New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage‐specific genes. It was recently reported that an excess of primate‐specific and human‐specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in (...) both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under‐characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We (...) use statistical methods and formal ontological principles as a first step towards finding answers to this question. (shrink)

MicroRNAs are non‐coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts (...) decisively to improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. (...) Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential (...) in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

The major transcript variants of human protein‐coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes—they can be protein‐coding, noncoding, or pseudogenes—and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced (...) micro‐exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re‐assignments. The emerging human pan‐genome is necessitating distinctive annotations incorporating differences between individuals and between populations. (shrink)

We present an annotated bibliography of peer reviewed scientific research highlighting the human health, animal welfare, and environmental risks associated with genetic modification. Risks associated with the expression of the transgenic material include concerns over resistance and non-target effects of crops expressing Bt toxins, consequences of herbicide use associated with genetically modified herbicide-tolerant plants, and transfer of gene expression from genetically modified crops through vertical and horizontal gene transfer. These risks are not connected to the technique of genetic (...) modification as such, but would be present for any conventionally produced crops with the same heritable traits. In contrast, other risks are a direct consequence of the method used in gene manipulation. These come about because of the unstable nature of the transgene and vectors used to insert it, and because of unpredictable interactions between the transgene and the host genome. The debate over the release of genetically modified organisms is not merely a scientific one; it encompasses economics, law, ethics, and policy. Any discussion on these levels does, however, need to be informed by sound science. We hope that the scientific references provided here will provide a useful starting point for further debate. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

The purpose of this article is to update and defend syntax-based gene concepts. I show how syntax-based concepts can and have been extended to accommodate complex cases of processing and gene expression regulation. In response to difficult cases and causal parity objections, I argue that a syntax-based approach fleshes out a deflationary concept defining genes as genomic sequences and organizational features of the genome contributing to a phenotype. These organizational features are an important part of accepted molecular explanations, (...) provide the theoretical basis for a large number of experimental techniques and practical applications, and play a crucial role in in annotating the genome, deriving predictions and constructing bioinformatics models. (shrink)

NCG 4.0 is the latest update of the Network of Cancer Genes, a web-based repository of systems-level properties of cancer genes. In its current version, the database collects information on 537 known (i.e. experimentally supported) and 1463 candidate (i.e. inferred using statistical methods) cancer genes. Candidate cancer genes derive from the manual revision of 67 original publications describing the mutational screening of 3460 human exomes and genomes in 23 different cancer types. For all 2000 cancer genes, duplicability, evolutionary origin, expression, (...) functional annotation, interaction network with other human proteins and with microRNAs are reported. In addition to providing a substantial update of cancer-related information, NCG 4.0 also introduces two new features. The first is the annotation of possible false-positive cancer drivers, defined as candidate cancer genes inferred from large-scale screenings whose association with cancer is likely to be spurious. The second is the description of the systems-level properties of 64 human microRNAs that are causally involved in cancer progression (oncomiRs). Owing to the manual revision of all information, NCG 4.0 constitutes a complete and reliable resource on human coding and non-coding genes whose deregulation drives cancer onset and/or progression. NCG 4.0 can also be downloaded as a free application for Android smart phones. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Over the past decade, high‐throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non‐coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the process of (...) translation rather than the resulting peptides that serves a function. Here, we review annotation studies in zebrafish to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein‐encoding mRNAs to potentially non‐functional peptide‐producing RNAs to non‐coding RNAs. As highlighted by the discovery of the novel signaling peptide Apela/ELABELA/Toddler, accurate annotations can give rise to exciting opportunities to identify the functions of previously uncharacterized transcripts. (shrink)

Both language and genes evolve by transmission over generations with opportunity for differential replication of forms. The understanding that gene frequencies change at random by genetic drift, even in the absence of natural selection, was a seminal advance in evolutionary biology. Stochastic drift must also occur in language as a result of randomness in how linguistic forms are copied between speakers. Here we quantify the strength of selection relative to stochastic drift in language evolution. We use time series derived (...) from large corpora of annotated texts dating from the 12th to 21st centuries to analyse three well-known grammatical changes in English: the regularization of past-tense verbs, the introduction of the periphrastic ’do’, and variation in verbal negation. We reject stochastic drift in favour of selection in some cases but not in others. In particular, we infer selection towards the irregular forms of some past-tense verbs, which is likely driven by changing frequencies of rhyming patterns over time. We show that stochastic drift is stronger for rare words, which may explain why rare forms are more prone to replacement than common ones. This work provides a method for testing selective theories of language change against a null model and reveals an underappreciated role for stochasticity in language evolution. (shrink)

There are remarkable behavioral, neural, and genetic similarities between the way songbirds learn to sing and human infants learn to speak. Furthermore, the brain regions involved in birdsong learning, perception, and production have been identified and characterized in detail. In particular, the caudal medial nidopallium (the avian analog of the mammalian auditory‐association cortex) has been found to contain the neural substrate of auditory memory, paving the way for analyses of the underlying molecular mechanisms. Recently, the zebra finch genome was sequenced, (...) and annotated cDNA databases representing over 15,000 unique brain‐expressed genes are available, enabling high‐throughput gene expression analyses. Here we review the involvement of immediate early genes (e.g. zenk and arc), their downstream targets (e.g. synapsins), and their regulatory signaling pathways (e.g. MAPK/ERK) in songbird memory. We propose that in‐depth investigations of zenk‐ and ERK‐dependent cascades will help to further unravel the molecular basis of auditory memory. (shrink)

Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non‐coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non‐coding DNA sequences and methodologies to characterize their three‐dimensional (3D) organization in (...) the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene‐intergenic fusion transcripts at the SV breakpoints. (shrink)

For some, biology explains all there is to know about the mind. Yet many big questions remain: is the mind shaped by genes or the environment? If mental traits are the result of adaptations built up over thousands of years, as evolutionary psychologists claim, how can such claims be tested? If the mind is a machine, as biologists argue, how does it allow for something as complex as human consciousness? The Biological Mind: A Philosophical Introduction explores these questions and more, (...) using the philosophy of biology to introduce and assess the nature of the mind. Drawing on the four key themes of evolutionary biology; molecular biology and genetics; neuroscience; and biomedicine and psychiatry Justin Garson addresses the following key topics: moral psychology, altruism and levels of selection evolutionary psychology and modularity genes, environment and the nature-nurture debate neuroscience, reductionism and the relation between biology and free will function, selection and mental representation psychiatric classification and the maladapted mind. Extensive use of examples and case studies is made throughout the book, and additional features such as chapter summaries, annotated further reading and a glossary make this an indispensable introduction to those teaching philosophy of mind and philosophy of psychology. It will also be an excellent resource for those in related fields such as biology. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. (...) Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Complex‐trait genetics has advanced dramatically through methods to estimate the heritability tagged by SNPs, both genome‐wide and in genomic regions of interest such as those defined by functional annotations. The models underlying many of these analyses are inadequate, and consequently many SNP‐heritability results published to date are inaccurate. Here, we review the modelling issues, both for analyses based on individual genotype data and association test statistics, highlighting the role of a low‐dimensional model for the heritability of each SNP. We use (...) state‐of‐art models to present updated results about how heritability is distributed with respect to functional annotations in the human genome, and how it varies with allele frequency, which can reflect purifying selection. Our results give finer detail to the picture that has emerged in recent years of complex trait heritability widely dispersed across the genome. Confounding due to population structure remains a problem that summary statistic analyses cannot reliably overcome. Also see the video abstract here: https://youtu.be/WC2u03V65MQ. (shrink)

The God Dialogues is an intriguing and extensive philosophical debate about the existence of God. Engaging and accessible, it covers all the main arguments for and against God's existence, from traditional philosophical "proofs" to arguments that involve the latest developments in biology and physics. Three main characters represent the principal views: Theodore Logan, the theist; Eva Lucien, the atheist; and Gene Sesquois, the agnostic. Their debate takes place during a post-college cross-country road trip during which Gene expresses dismay (...) over his future. He wants to do something meaningful with his life but is at a loss as to how to proceed, despite having just earned a degree in engineering. Gene's quandary precipitates a discussion of the meaning of life and its connection to God's existence. This in turn leads to vigorous debates about morality and theism, evidence for and against God's existence, probability and the rationality of belief, and the relationship between faith and reason. The strongest arguments from all three perspectives are fairly represented. An annotated list of suggested readings directs readers to relevant and helpful primary sources.Assuming no background knowledge, The God Dialogues is ideal for courses in the philosophy of religion, an excellent supplement for introduction to philosophy courses, and a compelling introduction for anyone with an interest in the subject. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re‐evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective (...) miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (...) (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also (...) provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Several recently discovered small proteins of less than 100 amino acids control important, but sometimes surprising, steps in the metabolism of cyanobacteria. There is mounting evidence that a large number of small protein genes have also been overlooked in the genome annotation of many other microorganisms. Although too short for enzymatic activity, their functional characterization has frequently revealed the involvement in processes such as signaling and sensing, interspecies communication, stress responses, metabolism, regulation of transcription and translation, and in the (...) formation of multisubunit protein complexes. Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. They thrive under a wide variety of conditions as long as there is light and must cope with dynamic changes in the environment. To acclimate to these fluctuations, frequently small regulatory proteins become expressed that target key enzymes and metabolic processes. The consequences of their actions are profound and can even impact the surrounding microbiome. This review highlights the diverse functions of recently discovered small proteins that control cyanobacterial metabolism. It also addresses why many of these proteins have been overlooked so far and explores the potential for implementing metabolic engineering strategies to improve the use of cyanobacteria in biotechnological applications. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has (...) been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support (...) advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental (...) stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Books Reviewed in this Article: Reason, Truth and History. By Hilary Putnam. Pp.xii, 222, Cambridge University Press, 1982, £15.00 , £4.95 . Fundamentals of philosophy. By David Stewart and H. Gene Blocker. Pp.xiii, 378, New York, Macmillan, 1982, £12.95. Modern Philosophy: An Introduction. By A.R. Lacey. Pp.vii, 246, London and Boston, Routledge & Kegan Paul, 1982, £7.95 , £3.95 . Merleau‐Ponty's Philosophy. By Samuel B. Mallin. Pp.xi, 302, New Haven and London, Yale University Press, 1979, £14.20. Thought and Object: (...) Essays on Intentionality. Edited by Andrew Woodfield. Pp.xvi, 316, Oxford, Clarendon Pressl Oxford University Press, 1982, £16.00. Philosophical Ethics: An Introduction to Moral Philosophy. By Tom L. Beauchamp. Pp.xv, 396, New York & London, McGraw‐Hill, 1982, £14.25. The Limits of Obligation. By James S. Fishkin. Pp.viii, 184, New Haven and London, Yale University Press, 1982, £12.95. Religion and the One: Philosophies East and West. By Frederick Copleston. Pp.281, London, Search Press, 1982, £10.50. Religious Experience and Christian Faith. By F.W. Dillistone. Pp.viii, 120. London, SCM Press, 1982, £4.95. Exploring Inner Space: Scientists and Religious Experience. By David Hay. Pp.256, Harmondsworth, Penguin Books, 1982, £2.95. Judaism and Psychoanalysis. Edited by Mortimer Ostrow. Pp.ix, 305, New York, Ktav, 1982, $20.00. Ecclesial Reflection: An Anatomy of Theological Method. By Edward Farley. Pp.xix, 380, Philadelphia, Fortress Press, 1982, $29.95. The Pastoral Nature of the Ministry. By Frank Wright. Pp.89, London, SCM Press, 1980, £2.50. Power and Authority in the Catholic Church. By Charles Dahm in collaboration with Robert Ghelardi. Pp.xviii, 334, Notre Dame, University of Notre Dame Press, 1981, £12.35. Religion in Sociological Perspective. By Bryan Wilson. Pp.vii. 187, Oxford University Press, 1982, £8.50. Myth, Religion and Society: Structuralist Essays. By M. Detienne, L. Gernet, J.‐P. Vernant and P. Vidal‐Naquet. Pp.xviii, 306, Cambridge University Press, 1981, £20.00 , £6.95 . Seven Theories of Human Society. By Tom Campbell. Pp.244, Oxford, Clarendon Press: Oxford University Press, 1981, £10.00. The Aims of Education Restated. By John White. Pp.xi, 177, London, Routledge & Kegan Paul, 1982, £8.95 , £4.95 . Love and Meaning in Religious Education: An Incarnational Approach to Teaching Christianity. By D.J. O'Leary and T. Sallnow. Pp.147, Oxford University Press, 1982, £3.50. Servant and Son: Jesus in Parable and Gospel. By J. Ramsey Michaels. Pp.xiii, 323, Atlanta, John Knox Press, 1981, £7.80. Parables for Now. By Edmund Flood. Pp.98, London, Darton, Longman and Todd, 1981, £2.50. More Parables for Now. By Edmund Flood. Pp.102, London, Darton, Longman and Todd, 1981, £2.50. Councils and Synods: With other Documents relating to the English Church, Vol.1 , A.D. 871–1204. Edited by D. Whitelock, M. Brett and C.N. Brooke. Pp.1 xxix, xii, 1151, Oxford University Press, 1981, £65.00. The Architectural History of Canterbury Cathedral. By Francis Woodman. Pp.xviii, 282, London, Routledge and Kegan Paul, 1981, £35.00. The Correspondence of Erasmus, Volume VI. Translated by R.A.B. Mynors and D.F.S. Thomson, annotated by Peter G. Bietenholz. Pp.xxii, 448, Toronto, University of Toronto Press, 1982, £56.25. Erasme: Vie de Jean Vitrier et de John Colet. Edited by Andrd Godin. Pp.160, Angers, Editions Moreana, 1982, $7.00. Erasme, lecteur d'Origène. By André Godin. Pp.ix, 724, Geneva, Librairie Droz, 1982, no price given. Thomas More: history and providence. By Alistair Fox. Pp.xi, 271, Oxford, Basil Blackwell, 1982, no price given. Thomas More: Essays on the Icon. Edited by D. Grace and B. Byron. Pp.129, Melbourne, Dove Communications, 1980, no price given. The Cambridge Connection and the Elizabethan Settlement of 1559. By W.S. Hudson. Pp.x, 158, Durham , Duke University Press, 1980, $14.75. Faith by Statute: Parliament and the Settlement of Religion, 1559. By Norman L. Jones. Pp.viii, 245 , London, Royal Historical Society, 1982, £17.52. Richard Hooker and the Politics of a Christian England. By Robert K. Faulkner. Pp.x, 190, Berkeley, University of California Press, 1981, £15.75. Icon and Conquest. By Bernadette Bucher. Pp.xvii, 220, Chicago, The University of Chicago Press, 1981, £9.95. The Wooden Churches of Eastern Europe: An Introductory Survey. By David Buxton. Pp.viii, 405, Cambridge University Press, 1982, £42.50. American Catholics: A History of the Roman Catholic Community in the United States. By James Hennessey. Pp.xii, 397, New York, Oxford University Press, 1981, £13.50. Peter Maurin: Prophet in the Twentieth Century. By Marc H. Ellis. Pp.191, Ramsey, New Jersey and Leominster, England, Paulist Press/Fowler Wright Books, 1981, £7.45. The Newman Movement: Roman Catholics in American Higher Education, 1883–1971. By John Whitney Evans. Pp.xvi, 248, Notre Dame, University of Notre Dame Press, 1980, $14.95. Priests and People in Pre‐Famine Ireland, 1780–1845. By S.J. Connolly. Pp.338, Dublin, Gill & Macmillan, 1982, £17.00. The Nonconformist Conscience: Chapel and Politics, 1870–1914. By D.W. Bebbington. Pp.x, 193, London, George Allen and Unwin, 1982, £10.00. Heinrich Pesch: sein Leben und seine Lehre. By Franz H. Mueller. Pp.220, Cologne, J.P. Bachem, 1980, no price given. Beyond Survival: Reflections on the Future of Judaism. By Dow Marmur. Pp.xix, 218, London, Darton, Longman and Todd, 1982, £7.95. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Genetic Testing and Genetic ScreeningPat Milmoe McCarrick (bio)In recent years there has been an enormous expansion in the knowledge that may be gleaned from the testing of an individual's genetic material to predict present or future disability or disease either for oneself or one's offspring. The Human Genome Project, which is currently mapping the entire human gene system, is identifying progressively more genetic sequencing information (see Scope Note (...) 17, The Human Genome Project). Information obtained from genetic testing raises ethical and legal questions about its uses by society. The ethical dilemmas were foreseen two decades ago by bioethicists who asked whether questionable applications could stop "legitimate pursuits" (IV, Gaylin 1972) and whether genetic disease might come to be viewed as "transmissible" in the sense of being contagious (IV, Veatch 1974).Not only has knowledge expanded, but the practice of genetic testing and screening has greatly increased as well. For example, in the case of testing for cystic fibrosis (CF), the U.S. Congress' Office of Technology Assessment (OTA) estimates that instances of screening jumped from 9310 tests in 1991 to 63,000 tests in 1992 (I, OTA [Cystic Fibrosis] 1992). In addition, the OTA estimates that within the next few years, the six million women who become pregnant each year routinely will be informed of available CF carrier tests (I, OTA [Cystic Fibrosis] 1992).Following the recent identification of a gene linked to breast cancer, Dr. Francis Sellers Collins, director of the National Center for Human Genome Research, said that "it is not inconceivable that every woman in America may want to be screened for this gene. The economic, ethical, and counseling issues will be very daunting." Dr. Collins opines that in the near future physical examinations for 18-year-olds will include DNA testing for diseases with genetic components and that physicians, in the interests of preventive medicine, will make risk-based recommendations for a healthy life-style (IV, Breo 1993). The U.S. President's Commission for the Study of Ethical Problems in Medicine and Biomedical and Behavioral Research predicted as early as 1983 that before the end of the century genetic screening and counseling would become major components of both public health and individual medical care (I, U.S. President's Commission 1983). [End Page 333]The OTA defines genetic testing as "the use of specific assays to determine the genetic status of individuals already suspected to be at high risk for a particular inherited condition. The terms genetic test, genetic assay, and genetic analysis are used interchangeably to mean the actual laboratory examination of samples." In contrast, genetic screening usually uses the same assays employed for genetic testing but is distinguished from genetic testing by its target population (I, OTA [Genetic Monitoring] 1990). The National Academy of Sciences (NAS) defines screening as the systematic search of populations for persons with latent, early, or asymptomatic disease (III, NAS 1975). Some of the literature annotated for this Scope Note appears to use the terms "testing" and "screening" interchangeably.Philip Boyle of the Hastings Center points out that the language used to describe genetic variation is important and asks what words should be used: "Defects, flaws, deleterious genes, disorders, or the more neutral conditions? Using words such as normal—and its corollary, abnormal—is likely to foster stigmatization and discrimination" (III, Genetic Grammar, Boyle 1992).Areas of focus in genetic testing include: prenatal diagnosis, newborn screening, carrier screening, forensic screening, and susceptibility screening.Prenatal diagnosis discerns whether a fetus is at risk for various identifiable genetic diseases or traits. Prenatal diagnosis is made using amniotic fluid, fetal cells, and fetal or maternal blood cells obtained during amniocentesis testing; alpha fetoprotein assays or chorionic villus sampling; or ultrasound tomography, which creates fetal images on a screen. Another method, known as fetoscopy, uses a camera on a needle inserted in the uterus to view the fetus. Since prenatal screening began in 1966 (I, U.S. President's Commission 1983), the number of metabolic defects and genetic disorders that can be diagnosed prenatally has expanded greatly. There is also discussion of requiring testing for parents who are participating in an in vitro fertilization program and are at genetic... (shrink)

High‐throughput genomic technologies are revolutionizing human genetics. So far the focus has been on the 1.5% of the genome, which is coding, in spite of the fact that the great majority of genomic variants fall outside the coding regions. Recent efforts to annotate the non‐coding sequence show that over 80% of the genome is biochemically active. The genome is divided into regulatory domains consisting of sequence regions that enhance and/or silence the expression of nearby genes and are, in some cases, (...) separated by boundaries with insulator activity. In this paper, we review the recent advances in the identification of variations that influence gene regulation and their consequences for human disease. We hypothesize that structural variations outside of the coding genome can interfere with normal gene regulation by disrupting the regulatory landscape. Therefore, the regulatory landscape of the genome has also to be taken into consideration when investigating the pathology of human disease. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Sponges are important but often‐neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non‐specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to (...) understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies. (shrink)

Understanding the functional mechanisms underlying genetic signals associated with complex traits and common diseases, such as cancer, diabetes and Alzheimer's disease, is a formidable challenge. Many genetic signals discovered through genome‐wide association studies map to non‐protein coding sequences, where their molecular consequences are difficult to evaluate. This article summarizes concepts for the systematic interpretation of non‐coding genetic signals using genome annotation data sets in different cellular systems. We outline strategies for the global analysis of multiple association intervals and the (...) in‐depth molecular investigation of individual intervals. We highlight experimental techniques to validate candidate (potential causal) regulatory variants, with a focus on novel genome‐editing techniques including CRISPR/Cas9. These approaches are also applicable to low‐frequency and rare variants, which have become increasingly important in genomic studies of complex traits and diseases. There is a pressing need to translate genetic signals into biological mechanisms, leading to prognostic, diagnostic and therapeutic advances. (shrink)

This article outlines the rationale for a molecular genetic study of social behavior, and explains why social insects are good models. Summaries of research on brain and behavior in two species, honey bees and fire ants, are presented to illustrate the richness of the behavioral phenomena that can be addressed with social insects and to show how they are beginning to be used to study genes that influence social behavior. We conclude by considering the problems and potential of this emerging (...) field. (shrink)

By rasing the form-critical questions our attention will be drawn directly to the text itself, and what it communicates concerning the prophetic role, the broad question of authority and validity in religious language, and the specific issue of the authentication of prophetic words... these are issues which refuse to be confined to the eighth century B.C. in Israel.

Time was when you could bite a tomato and not ingest fish genes. Time was when you could eat french fries and just worry about the fat and salt, not the bacterial genes that produce insecticides in the potato. Those times are over, thanks to corporate control over both genetic engineering and the lack of food-labeling. Unless you are a “hard core” consumer of organic foods, you eat genetically engineered foods everyday. While 80-90% of US consumers believe genetically engineered foods (...) should be labeled, only 3% know they already on the market.[1] Today 60-70% of the food in a grocery store contains components from genetically modified crops. Moreover, this technology was unleashed on over 45 million acres of US farmland last year alone, after having been commercially introduced only four years ago.[2] Here we will provide a brief background on the types of genetically engineered crops that are being surreptitiously forced upon consumers, then argue against their current widespread use. (shrink)

This paper attempts to explicate the philosophical and theological premisses involved in Fr. Paneloux’s second sermon in Camus’ The Plague. In that sermon Fr. Paneloux says that the suffering of children is our bread of affliction. The article shows where one must start in order to get to that point, and what follows from it. Whether or not the argument given should be called a theodicy or a reductio ad absurdum of religious belief is an open question for a philosopher, (...) but the argument is shown to cohere with the traditional belief in God’s omnipotent goodness. (shrink)