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METHOD Open Access Method Integrating phenotype ontologies across multiple species
"... Multi-species A the across truly phenotypic analysis cross multiple species of Phenotype ontology phenotype-genotype species, translational that paving ontologies can the research. be way used data for Phenotype ontologies are typically constructed to serve the needs of a particular community, such ..."
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these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology. Background The completion of the Human Genome Project [1,2] has resulted in an increase in high-throughput systematic projects aimed at elucidating the molecular basis of human disease
Original article PhenoMiner: quantitative phenotype curation at the rat genome database
"... The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses>40 000 rat gene records as well as human and mouse orthologs,>2000 rat and 1900 human quantitative trait loci (QTLs) records and>2900 rat strain records. Biological information curat ..."
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curated for these data objects includes disease associations, pheno-types, pathways, molecular functions, biological processes and cellular components. Recently, a project was initiated at RGD to incorporate quantitative phenotype data for rat strains, in addition to the currently existing qualitative
CLINICAL ONTOLOGIES FOR DISCOVERY APPLICATIONS
"... Abstract: The recent achievements in the Human Genome Project have made possible a high-throughput “systems approach ” for accelerating bioinformatics research. In addition, the NIH Whole Genome Association Studies will soon supply abundant clinical data annotated to clinical ontologies for mining. ..."
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Cited by 1 (0 self)
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. The elucidation of the molecular underpinnings of human diseases will require the use of genomic and ontology-anchored clinical databases. The objective of this chapter is to provide the background required to conduct biological discovery research with clinical ontologies. We first provide a description
Capturing phenotypes for precision medicine | COMMENTARY Molecular Case Studies
"... Abstract Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natu ..."
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as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers
A plant disease extension of the Infectious Disease Ontology
"... Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plan ..."
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and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease On-‐ tology (IDOPlant). The IDOPlant is envisioned as a reference
Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma
, 2014
"... Suicidal behavior is a complex disorder, with evidence for genetic risk independent of other genetic risk factors including psychiatric disorders. Since 1996, over 3000 DNA samples from Utah suicide decedents have been collected and banked for research use through the Utah Medical Examiner. In addi ..."
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. Genotyping was done using the Infinium HumanExome BeadChip. For analysis, we used the pedigree extension of Variant Annotation, Analysis and Search Tool (pVAAST) to calculate the disease burden of each gene. The Phenotype Driven Variant Ontological Re-ranking tool (Phevor) then re-ranked our pVAAST results
Chapter 5 CLINICAL ONTOLOGIES FOR DISCOVERY APPLICATIONS
"... Abstract: The recent achievements in the Human Genome Project have made possible a high-throughput “systems approach ” for accelerating bioinformatics research. In addition, the NIH Whole Genome Association Studies will soon supply abundant clinical data annotated to clinical ontologies for mining. ..."
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. The elucidation of the molecular underpinnings of human diseases will require the use of genomic and ontology-anchored clinical databases. The objective of this chapter is to provide the background required to conduct biological discovery research with clinical ontologies. We first provide a description
Phenotypic checkpoints regulate neuronal development. Trends Neurosci
- in the presymptomatic stage. Neural Plast. 2012, 976164. doi: 10.1155/2012/976164 Chapleau
, 2010
"... 2 Abstract Nervous system development proceeds by sequential gene expression mediated by cascades of transcription factors in parallel with sequences of patterned network activity driven. These sequences are cell type-and developmental stage-dependent and modulated by paracrine actions of substance ..."
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Cited by 4 (0 self)
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biological function of the polarity of GABA's effects (65). If this conversion in polarity of GABA signals is prevented, subsequent stages of development are blocked. Thus the switch from depolarization to hyperpolarization is an important phenotypic checkpoint during development. Phenotypic checkpoints
Linking molecular insight and ecological research.
- Trends Ecol. Evol.
, 2002
"... 409 Opinion Throughout the 20th century, individual disciplines in biology succeeded by specializing in different scales of size and organization. Effective in many respects, this traditional partitioning sometimes hindered our understanding of how organisms function and interact with each other an ..."
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Cited by 8 (3 self)
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to provide a mechanistic basis for some ecological processes. Many molecular tools developed using model systems can now be applied to other organisms, removing the technical barriers to examining biological mechanisms in nature. Acquiring a detailed genomic understanding Linking molecular insight
Molecular and clinical classification of human prion disease
, 2003
"... While rare in humans, the prion diseases have become an area of intense clinical and scientific interest. The recognition that variant Creutzfeldt-Jakob disease is caused by the same prion strain as bovine spongiform encephalopathy in cattle has dramatically highlighted the need for a precise unders ..."
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Cited by 9 (4 self)
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understanding of the molecular biology of human prion diseases. Detailed clinical, pathological and molecular data from a large number of human prion disease cases have shown that distinct abnormal isoforms of prion protein are associated with prion protein gene polymorphism and neuropathological phenotypes. A
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