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Results for “FAIR principles”

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At least 19 recordsLinked to original sources

PubMed2026

Q&A with Michèle Ramsay.

Michèle Ramsay, PhD, is Director of the Sydney Brenner Institute for Molecular Bioscience, Professor in Human Genetics, and South African Research Chair in Genomics and Bioinformatics of African Populations at the University of the Witwatersrand, Johannesburg. While promoting research excellence in Africa and contributing to research that accurately represents African populations in global science, she supports capacity strengthening in the fields of genomics and precision medicine. Michèle is a founding member of the Human Heredity and Health in Africa Consortium, co-chair of the International Health Cohorts Consortium, member of the WHO Technical Advisory Group for Genomics (TAG-G), and co-chair of the Lancet Commission on Precision Health. She contributes low- and middle-income countries' perspectives to global genomics, promoting ethical, equitable and fair principles and practices.

Humans↗

PubMed2025

MelanoDB: A dataset of clinical and molecular features of patients with advanced melanoma treated with MAPK inhibitors.

MAPK inhibitors (MAPKi) have revolutionized the treatment of patients with advanced melanoma. However, primary and acquired resistance mechanisms limit their efficacy. Predicting MAPKi response from the tumor baseline features remains challenging due to the limited size of patient cohorts. Therefore, we collected data from nine different patient cohorts (total n = 417 patients with advanced melanoma treated with MAPKi) to identify clinical and molecular features. Our curated dataset, named MelanoDB, includes whole or partial exome sequencing data for 191 patients, copy number alteration information for 66 patients, and gene expression data for 132 patients. We provide a web application to explore the integrated dataset and data distribution across the collected studies, and we share this dataset with the scientific community according to the Findable, Accessible, Interoperable, Reusable (FAIR) principles.

Humans↗

PubMed2026

The need for standardization and improved open (meta)data practices in metaproteomics.

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.

Proteomics↗

PubMed1992

The United States: breakthroughs and waste.

The health system of the United States is in a paradoxical position. At its best, the system is a magnet for those seeking the latest technical breakthroughs. It can offer that excellence because there have never been effective financial constraints on the imagination; the system has become a major economic frontier, at which professional and other entrepreneurs successfully seek their fortune. At the same time, the system is leaving increasing numbers of Americans frustrated and disillusioned. It is beset by excess capacity in many areas, is needlessly expensive, and often bestows unnecessary health services. Yet only the experts are aware of these flaws; most Americans still express high satisfaction with the quality of the services they receive from their doctors and hospitals. The public's major misgivings arise over the awkward and inequitable way in which American health care is financed. The typical private health insurance policy, for example, is tied to a particular job. If the job is lost, so is the health insurance. Furthermore, these policies are priced on actuarially "fair" principles, so sick individuals are forced to pay higher insurance premiums than relatively healthy ones and chronically ill persons often cannot obtain health insurance coverage at any price. Although there are public programs to catch many persons not privately insured, the coverage tends to be insufficiently extensive and deep. Some 35 million Americans, mostly poor, have no health insurance whatsoever. Unfortunately, at this time there is no political force in the United States strong enough to reform the American health system toward greater social equity and economic efficiency, whereas there are numerous groups powerful enough to block whatever reform might harm their own narrow economic interests. Other nations can learn from America's clinical and organizational innovations in health care delivery. They can also learn what not to do by studying the unseemly way in which American health care is financed.

Cost Control↗

PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS: To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS: Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗

PubMed2025

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.

As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud-based research continue to expand. Besides the potential for accelerated and diverse biomedical discovery that comes from a harmonized data ecosystem, the cloud also presents a shift away from the standard practice of duplicating data to computational clusters or local computers for analysis. However, despite these benefits, researcher migration to the cloud has lagged, in part due to insufficient educational resources to train biomedical scientists on cloud infrastructure. There exists a conceptual lack especially around the crafting of custom analytic pipelines that require software not pre-installed by cloud analysis platforms. We here present three fundamental concepts necessary for custom pipeline creation in the cloud. These overarching concepts are workflow and cloud provider agnostic, extending the utility of this education to serve as a foundation for any computational analysis running any dataset in any biomedical cloud platform. We illustrate these concepts using one of our own custom analyses, a study using the case-parent trio design to detect sex-specific genetic effects on orofacial cleft (OFC) risk, which we crafted in the biomedical cloud analysis platform CAVATICA.

Cloud Computing↗

PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗

PubMed2026

The Lipid Interactome: an interactive and open access platform for exploring cellular lipid-protein interactions.

SUMMARY: Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized lipid probes-equipped with photoactivatable crosslinkers, affinity handles, and photocleavable protecting groups-have enabled proteomics-based identification of lipid interacting proteins with unprecedented specificity and resolution. Despite the growing number of published lipid interactomes, there remains no centralized effort to harmonize, compare, or integrate these datasets. The Lipid Interactome addresses this gap by providing a structured, interactive web portal that adheres to FAIR data principles-ensuring that lipid interactome studies are Findable, Accessible, Interoperable, and Reusable. Through standardized data formatting, interactive visualizations, and direct cross-study comparisons, this resource enables researchers to systematically explore the protein-binding partners of diverse bioactive lipids. By consolidating and curating lipid interactome proteomics data from multiple studies, the Lipid Interactome database serves as a critical tool for deciphering the biological functions of lipids in cellularsystems. AVAILABILITY AND IMPLEMENTATION: This site can be viewed at LipidInteractome.org. All data are available for download. No user information is collected or necessary for data navigation, interaction, or download.

Proteins↗

PubMed1977

When may research be stopped?

The prohibition of research with recombinant DNA must rely upon some argument that both establishes a principle, applicable to research in any sphere, identifying kinds of defect or hazard that are intolerable, and shows that recombinant DNA research is intolerably defective or hazardous in the ways specified by that principle. No such argument succeeds. Of arguments proposed to defend prohibition it may be fairly said either that the major premise (the principle of prohibition) is false, or when sound principles are put forward, that the minor premise (specifying recombinant DNA research as defective or hazardous in the ways called for) is far from established. There is no valid practical syllogism, having true premises, whose conclusion is that research with recombinant DNA should be stopped.

DNA, Recombinant↗

PubMed1992

The method of 'principlism': a critique of the critique.

Several scholars have recently criticized the dominant emphasis upon mid-level principles in bioethics best exemplified by Beauchamp and Childress's Principles of Biomedical Ethics. In Part I of this essay, I assess the fairness and cogency of three broad criticisms raised against 'principlism' as an approach: (1) that principlism, as an exercise in applied ethics, is insufficiently attentive to the dialectical relations between ethical theory and mortal practice; (2) that principlism fails to offer a systematic account of the principles of non-maleficence, beneficence, respect for autonomy, and justice; and (3) that principlism, as a version of moral pluralism, is fatally flawed by its theoretical agnosticism. While acknowledging that Beauchamp and Childress's reliance upon Ross's version of intuitionism is problematic, I conclude that the critics of principlism have failed to make a compelling case against its theoretical or practical adequacy as an ethical approach. In Part II, I assess the moral theory developed by Bernard Gert in Mortality: A New Justification of the Moral Rules, because Gert has recommended his approach as a systematic alternative to principlism. I judge Gert's theory to be seriously incomplete and, in contrast to principlism, unable to generate coherent conclusions about cases of active euthanasia and paternalism.

Beneficence↗

PubMed1992

Cost-effectiveness and cost-benefit analyses in the medical literature. Are the methods being used correctly?

OBJECTIVE: To determine whether published cost-effectiveness and cost-benefit analyses have adhered to basic analytic principles. DESIGN: Structured methodologic review of published articles. STUDY SAMPLE: Seventy-seven articles published either from 1978 to 1980 or from 1985 to 1987 in general medical, general surgical, and medical subspecialty journals. MAIN OUTCOME MEASUREMENTS: Articles were reviewed to assess the use and reporting of six fundamental principles of analysis. These principles were derived by reviewing widely cited textbooks and articles describing the methods for performing economic analyses and by selecting the methods universally recommended. MAIN RESULTS: Overall performance was only fair. Three articles adhered to all six principles, and the median number of principles to which articles adhered was three. Among the problems noted were failure to make underlying assumptions explicit and, therefore, verifiable, and failure to test assumptions with sensitivity analyses. No improvement in performance was observed between 1978 and 1987. Articles in general medical journals, however, were more likely to use analytic methods appropriately than articles in the general surgical or medical subspecialty literature. CONCLUSIONS: Greater attention should be devoted to ensuring the appropriate use of analytic methods for economic analyses, and readers should make note of the methods used when interpreting the results of economic analyses.

Cost-Benefit Analysis↗

PubMed1975

Some toxic, physical and chemical properties of the oral secretion of the sand tampan, Ornithodoros savignyl Audouin (1827).

Mice, exposed to the effects of the oral secretion of Ornithodorus savignyi by injection, revealed that a potent toxin is present in the secretion. Electrophoretic and chromatographic separations of the secretion showed a heterogeneous pattern of protein-like substances. Toxicity trials on these fractions showed that the toxic principle is protein in nature and fairly heat stable.

Amino Acids↗

PubMed1976

Evaluation of a new spirometer based on a fluidistor technique.

Using a mechanical model and human subjects a new spirometer based on fluidistor principles was evaluated. At normal minute volumes the fluidistor was accurate to within +/-5% when compared with a Bernstein spirometer. It underread at low volumes and overread at high. Prolonged expiratory time constant as well as the use of gas with low density increased the error. The instrument was somewhat sensitive to variation in breathing frequency and gas flow pattern but insensitive to moisture. The resistance to gas flow of the instrument itself was fairly high. The fluidistor is based on a sound and simple principle (no movable parts). It proved to be stable and easy to handle and accurate enough for clinical use in anaesthesia and intensive care. The tendency of the spirometer to underread at low flow and to overread at high flow could possibly be substantially reduced if the instrument was provided with several flow heads so that the oscillation volume could be individually adapted to the gas flow rate to be studied.

Airway Resistance↗

PubMedDate not supplied

Patient complaints: guidance for nurses.

In response to the debate at RCN Congress in 1990, the College has produced the following guidelines for good practice on handling complaints about care, treatment and services. These guidelines have been written to help nurses, midwives and health visitors to handle complaints in ways which are fair to patients and in which they feel confident. The principles are readily applicable to other disciplines and an effective complaints procedure can only be established on a multidisciplinary basis. They may be used and adapted to form local policies and should be considered in conjunction with the recommendations of the Association of Community Health Councils and government recommendations and proposals to improve patients' satisfaction and confidence in health care services.

Humans↗

PubMed2025

"It just feels morally not right to Sell the data": Ethical and social perspectives on human genomic data sharing in Uganda-A phenomenological qualitative study.

While genomic data sharing enhances transparency and research efficiency, it also raises significant ethical and social challenges. This study explored stakeholders' perspectives on these issues, particularly around privacy, confidentiality, and equity in collaborative research. A phenomenological qualitative study was conducted between August and December 2023 at Makerere University College of Health Sciences, other research-intensive institutions, and national regulatory bodies. The study engaged 86 participants: 47 key informants (16 researchers, 14 ethics committee members, nine community advisory board members, and eight research regulators) and four deliberative focus group discussions with 39 participants. Interviews were transcribed verbatim, and thematic analysis was conducted using NVivo 14. Three major themes emerged: (1) stakeholders' experiences in genomic research, including their roles as participants, implementers, or overseers; (2) ethical concerns, such as informed consent, third-party data access, inequities between high-income and low- and middle-income country (LMIC) researchers and participants, and the lack of benefit-sharing frameworks; and (3) social implications, including stigma, discrimination, labeling, community perceptions of fairness, and the need for meaningful engagement. Participants emphasized the importance of protecting participant rights, promoting equity, and ensuring robust data governance and security. The theoretical frameworks of principlism and distributive justice provided a valuable lens for examining these concerns, particularly by highlighting the need to safeguard privacy and fairly distribute responsibilities and benefits in global collaborations. Participants also noted that perceptions of fairness are shaped by trust, local context, and past experiences with research factors that are critical for building equitable and respectful partnerships. This study underscores the urgent need to strengthen protections for research participants and promote fairness in genomic data sharing. Policies should, if adopted, emphasize culturally contextualized consent, active community engagement, restricted third-party data access, and strong data protection mechanisms to address existing inequities and prevent misuse.

LMICs↗

PubMedDate not supplied

Genetics and the moral mission of health insurance.

Deciding whether genetic differences among individuals are morally relevant to health insurance requires us to ask, What kind of good is health care? and, What principles should govern its distribution? There are good reasons to doubt that "actuarial fairness" is an adequate description of genuine fairness in health insurance.

Actuarial Analysis↗

PubMed1976

An approach to general oncology: principles and procedures.

The obstetrician-gynecologist is frequently the only physician to attend women during their reproductive years. Malignant disease outside the pelvic organs is a fairly frequent occurence in this age group. Certain findings in the patient's history and physical examination can suggest malignant disease. The routine laboratory examination can also provide indications of the presence of a neoplastic process. Once this process is suspected, histologic proof of malignancy must be obtained before further staging and therapy are considered. The extent of the disease is important for the planning of therapy, i.e., whether it is to be surgery, radiotherapy, chemotherapy or some combination of the three. Adjuvant chemotherapy is recognized as a form of treatment designed to eradicate micrometastases, prevent the occurrence of subsequent clinical metastatic disease and, as a result, improve survival.

Adult↗

PubMed1976

Selecting a few residents from many applicants: a new way to be fair and efficient.

Selection of residents from among the large number of qualified applicants is an annual task requiring a significant commitment of resources by teaching hospitals. A method based on sound principles of decision-making and utilizing a computer analysis for initial ranking of applicants was developed to improve the selection process. The result was satisfactory selection with significant savings of time and effort for the residency program faculty.

Decision Making↗