Presentations and Papers

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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.


Recent Submissions

Now showing 1 - 20 of 57
  • Presentation
    MBLWHOI Library’s Institutional Repository – WHOAS: DSpace 7.2 migration
    (Woods Hole Oceanographic Institution, 2022-12-01) Roth, Deborah J. ; Mickle, Audrey
    The MBLWHOI Library’s Institutional Repository (IR) is a DSpace repository. We are migrating from version 5.6 to 7.2. This presentation will demonstrate new DSpace 7 features in our repository, while discussing our story and our takeaways from our migration.
  • 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.
  • Presentation
    MBLWHOI Library’s institutional repository stewardship responsibility
    (Woods Hole Oceanographic Institution, 2020-12-03) Roth, Deborah J. ; Raymond, Lisa
    The MBLWHOI Library’s Institutional Repository (IR) is a CoreTrustSeal certified repository. We chose to go through this process to demonstrate our commitment to quality stewardship and to be a trusted option for our researchers facing funder and publisher requirements that data be accessible, and more recently, also citable with a DOI. The Library always recommends that researchers deposit data in an appropriate subject or community repository, but there are many cases where the dataset needing a DOI does not fit that scenario. The ability to quickly and easily deposit data in a certified repository is a value added service for our users. Some funders now mandate the data must be deposited in a FAIR repository. Being a CoreTrustSeal certified repository ensures that the MBLWHOI Library’s Institutional Repository practices FAIR principles. This lighting talk will show the steps we went through to become certified, some of the hurdles and benefits, as well our current status as an application reviewer. This process enabled us to review our internal process and procedures and re-examine any outdated practices. It shined a light on places we could improve our documentation and more clearly state our policies. The importance of demonstrating our commitment to quality and the Library’s continued efforts with the repository to remain on the forefront of technology with linked open data,, etc.
  • 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.
  • Still Image
    MBLWHOI Library Banner
    ( 2019-09) Batyuk, Kirill
  • Working Paper
    MBLWHOI LIBRARY Recommendation for Webinar Series
    ( 2018-12-14) Corlett, Rebecca S.
    This report was completed for a graduate level class at Syracuse University entitled IST 613 Library Planning, Marketing, and Assessment. This report was completed in partnership with Lisa Raymond and Jennifer Walton, Co-Directors of the MBLWHOI Library in Woods Hole, Massachusetts. The following report delivers information on the existing value and impact areas of the library including an analysis of the existing stakeholders, services, and resources. The MBLWHOI Library is a vital resource to the five science institutions located in Woods Hole, Massachusetts, as it provides both strong core and specialized services to assist patrons in furthering their endeavors in discovery, education, and research; however, communicating the value and impact of the library and its specialized services to its busy user community can be challenging. Bridging this gap is how the recommendation of the monthly lunch and learn webinar series was developed. The lunch and learn webinar series will not only help the library to share its specialized services and resources with its community, but it will also allow the library to meet and expand a good number of the goals listed within its Strategic Plan for 2018. A focus on identifying user needs via assessment will be key to creating a webinar series that is both relevant and inviting to the library’s community. By using webinar services that are provided at no cost by the institutions, the library can reinforce communication with its users, while also ensuring that the library budget remains primarily focused on resources, such as journal articles, that are of great importance to library patrons. Strengths for the recommendation stem from dedicated library staff, evidence of user needs for instruction on specialized services, as well as the library’s strong core values of furthering the education and research projects within the Woods Hole community. Marketing of the webinar series via flyers, social media, and email newsletters will refresh the library’s presence on campus, thus helping it to meet its goal of being viewed by the community as the primary knowledge resource on campus. The increased communication efforts will be tailored to various audience types by using key messages for each user group, as well as ensuring that the communication initiated by the library is brief, informative, and timely. Assessing the webinar series will be essential, and the continued success of the program will rest on the library’s ability to identify strengths and weaknesses in the series, as well as user need areas. User surveys, focus groups, informal conversations, and library statistics will all be collected and used as assessment tools. Assessment of the webinar series will help the library to ensure that the series’ outcomes and strategic plan goals are being met. Available library staff time and library budget will determine the ability of the library to implement the webinar series; however, the benefits of implementing the webinar series will not only create a platform for the increased exchange of knowledge between the library and its users, but it will also bring renewed focus to the library that will allow for the library to maximize the value and impact they are able to bestow on their user community.
  • 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
    Using linked open data to search across geoscience repositories [poster]
    ( 2017-10) 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
    Leveraging the GeoLink Knowledge Base for Cruise Information
    (Federation of Earth Science Information Partners, 2016-12-21) Mickle, Audrey ; Fils, Douglas ; Shepherd, Adam
    Open Linked Data (LOD) is providing an excellent opportunity for repositories, libraries, and archives to expand the use of their holdings and advance the work of researchers. The implementation of the GeoLink Knowledgebase has created an exciting LOD framework for organizations specializing in Earth Sciences. As an NSF EarthCube Building Block, GeoLink brings together several powerful data sources, such as BCO-DMO, Rolling Deck to Repository (R2R), Data One, IEDA, IODP, and LTER, with publication providers such as the MBLWHOI Library’s Woods Hole Open Access Server (WHOAS), ESIP, and AGU. While publishing to the GeoLink knowledgebase offers a great way to make collections and metadata more findable and relevant, becoming a linked data publisher is not the only way to engage with linked data or the GeoLink project. Any repository can use simple, easily customizable code developed by members of the GeoLink team to add live GeoLink content to a page based on the item's metadata, leveraging GeoLink’s powerful framework for searching across repositories, organizations, and disciplines.
  • Presentation
    Getting Started with Data Management & DMPTool at WHOI
    ( 2017-01-25) Mickle, Audrey
    Introduction to DMP Tool for WHOI staff given on January 26th, 2017. Presentation adapted from
  • Presentation
    Open Access : the Power of One (or, how one individual moved an institution toward adopting an open access policy)
    ( 2016-10-25) Manning, Cara C.
    A presentation and discussion on the ongoing process to elevate open access in Woods Hole, sponsored by the MBLWHOI Library in observance of International Open Access week. Presented 25 October 2016 at the Smith Lab, Woods Hole Oceanographic Institution, Woods Hole, MA
  • Preprint
    Key components of data publishing : using current best practices to develop a reference model for data publishing
    ( 2015-12-04) Austin, Claire C ; Bloom, Theodora ; Dallmeier-Tiessen, Sunje ; Khodiyar, Varsha ; Murphy, Fiona ; Nurnberger, Amy ; Raymond, Lisa ; Stockhause, Martina ; Tedds, Jonathan ; Vardigan, Mary ; Whyte, Angus
    Availability of workflows for data publishing could have an enormous impact on researchers, research practices and publishing paradigms, as well as on funding strategies and career and research evaluations. We present the generic components of such workflows in order to provide a reference model for these stakeholders. Methods: The RDA-WDS Data Publishing Workflows group set out to study the current data publishing workflow landscape across disciplines and institutions. A diverse set of workflows were examined to identify common components and standard practices, including basic self-publishing services, institutional data repositories, long term projects, curated data repositories, and joint data journal and repository arrangements. Results: The results of this examination have been used to derive a data publishing reference model comprised of generic components. From an assessment of the current data publishing landscape, we highlight important gaps and challenges to consider, especially when dealing with more complex workflows and their integration into wider community frameworks. Conclusions: It is clear that the data publishing landscape is varied and dynamic, and that there are important gaps and challenges. The different components of a data publishing system need to work, to the greatest extent possible, in a seamless and integrated way. We therefore advocate the implementation of existing standards for repositories and all parts of the data publishing process, and the development of new standards where necessary. Effective and trustworthy data publishing should be embedded in documented workflows. As more research communities seek to publish the data associated with their research, they can build on one or more of the components identified in this reference model.
  • Book
    Ocean data publication cookbook
    (UNESCO, 2013) Leadbetter, Adam ; Raymond, Lisa ; Chandler, Cynthia L. ; Pikula, Linda ; Pissierssens, Peter ; Urban, Edward
    Executive summary: This “Cookbook” has been written for data managers and librarians who are interested in assigning a permanent identifier to a dataset for the purposes of publishing that dataset online and for the citation of that dataset within the scientific literature. A formal publishing process adds value to the dataset for the data originators as well as for future users of the data. Value may be added by providing an indication of the scientific quality and importance of the dataset (as measured through a process of peer review), and by ensuring that the dataset is complete, frozen and has enough supporting metadata and other information to allow it to be used by others. Publishing a dataset also implies a commitment to persistence of the data and allows data producers to obtain academic credit for their work in creating the datasets. One form of persistent identifier is the Digital Object Identifier (DOI). A DOI is a character string (a "digital identifier") used to provide a unique identity of an object such as an electronic document. Metadata about the object is stored in association with the DOI name and this metadata may include a location where the object can be found. The DOI for a document is permanent, whereas its location and other metadata may change. Referring to an online document by its DOI provides more stable linking than simply referring to it by its URL, because if its URL changes, the publisher need only update the metadata for the DOI to link to the new URL. A DOI may be obtained for a variety of objects, including documents, data files and images. The assignment of DOIs to peer-reviewed journal articles has become commonplace. This cookbook provides a step-by-step guide to the data publication process and showcases some best practices for data publication.
  • Presentation
    No Repository is an Island: Putting the WHOAS community repository in a geoscience context [poster]
    (E-Science Symposium, University of Massachusetts Medical School, 2016-04-06) Mickle, Audrey
    The MBLWHOI Library is partner in the NSF-funded EarthCube building block, GeoLink, whose goal is to push the boundaries of semantic technology in cross-repository discovery within the geosciences field. GeoLink has created ontology design patterns that link together: the MBLWHOI Library’s Woods Hole Open Access Server (WHOAS); data repositories, including Rolling Deck to Repository (R2R), Biological and Chemical Oceanography Data Management Office (BCO-DMO), Integrated Earth Data Applications (IEDA), Long-Term Ecological Research Network (LTER), DataONE and the International Ocean Discovery Program (IODP); the National Science Foundation (NSF) funded awards; and American Geophysical Union (AGU) conference presentations. ­ The Library created WHOAS, a DSpace repository, more than 10 years ago. As part of the GeoLink project we have been collaborating with @mire, a leader in open source DSpace development to develop modular code that can be integrated into other DSpace installations to improve LOD functionality. Our DSpace goals are to provide a built-in SPARQL endpoint for easy access to the data, implement editable authority concepts with URIs, and be able to integrate concepts from other authoritative sources using SPARQL queries. There is a second layer that takes dc-based DSpace triples and constructs triples based on GeoLink patterns which describes the data in a geoscience context. This provides flexibility and serves as a model for organizations contributing data to multiple LOD communities. This code is freely available to the 1700 registered DSpace repositories worldwide.
  • Presentation
    Publishing returns to the Academy
    (MBLWHOI Library, 2015-10-23) Goldstone, Heather M. H. ; Skomal, Susan ; Markie, Michael ; Brand, Amy ; Gray, Joshua P.
    Panel and audience conversations about exploring some of the new models through which science publishing can evolve, empowering researchers and the research community to have more critical input in the publishing process
  • 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.
  • 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.
  • Working Paper
    Report of the Research Coordination Network RCN : OceanObsNetwork, facilitating open exchange of data and information
    (NSF/Ocean Research Coordination Network, 2013-05) Gallagher, James ; Orcutt, John A. ; Pissierssens, Peter ; Raymond, Lisa ; Simpson, Pauline ; Pearlman, Jay ; Williams, Albert J. ; Simpson, Pauline
    The OceanObsNetwork goals and objectives are to foster a broad, multi-disciplinary dialogue, enabling more effective use of sustained ocean observatories and observing systems. To achieve these, the activities for the RCN include a working group titled “Facilitating Open Exchange of Data and Information.” Within this area 3 task teams were created dealing with elements that impact on open exchange of data and information. This report examines the foundation of Open Data and its importance to the international community, science, innovation and jobs. While the goal may be similar, the paths to Open Data are varied and drawing together a pervasive approach will take time. There are however, near term steps, technical and social, that could have significant impacts. Stimulating interdisciplinary collaboration occurs through adoption of common standards for data exchange, creation of information brokering for improved discovery and access and working toward common or defined vocabularies. Simply finding other scientists’ data has been noted as a major barrier for research. Open Data impinges on existing reward systems and social interactions. Areas that need to be addressed are the academic reward system (in terms of promotion and resources), the peer review panels and grant selection processes (in terms of acknowledging the importance and challenge of data collection) and the needs for acceptable citation mechanisms. Intellectual property should not be abandoned in an Open Data environment and managing IPR is necessary. A sustainable Open Data Policy is essential and sustainability is a matter for all parties, government, private sector, academia and non-profit organizations. As full implementation of Open Data will involve a change in practices in a number of research and publication activities, an end-to-end perspective and strategy would most likely allow a long-term sustainable path to be pursued. Various business models are discussed in the paper that would not have been considered a decade ago. These range from cloud storage to publication of data with Digital Object Identifiers. These set a possible foundation for the future.
  • 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
    Pilot projects for publishing and citing ocean data
    (American Geophysical Union, 2012-10-23) Urban, Edward ; Leadbetter, Adam ; Moncoiffe, Gwenaelle ; Pissierssens, Peter ; Raymond, Lisa ; Pikula, Linda
    In the ocean sciences, a project was started in 2008 to bring together scientists, data managers, and library experts to explore means to (1) increase the submission of data to data centers, (2) make data more accessible for reuse, (3) link data more closely to traditional journal publications, and (4) create a system that gives more credit to data generators. This project is a joint effort among the Scientific Committee on Oceanic Research, the International Oceanographic Data and Information Exchange (IODE) of the United Nations Educational, Scientific and Cultural Organization’s Intergovernmental Oceanographic Commission, and the Marine Biological Laboratory Woods Hole Oceanographic Institution (MBLWHOI) Library.