FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies

ToLeRating UR-STD

A new emerging paradigm of Uncertain Risk of Suspicion, Threat and Danger, observed across the field of information security, is described. Based on this paradigm a novel approach to anomaly detection is presented. Our approach is based on a simple yet powerful analogy from the innate part of the human immune system, the Toll-Like Receptors. We argue that such receptors incorporated as part of an anomaly detector enhance the detector’s ability to distinguish normal and anomalous behaviour. In addition we propose that Toll-Like Receptors enable the classification of detected anomalies based on the types of attacks that perpetrate the anomalous behaviour. Classification of such type is either missing in existing literature or is not fit for the purpose of reducing the burden of an administrator of an intrusion detection system. For our model to work, we propose the creation of a taxonomy of the digital Acytota, based on which our receptors are created

In defense of the organism: Thomas Pradeu (Elizabeth Vitanza, trans.): The limits of the self: immunology and biological identity. New York: Oxford University Press, 2012, ix+302 pp, ISBN: 978-0-19-977528-6, $65 HB.

pre-printThomas Pradeu's The Limits of the Self provides a precise account of biological identity developed from the central concepts of immunology. Yet the central concepts most relevant to this task (self and nonself ) are themselves deemed inadequate, suffering from ambiguity and imprecision. Pradeu seeks to remedy this by proposing a new guiding theory for immunology, the continuity theory. From this, an account of biological identity is provided in terms of uniqueness and individuality, ultimately leading to a defense of the heterogeneous organism as expressing the highest degree of individuality. Organisms are under attack. Pathogens, environmental stress, and endogenous factors, among many others, threaten the survival of an organism. To persist, organisms must be able to mount an effective response, and a variety of strategies for regulating these stressors have evolved. Collectively, these are the immune system. The organism is also under attack as a scientific concept. Samir Okasha (2011) has argued that organism is an anachronistic hierarchical rank, and that we should abandon this vestige of classification in favor of a rank-free ecological hierarchy. I have argued for a neighboring view (Haber 2013), observing that the term organism, much like species, is used to refer to a disparate group of entities, and that we ought to follow the lead of species eliminativists like Marc Ereshefsky (1992) and Brent Mishler (1999) and ‘get rid of organisms'

An ontology for major histocompatibility restriction

BACKGROUND: MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. PURPOSE: To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. DESCRIPTION: This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. CONCLUSIONS: Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13326-016-0045-5) contains supplementary material, which is available to authorized users

Introduction: History and Future of Ranaviruses

Dr. Allan Granoff (1923–2012), who isolated the first ranavirus (Granoff et al. 1966), had, scattered throughout his office at St. Jude Children’s Research Hospital, a variety of frog-related items including the poem cited above. Although one of Allan’s isolates, Frog virus 3 (FV3), subsequently became the best-characterized member of both the genus (Ranavirus) and the family (Iridoviridae); the impact of that discovery was not fully appreciated at the time. FV3 was neither the first iridoviridae to be recognized as a pathogen of lower vertebrates or the first isolated. Those honors belonged to lymphocystis disease virus (LCDV) and Invertebrate iridovirus 1 (IIV1), respectively (Wissenberg 1965; Xeros 1954). LCDV is responsible for a generally non-life threatening, but disfiguring, disease in fish characterized by the appearance of wart-like growths on the skin and (rarely) internal organs, whereas IIV1 is the causative agent of latent and patent infections in crane fly larvae. Despite its lack of primacy, FV3 was studied because, in keeping with the mission of St. Jude Hospital, it was initially thought to be linked to adenocarcinoma in frogs and thus could be a useful model of human malignancies. Furthermore, unlike LCDV and IIV1, it could be readily grown in cultured cells and was thus amenable to detailed molecular characterization. Although its role in tumor development was soon proven incorrect, FV3 served as a gateway into understanding the replication strategy of a heretofore poorly studied virus family. Moreover, over the next 20 years, its study led to important insights not only into iridoviridae replication, but also eukaryotic biology, virus evolution, and host–virus interactions

Studies on the Morphogenesis of Murine Cytomegalovirus

Two modes of assembly of murine cytomegalovirus (MCMV) were observed in cultured mouse embryo fïbroblasts, generating two morphologically different types of viral particles: monocapsid virions and multicapsid virions. The assembly of nucleocapsids appeared to be the same for both types of morphogenesis. Three successive stages of intranuclear capsid formation could be distinguished: capsids with electron-lucent cores, coreless capsids, and capsids with dense cores. Some of the capsids were enveloped at the inner nuclear membrane to form monocapsid virions, which were first detectable in the perinuclear cisterna. Other capsids left the nucleus via nuclear pores and usually entered cytoplasmic capsid aggregates that received an envelope by budding into extended cytoplasmic vacuoles, thereby forming multicapsid virions. Since the formation of multicapsid virions is not restricted to cell culture conditions and also occurs in vivo in immunosuppressed mice, multicapsid virions may play a role in the pathogenesis of cytomegalovirus infection

Single-cell transcriptomics to explore the immune system in health and disease

The immune system varies in cell types, states, and locations. The complex networks, interactions, and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as massively parallel single-cell RNA sequencing and sophisticated computational methods are catalyzing a revolution in our understanding of immunology. Here we provide an overview of the state of single-cell genomics methods and an outlook on the use of single-cell techniques to decipher the adaptive and innate components of immunity.National Institute of Allergy and Infectious Diseases (U.S.) (Grant U24AI118672)National Institute of Allergy and Infectious Diseases (U.S.) (Grant R24AI072073

Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology

Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from IDOCore, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus-specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally the present pandemic has motivated construction of a more specific extension of CIDO covering terminological contents specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choicepoints for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine-learning projects