BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results

<p>Abstract</p> <p>Background</p> <p>High-throughput screening (HTS) is one of the main strategies to identify novel entry points for the development of small molecule chemical probes and drugs and is now commonly accessible to public sector research. Large amounts of data generated in HTS campaigns are submitted to public repositories such as PubChem, which is growing at an exponential rate. The diversity and quantity of available HTS assays and screening results pose enormous challenges to organizing, standardizing, integrating, and analyzing the datasets and thus to maximize the scientific and ultimately the public health impact of the huge investments made to implement public sector HTS capabilities. Novel approaches to organize, standardize and access HTS data are required to address these challenges.</p> <p>Results</p> <p>We developed the first ontology to describe HTS experiments and screening results using expressive description logic. The BioAssay Ontology (BAO) serves as a foundation for the standardization of HTS assays and data and as a semantic knowledge model. In this paper we show important examples of formalizing HTS domain knowledge and we point out the advantages of this approach. The ontology is available online at the NCBO bioportal <url>http://bioportal.bioontology.org/ontologies/44531</url>.</p> <p>Conclusions</p> <p>After a large manual curation effort, we loaded BAO-mapped data triples into a RDF database store and used a reasoner in several case studies to demonstrate the benefits of formalized domain knowledge representation in BAO. The examples illustrate semantic querying capabilities where BAO enables the retrieval of inferred search results that are relevant to a given query, but are not explicitly defined. BAO thus opens new functionality for annotating, querying, and analyzing HTS datasets and the potential for discovering new knowledge by means of inference.</p

CLO: The cell line ontology

Abstract Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.http://deepblue.lib.umich.edu/bitstream/2027.42/109554/1/13326_2013_Article_185.pd

Characterization of the 5 ' flanking region of the Xenopus laevis transforming growth factor-\beta5 (TGF-\beta 5) gene

Transforming growth factors-beta are potent regulators of cellular proliferation, differentiation and morphogenesis. 2.41 kb of the 5' flanking region of the transforming growth factor-beta 5 (TGF-beta 5) gene has been isolated from a Xenopus laevis genomic library and sequenced. The transcription start site of this gene was determined by 5' RACE method. Promoter activity was demonstrated by transient transfection experiments using luciferase reporter gene constructs in XTC cells. A number of putative recognition sites for transcription factors were found in the 5' flanking region of the TGF-beta 5 gen

Mouse models of oxidative phosphorylation dysfunction and disease

Oxidative phosphorylation (OXPHOS) deficiency results in a number of human diseases, affecting at least one in 5000 of the general population. Altering the function of genes by mutations are central to our understanding their function. Prior to the development of gene targeting, this approach was limited to rare spontaneous mutations that resulted in a phenotype. Since its discovery, targeted mutagenesis of the mouse germline has proved to be a powerful approach to understand the in vivo function of genes. Gene targeting has yielded remarkable understanding of the role of several gene products in the OXPHOS system. We provide a “tool box” of mouse models with OXPHOS defects that could be used to answer diverse scientific questions

Isolation and characterization of a transforming growth factor-β\beta Type II receptor cDNA from Xenopus laevis

Transforming Growth Factor-$\beta$ $(TGF-\beta)$ and their receptors have been characterized from many organisms. Two $TGF-\beta$ signaling receptors called Type I and II have been described for various ligands of the superfamily from organisms ranging from Drosophila to humans. In Xenopus laevis, $TGF-\beta 2$ and 5 have been reported and presumably, play important roles during early development. Several Type I and type II receptors for many ligands of the $TGF-\beta$ superfamily except $TGF-\beta$ type II receptor $(T \beta IIR)$, have been characterized in Xenopus laevis. A chemical cross linking experiment using iodinated $TGF-\beta 1$ and -$\beta 5$, revealed four specific binding proteins on XTC cells. In order to understand the $TGF-\beta$ involvement during Xenopus development, a $TGF-\beta$ type II receptor $(XT \beta IIR)$ has been isolated from a XTC cDNA library. $XT \beta IIR$ was a partial cDNA lacking a portion of the signal peptide. The sequence analysis and homology comparison with the human $T\beta IIR$ revealed 67% amino acid similarity in the extra cellular domain, 60% similarity in the transmembrane domain and 87% similarity in the cytoplasmic kinase domain, suggesting that $XT \beta IIR$ is a putative $TGF-\beta$ type II receptor. In addition, the consensus amino acid motif for serine threonine receptor kinases was also present. Further, a dominant negative expression construct lacking the cytoplasmic kinase domain (engineered with the signal peptide from human $TGF-\beta$ type II receptor), was able to abolish $TGF-\beta$ mediated induction of a luciferase reporter plasmid, in a transient cell transfection assay. This substantiates the notion that $XT \beta IIR$ cDNA can act as a receptor for $TGF-\beta$. RT-PCR analysis using RNA isolated from various developmental stages of Xenopus laevis revealed expression of this gene in all the early stages of development and in the adult organs, except in stages 46/48

Mouse models of oxidative phosphorylation defects: Powerful tools to study the pathobiology of mitochondrial diseases

Defects in the oxidative phosphorylation system (OXPHOS) are responsible for a group of extremely heterogeneous and pleiotropic pathologies commonly known as mitochondrial diseases. Although many mutations have been found to be responsible for OXPHOS defects, their pathogenetic mechanisms are still poorly understood. An important contribution to investigate the in vivo function of several mitochondrial proteins and their role in mitochondrial dysfunction, has been provided by mouse models. Thanks to their genetic and physiologic similarity to humans, mouse models represent a powerful tool to investigate the impact of pathological mutations on metabolic pathways. In this review we discuss the main mouse models of mitochondrial disease developed, focusing on the ones that directly affect the OXPHOS system

Transforming growth factor-β5\beta 5 expression during early development of Xenopus laevis

Members of the transforming growth factor-\beta $(TGF-\beta)$ superfamily play various roles during development in both vertebrates and invertebrates. Two isoforms, $TGF-\beta 2$ and -$\beta 5$, have been isolated from Xenopus laevis. We describe here the localization of $TGF-\beta 5$ mRNA in early embryos of X. laevis, assessed by whole-mount in situ hybridization. The first detectable expression of $TGF-\beta 5$ was seen in the stage 14 embryo at the posterior tip of notochord, which continued to later stages, accompanied by the expression in bilateral regions of posterior wall in the tail region next to the notochord. At later stages, transient expression was seen in the cement gland (around stage 21) and in the somites (stages 24–27). In addition, expression was present in the branchial arches (stage 29–36) and olfactory placodes (stage 36)

BioAssay ontology annotations facilitate cross-analysis of diverse high-throughput screening data sets

High-throughput screening data repositories, such as PubChem, represent valuable resources for the development of small-molecule chemical probes and can serve as entry points for drug discovery programs. Although the loose data format offered by PubChem allows for great flexibility, important annotations, such as the assay format and technologies employed, are not explicitly indexed. The authors have previously developed a BioAssay Ontology (BAO) and curated more than 350 assays with standardized BAO terms. Here they describe the use of BAO annotations to analyze a large set of assays that employ luciferase- and β-lactamase-based technologies. They identified promiscuous chemotypes pertaining to different subcategories of assays and specific mechanisms by which these chemotypes interfere in reporter gene assays. Results show that the data in PubChem can be used to identify promiscuous compounds that interfere nonspecifically with particular technologies. Furthermore, they show that BAO is a valuable toolset for the identification of related assays and for the systematic generation of insights that are beyond the scope of individual assays or screening campaigns

A Consensus RNA Signal That Directs Germ Layer Determinants to the Vegetal Cortex of Xenopus Oocytes

RNA localization is an important mechanism for generating cellular diversity and polarity in the early embryo. In Xenopus, the correct localization of the RNA encoding the T-box transcription factor VegT is essential for the correct spatial organization and identity of endoderm and mesoderm. Although localization signals in the 3′ UTR have been identified for many localized RNAs, insight into what constitutes an RNA localization signal remains elusive. To investigate possible common features between signals that direct different RNAs to the same subcellular region, we carried out a detailed analysis of the uncharacterized VegT RNA localization signal and compared it with the well-studied Vg1 localization signal. Both RNAs localize to the vegetal cortex during the same period of oogenesis. Our results suggest a common RNA localization signal at the level of clustered redundant protein-binding motifs and trans-acting factors. We propose that what characterizes RNA localization signals in general is not the nucleotide sequence or secondary structure per se, but the critical clustering of specific redundant protein-binding motifs