Findable, Accessible, Interoperable, Reusable Principles Research Articles

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.

Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data – such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles – also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock–Cooper–Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales.

Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey.

Background Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusions The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.

Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database.

Improving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with a number of limitations, for instance, the ad hoc curation protocol and the inclusion of only digenic cases. The OLIgogenic diseases DAtabase (OLIDA) presents a novel, transparent and rigorous curation protocol, introducing a confidence scoring mechanism for the published oligogenic literature. The application of this protocol on the oligogenic literature generated a new repository containing 916 oligogenic variant combinations linked to 159 distinct diseases. Information extracted from the scientific literature is supplemented with current knowledge support obtained from public databases. Each entry is an oligogenic combination linked to a disease, labelled with a confidence score based on the level of genetic and functional evidence that supports its involvement in this disease. These scores allow users to assess the relevance and proof of pathogenicity of each oligogenic combination in the database, constituting markers for reporting improvements on disease-causing oligogenic variant combinations. OLIDA follows the FAIR principles, providing detailed documentation, easy data access through its application programming interface and website, use of unique identifiers and links to existing ontologies.Database URL https://olida.ibsquare.be

Guidelines for Publicly Archiving Terrestrial Model Data to Enhance Usability, Intercomparison, and Synthesis

Scientific communities are increasingly publishing data to evaluate, accredit, and build on published research. However, guidelines for curating data for publication are sparse for model-related research, limiting the usability of archived simulation data. In particular, there are no established guidelines for archiving data related to terrestrial models that simulate land processes and their coupled interactions with climate. Terrestrial modelers have a unique set of challenges when publishing data due to the diversity of scientific domains, research questions, and the types and scales of simulations. Researchers in the U.S. Department of Energy’s (DOE) projects use a variety of multiscale models to advance robust predictions of terrestrial and subsurface ecosystem processes. Here, we synthesize archiving needs for data associated with different DOE models, and provide guidelines for publishing terrestrial model data components following FAIR (Findable, Accessible, Interoperable, Reusable) principles. The guidelines recommend archiving model inputs and testing data used in final simulation runs along with associated codes, workflow scripts, and metadata in public repositories. Researchers should consider archiving model outputs if they are within the storage limits of the repository. We also provide considerations for how to bundle files into different data publications with citable digital object identifiers. Finally, we identify repository features and tools that would enable storage and reuse of model data. Given the diversity of DOE terrestrial models, these guidelines are transferable to other model types and will enable efficient reuse of simulation data for purposes such as model intercomparisons, initialization, benchmarking, synthesis, and comparisons with field observations.

Дослідження принципів, моделей та методів парадигми менеджменту наукових даних FAIR для аналізу метаданих BIG DATA

In this research work we considere the basic principles, models and methods of the FAIR (Findable, Accessible, Interoperable, Reusable) scientific data management paradigm as a separate case of Big Data. This paradigm is focused on the reuse of scientific research results.Basic principles of FAIR apply to three types of entities: data (or any digital object), metadata (information about this digital object) and infrastructure. Information on various projects, initiatives and communities working on solving the problems of scientific data and their metadata integration is examined. We analyze how the properties of FAIR data contribute to the unification and integration of the scientific infrastructure in the paradigm of open science, which is based on free access to research results and open data.

Grapevine and Wine Metabolomics-Based Guidelines for FAIR Data and Metadata Management.

In the era of big and omics data, good organization, management, and description of experimental data are crucial for achieving high-quality datasets. This, in turn, is essential for the export of robust results, to publish reliable papers, make data more easily available, and unlock the huge potential of data reuse. Lately, more and more journals now require authors to share data and metadata according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. This work aims to provide a step-by-step guideline for the FAIR data and metadata management specific to grapevine and wine science. In detail, the guidelines include recommendations for the organization of data and metadata regarding (i) meaningful information on experimental design and phenotyping, (ii) sample collection, (iii) sample preparation, (iv) chemotype analysis, (v) data analysis (vi) metabolite annotation, and (vii) basic ontologies. We hope that these guidelines will be helpful for the grapevine and wine metabolomics community and that it will benefit from the true potential of data usage in creating new knowledge being revealed.

Exploring the Current Practices, Costs and Benefits of FAIR Implementation in Pharmaceutical Research and Development: A Qualitative Interview Study

The findable, accessible, interoperable, reusable (FAIR) principles for scientific data management and stewardship aim to facilitate data reuse at scale by both humans and machines. Research and development (R&D) in the pharmaceutical industry is becoming increasingly data driven, but managing its data assets according to FAIR principles remains costly and challenging. To date, little scientific evidence exists about how FAIR is currently implemented in practice, what its associated costs and benefits are, and how decisions are made about the retrospective FAIRification of data sets in pharmaceutical R&D. This paper reports the results of semi-structured interviews with 14 pharmaceutical professionals who participate in various stages of drug R&D in seven pharmaceutical businesses. Inductive thematic analysis identified three primary themes of the benefits and costs of FAIRification, and the elements that influence the decision-making process for FAIRifying legacy data sets. Participants collectively acknowledged the potential contribution of FAIRification to data reusability in diverse research domains and the subsequent potential for cost-savings. Implementation costs, however, were still considered a barrier by participants, with the need for considerable expenditure in terms of resources, and cultural change. How decisions were made about FAIRification was influenced by legal and ethical considerations, management commitment, and data prioritisation. The findings have significant implications for those in the pharmaceutical R&D industry who are engaged in driving FAIR implementation, and for external parties who seek to better understand existing practices and challenges.

Customized e-floras: How to develop your own project on the Pl@ntNet platform

Customized e-floras: How to develop your own project on the Pl@ntNet platform

Systematic review of the status of veterinary epidemiological research in two species regarding the FAIR guiding principles

BackgroundThe FAIR (Findable, Accessible, Interoperable, Reusable) principles were proposed in 2016 to set a path towards reusability of research datasets. In this systematic review, we assessed the FAIRness of datasets associated with peer-reviewed articles in veterinary epidemiology research published since 2017, specifically looking at salmonids and dairy cattle. We considered the differences in practices between molecular epidemiology, the branch of epidemiology using genetic sequences of pathogens and hosts to describe disease patterns, and non-molecular epidemiology.ResultsA total of 152 articles were included in the assessment. Consistent with previous assessments conducted in other disciplines, our results showed that most datasets used in non-molecular epidemiological studies were not available (i.e., neither findable nor accessible). Data availability was much higher for molecular epidemiology papers, in line with a strong repository base available to scientists in this discipline. The available data objects generally scored favourably for Findable, Accessible and Reusable indicators, but Interoperability was more problematic.ConclusionsNone of the datasets assessed in this study met all the requirements set by the FAIR principles. Interoperability, in particular, requires specific skills in data management which may not yet be broadly available in the epidemiology community. In the discussion, we present recommendations on how veterinary research could move towards greater reusability according to FAIR principles. Overall, although many initiatives to improve data access have been started in the research community, their impact on the availability of datasets underlying published articles remains unclear to date.

Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure.

Advance access and reuse mechanisms for large-scale Mass Spectrometry (MS) data are essential for democratizing data for the omics research community and making it adhere to FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although a number of centralized data repositories have been established, they have been limited to search mechanisms that depend on the meta-data associated with these MS datasets. Furthermore, they require constant influx of resources for maintenance. In this paper, we proposed an alternative novel distributed infrastructure for direct MS/MS spectral search. We designed and developed a simulation testbed using concepts from computer networks, queuing theory, and stochastic simulation methods. Results show that a distributed MS search based on raw MS/MS spectra can scale gracefully for up-to 2000 participating nodes, while simultaneously processing queries using the proposed networked infrastructure on the order of milliseconds to a few seconds for up-to a total of fifty billion MS/MS spectra.

Archaeological Digital Archiving in Turkey

This article provides a brief overview of archaeological digital archiving in Turkey. It introduces the legal framework and the stakeholders involved in conducting archaeological excavations and surveys. The current situation in archiving born-digital and digitised documentation produced during archaeological fieldwork is then introduced. Existing repositories serving as hubs for archaeological and heritage archiving are listed and briefly discussed. Analysis of online publishing practices for archaeological digital resources points to an eclectic landscape that only minimally complies with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. We conclude that guidelines for best practice in metadata and semantic technologies, locally applicable standards (especially controlled vocabularies), technical know-how, and a larger acceptance of open data and scholarship remain much-needed assets for archaeological digital archiving in Turkey. We also conclude that the future promises progress towards more interoperable archaeological digital archives thanks to international training, network and knowledge transfer opportunities (e.g. SEADDA Project).

Making Linked Data accessible for One Health Surveillance with the "One Health Linked Data Toolbox"

In times of emerging diseases, data sharing and data integration are of particular relevance for One Health Surveillance (OHS) and decision support. Furthermore, there is an increasing demand to provide governmental data in compliance to the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Semantic web technologies are key facilitators for providing data interoperability, as they allow explicit annotation of data with their meaning, enabling reuse without loss of the data collection context. Among these, we highlight ontologies as a tool for modeling knowledge in a field, which simplify the interpretation and mapping of datasets in a computer readable medium; and the Resource Description Format (RDF), which allows data to be shared among human and computer agents following this knowledge model. Despite their potential for enabling cross-sectoral interoperability and data linkage, the use and application of these technologies is often hindered by their complexity and the lack of easy-to-use software applications. To overcome these challenges the OHEJP Project ORION developed the Health Surveillance Ontology (HSO). This knowledge model forms a foundation for semantic interoperability in the domain of One Health Surveillance. It provides a solution to add data from the target sectors (public health, animal health and food safety) in compliance with the FAIR principles of findability, accessibility, interoperability, and reusability, supporting interdisciplinary data exchange and usage. To provide use cases and facilitate the accessibility to HSO, we developed the One Health Linked Data Toolbox (OHLDT), which consists of three new and custom-developed web applications with specific functionalities. The first web application allows users to convert surveillance data available in Excel files online into HSO-RDF and vice versa. The web application demonstrates that data provided in well-established data formats can be automatically translated in the linked data format HSO-RDF. The second application is a demonstrator of the usage of HSO-RDF in a HSO triplestore database. In the user interface of this application, the user can select HSO concepts based on which to search and filter among surveillance datasets stored in a HSO triplestore database. The service then provides automatically generated dashboards based on the context of the data. The third web application demonstrates the use of data interoperability in the OHS context by using HSO-RDF to annotate meta-data, and in this way link datasets across sectors. The web application provides a dashboard to compare public data on zoonosis surveillance provided by EFSA and ECDC. The first solution enables linked data production, while the second and third provide examples of linked data consumption, and their value in enabling data interoperability across sectors. All described solutions are based on the open-source software KNIME and are deployed as web service via a KNIME Server hosted at the German Federal Institute for Risk Assessment. The semantic web extension of KNIME, which is based on the Apache Jena Framework, allowed a rapid an easy development within the project. The underlying open source KNIME workflows are freely available and can be easily customized by interested end users. With our applications, we demonstrate that the use of linked data has a great potential strengthening the use of FAIR data in OHS and interdisciplinary data exchange.

Reassessing the lithosphere: SeisDARE, an open-access seismic data repository

Abstract. Seismic reflection data (normal incidence and wide angle) are unique assets for solid Earth sciences as they provide critical information about the physical properties and structure of the lithosphere as well as about the shallow subsurface for exploration purposes. The resolution of these seismic data is highly appreciated; however they are logistically complex and expensive to acquire, and their geographical coverage is limited. Therefore, it is essential to make the most of the data that have already been acquired. The collation and dissemination of seismic open-access data are then key to promote accurate and innovative research and to enhance new interpretations of legacy data. This work presents the Seismic DAta REpository (SeisDARE), which is, to our knowledge, one of the first comprehensive open-access online databases that stores seismic data registered with a permanent identifier (DOI). The datasets included here are openly accessible online and guarantee the FAIR (findable, accessible, interoperable, reusable) principles of data management, granting the inclusion of each dataset in a statistics referencing database so its impact can be measured. SeisDARE includes seismic data acquired in the last 4 decades in the Iberian Peninsula and Morocco. These areas have attracted the attention of international researchers in the fields of geology and geophysics due to the exceptional outcrops of the Variscan and Alpine orogens and wide foreland basins, the crustal structure of the offshore margins that resulted from a complex plate kinematic evolution, and the vast quantities of natural resources contained within. This database has been built thanks to a network of national and international institutions, promoting a multidisciplinary research and is open for international data exchange and collaborations. As part of this international collaboration, and as a model for inclusion of other global seismic datasets, SeisDARE also hosts seismic data acquired in Hardeman County, Texas (USA), within the COCORP project (Consortium for Continental Reflection Profiling). SeisDARE aims to make easily accessible old and recently acquired seismic data and to establish a framework for future seismic data management plans. SeisDARE is freely available at https://digital.csic.es/handle/10261/101879 (a detailed list of the datasets can be found in Table 1), bringing endless research and teaching opportunities to the scientific, industrial, and educational communities.

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.

The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted in a substantial reduction in spurious annotation. The hierarchical collection of protein family models (PFMs) used by PGAP as evidence for structural and functional annotation was expanded to over 35 000 protein profile hidden Markov models (HMMs), 12 300 BlastRules and 36 000 curated CDD architectures. As a result, >122 million or 79% of RefSeq proteins are now named based on a match to a curated PFM. Gene symbols, Enzyme Commission numbers or supporting publication attributes are available on over 40% of the PFMs and are inherited by the proteins and features they name, facilitating multi-genome analyses and connections to the literature. In adherence with the principles of FAIR (findable, accessible, interoperable, reusable), the PFMs are available in the Protein Family Models Entrez database to any user. Finally, the reference and representative genome set, a taxonomically diverse subset of RefSeq prokaryotic genomes, is now recalculated regularly and available for download and homology searches with BLAST. RefSeq is found athttps://www.ncbi.nlm.nih.gov/refseq/.

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences.

Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the life sciences. Our implementation follows principles and guidelines recommended by the maturity indicator authoring group and integrates concepts from the literature. In addition, we propose a FAIR balloon plot to summarize and compare dataset FAIRness. We evaluated the feasibility of our method on three real use cases where researchers looked for six datasets to answer their scientific questions. We retrieved information from repositories (ArrayExpress, Gene Expression Omnibus, eNanoMapper, caNanoLab, NanoCommons and ChEMBL), a registry of repositories, and a searchable resource (Google Dataset Search) via application program interfaces (API) wherever possible. With our analysis, we found that the six datasets met the majority of the criteria defined by the maturity indicators, and we showed areas where improvements can easily be reached. We suggest that use of standard schema for metadata and the presence of specific attributes in registries of repositories could increase FAIRness of datasets.

FAIR data sharing: The roles of common data elements and harmonization.

The value of robust and responsible data sharing in clinical research and healthcare is recognized by patients, patient advocacy groups, researchers, journal editors, and the healthcare industry globally. Privacy and security concerns acknowledged, the act of exchanging data (interoperability) along with its meaning (semantic interoperability) across studies and between partners has been difficult, if not elusive. For shared data to retain its value, a recommendation has been made to follow the Findable, Accessible, Interoperable, Reusable (FAIR) principles. Without applying appropriate data exchange standards with domain-relevant content standards and accessible rich metadata that uses applicable terminologies, interoperability is burdened by the need for transformation and/or mapping. These obstacles to interoperability limit the findability, accessibility and reusability of data, thus diminishing its value and making it impossible to adhere to FAIR principles. One effort to standardize data collection has been through common data elements (CDEs). CDEs are data collection units comprising one or more questions together with a set of valid values. Some CDEs contain standardized terminology concepts that define the meaning of the data, and others include links to unique terminology concept identifiers and unique identifiers for each CDE; however, usually CDEs are defined for specific projects or collaborations and lack traceable or machine readable semantics. While the name implies that these are 'common', this has not necessarily been a requirement, and many CDEs have not been commonly used. The National Institutes of Health (NIH) CDEs are, in fact, a conglomerate of CDEs developed in silos by various NIH institutes. Therefore, CDEs have not brought the anticipated benefit to the industry through widescale interoperability, nor is there widespread reuse of CDEs. Certain institutes in the NIH recommend, albeit do not enforce, institute-specific preferred CDEs; however, at the NIH level a preponderance of choice and a lack of any overarching harmonization of CDEs or consistency in linking them to controlled terminology or common identifiers create confusion for researchers in their efforts to identify the best CDEs for their protocol. The problem of comparing data among studies is exacerbated when researchers select different CDEs for the same variable or data collection field. This manuscript explores reasons for the disappointingly low adoption of CDEs and the inability of CDEs or other clinical research standards to broadly solve the interoperability and data sharing problems. Recommendations are offered for rectifying this situation to enable responsible data sharing that will help in adherence to FAIR principles and the realization of Learning Health Systems for the sake of all of us as patients.

3339 Development of a Competency-based Informatics Course for Translational Researchers

OBJECTIVES/SPECIFIC AIMS: Translational researchers often require the use of informatics methods in their work. Lack of an understanding of key informatics principles and methods limits the abilities of translational researchers to successfully implement Findable, Accessible, Interoperable, Reusable (FAIR) principles in grant proposal submissions and performed studies. In this study we describe our work in addressing this limitation in the workforce by developing a competency-based, modular course in informatics to meet the needs of diverse translational researchers. METHODS/STUDY POPULATION: We established a Translational Research Informatics Education Collaborative (TRIEC) consisting of faculty at the University of Utah (UU) with different primary expertise in informatics methods, and working in different tiers of the translational spectrum. The TRIEC, in collaboration with the Foundation of Workforce Development of the Utah Center for Clinical and Translational Science (CCTS), gathered informatics needs of early investigators by consolidating requests for informatics services, assistance provided in grant writing, and consultations. We then reviewed existing courses and literature for informatics courses that focused on clinical and translational researchers [3–9]. Using the structure and content of the identified courses, we developed an initial draft of a syllabus for a Translational Research Informatics (TRI) course which included key informatics topics to be covered and learning activities, and iteratively refined it through discussions. The course was approved by the UU Department of Biomedical Informatics, UU Graduate School and the CCTS. RESULTS/ANTICIPATED RESULTS: The TRI course introduces informatics PhD students, clinicians, and public health practitioners who have a demonstrated interest in research, to fundamental principles and tools of informatics. At the completion of the course, students will be able to describe and identify informatics tools and methods relevant to translational research and demonstrate inter-professional collaboration in the development of a research proposal addressing a relevant translational science question that utilizes the state-of-the-art in informatics. TRI covers a diverse set of informatics content presented as modules: genomics and bioinformatics, electronic health records, exposomics, microbiomics, molecular methods, data integration and fusion, metadata management, semantics, software architectures, mobile computing, sensors, recruitment, community engagement, secure computing environments, data mining, machine learning, deep learning, artificial intelligence and data science, open source informatics tools and platforms, research reproducibility, and uncertainty quantification. The teaching methods for TRI include (1) modular didactic learning consisting of presentations and readings and face-to-face discussions of the content, (2) student presentations of informatics literature relevant to their final project, and (3) a final project consisting of the development, critique and chalk talk and formal presentations of informatics methods and/or aims of an National Institutes of Health style K or R grant proposal. For (3), the student presents their translational research proposal concept at the beginning of the course, and works with members of the TRIEC with corresponding expertise. The final course grade is a combination of the final project, paper presentations and class participation. We offered TRI to a first cohort of students in the Fall semester of 2018. DISCUSSION/SIGNIFICANCE OF IMPACT: Translational research informatics is a sub-domain of biomedical informatics that applies and develops informatics theory and methods for translational research. TRI covers a diverse set of informatics topics that are applicable across the translational spectrum. It covers both didactic material and hands-on experience in using the material in grant proposals and research studies. TRI’s course content, teaching methodology and learning activities enable students to initially learn factual informatics knowledge and skills for translational research correspond to the ‘Remember, Understand, and Apply’ levels of the Bloom’s taxonomy [10]. The final project provides opportunity for applying these informatics concepts corresponding to the ‘Analyze, Evaluate, and Create’ levels of the Bloom’s taxonomy [10]. This inter-professional, competency-based, modular course will develop an informatics-enabled workforce trained in using state-of-the-art informatics solutions, increasing the effectiveness of translational science and precision medicine, and promoting FAIR principles in research data management and processes. Future work includes opening the course to all Clinical and Translational Science Award hubs and publishing the course material as a reference book. While student evaluations for the first cohort will be available end of the semester, true evaluation of TRI will be the number of trainees taking the course and successful grant proposal submissions.

A FAIR guide for data providers to maximise sharing of human genomic data.

It is generally acknowledged that, for reproducibility and progress of human genomic research, data sharing is critical. For every sharing transaction, a successful data exchange is produced between a data consumer and a data provider. Providers of human genomic data (e.g., publicly or privately funded repositories and data archives) fulfil their social contract with data donors when their shareable data conforms to FAIR (findable, accessible, interoperable, reusable) principles. Based on our experiences via Repositive (https://repositive.io), a leading discovery platform cataloguing all shared human genomic datasets, we propose guidelines for data providers wishing to maximise their shared data’s FAIRness.

IndexMEED cases studies using "Omics" data with graph theory

Data produced within marine and terrestrial biodiversity research projects that evaluate and monitor Environmental Status, have a high potential for use by stakeholders involved in environmental management. However, environmental data, especially in ecology, are not readily accessible to various users. The specific scientific goals and the logics of project organization and information gathering lead to a decentralized data distribution. In such a heterogeneous system across different organizations and data formats, it is difficult to efficiently harmonize the outputs. Few tools are available to assist. For instance standards and specific protocols can be applied to interconnect databases. Such semantic approaches greatly increase data interoperability. This communication present the recent results and the consortium IndexMEED (Indexing for Mining Ecological and Environmental Data) activity that aims to build new approaches to investigate complex research questions, and support the emergence of new scientific hypotheses based on graph theory Auber et al. 2014). Current developments in data mining based on graphs, as well as the potential for relevant contributions to environmental research, particularly about strategic decision-making, and new ways of organizing data will be presented (David et al. 2015). In particular, the consortium makes decisions on how i) to analyze heterogeneous distributed data spread throughout different databases combining molecular and habitat characteristics data [3], ii) to create matches and incorporate some approximations, iii) to identify statistical relationships between observed data and the emergence of contextual patterns using a calculation library and distributed calculation center at the European level, iv) to encourage openness and sharing data while complying with the general principles of FAIR (Findable, Accessible, Interoperable, Re-usable and citable) in order to enhance data value and their utilization. IndexMEED participants are now exploring the ability of two scientific communities (ecology sensu lato and computer sciences) to work together, using several studies cases. The ECOSCOPE project aims to meet the need to access structured and complementary omics-datasets to better understand biodiversity state and its dynamics. Indeed, the ECOSCOPE case study targets to visualize, through the graph approach, links between datasets and databases from genetics to ecosystems. Another case study, displaying anthropology fossils and omics on the same graph, will also be presented. DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) and CIGESMED (Coralligenous based Indicators to evaluate and monitor the Good Environmental Status of the MEDiterranean coastal water) European projects, conducted by IMBE, are focused on photo quadrats, cartography and omics data of the marine hard bottom in order to discover context patterns helpful to build decision support system building. Study case “65 Millions d’observateurs” French project is testing AskOmics to provide a graph-based querying interface using RDF (Resource Description Framework) and SPARQL technologies. Scientific questions can be resolved by the new data mining approaches that offer new ways to investigate heterogeneous environmental data with graph mining (Munoz et al. 2017). The uses of data from biodiversity research demonstrate the prototype functionalities (David et al. 2016) and introduce new perspectives to analyze environmental and societal responses including decision-making at large scale, both at the information system level and the observing system level than at the observed system level.

A FAIR-Based Approach to Enhancing the Discovery and Re-Use of Transcriptomic Data Assets for Nuclear Receptor Signaling Pathways

Public transcriptomic assets in the nuclear receptor (NR) signaling field hold considerable collective potential for exposing underappreciated aspects of NR regulation of gene expression. This potential is undermined however by a series of enduring informatic pain points that retard the routine re-use of these datasets. Here we describe a coordinated biocuration and web development approach to redress this situation that is closely aligned with ideals articulated in the FAIR (findable, accessible, interoperable, re-usable) principles on data stewardship. To improve findability, biocurators engage authors of studies in collaborating journals to secure datasets for deposition in public archives. Annotated derivatives of the archived datasets are assigned digital object identifiers and regulatory molecule identifiers that support persistent linkages between datasets and their associated research articles, integration in relevant records in gene and small molecule knowledgebases, and indexing by dataset search engines. To enhance their accessibility and interoperability, datasets are visualizable in responsively designed web pages, retrievable in machine-readable spreadsheets, or through an application programming interface. Re-use of the datasets is supported by their interrogation as a universe of data points through the Transcriptomine search engine, highlighting transcriptional intersections between NR signaling pathways, physiological processes and disease states. We illustrate the value of our approach in connecting disparate research communities using a use case of persistent interoperability between the Nuclear Receptor Signaling Atlas and the Pharmacogenomics Knowledgebase. Our FAIR-aligned model demonstrates the enduring value of discovery-scale datasets that accrues from their systematic compilation, biocuration and distribution across the digital biomedical research enterprise.