112 research outputs found
The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease
Clinical management; Medical action ontology; OntologyGestión clínica; Ontología de la acción médica; OntologíaGestió clínica; Ontologia de l'acció mèdica; OntologiaBackground
Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions.
Methods
MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo Disease Ontology.
Findings
MAxO encompasses 1,757 terms spanning a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. These terms annotate phenotypic features associated with specific disease (using HPO and Mondo). Presently, there are over 16,000 MAxO diagnostic annotations that target HPO terms. Through POET, we have created 413 MAxO annotations specifying treatments for 189 rare diseases.
Conclusions
MAxO offers a computational representation of treatments and other actions taken for the clinical management of patients. Its development is closely coupled to Mondo and HPO, broadening the scope of our computational modeling of diseases and phenotypic features. We invite the community to contribute disease annotations using POET (https://poet.jax.org/). MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO).This study was supported by the National Institutes of Health (NIH): NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04. R.H. is a Wellcome Trust Investigator (109915/Z/15/Z), who receives support from the Medical Research Council (UK) (MR/V009346/1), the Addenbrookes Charitable Trust (G100142), the Evelyn Trust, the Stoneygate Trust, the Lily Foundation, Action for AT and an MRC strategic award to establish an International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD) MR/S005021/1. This research was supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014). The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care
Gleam: the GLAST Large Area Telescope Simulation Framework
This paper presents the simulation of the GLAST high energy gamma-ray
telescope. The simulation package, written in C++, is based on the Geant4
toolkit, and it is integrated into a general framework used to process events.
A detailed simulation of the electronic signals inside Silicon detectors has
been provided and it is used for the particle tracking, which is handled by a
dedicated software. A unique repository for the geometrical description of the
detector has been realized using the XML language and a C++ library to access
this information has been designed and implemented.Comment: 10 pages, Late
GA4GH Phenopackets: A Practical Introduction.
The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases
GA4GH Phenopackets: A Practical Introduction
The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases
Improved Adaptive Group Testing Algorithms with Applications to Multiple Access Channels and Dead Sensor Diagnosis
We study group-testing algorithms for resolving broadcast conflicts on a
multiple access channel (MAC) and for identifying the dead sensors in a mobile
ad hoc wireless network. In group-testing algorithms, we are asked to identify
all the defective items in a set of items when we can test arbitrary subsets of
items. In the standard group-testing problem, the result of a test is
binary--the tested subset either contains defective items or not. In the more
generalized versions we study in this paper, the result of each test is
non-binary. For example, it may indicate whether the number of defective items
contained in the tested subset is zero, one, or at least two. We give adaptive
algorithms that are provably more efficient than previous group testing
algorithms. We also show how our algorithms can be applied to solve conflict
resolution on a MAC and dead sensor diagnosis. Dead sensor diagnosis poses an
interesting challenge compared to MAC resolution, because dead sensors are not
locally detectable, nor are they themselves active participants.Comment: Expanded version of a paper appearing in ACM Symposium on Parallelism
in Algorithms and Architectures (SPAA), and preliminary version of paper
appearing in Journal of Combinatorial Optimizatio
The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease.
BACKGROUND: Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions.
METHODS: MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo Disease Ontology.
FINDINGS: MAxO encompasses 1,757 terms spanning a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. These terms annotate phenotypic features associated with specific disease (using HPO and Mondo). Presently, there are over 16,000 MAxO diagnostic annotations that target HPO terms. Through POET, we have created 413 MAxO annotations specifying treatments for 189 rare diseases.
CONCLUSIONS: MAxO offers a computational representation of treatments and other actions taken for the clinical management of patients. Its development is closely coupled to Mondo and HPO, broadening the scope of our computational modeling of diseases and phenotypic features. We invite the community to contribute disease annotations using POET (https://poet.jax.org/). MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO).
FUNDING: NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04
Fermi Large Area Telescope Constraints on the Gamma-ray Opacity of the Universe
The Extragalactic Background Light (EBL) includes photons with wavelengths
from ultraviolet to infrared, which are effective at attenuating gamma rays
with energy above ~10 GeV during propagation from sources at cosmological
distances. This results in a redshift- and energy-dependent attenuation of the
gamma-ray flux of extragalactic sources such as blazars and Gamma-Ray Bursts
(GRBs). The Large Area Telescope onboard Fermi detects a sample of gamma-ray
blazars with redshift up to z~3, and GRBs with redshift up to z~4.3. Using
photons above 10 GeV collected by Fermi over more than one year of observations
for these sources, we investigate the effect of gamma-ray flux attenuation by
the EBL. We place upper limits on the gamma-ray opacity of the Universe at
various energies and redshifts, and compare this with predictions from
well-known EBL models. We find that an EBL intensity in the optical-ultraviolet
wavelengths as great as predicted by the "baseline" model of Stecker et al.
(2006) can be ruled out with high confidence.Comment: 42 pages, 12 figures, accepted version (24 Aug.2010) for publication
in ApJ; Contact authors: A. Bouvier, A. Chen, S. Raino, S. Razzaque, A.
Reimer, L.C. Reye
A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope
Globular clusters with their large populations of millisecond pulsars (MSPs)
are believed to be potential emitters of high-energy gamma-ray emission. Our
goal is to constrain the millisecond pulsar populations in globular clusters
from analysis of gamma-ray observations. We use 546 days of continuous
sky-survey observations obtained with the Large Area Telescope aboard the Fermi
Gamma-ray Space Telescope to study the gamma-ray emission towards 13 globular
clusters. Steady point-like high-energy gamma-ray emission has been
significantly detected towards 8 globular clusters. Five of them (47 Tucanae,
Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices and clear evidence for an exponential cut-off in the range
1.0-2.6 GeV, which is the characteristic signature of magnetospheric emission
from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral
indices , however the presence of an exponential cut-off
can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC
6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral
properties. From the observed gamma-ray luminosities, we estimate the total
number of MSPs that is expected to be present in these globular clusters. We
show that our estimates of the MSP population correlate with the stellar
encounter rate and we estimate 2600-4700 MSPs in Galactic globular clusters,
commensurate with previous estimates. The observation of high-energy gamma-ray
emission from a globular cluster thus provides a reliable independent method to
assess their millisecond pulsar populations that can be used to make
constraints on the original neutron star X-ray binary population, essential for
understanding the importance of binary systems in slowing the inevitable core
collapse of globular clusters.Comment: Accepted for publication in A&A. Corresponding authors: J.
Kn\"odlseder, N. Webb, B. Pancraz
Gammaherpesvirus Latency Accentuates EAE Pathogenesis: Relevance to Epstein-Barr Virus and Multiple Sclerosis
Epstein-Barr virus (EBV) has been identified as a putative environmental trigger of multiple sclerosis (MS), yet EBV's role in MS remains elusive. We utilized murine gamma herpesvirus 68 (γHV-68), the murine homolog to EBV, to examine how infection by a virus like EBV could enhance CNS autoimmunity. Mice latently infected with γHV-68 developed more severe EAE including heightened paralysis and mortality. Similar to MS, γHV-68EAE mice developed lesions composed of CD4 and CD8 T cells, macrophages and loss of myelin in the brain and spinal cord. Further, T cells from the CNS of γHV-68 EAE mice were primarily Th1, producing heightened levels of IFN-γ and T-bet accompanied by IL-17 suppression, whereas a Th17 response was observed in uninfected EAE mice. Clearly, γHV-68 latency polarizes the adaptive immune response, directs a heightened CNS pathology following EAE induction reminiscent of human MS and portrays a novel mechanism by which EBV likely influences MS and other autoimmune diseases
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO\u27s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes
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