarly literature through increased dissemination and re-use.
  • Moving Image
    Collaborative research : EarthCube building blocks, leveraging semantics and linked data for geoscience data sharing and discovery, OceanLink
    ( 2013-10-28) Wiebe, Peter H. ; Chandler, Cynthia L. ; Raymond, Lisa ; Shepherd, Adam ; Finin, Tim ; Narock, Tom ; Arko, Robert A. ; Carbotte, Suzanne M. ; Hitzler, Pascal ; Cheatham, Michelle ; Krisnadhi, Adila
    The OceanLink EarthCube project will apply state-of-the-art Semantic Web Technologies to support data representation, discovery, analysis, sharing, and integration of datasets from the global oceans, and related resources including meeting abstracts and library holdings. Ships are a principal platform from which a wide spectrum of oceanographic data are collected. At the University of Maryland, Baltimore County, semantic relationships will be extracted from text for use in developing methods that efficiently identify relationships across distributed oceanographic datasets. At Wright State University integration of disparate data will occur by refining and applying leading edge technology from the Semantic Web, ontologies, and linked data. From the MBLWHOI Library, DSpace content will be published as Linked Open Data, providing relationships between oceanographic datasets, publications, conference presentations, and funded National Science Foundation projects. Teams of researchers at the Lamont-Doherty Earth Observatory and the Woods Hole Oceanographic Institution will develop Use Cases that represent the needs of the oceanographic research community and will publish oceanographic dataset catalogs as Linked Open Data. A key contribution will be semantically-enabled cyberinfrastructure components capable of automated data integration across distributed repositories. These efforts will ultimately lead to generalized computational techniques applicable to all of EarthCube.
  • Presentation
    Data Science Training Camp at Woods Hole Oceanographic Institution: Syllabus and slide presentations in 2020
    (Woods Hole Oceanographic Institution, 2020-08-21) Beaulieu, Stace E. ; Raymond, Lisa ; Mickle, Audrey ; Futrelle, Joe ; Symmonds, Nick ; Mazzoli, Roberta ; Brey, Rich ; Kinkade, Danie ; Rauch, Shannon
    With data and software increasingly recognized as scholarly research products, and aiming towards open science and reproducibility, it is imperative for today's oceanographers to learn foundational practices and skills for data management and research computing, as well as practices specific to the ocean sciences. This educational package was developed as a data science training camp for graduate students and professionals in the ocean sciences and implemented at the Woods Hole Oceanographic Institution (WHOI) in 2019 and 2020. Here we provide materials for the 2020 camp which was delivered in-person during two afternoons (total of 8 hours), with two modules per afternoon. We aimed for ~40 participants per camp, with disciplines spanning Earth and life sciences and engineering. Disciplines at each table were mixed on the first afternoon but similar on the second afternoon. Contents of this package include the syllabus and slide presentations for each of the four modules: 1 "Good enough practices in scientific computing," 2 Data management, 3 Software development and research computing, and 4 Best practices in the ocean sciences. The 3rd module is split into two parts. We also include a poster presented at the 2020 Ocean Science Meeting, which has some results from pre- and post-surveys. Funding: The camp was funded by WHOI Academic Programs Office through a Doherty Chair in Education Award, with additional support from WHOI Ocean Informatics Working Group, WHOI Information Services, MBLWHOI Library, the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO), and an NSF-funded XSEDE Jetstream Education Allocation TG-OCE190011. We also utilized resources from the NSF-funded Pangeo project.
  • Presentation
    Dataset to DOI using SWORD [poster]
    ( 2012-03-12) Devenish, Ann ; Chandler, Cynthia L. ; Dorsk, Alexander ; Raymond, Lisa ; Work, Tobias
    This poster describes the tools and processes by which datasets are deposited in an institutional repository (IR) and digital object identifiers (DOI) are acquired. The Marine Biological Laboratory/Woods Hole Oceanographic Institution (MBLWHOI) Library and the Biological and Chemical Oceanography Data Management Office (BCO-DMO) have developed tools and processes to automate the ingestion of datasets and metadata from BCO-DMO for deposit into the Woods Hole Open Access Server (WHOAS) institutional repository. The system also incorporates functionality for BCO-DMO to request a DOI from the Library and streamlines the process by which XML files are generated for DOI deposit with CrossRef, a DOI registration agency. This partnership allows the Library to work with a trusted data repository to ensure high quality data while the data repository utilizes library services and is assured of a permanent archive of the copy of the data extracted from the repository database. This research is being conducted by a team of librarians, data managers and scientists that are collaborating with representatives from the Scientific Committee on Oceanic Research (SCOR) and the International Oceanographic Data and Information Exchange (IODE) of the Intergovernmental Oceanographic Commission (IOC).
  • Presentation
    Digital libraries, archives and large data sets
    ( 2004-06-03) McCray, Alexa T.
    PowerPoint slides for a presentation given at Woods Hole Oceanographic Institution under the auspices of the MBLWHOI Library on June 3, 2004
  • Presentation
    A DSpace institutional repository : WHOAS
    ( 2006-06-08) Devenish, Ann
    This presentation looked at the implementation of a DSpace institutonal respository for the Woods Hole (Massachusetts) science community, including description of content recruitment techniques.
  • Article
    The Encyclopedia of Life, Biodiversity Heritage Library, biodiversity informatics and beyond Web 2.0
    (Great Cities Initiative of the University of Illinois at Chicago Library, 2008-08-04) Norton, Cathy N.
    E.O. Wilson, the noted entomologist at Harvard, "wished" for an authoritative encyclopedia of life that would be freely available on the worldwide web for the entire world. On 9 May 2007, The Encyclopedia of Life (EOL) was launched as a multi-institutional initiative whose mission is to create 1.8 million Web sites detailing all the known attributes, history, and behavior, about every known and described species and portraying that information through video, audio, and literature, via the Internet. A major contributor to the Encyclopedia is the Biodiversity Heritage Library that is currently scanning all the core biodiversity literature.
  • Working Paper
    Envisioning the future of science libraries at academic research institutions : a discussion
    ( 2012-12-20) Feltes, Carol ; Gibson, Donna S. ; Miller, Holly ; Norton, Cathy N. ; Pollock, Ludmila
    A group of librarians, other information professionals, scientists and research administrators met to discuss the challenges that research libraries are currently facing. After the meeting a survey was conducted to obtain additional input from the group on several key challenges that arose from the discussions. The purpose of the meeting and survey was threefold: 1. Examine in detail, from a variety of perspectives, how the world of research is changing and the impact these changes have on the direction of research libraries. 2. Create an informed vision of how research libraries can be a vital partner to researchers. 3. Suggest a strategic approach for realizing this vision. The strategic approach presented in this white paper incorporates feedback from various sized research libraries, each with its own mission. The expectation is that individual libraries will use it as a guide in formulating strategies that are appropriate to their research communities, financial circumstances, and organizational reporting structure.
  • Article
  • Article
    Exploring historical trends using taxonomic name metadata
    (BioMed Central, 2008-05-13) Sarkar, Indra Neil ; Schenk, Ryan ; Norton, Cathy N.
    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.
  • Preprint
    Facilitating open exchange of data and information
    ( 2014-09-22) Gallagher, James ; Orcutt, John A. ; Simpson, Pauline ; Wright, Dawn J. ; Pearlman, Jay ; Raymond, Lisa
    By broad consensus, Open Data presents great value. However, beyond that simple statement, there are a number of complex, and sometimes contentious, issues that the science community must address. In this review, we examine the current state of the core issues of Open Data with the unique perspective and use cases of the ocean science community: interoperability; discovery and access; quality and fitness for purpose; and sustainability. The topics of Governance and Data Publication are also examined in detail. Each of the areas covered are, by themselves, complex and the approaches to the issues under consideration are often at odds with each other. Any comprehensive policy on Open Data will require compromises that are best resolved by broad community input. In the final section of the review, we provide recommendations that serve as a starting point for these discussions.
  • Article
    The fate of the ocean
    (Foundation for National Progress, 2006-03) Whitty, Julia
    Our oceans are under attack, and approaching a point of no return. Can we survive if the seas go silent?
  • Article
    GenBank and PubMed : how connected are they?
    (BioMed Central, 2009-06-09) Miller, Holly ; Norton, Cathy N. ; Sarkar, Indra Neil
    GenBank(R) is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs). Here we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences. Our analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.