FAIR semantics and the NVS

The FAIR principles provide guidelines for the publication of digital resources such as datasets, code, workflows, and research objects aiming at making them Findable, Accessible, Interoperable, and Reusable(1). Amongst them, the I of the FAIR promotes interoperability and more specifically principle I2 suggests that metadata should use vocabularies that themselves follow the FAIR principles. Recently, FAIRsFAIR1 project officially published a first iteration of recommendations for making vocabularies FAIR (2). These recommendations include 17 general recommendations aligned with the different FAIR Principles and 10 Best Practice recommendations. The main objective of these recommendations is to provide a set of guidelines for creating a harmonised and interoperable semantic landscape easing the use and reuse of semantic artefacts from multiple different scientific domains

Emerging Role of Librarians in Data Publication

Purpose: This poster demonstrates the procedures and tools developed to deposit datasets in an Institutional Repository (IR) and assign Digital Object Identifiers (DOIs). Setting/Participants/Resources: 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). The goal is to identify best practices for tracking data provenance and clearly attributing credit to data collectors/providers. Description: Current literature on the topic of data publication suggests that success is best achieved when there is a partnership between scientists, data managers, and librarians. 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 metadata from BCO-DMO for deposit with datasets into the Institutional Repository (IR) Woods Hole Open Access Server (WHOAS). The system also incorporates functionality for BCO-DMO to request a Digital Object Identifier (DOI) from the Library. 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. While the WHOI Data Library and Archives has long been recognized as a valuable local resource, this project is an example of an important new role for the facility in providing the essential service of scientific data publication. The diversity and volume of modern research data sets precludes their publication in the peer reviewed journals that are the currency of scientific research. The process of developing the initial publication system required active engagement of the research community and the working system provides a valuable resource that supports networked science by improving access to data, enabling accurate reuse of data and facilitating proper citation of data resources. Results/Outcome: The assignment of persistent identifiers enables accurate data citation. The Library can assign a DOI to appropriate datasets deposited in WHOAS. A primary activity is working with authors to deposit datasets associated with published articles. The DOI would ideally be assigned before submission and be included in the published paper so readers can link directly to the dataset, but DOIs are also being assigned to datasets related to articles after publication. WHOAS metadata records link the article to the datasets and the datasets to the article. The assignment of DOIs has enabled another important collaboration with Elsevier, publisher of educational and professional science journals. Elsevier can now link from articles in the Science Direct database to the datasets available from WHOAS that are related to that article. The data associated with the article are freely available from WHOAS and accompanied by a Dublin Core metadata record. In addition, the Library has worked with researchers to deposit datasets in WHOAS that are not appropriate for national, international, or domain specific data repositories. These datasets currently include audio, text and image files. Related Publications: http://www.iode.org/index.php?option=com_oe&task=viewDocumentRecord&docID=2457 http://www.iode.org/index.php?option=com_oe&task=viewDocumentRecord&docID=5437 http://www.iode.org/index.php?option=com_oe&task=viewDocumentRecord&docID=8098 http://tw.rpi.edu/proj/portal.wiki/images/3/3b/JewettSummary.pd

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

InteroperAble Descriptions of Observable Property Terminologies (I-ADOPT) WG - outputs and recommendations

The InteroperAble Description of Observable Property Terminologies Working Group (I-ADOPT WG) was formed in June 2019 under the auspices of the Research Data Alliance’s Vocabulary and Semantic Services Interest Group. Its objective was to develop a framework to harmonise the way observable properties are named and conceptualised, in various communities within and across scientific domains. There was a realisation that the rapid demand for controlled vocabularies specialised in describing observed properties (i.e. measured, simulated, counted quantities, or qualitative observations) was presenting a risk of proliferation of semantic resources that were poorly aligned. This, in turn, was becoming a source of confusion for the end-users and a hindrance to data interoperability. The development of the I-ADOPT Framework proceeded in multiple phases. Following the initial phase dedicated to the collection of user stories, the identification of key requirements, and an in-depth analysis of existing semantic representations of scientific variables and of terminologies in use, the group focused on identifying the essential components of the conceptual framework, reusing as much as possible concepts that were common to existing operational resources. The proposed framework was then tested against a variety of examples to ensure that it could be used as a sound basis for the creation of new variable names as needed. The results were formalised into the I-ADOPT ontology and subsequently extended with usage guidelines to form the I-ADOPT Framework presented in this document. The output can now be used to facilitate interoperability between existing semantic resources and to support the provision of machine-readable variable descriptions whose components are mapped to FAIR vocabulary concepts. The group also issued the following six key recommendations: 1. Data creators, curators or publishers should describe the variable(s) held in datasets in both a human- and a machine-readable format. 2. The variable’s description should enable data reuse with minimum reliance on externally held free-text documentation. 3. The machine-readable description should make use of FAIR terminologies (e.g., controlled vocabularies, ontological relationships) adhering to Linked Data principles. 4. The translation from human readable to machine readable form should follow a decomposition approach that is compatible with the classes and relations defined in the I-ADOPT ontology (https://w3id.org/iadopt/). 5. Users should preferably reuse terminologies that are already aligned with the I-ADOPT Framework by either reusing existing concepts or extending collections, or by creating new concepts based on the I-ADOPT Framework. 6. For variables based on a different schema, a mapping to the I-ADOPT Framework should be provided. The group also set up public repositories to continue open collaboration and give access to resources that will be maintained and/or developed beyond the lifetime of the official RDA working group: 1) a catalogue of terminologies relevant to observable properties, 2) a repository of design patterns; 3) a step-by-step guide for minting new variables, 4) use-case specific guidelines on implementing the framework, 5) a repository of applications, and user implementation stories; 6) additional materials including a list of alignments with other ontological resources

Aligning Observable Property Terminologies using the I-ADOPT framework

During its lifetime, the RDA WG InteroperAble Descriptions of Observable Property Terminologies (I-ADOPT) developed a semantic framework to represent scientific variables and give a detailed account of what has been measured or otherwise been observed. The framework breaks down complex variable descriptions into essential atomic components, e.g., what quality or quantity kind of which object or phenomenon kind are the subject of the measurement or observation. While the ecological domain served as a starting point, we took into account other domains as part of the development. As a result, the I-ADOPT model is a generic framework to describe observational properties. The recommendations of the IADOPT WG have been published along with several outputs including the I-ADOPT ontology itself and a collection of terminologies to be used as atomic components. The I-ADOPT WG is now in maintenance mode but work is continuing on testing and supporting real-life implementation scenarios. Multiple terminology providers and data repositories have started aligning their variables to the I-ADOPT framework. This results in an increasing number of I-ADOPT-compliant variable descriptions from different stakeholders. We are now ready to test whether one of the main goals of the I-ADOPT WG has actually been achieved: does the I-ADOPT framework enable semantic interoperability of variable descriptions across datasets annotated using different controlled vocabularies? This poster highlights how the I-ADOPT model has been applied to existing terminologies of observational variables, providing detailed semantic context information. We present current efforts to exploit these details while aligning terminologies of different origins. We want to encourage other terminology providers and domains to explore the I-ADOPT framework to grow an increasing network of interoperable terminologies for observational variables

Pilot projects for publishing and citing ocean data

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Eos 93, no. 43 (2012): 425-426.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.2013-04-2

More than just DOIs, how to pragmatically make 50 years of diverse data centre holdings and services citable, the perspective and aspirations of the British Oceanographic Data Centre

The British Oceanographic Data Centre (BODC) celebrated its 50th anniversary in 2019. It holds data collected from 1773 to the present day. Holdings are multidisciplinary, heterogeneous data reflecting the full range of disciplines, platforms, temporal and spatial fieldwork scales typically encountered in oceanographic research and monitoring. These collections vary in granularity and contain data which are at different stages of curation ranging from raw data to standardised data products. BODC need to improve data services to meet the developing the expectations of the research community. These include the FAIR data principles, TRUSTed repository guidelines and CoreTrustSeal accreditation. This is a significant challenge within the constraints of resource available (both financial and human). The initial focus for BODC is making holdings citable with the following aspirations: Application of DOIs to data at the point of receipt by BODC. Publication of data papers and publication of DOIs for data products. Application of persistent identifiers to low level data granules where DOIs are not feasible. Application of persistent identifiers to datasets included in BODC API services and versioning of these data. Work with organisations or groups who include data curated by BODC in their products to enable the provenance of data to be unambiguous. Work with communities on joint data papers where BODC are a partner organisation. This will enable each type of data served by BODC to be unambiguously citable. The initial effort is being directed towards the application of DOIs to data submissions and publication of data papers for BODC curated data products

Applying VocPrez to operational semantic repositories: the NVS experience

The Natural Environment Research Council’s (NERC) Vocabulary Server (NVS1) has been serving the marine and wider community with controlled vocabularies for over a decade. NVS provides access to standardised lists of terms which are used for data mark-up, facilitating interoperability and discovery in the marine and associated earth science domains. The NVS controlled vocabularies are published as Linked Data on the web using the data model of the Simple Knowledge Organisation System (SKOS). They can also be accessed as web services (RESTFul, SOAP) or through a sparql endpoint. NVS is an operational semantic repository, which underpins data systems like SeaDataNet, the pan-European infrastructure of marine data management, and is embedded in SeaDataNet-specific tools like MIKADO. Its services are being constantly monitored by the SeaDataNet Argo monitoring system, ensuring a guarantee of reliability and availability. In this presentation we will discuss the pathway of challenges we encountered while enhancing an operational semantic repository like NVS with VocPrez, a read-only web delivery system for Simple Knowledge Organization System (SKOS)-formulated RDF vocabularies. We will also present our approach on implementing CI/CD delivery and the added value of VocPrez to NVS in terms of FAIRness. Finally we will discuss the lessons learnt during the lifecycle of this development. VocPrez2 is an open-source, pure Python, application that reads vocabularies from one or more sources and presents them online (HTTP) in several different ways: as human-readable web pages, using simple HTML templates for different SKOS objects and as machine-readable RDF or other formats, using mapping code. The different information model views supported by VocPrez are defined by profiles, that is, by formal specifications. VocPrez supports both different profiles and different formats (Media Types) for each profile. VocPrez enhanced the publication of NVS both for human users and machines. Humans accessing NVS are presented with a new look and feel that is more user friendly, providing filtering of collections, concepts and thesauri, and sorting of results using different options. For machine-to-machine communication, VocPrez presents NVS content in machine-readable formats which Internet clients can request directly using the Content Negotiation by Profile standard3. The profiles and formats available are also listed on an “Alternate Profiles” web page which is automatically generated per resource thus allowing for discovery of options. As a result, human or machine end users can access NVS collections, thesauri and concepts according to different information models such as DCAT, NVS’ own vocabulary model or pure SKOS and also in different serializations like JSON-LD , turtle, etc. using content negotiation

The I-ADOPT Interoperability Framework: a proposal for FAIRer observable property descriptions

Global environmental challenges like climate change, pollution, and biodiversity loss are complex. To understand environmental patterns and processes and address these challenges, scientists require the observations of natural phenomena at various temporal and spatial scales and across many domains. The research infrastructures and scientific communities involved in these activities are often following their own data management practices which inevitably leads to a high degree of variability and incompatibility of approaches. Consequently, a variety of metadata standards and vocabularies have been proposed to describe observations and are actively used in different communities. However, this diversity in approaches now causes severe issues regarding the interoperability across datasets and hampers their exploitation as a common data source. Projects like ENVRI-FAIR, FAIRsFAIR, FAIRplus are addressing this difficulty by working on the full integration of services across research infrastructures based on FAIR Guiding Principles supporting the EOSC vision towards an open research culture. Beyond these projects, we need collaboration and community consensus across domains to build a common framework for representing observable properties. The Research Data Alliance InteroperAble Descriptions of Observable Property Terminology Working Group (RDA I-ADOPT WG) was formed in October 2019 to address this need. Its membership covers an international representation of terminology users and terminology providers, including terminology developers, scientists, and data centre managers. The group’s overall objective is to deliver a common interoperability framework for observable property variables within its 18-month work plan. Starting with the collection of user stories from research scientists, terminology managers, and data managers or aggregators, we drafted a set of technical and content-related requirements. A survey of terminology resources and annotation practices provided us with information about almost one hundred terminologies, a subset of which was then analysed to identify existing conceptualisation practices, commonalities, gaps, and overlaps. This was then used to derive a conceptual framework to support their alignment. In this presentation, we will introduce the I-ADOPT Interoperability Framework highlighting its semantic components. These represent the building blocks for specific ontology design patterns addressing different use cases and varying degrees of complexity in describing observed properties. We will demonstrate the proposed design patterns using a number of essential climate and essential biodiversity variables. We will also show examples of how the I-ADOPT framework will support interoperability between existing representations. This work will provide the semantic foundation for the development of more user-friendly data annotation tools capable of suggesting appropriate FAIR terminologies for observable properties