Structured vocabularies describing concepts from the fields of biology and relationships between concepts.
A specified list of terms with a fixed and unalterable meaning, and from which a selection is made when CATALOGING; ABSTRACTING AND INDEXING; or searching BOOKS; JOURNALS AS TOPIC; and other documents. The control is intended to avoid the scattering of related subjects under different headings (SUBJECT HEADINGS). The list may be altered or extended only by the publisher or issuing agency. (From Harrod's Librarians' Glossary, 7th ed, p163)
Organized activities related to the storage, location, search, and retrieval of information.
Sets of structured vocabularies used for describing and categorizing genes, and gene products by their molecular function, involvement in biological processes, and cellular location. These vocabularies and their associations to genes and gene products (Gene Ontology annotations) are generated and curated by the Gene Ontology Consortium.
The terms, expressions, designations, or symbols used in a particular science, discipline, or specialized subject area.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
A branch of biology dealing with the structure of organisms.
Databases devoted to knowledge about specific genes and gene products.
Sequential operating programs and data which instruct the functioning of a digital computer.
Software designed to store, manipulate, manage, and control data for specific uses.
Computer processing of a language with rules that reflect and describe current usage rather than prescribed usage.
The portion of an interactive computer program that issues messages to and receives commands from a user.
The relationships between symbols and their meanings.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Specific languages used to prepare computer programs.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Systematic organization, storage, retrieval, and dissemination of specialized information, especially of a scientific or technical nature (From ALA Glossary of Library and Information Science, 1983). It often involves authenticating or validating information.
Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.
The field of knowledge, theory, and technology dealing with the collection of facts and figures, and the processes and methods involved in their manipulation, storage, dissemination, publication, and retrieval. It includes the fields of COMMUNICATION; PUBLISHING; LIBRARY SCIENCE; and informatics.
Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.
A research and development program initiated by the NATIONAL LIBRARY OF MEDICINE to build knowledge sources for the purpose of aiding the development of systems that help health professionals retrieve and integrate biomedical information. The knowledge sources can be used to link disparate information systems to overcome retrieval problems caused by differences in terminology and the scattering of relevant information across many databases. The three knowledge sources are the Metathesaurus, the Semantic Network, and the Specialist Lexicon.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
Controlled vocabulary of clinical terms produced by the International Health Terminology Standards Development Organisation (IHTSDO).
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
Biological activities and function of the whole organism in human, animal, microorgansims, and plants, and of the biosphere.
One of the BIOLOGICAL SCIENCE DISCIPLINES concerned with the origin, structure, development, growth, function, genetics, and reproduction of animals, plants, and microorganisms.
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
Methods for determining interaction between PROTEINS.
A family of soil bacteria. It also includes some parasitic forms.
A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.
A soil-dwelling actinomycete with a complex lifecycle involving mycelial growth and spore formation. It is involved in the production of a number of medically important ANTIBIOTICS.
A chronic progressive subcutaneous infection caused by species of fungi (eumycetoma), or actinomycetes (actinomycetoma). It is characterized by tumefaction, abscesses, and tumor-like granules representing microcolonies of pathogens, such as MADURELLA fungi and bacteria ACTINOMYCETES, with different grain colors.
Class of BACTERIA with diverse morphological properties. Strains of Actinobacteria show greater than 80% 16S rDNA/rRNA sequence similarity among each other and also the presence of certain signature nucleotides. (Stackebrandt E. et al, Int. J. Syst. Bacteriol. (1997) 47:479-491)
Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
An actinomycete from which the antibiotics STREPTOMYCIN, grisein, and CANDICIDIN are obtained.

Evaluation of research in biomedical ontologies. (1/26)

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Towards Web 3.0: taxonomies and ontologies for medical education -- a systematic review. (2/26)

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Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers. (3/26)

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FYPO: the fission yeast phenotype ontology. (4/26)

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Effects of guideline-based training on the quality of formal ontologies: a randomized controlled trial. (5/26)

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OntoQuery: easy-to-use web-based OWL querying. (6/26)

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The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. (7/26)

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The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. (8/26)

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Phenotype data for mouse gene Zdhhc21. Discover Zdhhc21s significant phenotypes, expression, images, histopathology and more. Data for gene Zdhhc21 is all freely available for download.
Phenotype data for mouse gene Cenpo. Discover Cenpos significant phenotypes, expression, images, histopathology and more. Data for gene Cenpo is all freely available for download.
In order to identify the function of genes, the consortium uses a series of response (ABR) test conducted at 14 weeks of age. Hearing is assessed at five frequencies - 6kHz, 12kHz, 18kHz, 24kHz and 30kHz - as well as a broadband click stimulus. Increased thresholds are indicative of abnormal hearing. Abnormalities in adult ear morphology are recorded as part of the Combined SHIRPA and Dysmorphology (CSD) protocol, which includes a response to a click box test (absence is indicative of a strong hearing deficit) and visual inspection for behavioural signs that may indicate vestibular dysfunction e.g. head bobbing or circling. ...
TY - JOUR. T1 - Ventriculoperitoneal shunt infection due to listeria monocytogenes. AU - Dominguez, Edward A.. AU - Patil, Aron A.. AU - Johnson, William M.. PY - 1994/7. Y1 - 1994/7. UR - http://www.scopus.com/inward/record.url?scp=0028291853&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0028291853&partnerID=8YFLogxK. U2 - 10.1093/clinids/19.1.223. DO - 10.1093/clinids/19.1.223. M3 - Article. C2 - 7677812. AN - SCOPUS:0028291853. VL - 19. SP - 223. EP - 224. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 1. ER - ...
TY - JOUR. T1 - Perineal anatomy and urine-voiding characteristics of young women with and without recurrent urinary tract infections. AU - Hooton, Thomas M.. AU - Stapleton, Ann E.. AU - Roberts, Pacita L.. AU - Winter, Carol. AU - Scholes, Delia. AU - Bavendam, Tamara. AU - Stamm, Walter E.. PY - 1999/12/1. Y1 - 1999/12/1. UR - http://www.scopus.com/inward/record.url?scp=0033371663&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0033371663&partnerID=8YFLogxK. U2 - 10.1086/313528. DO - 10.1086/313528. M3 - Article. C2 - 10585838. AN - SCOPUS:0033371663. VL - 29. SP - 1600. EP - 1601. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 6. ER - ...
TY - JOUR. T1 - Vancomycin telephone. AU - Drekonja, Dimitri M.. N1 - Copyright: Copyright 2011 Elsevier B.V., All rights reserved.. PY - 2011/7/15. Y1 - 2011/7/15. UR - http://www.scopus.com/inward/record.url?scp=79959742278&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=79959742278&partnerID=8YFLogxK. U2 - 10.1093/cid/cir311. DO - 10.1093/cid/cir311. M3 - Letter. C2 - 21690636. AN - SCOPUS:79959742278. VL - 53. SP - 211. EP - 212. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 2. ER - ...
TY - JOUR. T1 - Safety, censoring, and intent-to-treat analysis. T2 - Dangers to generalizability. AU - Boulware, David R.. N1 - Copyright: Copyright 2011 Elsevier B.V., All rights reserved.. PY - 2010/10/15. Y1 - 2010/10/15. UR - http://www.scopus.com/inward/record.url?scp=77957824492&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=77957824492&partnerID=8YFLogxK. U2 - 10.1086/656436. DO - 10.1086/656436. M3 - Letter. C2 - 20858076. AN - SCOPUS:77957824492. VL - 51. SP - 985. EP - 986. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 8. ER - ...
To assess the mortality and resource utilization that results from acute renal failure associated with amphotericin B therapy, 707 adult admissions in which parenteral amphotericin B therapy was given were studied at a tertiary-care hospital. Main outcome measures were mortality, length of stay, and costs; we controlled for potential confounders, including age, sex, insurance status, baseline creatinine level, length of stay before beginning amphotericin B therapy, and severity of illness. Among 707 admissions, there were 212 episodes (30%) of acute renal failure. When renal failure developed, the mortality rate was much higher: 54% versus 16% (adjusted odds of death, 6.6). When acute renal failure occurred, the mean adjusted increase in length of stay was 8.2 days, and the adjusted total cost was $29,823. Although residual confounding exists despite adjustment, the increases in resource utilization that we found are large and the associated mortality is high when acute renal failure occurs ...
Background. Because antiretrovirals are becoming increasingly available in developing countries, we reviewed the findings of studies that have documented highly active antiretroviral therapy (HAART) use in Africa to identify lessons learned. With the World Health Organization (WHO) guidelines used as a frame of reference, we assessed the feasibility of implementing such programs in Africa. Moreover, clinical and laboratory outcomes were compiled to determine the effectiveness of HAART programs.. Methods. We searched academic databases and recent conference abstracts for studies, and we included all studies that documented patients receiving HAART in Africa. In particular, we examined studies for such program features as type of regimen and frequency of monitoring, in addition to evaluations of patient outcomes.. Results. Twenty-eight articles and abstracts involving studies from 14 African countries were reviewed. Overall, 6052 patients (96.4%) were receiving HAART, mainly consisting of 2 ...
Babesia microti causes babesiosis-a zoonosis acquired chiefly in the coastal areas and islands off the northeastern coast of the United States (e.g., Nantucket Island). The sporozoan organism is endemic in rodents and is transmitted by the bite of the tick Ixodes dammini (renamed I. scapularis), the same species of tick that transmits Borrelia burgdorferi, the agent of Lyme disease. Babesia infects red blood cells, causing them to lyse, but unlike plasmodia, it has no exoerythrocytic phase. Asplenic patients and patients being treated with rituximab are affected more severely. ...
Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A. Jähn, Roger James, Roland Krause, Stanley J.F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W.M. Veltman, Tom Vulliamy, Jing Yu, Julie Von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O.B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa Haendel, Peter N. Robinson ...
POSTER 8 - 3-D VISUALIZATION OF MOUSE EMBRYOS WITH OPTICAL PROJECTION TOMOGRAPHY Walls JR 1, Sled JG 1, Bruneau BG 2, Sharpe J 3, Henkelman RM 1 1 Mouse Imaging Centre, Hospital for Sick Children, Toronto, Canada, 2 Hospital for Sick Children, Toronto, Canada, 3 Human Genetics Unit, Medical Research Council, Edinburgh, United Kingdom The ability to visualize the 3D organization of biological tissue is essential to unravelling its complexities. A new imaging technique called Optical Projection Tomography (OPT), essentially an optical version of X-Ray computed tomography (CT), fills a gap among current imaging modalities by creating molecularly specific, cellular resolution images of specimens up to 1 cc in size. The visualization of a specific genes pattern of expression is essential to gain an understanding of its role. Mutant comparisons performed with OPT are more sensitive to spatial complexity than comparisons performed with serial sectioning techniques that might alter subtle morphology. ...
Church DM, Agarwala R, Chen H-C, Chetvernin S, Ermolaeva O, Geer R, Hlavina W, Jang W, Johnson P, Kans J, Katz K, Kitts P, Lipman D, Meric P, Ostell J, Pruitt K, Resenchuk S, Sapojnikov V, Schuler G, Sherry S, Shkeda A, Wagner L, Tatusova T, Maglott D. 136. THE MOUSE GENOME INFORMATICS DATABASE: A COMPREHENSIVE ONLINE RESOURCE FOR THE MAMMALIAN GENOMICS RESEARCH COMMUNITY ...
Most of the classes in the pre-composed phenotype ontologies are gross anatomy phenotypes - they can be defined in terms of a quality of some part of the body. For example: MP:decreased diameter of femur*; MP:hypothalamus hypoplasia; MP:large lymphoid organs; MP:muscular atrophy; MP:truncated notochord*; MP:motor neuron degeneration*; MP:axon degeneration*; HP:narrow pelvis*; TO:leaf area*; WP:shrunken intestine*; MP:situs inversus* (examples marked with an asterisk are shown in Table 4).. The first step to creating mappings for these pre-composed phenotypes is selection of the appropriate anatomical ontology. For worm and plant phenotypes, there is a single unified gross anatomy ontology covering each. For human phenotypes from HP, we use the FMA, and although the FMA does not include developing structures, this is not currently a limitation because the HP does not include many phenotypes for developing structures such as neural tube.. The MP is intended as a mammalian phenotype ontology. ...
Historically, IFOMIS originated in April 2002 utilizing the Wolfgang Paul Award of the Alexander von Humboldt Foundation to Prof. Barry Smith. Substantial funding was provided also by the Volkswagen Foundation and by the European Commission. IFOMIS comprehends an interdisciplinary research group, with members from Philosophy, Computer and Information Science, Logic, Medicine, and Medical Informatics. Inquiries regarding long- and short-term research visits are welcome. ...
Improving efficiency of disease diagnosis based on phenotype ontology is a critical yet challenging research area. Recently, Human Phenotype Ontology (HPO)-based semantic similarity has been affectively and widely used to identify causative genes and diseases. However, current phenotype similarity measurements just consider the annotations and hierarchy structure of HPO, neglecting the definition description of phenotype terms. In this paper, we propose a novel phenotype similarity measurement, termed as DisPheno, which adequately incorporates the definition of phenotype terms in addition to HPO structure and annotations to measure the similarity between phenotype terms. DisPheno also integrates phenotype term associations into phenotype-set similarity measurement using gene and disease annotations of phenotype terms. Compared with five existing state-of-the-art methods, DisPheno shows great performance in HPO-based phenotype semantic similarity measurement and improves the efficiency of disease
Unsere breite Palette Geheimratskäse diagnostischen Spielbank Esplanade und Lösungen bieten wertvolle Unterstützung für die klinische Entscheidungsfindung. The severity of the flu season, which varies from year to year, and any spread of Ebola in Las Vegas Essen United States, will be critical factors in how strained hospital resources may become. Edward T. Flu season typically begins in November and peaks in January or February. Clinical Infectious Diseases ;57(S3):S-70 and Chief, Division of Infectious Disease Diagnostics, North Shore-Long Island Jewish Health System. North Shore-Long Island Jewish Research Institute; Original Assignee: North Shore-Long Island Jewish claims description 3; Candida infections Diseases claims description 3 heat treatment Methods description 1; heteroatoms Chemical ID=​ The woman had been to South Africa, more than 3, miles (5, km) from the Dr. Bruce Hirsch, an infectious diseases specialist at North Shore University. North Shore-Long Island Jewish Research ...
Faden, R.R., Taylor, H.A., Seiler, N.K. (2003). Consent and compensation: A social compact for smallpox vaccine policy in the event of an attack. Clinical Infectious Diseases, 36(12), 1547-1551.. ...
Shulman, ST; Bisno, AL; Clegg, HW; Gerber, MA; Kaplan, EL; Lee, G; Martin, JM; Van Beneden, C (Sep 9, 2012). Clinical Practice Guideline for the Diagnosis and Management of Group A Streptococcal Pharyngitis: 2012 Update by the Infectious Diseases Society of America.. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 55 (10): e86-102. doi:10.1093/cid/cis629. PMID 22965026. ...
h1,HIV Drug Appears to Prevent Infection Even in High-Risk Settings,/h1, ,p class=byline,by Hannah Guzik, California Health Report ,br /,September 2, 2015,/p, ,p,An HIV drug appears to prevent infection, even in high-risk settings, according to the results of a new study.,/p, ,p,Despite often not using condoms, none of the 657 patients taking the medication in the study had a new HIV infection during two-and-a-half years of observation by researchers at Kaiser Permanente San Francisco Medical Center. The results were ,a href=http://cid.oxfordjournals.org/content/early/2015/09/01/cid.civ778.full.pdf+html,published online,/a, Tuesday by the peer-reviewed journal Clinical Infectious Diseases.,/p, ,p,Nearly all - 99 percent - of the patients in the study were men who have sex with men.,/p, ,p,The results of the study also suggest that patients taking the drug, commercially called Truvada, may be less likely to use condoms than they were before, potentially making them more vulnerable to other ...
ORCID: https://orcid.org/0000-0002-9109-350X (2018) Bacterial risk factors for treatment failure and relapse among patients with isoniazid resistant tuberculosis. BMC Infectious Diseases, Vol 18, Issue 1. Thomas, J. E., Bunn, J., Kleanthous, H., Monath, T. P., Harding, M., Coward, W. A. and Weaver, L. T. (2004) Specific immunoglobulin A antibodies in maternal milk and delayed Helicobacter pylori colonization in Gambian infants. Clinical Infectious Diseases, Vol 39, Issue 8, pp. 1155-1160. Thomas, Jennifer Dolan, Hatcher, Cynthia P, Satterfield, Dara A, Theodore, M Jordan, Bach, Michelle C, Linscott, Kristin B, Zhao, Xin, Wang, Zin, Mair, Raydel, Schmink, Susanna, Arnold, Kathryn E, Stephens, David S, Harrison, Lee H, Hollick, Rosemary A, Andrade, Ana Lucia, Lamaro-Cardosa, Juliana, de Lemos, Ana Paula S, Gritzfeld, Jenna, Gordon, Stephen ...
Shlaes, D.M., Gerding, D.N., John Jr., J.F., et al. (1997) Society for Healthcare Epidemiology of America and Infectious Diseases Society of America Joint Committee on the Prevention of Antimicrobial Resistance Guidelines for the prevention of antimicrobial resistance in hospitals. Clinical Infectious Diseases, 25, 584-599.
Clinical Infectious Disease Specialists 2435 Fire Mesa St., Ste 120 • Las Vegas, NV 89128 702-968-2437 2610 W. Horizon Ridge, Ste. 103 • Henderson, NV 89052 702-586-0202. Dr. Rajat Sood MD, ...
Simon Collins, HIV i-Base. Experience of PrEP use outside a clinical trial in a high incidence population were presented from a retrospective analysis of people accessing care at the Kaiser Permanente Medical Centre in San Francisco, California.. This analysis described all patients at the centre who were evaluated for and started on PrEP from July 2012 (when PrEP was approved in the US) to February 2015. The results were reported by Jonathan Volk and colleagues and are available as an open access paper in the 1 September edition of Clinical Infectious Diseases. [1]. Use was low during the first year (less than 5 to 10 people starting PrEP each month), steadily increasing to approximately 40 people a month at the end of the second year and reaching 50 to 60 for the last six months. Approximately 80% of the 1045 referrals led to an evaluation with at least one clinic visit (n=908) and of these, 657 individuals started PrEP. This cohort was 99% gay men, with one heterosexual women and one ...
Bakker, O. J., Van Santvoort, H. C., Van Brunschot, S., Geskus, R. B., Besselink, M. G., Bollen, T. L., … Timmer, R. (2012). Endoscopic Transgastric vs Surgical Necrosectomy for Infected Necrotizing Pancreatitis: A Randomized Trial. JAMA, 307(10), 1053-1061. doi:10.1001/jama.2012.276. Baron, T.H., & Morgan, D.E. (1999). Acute necrotizing pancreatitis The New England journal of medicine, 340 (18), 1412-1417. Beger, H.G. (1986). Bacterial contamination of pancreatic necrosis. A prospective clinical study. Gastroenterology, 91 (2), 433-438. Bradley, E. L. (1993). A Clinically Based Classification System for Acute Pancreatitis: Summary of the International Symposium on Acute Pancreatitis. Archive Surgery, 128(5), 586590. doi:10.1001/archsurg.1993.01420170122019. Chiu, C. H., Lin, T.Y., & Wu, J. L. (1996). Acute Pancreatitis Associated with Streptococcal Toxic Shock Syndrome, Clinical Infectious Diseases, 22(4), 724-726. doi:/10.1093/clinids/22.4.724. Cusack, T. P., Ashley, E. A., Ling, C. L., ...
In addition to the history and physical examination, clinical diagnosis of CNS infections requires a spinal fluid analysis combined with neuroimaging using either magnetic resonance imaging (MRI) or computed tomography (CT) scan. Microbiologic diagnosis of bacterial infections frequently is made using Gram stain and culture of spinal fluid and blood. Polymerase chain reaction (PCR) assays and serologic tests are also useful. Antimicrobial therapy requires that the antibiotics be bactericidal and that they penetrate the blood-brain barrier. Some CNS infections, such as a brain abscess, often require surgical drainage. ...
aDepartment of Infectious Disease Epidemiology, TB Modelling Group, TB Centre, Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine bDepartment of Infection and Population Health, Centre for Infectious Disease Epidemiology, University College London, London, UK cDepartment of Medicine, Institute of Infectious Disease and Molecular Medicine, University of Cape Town dDivision of Clinical Pharmacology, University of Cape Town, Cape Town, South Africa eTuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA fCentre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa gDepartment of Medicine, Imperial College London hThe Francis Crick Institute Mill Hill Laboratory, London, UK iInstitute of Infectious Diseases and ...
Adachi K, Xu J, Ank B, Watts HD, Mofenson LM, Pilotto JH, Joao E, Santos B, Fonseca R, Kreitchmann R et al.. 2017. Cytomegalovirus Urinary Shedding in HIV-infected Pregnant Women and Congenital Cytomegalovirus Infection.. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. Abstract ...
Adachi K, Xu J, Ank B, Watts HD, Mofenson LM, Pilotto JH, Joao E, Santos B, Fonseca R, Kreitchmann R et al.. 2017. Cytomegalovirus Urinary Shedding in HIV-infected Pregnant Women and Congenital Cytomegalovirus Infection.. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. Abstract ...
by Physicians Weekly , Dec 13, 2012. Recent estimates suggest that the direct annual costs of sinusitis are approximately $5.8 billion in the United States, and nearly one in seven Americans is diagnosed with a sinus infection every year. Rhinosinusitis is one of the most common reasons patients seek medical help. It ranks among the top five reasons for antibiotic prescriptions for adults. However, 90% to 98% of patients presenting with symptoms of sinusitis have viral causes and will not benefit from antibiotics. The overuse of antibiotics among this population has contributed largely to the emergence of antimicrobial resistance. The Need for Guidance Clinicians need clear guidance on how to treat patients with rhinosinusitis and on how to differentiate viral from bacterial infections, says Thomas M. File, Jr., MD. In the April 15, 2012 issue of Clinical Infectious Diseases, Dr. File coauthored guidelines from the Infectious Disease Society of America (IDSA) on acute bacterial rhinosinusitis ...
The devastation of the last two years of the Ebola crisis in West Africa was made all the more daunting by a predictable aspect of its toll. The health workers who represented the best hope of controlling the outbreak were also at the greatest risk of illness and death. By the dwindling days of the epidemic across Guinea, Sierra Leone and Liberia, at least 500 of the more than 11,300 people who had lost their lives to virus were health workers.. That illness is an occupational hazard on the front lines of health care is not new, a Clinical Infectious Diseases supplement on tuberculosis control in health settings notes, but it continues to be neglected at every level. And, as authors of one article note, while the death toll of the 2014-2015 Ebola outbreak is replicated by tuberculosis every three days worldwide, health workers in high burden and low-resource settings face risks at least three times those of the general population. They include doctors, nurses, counselors, administrative staff, ...
After an airline passenger vomited on a plane, almost half of flight attendants who subsequently worked on the same plane developed gastrointestinal symptoms, and two who submitted stool samples were infected with norovirus, according to a study in Clinical Infectious Diseases. Researchers analyzed data from nine flights over 6 days of a Boeing 777-200 after a passenger vomited on the plane and flight attendants subsequently began getting sick. Eight of the flights were international legs that lasted longer than 10 hours. Of the 77 attendants who worked those flights, 63 provided information, and, of those, 27 (43%) met the case definition for gastroenteritis. The attack rate rose to 79% for crew supervisors and declined over time. Two patients who worked different flights provided stool samples, both of which tested positive for norovirus. The authors write, Findings from our investigation suggest that flight attendants were infected through their work on the airplane, with transmission ...
Source: Donald A. Henderson, etal, Smallpox Vaccination in 2003: Key Information for Clinicians, Clinical Infectious Diseases, Vol. 36: 883-902, (2003).. Now, four months after the campaign has commenced, impediments to participation have brought it to a virtual standstill. The program has proven to be less popular, medically riskier and more expensive than anticipated. Many health care professionals maintain the benefits of the program do not justify the risks and recommend it be delayed until there is clear evidence a smallpox attack is imminent.[3] Furthermore, more than a dozen states have suspended vaccination until more is learned about its recent link to myocarditis and heart attacks.[4]. What measures can be taken to bolster this policys waning success, and should they be taken? Initiating a large-scale vaccination effort against a disease that is no longer a natural threat presents many challenges for the medical community. A look at the history of smallpox in the U.S. and the ...
The Holy Grail of neurosyphilis is a specific and sensitive diagnostic test that can be done on cerebrospinal fluid (CSF) to diagnosis this disease. The goal of the study by Vanhaecke et al, reported in this issue of Clinical Infectious Diseases, was to study the utility of polymerase chain reaction (PCR) for the tpp47 gene of Treponema pallidum in 40 patients with well-documented neurosyphilis [1]. But, as the authors themselves state, Neurosyphilis has multiple clinical presentations, and there is no consensus concerning its definition. For reasons that I will explore below, confusion over the diagnosis of neurosyphilis leaves this reader uncertain as to which patients in Vanhaecke et als series of 40 cases actually had neurosyphilis. In this context, the addition of PCR does not look to be very helpful. During the incubation period leading up to the appearance of a chancre, and while the chancre is present, T. pallidum disseminates widely throughout the body. Organisms may be found in ...
Patients are not at increased risk of Guillain-Barre syndrome in the six-week period after vaccination with any vaccine, including influenza, according to a Kaiser Permanente study published in Clinical Infectious Diseases.. The retrospective study by researchers at the Kaiser Permanente Vaccine Study Center spanned 13 years and was controlled for seasonality.. If there is a risk of Guillain-Barré syndrome following any vaccine, including influenza vaccines, it is extremely low, said Roger Baxter, MD, co-director of the Kaiser Permanente Vaccine Study Center.. During the 13-year period (1994-2006), 415 confirmed cases of Guillain-Barré syndrome were observed. Within this group, the researchers found only 25 patients had received any vaccine in the six weeks prior to the onset of the disease. The study also found that 277 patients had a respiratory or gastrointestinal illness in the 90 days preceding the onset.. Guillain-Barré syndrome is an acute disease thought to be an autoimmune disorder ...
For a number of years it was widely felt that the first of the new so-called 5th Generation, or anti-MRSA cephalosporins would be ceftobiprole. This drug, a joint venture by the Swiss company Basilea and Johnson & Johnson had come under some fire from the FDA (see my blog entry from Dec 31, 2009) and now looks like it has pretty much been abandoned, at least here in the US. Even in Canada, where it had been approved for complicated skin and skin structure infections (cSSSI), as of April 2010 sales have been discontinued.. While all of the hoopla surrounded ceftobiprole, another drug was pretty quietly making its way through the clinical trial process; ceftaroline. Ceftaroline is being developed by Cerexa Inc., a wholly owned subsidiary of New Yorks Forest Pharmaceuticals under license from Takeda in Japan. This month has proven to be an important one for this antibiotic. In the September 15 issue of Clinical Infectious Diseases the results of their cSSSI trial, named the CANVAS study have ...
Originally published by CIDRAP News May 31. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) appears to be spreading further into the community and healthcare settings in Denmark, researchers reported yesterday in Clinical Infectious Diseases.. In the study, researchers evaluated data on all Danish patients who were registered as having had an episode of MRSA bloodstream infection (BSI) or skin and soft tissue infection (SSTI) from 2010 through 2015. Using molecular sequencing tests, they set out to determine how many were caused by LA-MRSA clonal complex 398 (CC398), which has been causing an increasing number of human infections in Denmark and other European countries with industrial pig production. While SSTIs caused by LA-MRSA CC398 have been studied and are mainly associated with livestock workers, less is known about the strains impact on BSIs.. The researchers also wanted to compare LA-MRSA CC398 BSI cases to SSTI cases caused by the strain and to BSI cases ...
PubMedID: 25995207 | Clinical Features of Patients With Ebola Virus Disease in Sierra Leone. | Clinical Infectious Diseases | 8/15/2015
Zanger, P., Nurjadi, D., Gaile, M., Gabrysch, S. and Kremsner, P.G. (2012) Hormonal Contraceptive Use and Persistent Staphylococcus aureus Nasal Carriage. Clinical Infectious Diseases, 55, 1625-1632.
The Src family kinase (SFK) member SRC is a major target in drug development because it is activated in many human cancers, yet deleterious SRC germline mutations have not been reported. We used genome sequencing and Human Phenotype Ontology patient coding to identify a gain-of-function mutation in SRC causing thrombocytopenia, myelofibrosis, bleeding, and bone pathologies in nine cases. Modeling of the E527K substitution predicts loss of SRCs self-inhibitory capacity, which we confirmed with in vitro studies showing increased SRC kinase activity and enhanced Tyr419 phosphorylation in COS-7 cells overexpressing E527K SRC. The active form of SRC predominates in patients platelets, resulting in enhanced overall tyrosine phosphorylation. Patients with myelofibrosis have hypercellular bone marrow with trilineage dysplasia, and their stem cells grown in vitro form more myeloid and megakaryocyte (MK) colonies than control cells. These MKs generate platelets that are dysmorphic, low in number, highly ...
These examples vividly illustrate how technology has brought beneficial change to entertainment, retailing and education, so the question is why cant we use technology to change the body politic?. As the founder of Social Revolution, I am trying to do just that. Social Revolution aims to harness innovative ideas through crowdsourcing, and distill them into a Business Plan for U.S.A. to help propel the country forward.. Were going to crowdsource ideas in five key areas - education, healthcare, business, finance and government. All these sectors are clearly ripe for a major disruption.. To manage the idea stream, were relying on an innovative crowdsourcing platform from Pleasanton, Calif.-based Spigit. If youre a company or individual that wants real change, and have a cogent idea about how to implement it, we want to hear from you. If youre using technology to make things better, we need to hear from you.. At Social Revolution, we believe that applying the new technologies offered by ...
Windows SharePoint Services manages what a user account can do with permissions. There is a large list of set permissions that are available at the web application level. These permissions, when applied to a user account, govern what it can do. Permissions are generally grouped together in what are called permission levels, to be applied to users based on the type of role they will play, or tasks they will perform in Windows SharePoint Services. There are a few default permission levels, such as full control (which usually is applied to administrators who require all permissions to be enabled), or contribute (which is usually applied to users who will be viewing content, adding content, editing content, etc.). Individual permissions cant be applied to users directly, but permission levels can. For the convenience of administrators, in addition to permission levels putting together useful permissions into role based combinations, Windows SharePoint Services uses another convention; the ...
TY - JOUR. T1 - Beyond knockouts: cre resources for conditional mutagenesis. AU - Murray, Stephen A. AU - Eppig, Janan. AU - Smedley, Damian. AU - Simpson, Elizabeth M. AU - Rosenthal, Nadia Alicia. PY - 2012. Y1 - 2012. N2 - With the effort of the International Phenotyping Consortium to produce thousands of strains with conditional potential gathering steam, there is growing recognition that it must be supported by a rich toolbox of cre driver strains. The approaches to build cre strains have evolved in both sophistication and reliability, replacing first-generation strains with tools that can target individual cell populations with incredible precision and specificity. The modest set of cre drivers generated by individual labs over the past 15+ years is now growing rapidly, thanks to a number of large-scale projects to produce new cre strains for the community. The power of this growing resource, however, depends upon the proper deep characterization of strain function, as even the best ...
Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, data integration and mining capabilities. Terminology resources devised for multiple purposes inherently diverge in content and structure. A major issue of biomedical data integration is the development of overlapping terms, ambiguous classifications and inconsistencies represented across databases and publications. The disease ontology (DO) was developed over the past decade to address data integration, standardization and annotation issues for human disease data. We have established a DO cancer project to be a focused view of cancer terms within the DO. The DO cancer project mapped 386 cancer terms from the Catalogue of Somatic Mutations in Cancer (COSMIC), The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium, Therapeutically Applicable
Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts. In this paper, we discuss a fact repository for causal chains of disease based on the disease ontology. It could be a valuable knowledge base for advanced medical information systems. We developed the fact repository for causal chains of diseases based on our disease ontology and abnormality ontology. This section summarizes these two ontologies. It is developed as linked data so that information scientists can access it using SPARQL queries
A free online platform is being developed that uses a crowdsourcing approach to make public gene expression data more accessible to biomedical researchers.
The trend of open collaboration has led to innovation across multiple industries. For decades, big pharma has been known as conservative and slow to change. Today however, there is a growing movement toward open access and crowdsourcing scientific information to accelerate research and development.
The trend of open collaboration has led to innovation across multiple industries. For decades, big pharma has been known as conservative and slow to change. Today however, there is a growing movement toward open access and crowdsourcing scientific information to accelerate research and development.
Are there additional ways that biochemists could benefit from crowdsourcing? What if there was a website for biochemists to compare notes in their roles as customers regarding their experiences with journals and with vendors. For example, 2011 has been a good year for my research group in terms of paper publishing. Four original research articles made it through the evaluation process, and two more are about to be submitted. Each of these will appear in a different journal, and my experience with each journal was distinct. The manuscript-submission websites varied in terms of ease of use, clarity and time required to complete the submission; the time for review varied significantly; the quality of the reviews differed; and each paper was subject to a different level of academic editor oversight. Scientists gossip about such differences, but what if there were a Biochemadvisor.com website with reviews of our experiences as customers of different journals? Whenever I am planning a trip to a new ...
Though DARPA very well may reap this reward, the agency is getting something else which is perhaps even more valuable - its collecting the hundreds of design ideas being submitted via contest entries and comments. Unlike typical crowdsourcing contests which ask participants to submit and/or vote on entries, the DARPA contest allows contestants to revise and resubmit their entries as often as they like, encouraging frequent comments from fellow participants at several stages along the way. The DARPA contest does have a voting component, though this has little to do with selecting a winner; that will be done by DARPA and Local Motors around March 15th. Instead, the votes, like the ubiquitous comments, are just part of the feedback generated by the contestants. In essence, the contest has produced a storehouse of collective intelligence and know-how that DARPA can return to for future projects whenever it likes ...
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are ...
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are ...
Extracellular matrices are essential for cellular and organismal function. Recent genome-wide and phenome-wide association studies started to reveal a broad spectrum of phenotypes associated with genetic variants. However, the phenome or spectrum of all phenotypes associated with genetic variants in extracellular matrix genes is unknown. Here, we analyzed over two million recorded genotype-to-phenotype relationships across multiple species to define their extracellular matrix phenomes. By using the previously defined matrisomes of humans, mice, zebrafish, Drosophila, and C. elegans, we found that the extracellular matrix phenome comprises of 3-10% of the entire phenome. Collagens (COL1A1, COL2A1) and fibrillin (FBN1) are each associated with ,150 distinct phenotypes in humans, whereas collagen COL4A1, Wnt- and sonic hedgehog (shh) signaling are predominantly associated in other species. We determined the phenotypic fingerprints of matrisome genes and found that MSTN, CTSD, LAMB2, HSPG2, and ...
Description: Ontology alignment, the task of identifying mappings between ontologies, is a key task for knowledge sharing between applications that use different ontologies. Manual alignment is time-consuming and difficult when dealing with large ontologies, which are common in biomedical domain, while automatic alignment shows low coverage. We present a tool with user-friendly GUI for semi-automatic ontology alignment, called NViz. It helps human experts focus on pairs of ontology clusters that are likely to have missing mappings. NViz utilizes a state of-the-art system of ontology alignment, called BOAT, and a hierarchical clustering method. Institution: Nanyang Technological University Contacts: Watson W.K. Chua, Jung-jae Kim, Bui Duc Hieu Home Page: http://nlp.sce.ntu.edu.sg/wiki/projects/nviz/NViz.html ...
The following is a list of libraries from ProgrammableWebs Library Directory that matched your search term. Although there many different interpretations of the word library among software developers, ProgrammableWeb adheres to a specific definition so as to clearly distinguish libraries from SDKs and frameworks in a way that will facilitate clean search results. In ProgrammableWebs parlance, the term library is strictly used to describe a platform-specific software tool that, when installed, results in the provisioning a specific API. Conversely, SDKs are exclusively for consuming APIs and Frameworks are agnostic to specific APIs. If you think a library, SDK, API, or other asset is missing from our directory, be sure to check our guidelines for making contributions to ProgrammableWeb ...
The administrator can assign their permission. Roles Permissions- Go to System Settings > Roles Permissions here we can create different Roles for staff users and then assign different user permission to this Role. To add new role enter Role Name then click on Save button all existing roles can be see from right side of this page. By default in Iskool School you will get 6 user roles SuperAdmin, Admin, Teacher, Accountant, Librarian, Receptionist. You can edit name or permission of these roles except SuperAdmin. To assign permission click on Assign Permission button from Action column. At this page you can see Module wise different Features and their different Permissions. Carefully assign different permissions on roles. After assigning permission, check where it is effecting in system. There are 4 types of permissions present here View, Add, Edit and Delete. Here note that if you are assigning Add/Edit or Delete permission then View permission should be given obviously if you have not given ...
There are currently no human or mouse genes associated with this disease in the MGI database. Synonyms: Andermann syndrome; Charlevoix disease; corpus callosum agenesis-neuronopathy syndrome
There are currently no human or mouse genes associated with this disease in the MGI database. Synonyms: Band-shaped keratopathy
I. Taxonomy of the producing organism, fermentation, HPLC analysis and biological activities". The Journal of Antibiotics. 46 ( ... "Finto: MeSH: Streptomyces antibioticus". finto: Finnish Thesaurus and Ontology Service. Retrieved 10 August 2015. Atta HM ( ... isolation and biological properties". Journal of Saudi Chemical Society. 19 (1): 12-22. doi:10.1016/j.jscs.2011.12.011. Oh DC, ...
Ontology-Based Integration and Preprocessing of Distributed Data. Biological and Medical Data Analysis. Springer Berlin ... The Protégé (software) is the standard tool for constructing an ontology.[citation needed] In general, the use of ontologies ... This application forms the ontology. From there, the ontology can be used to analyze data and process results. Fuzzy ... The idea is to build a dedicated ontology, which explains on a higher level what the problem is about. In regards to semantic ...
Biological database Biological data visualization InterMine - an open-source biological data warehouse system Doms, A.; ... constructed a lattice work of three ontologies (for anatomy and development of model organisms) on a novel framework ontology ... For example, various 'omics' datasets may be integrated to provide biological insights into biological systems. Examples ... in this ontology would return the heart plans for each of the vertebrate species whose ontologies were included. The stated ...
ISBN 0-7914-6938-7 The Species Problem: Biological Species, Ontology, and the Metaphysics of Biology. Lexington Books. 2004. ...
The Open Biological and Biomedical Ontologies: a community-based platform that integrates databases and tools of gene ontology ... 34, Database issue D344-D348 Gene Ontology Consortium (GOC): an international collaboration on developing gene ontology and ... The GO browser provides links to genes organised by gene ontology terms and the Expression Data Viewer provides both the access ... It also provides tools to search or browse the database with genes, species, sequences, orthologous groups, gene ontology (GO) ...
This augmented ontology increases the explanatory power of this conception. Descriptive aspect Most descriptions of mechanisms ... For example, natural selection is a mechanism of biological evolution; other mechanisms of evolution include genetic drift, ... For example, one influential characterization of neuro- and molecular biological mechanisms by Peter K. Machamer, Lindley ... There are three distinguishable aspects of this characterization: Ontic aspect The ontic constituency of biological mechanisms ...
Gene ontology analysis of both Hsp90A and Hsp90B interactomes indicate that each paralogs is associated with unique biological ... Jameel A, Skilton RA, Campbell TA, Chander SK, Coombes RC, Luqmani YA (Feb 1992). "Clinical and biological significance of ... Assembly of the reovirus cell attachment protein". The Journal of Biological Chemistry. 276 (35): 32822-7. doi:10.1074/jbc. ... The Journal of Biological Chemistry. 276 (18): 14649-57. doi:10.1074/jbc.M100200200. PMID 11297531. Peng Y, Chen L, Li C, Lu W ...
Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. ZFIN is based at the ... The Zebrafish Information Network (ZFIN) is an online biological database of information about the zebrafish (Danio rerio). The ... ZFIN's relational database interface provides query forms and display pages for the following biological data types: Genes, ... as well as biological resources such as laboratory protocols, a gene nomenclature guide, and anatomy information a relational ...
This theoretical representation of the data is called an ontology. The ontology is the theory behind the database's design. In ... biological information etc. Therefore, the data to be stored in the database must be determined in cooperation with a person ...
These models are actively undergoing a curation process aiming to provide annotations with biological ontologies such as Gene ... A repository of several hundred biological models encoded into CellML can be found on the CellML community website at CellML ... Ontology and to validate the models against standards of unit balance and biophysical constrains such as conservation of mass, ...
General Hymenoptera Anatomy Ontology project Hymenoptera Anatomy Glossary Hymenoptera Forum German and International ... Mayhew, Peter J. (2007). "Why are there so many insect species? Perspectives from fossils and phylogenies". Biological Reviews ... Biological Journal of the Linnean Society. 79 (2): 245-275. doi:10.1046/j.1095-8312.2003.00233.x. Schulmeister, S. "Symphyta". ... a biological image database Order Hymenoptera Insect Life Forms Systematics Hymenopteran Systematics Hymenoptera Online 1000+ ...
... aimed at developing gene ontology terms that capture biological processes occurring during the interactions between organisms, ... In addition, researchers working with P. syringae have played an integral role in the Plant-Associated Microbe Gene Ontology ... Since the 1970s, P. syringae has been implicated as an atmospheric "biological ice nucleator", with airborne bacteria serving ... 2010). "Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology". Microbiology ...
... fluxomic methods are considered a key enabling technology due to their unique position in the ontology of biological processes ... Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. ... Systems biology recognizes the complexity of biological systems and has the broader goal of explaining and predicting this ... While metabolomics can provide instantaneous information on the metabolites in a biological sample, metabolism is a dynamic ...
Chemical engineering is the application of chemical, physical and biological sciences to the process of converting raw ... "Ontology driven software engineering". 2012 25th IEEE Canadian Conference on Electrical and Computer Engineering (CCECE): 1-4. ...
... made by philosopher Hubert Dreyfus has marked new directions for integration of neurosciences with an embodied ontology. The ... Biological Research. 36 (1): 27-65. doi:10.4067/s0716-97602003000100005. PMID 12795206. Gallagher, Shaun (2009). " ...
"RNA Ontology Consortium (ROC)". ROC.bgsu.edu. Archived from the original on January 22, 2009. Birmingham A, Clemente JC, Desai ... Section D, Biological Crystallography. 66 (Pt 2): 213-21. doi:10.1107/S0907444909052925. PMC 2815670. PMID 20124702. Chen VB, ... Section D, Biological Crystallography. 66 (Pt 2): 213-21. doi:10.1107/S0907444909052925. PMC 2815670. PMID 20124702. Chen VB, ... Section D, Biological Crystallography. 66 (Pt 1): 12-21. doi:10.1107/S0907444909042073. PMC 2803126. PMID 20057044. Read RJ, ...
He did work on ontology translation and on semantic web services. McDermott was a prime mover, with James Hendler and others, ... and that therefore biological brains probably don't either. This interest culminated in the publication in 2001 of a book on ...
Gene ontology based enrichment analysis are provided by DAVID and gene set enrichment analysis (GSEA), pathway based analysis ... If two genes have fused, it is predicted that they have similar biological functions that make such co-regulation advantageous ... Together these measurement modalities endeavor to quantitate the various biological processes and improve our understanding of ... mostly multiplex techniques to measure the abundance of many or all gene products such as mRNAs or proteins within a biological ...
"The ontologies of industrial ecology?," Progress in Industrial Ecology, An International Journal 3, no. 1 (2006): 28-40. " ... 02 (2000). "Understanding industrial ecology from a biological systems perspective," co-written with W.E.Cooper, Environmental ...
While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Cytoscape can ... Import gene functional annotations from the Gene Ontology (GO) and KEGG databases. Directly import GO terms and annotations ...
"Biological Magnetic Resonance Bank". bmrb.wisc.edu. Berman, H. M. (January 2008). "The Protein Data Bank: a historical ... such as Gene ontology. Two forces converged to initiate the PDB: a small but growing collection of sets of protein structure ... The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as ... Biological Magnetic Resonance Data Bank (USA) wwPDB Documentation-documentation on both the PDB and PDBML file formats Looking ...
... exists at the intersection of several broad fields: biological science - includes bench sciences such as ... Imaging facilities design Imaging vocabularies and ontologies Data mining from medical images databases Transforming the ...
Similarity Calculator can be used to compute how well related two geographic concepts are in the Geo-Net-PT ontology. The OSM ... assessment with biological features and issues". Briefings in Bioinformatics. 13 (5): 569-585. doi:10.1093/bib/bbr066. PMID ... Semantic similarity measures have been applied and developed in biomedical ontologies. They are mainly used to compare genes ... Dong, Hai (2009). "A Hybrid Concept Similarity Measure Model for Ontology Environment". On the Move to Meaningful Internet ...
Acharya S, Saha S, Pradhan P (December 2018). "Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: ... The Journal of Biological Chemistry. 277 (33): 29874-80. doi:10.1074/jbc.M203915200. PMID 12019269. Grenier JM, Wang L, Manji ... Acharya S, Saha S, Pradhan P (December 2018). "Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: ... Acharya S, Saha S, Pradhan P (December 2018). "Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: ...
... ontology, epistemology, philosophy of science and ethics. His systemism includes the CESM (composition-environment-structure- ... biological dynamics and neurostimulation. Gerhard Chroust (born 1941) Austrian systems scientist, and Professor Emeritus for ...
A Biositemap is a way for a biomedical research institution of organisation to show how biological information is distributed ... Official website Biomedical Resource Ontology Biositemaps online editor. ... and Biomedical Resource Ontology (BRO). The IM is responsible for defining the data held in the metafields and the BRO controls ... Name Description URL Stage of development Organization Resource Ontology Label Keywords License Up-to-date documentation on the ...
This method can be used for any biological molecule in principle and is not restricted to serum antigens, nor is it required to ... ". "Radioimmunoassay". Ontology Search.{{cite web}}: CS1 maint: url-status (link) Smith, John. "Solution radioimmunoassay of ...
Series B, Biological Sciences. 136 (884): 378-388. Bibcode:1949RSPSB.136..378F. doi:10.1098/rspb.1949.0031. ISSN 0080-4649. ... Gene Ontology - GO:0005344: oxygen carrier activity. ... Series B, Containing Papers of a Biological Character. 111 (772 ... Globin enjoys a large biological distribution, not only occurring among more than 9 different phyla of animals but occurring in ... Lamy, Jean; Truchot, J.-P; Gilles, R; International Union of Biological Sciences; Section of Comparative Physiology and ...
Biodiversitas Journal of Biological Diversity. Talavera, Manalo, Baybay, Saludario, Dizon, Mauro, Porquerino, Novela, Yakit, ... Novellino, D. (2003). 'Contrasting landscapes, conflicting ontologies'. Assessing environmental conservation on Palawan Island ...
Gamble A (2018-07-01). "Biological Abstracts (Clarivate Analytics)". The Charleston Advisor. 20 (1): 19-25. doi:10.5260/chara. ... Semantics and Ontologies. 4 (1/2): 4. doi:10.1504/IJMSO.2009.026249. ISSN 1744-2621. Diospatonyi I, Horvai G, Braun T ( ...
Logic and Ontology) Lenn Evan Goodman (২০০৩), Islamic Humanism, পৃষ্ঠা ১৫৫, Oxford University Press, আইএসবিএন ০-১৯-৫১৩৫৮০-৬ ... "Al-Jahiz And the Rise of Biological Evolutionism", The Islamic Quarterly। London। Ehsan Masood, [১], Islam's evolutionary ... Logic and Ontology) Lenn Evan Goodman (২০০৩), Islamic Humanism, পৃষ্ঠা ১৫৫, Oxford University Press, আইএসবিএন ০-১৯-৫১৩৫৮০-৬ ... Logic and Ontology) Lenn Evan Goodman (২০০৩), Islamic Humanism, পৃষ্ঠা ১৫৫, Oxford University Press, আইএসবিএন ০-১৯-৫১৩৫৮০-৬ ...
The most general ontologies are called upper ontologies, which attempt to provide a foundation for all other knowledge and act ... similar to the way it is defined in biological intelligence. No established unifying theory or paradigm has guided AI research ... The semantics of an ontology is typically represented in description logic, such as the Web Ontology Language. AI research has ... A representation of "what exists" is an ontology: the set of objects, relations, concepts, and properties formally described so ...
... ontology of topics in medical education TNM Classification of Malignant Tumors Unified Medical Language System (UMLS) Victoria ... US billing system for outpatient services Biological database Classification of mental disorders Clinical coder German ...
This form of naturalism says that our psychological and biological limitations and abilities are relevant to the study of human ... Naturalized epistemology at PhilPapers Naturalized epistemology at the Indiana Philosophy Ontology Project "Naturalized ...
a critical examination of reductive accounts of the meaning and ontology of dispositional discourse Available for consultation ... chemical and biological kinds, for example), and that at least some natural kinds have distinctive dispositions (for example, ...
The length of inert appendages (hair, claws, nails, teeth) of biological specimens, in the direction of growth.[citation needed ... Swat, MJ; Grenon, P; Wimalaratne, S (2016). "ProbOnto: ontology and knowledge base of probability distributions". ...
This is accomplished because of the creation of a common vocabulary, called ontology, for varied search terms and varied data. ... Disciplines included in this index are agriculture, biological sciences, engineering, medical and life sciences, physical and ...
... and Ontology", 1950 W. V. O. Quine, "Two Dogmas of Empiricism", 1951 Errol Harris, The Foundations of Metaphysics in Science, ... Philosophy of Biological Science, 1974 Stephen Jay Gould and Richard Lewontin, "The Spandrels of San Marco and the Panglossian ... Biological Complexity and Integrative Pluralism, 2003 Denis Noble, The Music of Life: Biology Beyond the Genome, 2006 Samir ... The Growth of Biological Thought: Diversity, Evolution, and Inheritance, 1982 Elliott Sober, The Nature of Selection: ...
Store high resolution CT data Create ontologies for updating and populating matrix cells. These tasks are difficult or ... Biological Sciences and Computer and Information Science and Engineering. The significance of the scientific work on MorphoBank ...
"Weaving Traditional Ecological Knowledge into Biological Education: A Call to Action," Oxford Journals: Science & Mathematics, ... ontology in which the sacred in nature is wholly immanent. But Wilber's views are also criticized as not including an in-depth ... if other species are biological kin, not resources; or if the planet is our mother, not an opportunity-then we will treat each ...
ISBN 978-3-639-20265-6 Michael Eldred, Social Ontology: Recasting Political Philosophy Through a Phenomenology of Whoness Ontos ... biological species). Foucault originated and developed the concept of "docile bodies" in his book Discipline and Punish. He ...
... a text mining integrator for biological pathway visualizations". Bioinformatics. 26 (12): i374-81. doi:10.1093/BIOINFORMATICS/ ... machine reading of the cancer literature with probabilistic reasoning across cancer claims using specially-designed ontologies ... "Event extraction across multiple levels of biological organization". Bioinformatics. 28 (18): i575-i581. doi:10.1093/ ...
Gene ontology enrichment analysis reveals an association between progranulin and notch receptor signaling. Granulin has also ... The Journal of Biological Chemistry. 267 (18): 13073-13078. doi:10.1016/S0021-9258(18)42382-4. PMID 1618805. Bateman A, ... The Journal of Biological Chemistry. 268 (15): 10863-10869. doi:10.1016/S0021-9258(18)82064-6. PMID 8496151. Andersson B, ...
A "value-free" ontology like materialism leads of necessity to living "without value". Any attempt to remedy the situation by a ... Gebser emphasized that biological evolution is an enclosing process which particularizes a species to a limited environment. ... Mechanized slaughter of two world wars and the new atomic weapons exemplified and symbolized the expression of the ontology of ...
Its character is an interdisciplinary though, and focused on issues of an ontology aspect as well as issues concerning mutual ... The PAU's Natural Sciences section brings together representatives of the biological, agricultural, and geological sciences. ...
... ogenesis is the biological process by which steroids are generated from cholesterol and changed into other steroids. The ... "C19-steroid hormone biosynthetic pathway - Ontology Browser - Rat Genome Database". rgd.mcw.edu. Edgren RA, Stanczyk FZ (Dec ... Steroids have two principal biological functions: as important components of cell membranes that alter membrane fluidity; and ... in biological tissue or fluid). The amount isolated depends on the analytical method, but is generally less than one microgram ...
I. Taxonomy of the producing organism, fermentation, HPLC analysis and biological activities". The Journal of Antibiotics. 46 ( ... "Finto: MeSH: Streptomyces antibioticus". finto: Finnish Thesaurus and Ontology Service. Retrieved 10 August 2015. Atta HM ( ... isolation and biological properties". Journal of Saudi Chemical Society. 19 (1): 12-22. doi:10.1016/j.jscs.2011.12.011. Oh DC, ...
K. - L. Ma, "ICBO_2018_77: Big Data Visualization", in International Conference on Biomedical Ontology (ICBO 2018), Corvallis, ...
P. Manda, Beasley, L., and Mohanty, S., "ICBO_2018_18: Taking a Dive: Experiments in Deep Learning for Automatic Ontology-based ... "in International Conference on Biomedical Ontology (ICBO 2018), 2018.*BibTex ... Annotation of Scientific Literature", in International Conference on Biomedical Ontology (ICBO 2018), 2018.*BibTex ...
Filters: First Letter Of Last Name is B and Author is Ramona Walls [Clear All Filters] ...
IP21: FoodON: A Global Farm-to-Fork Food Ontology. International Conference on Biomedical Ontology and BioCreative (ICBO ... D104: Updates to the AberOWL ontology repository. International Conference on Biomedical Ontology and BioCreative (ICBO ... IT702: To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO) ... International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). *Google Scholar ...
Ontology-Based Integration and Preprocessing of Distributed Data. Biological and Medical Data Analysis. Springer Berlin ... The Protégé (software) is the standard tool for constructing an ontology.[citation needed] In general, the use of ontologies ... This application forms the ontology. From there, the ontology can be used to analyze data and process results. Fuzzy ... The idea is to build a dedicated ontology, which explains on a higher level what the problem is about. In regards to semantic ...
biological_process. 20091. metabolic process. 12359. organic substance metabolic process. 11881. macromolecule metabolic ... Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data ... OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog ...
biological_process. 15040. cellular process. 14011. cellular localization. 3100. localization within membrane. 620. ... Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data ... OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog ...
Ontologies used. Radiological Sciences Lab (RSL), Stanford University. Contacts: David Paik and Nathan Baker and Srikanth Adiga ... Biological process. *Cellular component. *Molecular function. *Mouse/Human Gene dictionary (JAXMGD). Center for Computational ... Ontologies used. Human and Molecular Genetics Center (HMGC), Medical College of Wisconsin. Contacts: Simon Twigger and Joey ... Ontologies used. Butte Lab, Center for Biomedical Informatics Research, Stanford University. Contacts: Atul Butte and Shai Shen ...
GO enrichment was studied for the GO ontologies Biological Process and Molecular Function. We used Fishers exact test to ... Biological material. The fish used in this study from aquaria housed stocks were kept and sampled in accordance with the ... A gene was determined to be expressed if at least one sample of the two biological replicates reached a library size-normalized ... and gene ontology (GO) term analysis (Supplementary Tables 16-21) revealed that several of these variants are most probably ...
Support of Ontologies for Biological Information Retrieval and Web Services - Change Management in Biomedical Ontologies - ... Ontologies for genetics, proteomics, diseases, privacy etc. - Conceptual models for biological and medical data - Semantics in ... Ontology mapping, merging, and alignment * Semantic Web data querying and reasoning * Document analysis and semantic extraction ... Dynamic ontology generation and adaptation - Languages, tools and methodologies for semantic annotations of web data - ...
... provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae. ... Gene Ontology Term: purine nucleotide metabolic process. GO ID. GO:0006163 Aspect. Biological Process. Description. The ... Gene Ontology Term ID. Gene Ontology Term. Aspect. Annotation Extension. Evidence. Method. Source. Assigned On. Reference. ... Gene Ontology Term ID. Gene Ontology Term. Aspect. Annotation Extension. Evidence. Method. Source. Assigned On. Reference. ...
... analysis platform for target prioritisation and broad-based biological knowledge discovery-was used to perform Gene Ontology ( ... Loo J, Spittle DA, Newnham M. COVID-19, immunothrombosis and venous thromboembolism: biological mechanisms. Thorax. 2021 Jan;76 ... Gene ontology (GO) pathway enrichment analyses were performed on the yellow, black, and magenta modules using Target-mine ... Figure 5: Gene ontology (GO) terms and Reactome enrichment analysis of the key modules.. Chord plots depicting the enriched top ...
... provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae. ... Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares ... Gene Ontology Details Gene Ontology GO Annotations consist of four mandatory components: a gene product, a term from one of the ... three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference ...
Besides, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis ... Gene Ontology (GO) analysis of target genes for treatment. The -axis shows a significantly rich "biological process" category ... Besides, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis ... These network models have shown us their value in biological researches. At present, the research on diseases mainly includes ...
... often helping with biological interpretation of high-throughput experiments. Results of Gene Ontology (GO) and miRBase microRNA ... Zhang, B., Kirov, S. & Snoddy, J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. ... The collected study material includes clinical and epidemiological data and biological samples from normal and complicated ... Somatic placental duplications were significantly enriched in genes belonging to biological pathways relevant to fetal ...
The Gene Ontology project describes genes (gene products) using terms from three structured vocabularies: biological process, ... Gene Ontology OBO file source. By default, each time geWorkbench starts, it downloads the latest Gene Ontology OBO file from ... Ontology Selection. Not currently implemented, this is intended to allow the loading of alternate ontologies besides the three ... Gene Ontology Term Analysis , Gene Ontology Viewer , GenomeSpace , genSpace , Grid Services , GSEA , Hierarchical Clustering , ...
... showed a biological signature of oogenesis, cell cycle regulation, epigenetic regulation and RNA maturation. In situ ... Functional annotation by gene ontology (GO) showed a biological signature of oogenesis, cell cycle regulation, epigenetic ...
... an introduction to the basic concepts and applications of ontologies ... ... Ontologies as a critical framework for the vast amounts of data in the postgenomic era: ... Given the current explosion of biological data in multiple dimensions, it is time to think systematically about strategies and ... what ontologies are; how ontologies are used; and what ontologies could be (which focuses on how ontologies could be used for ...
Gene Ontology analysis and informatic software used. Request a detailed protocol Differential proteins (adjusted p-value≤0.05) ... Graphs display the mean with SEM of 3 biological replicates. (C) Heatmap depicting the Log2 abundance ratio in Xrn1 KO HEK293T ... C) Gene ontology molecular function overrepresentation analysis by Pantherdb, graphed according to their P value. (D) Graphs ... Three biological replicates of control, WT, and D219A muSOX expressing cells were then separated into nuclear and cytoplasmic ...
It combines parts of several biological ontologies, covering domains such as anatomy, disease and chemical compounds. The EFO ... NanoParticle Ontology (NPO). The NanoParticle Ontology (NPO ) is loaded in NCI Metathesaurus, on LexEVS, and on the NCI Term ... Ontology Alignment Evaluation Initiative (OAEI). The OAEI is a collaborative effort in the ontology alignment community aimed ... Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking. Proceedings of the 12th ...
Ontology:. GO: Biological Process QuickGO AmiGO Relationships is a type of: biological regulation regulation of developmental ...
Gene Ontology:. Cellular Component:. NONE FOUND Biological Process:. peptidoglycan biosynthetic process [ISS. ] ...
... the biological, the social, the mathematical, and so on. In addition, a regional ontology might tell us what makes it possible ... fundamental ontology. There is both plurality in the form of multiple regional ontologies and unity arising from the fact we ... For Heidegger, all of these regional ontologies have at least one thing in common: they are interested in what it means to be a ... The question of the meaning of being in general, as underlying all regional ontologies, is what Heidegger has in mind when he ...
Ppy-lineage beta cells was performed using ShinyGO v0.61 Gene Ontology Enrichment Analysis. GO biological process output to ... including DEG and Gene Ontology (GO) analyses. ...
Gene Ontology:. Cellular Component:. cellular_component [ND] Biological Process:. biological_process [ND] ... 2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS ...
To identify the components that contribute to virulence and unveil those biological processes potentially related to ... Table S2: Gene Ontology enrichment analysis for differentially expressed proteins.. Supplementary 3 . Table S3: pathway ... To examine which biological pathways were apparently altered, we carried out a pathway analysis. Enriched pathways were grouped ... Gene Ontology (GO) enrichment analysis was then performed for the differentially expressed proteins for the categories " ...
biological questions for research projects. content and functions for computational resource projects. **The tasks for which ... Yu Lin - Brucellosis Ontology // Presentation. Burke Squires - Flu-IDO // Presentation. *2:00pm Session 2 continued ... The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to ... The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a ...
  • so that any textual annotation created in Laboratree would also have corresponding ontology concept annotations. (bioontology.org)
  • GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies ( Molecular Function , Biological Process , and Cellular Component ), a reference, and an evidence code. (yeastgenome.org)
  • The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. (philpapers.org)
  • This document is aimed at anyone interested in the metadata, and specifically the ontology annotations, required to capture variables and experimental factors related to a transcriptomics experiment. (elixir-europe.org)
  • Disease model annotations are made by assigning terms from this ontology to alleles shown to recapitulate an aspect of a human disease in Drosophila melanogaster . (flybase.org)
  • Prevalent gene ontology annotations for any target gene and candidate regulators also present proof of practical partnership. (aurorapathway.com)
  • The Gene Ontology project describes genes (gene products) using terms from three structured vocabularies: biological process, cellular component and molecular function. (columbia.edu)
  • the biological role answers the question how a chemical is involved in molecular processes in an organism. (hmdb.ca)
  • The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component. (yellowcouch.org)
  • The GO has three domains: the molecular function of gene products, the biological process (i.e. roles) in which they are involved and their cellular component (location). (flybase.org)
  • The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus . (biomedcentral.com)
  • K. - L. Ma , " ICBO_2018_77: Big Data Visualization " , in International Conference on Biomedical Ontology (ICBO 2018) , Corvallis, OR, 2008. (oregonstate.edu)
  • P. Manda , Beasley, L. , and Mohanty, S. , " ICBO_2018_18: Taking a Dive: Experiments in Deep Learning for Automatic Ontology-based Annotation of Scientific Literature " , in International Conference on Biomedical Ontology (ICBO 2018) , 2018. (oregonstate.edu)
  • International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). (oregonstate.edu)
  • Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. (biomedcentral.com)
  • Biological pathways are reaction-networks of the biological processes within a cell, which can be classified into three categories: gene regulatory networks, metabolic pathways and signaling pathways. (biomedcentral.com)
  • Due to the nature of concurrency of biological pathways, Petri nets have been used to model and analyze biological pathways in many studies [ 1 - 9 ]. (biomedcentral.com)
  • HFPNe-based modeling allows users to easily understand biological networks with a graphical representation and reveals the expressiveness when representing the dynamic behaviors of sophisticated biological pathways. (biomedcentral.com)
  • To improve the maintainability and reusability of HFPNe models, we have developed an XML format called the Cell System Markup Language (CSML) [ 11 ], with the aim of creating an exchange format for modeling, visualizing, and simulating biological pathways. (biomedcentral.com)
  • CSML is based on HFPNe, a graphical language, for modeling and simulation of biological pathways. (biomedcentral.com)
  • Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were referenced to identify important biological functions and signaling pathways related to these differentially expressed ARGs. (researchsquare.com)
  • These genes were enriched in the biological processes and signaling pathways related to autophagy. (researchsquare.com)
  • the biological role is limited to cellular levls, and will not include role at system process level, such as a chemical which has a role in a disease. (hmdb.ca)
  • Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. (biomedcentral.com)
  • Individual CV Term Reports can be reached either by clicking on the controlled vocabulary term where it is displayed in a report page (e.g. the Gene Ontology: Function, Process, and Cellular component section of the Gene Report), or by using the Vocabularies tool (previously known as TermLink), which allows users to search directly for controlled vocabulary terms from any of the controlled vocabularies used by FlyBase. (flybase.org)
  • Homologues of the S. cerevisiae sensors of cellular en ergetic state Snf1 and TOR have been widely identified in fila mentous fungi. (aurorapathway.com)
  • In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. (bioontology.org)
  • 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. (philpapers.org)
  • The KB offers programmable (API) access to natural language phenotype descriptions annotated with formal ontologies so that machines can understand and compute with the semantics of descriptions at scale. (phenoscape.org)
  • Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes. (yeastgenome.org)
  • Besides, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to systematically explore the potential mechanisms of Tusizi-Sangjisheng treating TA. (hindawi.com)
  • The Gene Ontology Enrichment component, also referred to as the "GO Terms" component, allows the genes in any such "changed-gene" list to be characterized using the Gene Ontology terms annotated to them. (columbia.edu)
  • In statistical terms, the analysis tests the null hypothesis that, for any particular ontology term, there is no difference in the proportion of genes annotated to it in the reference list and the proportion annotated to it in the test list. (columbia.edu)
  • The Ontologizer code uses the "true path" property of the Gene Ontology in counting genes assigned to a term, by which a gene annotated to any term is considered also annotated to all that term's parent terms. (columbia.edu)
  • Subsequently, a mathematically supported subset of genes, comprising those most consistently involved in persisting pain, was analysed by means of computational functional genomics in the Gene Ontology knowledgebase. (helsinki.fi)
  • GOssTo and GOssToWeb are tools to calculate the semantic similarity between genes or terms in the Gene Ontology . (paccanarolab.org)
  • Semantic similarity calculations aim to provide a quantifiable measure of functional relatedness of genes by assessing the similarity of the Gene Ontology terms with which they are annotated. (paccanarolab.org)
  • We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. (thebiogrid.org)
  • Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the online Database for Annotation, Visualization and Integrated Discovery (DAVID) tool. (omicsdi.org)
  • Gene ontology (GO) analysis was used to identify characteristic the biological attributes of differentially expressed genes (DEGs) between PTC and normal samples. (omicsdi.org)
  • Based on the premise that co-expressed genes and/or closely interconnected proteins are more likely to be related to a particular biological function, researchers have made an effort to identify groups of genes, called modules [ 3 ], to gain a better understanding of the biological system of interest. (biomedcentral.com)
  • We have therefore developed SSIM (Semantic Similarity-Integrated approach for Modularization), to integrate various gene-gene pairwise relationships including similarity measures based on GO biological process (BP) annotation of genes, gene expression pattern, and protein-protein interaction information. (biomedcentral.com)
  • We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (philpapers.org)
  • Attendees will learn how to use R packages such as RPhenoscape to access a knowledgebase of ontology-linked phenotypes, build character matrices that take anatomical dependencies into account, and use these to construct stochastic character maps on a phylogeny. (phenoscape.org)
  • A similarly rich set of tools, such as ontologies, data annotation models, and machine reasoners, have also recently been introduced allowing researchers to represent the semantics of phenotypes, traits, functions, and environmental properties in such a way that computers can access what had previously been the implicit knowledge of biological experts. (phenoscape.org)
  • At the epub biological and of its process with Canadian Electronic Library, UBC Press was not give any pages in competition to be and have authors of its accessible developments. (literary-liaisons.com)
  • A biological process occurring at the subcellular level, involving biochemical reactions. (foodb.ca)
  • Biological process: Mo-molybdopterin cofactor biosynthetic process. (expasy.org)
  • This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for Biomedical Ontology ( NCBO ). (bioontology.org)
  • The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. (bioontology.org)
  • The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics. (philpapers.org)
  • To identify the components that contribute to virulence and unveil those biological processes potentially related to attenuation, we used isobaric tags for relative and absolute quantification technology (iTRAQ) to compare the protein profiles of the virulent M. hyopneumoniae strain 168 and its attenuated highly passaged strain 168L. (hindawi.com)
  • Artificial intelligence and machine-learning techniques may combine this knowledge with results of genetic research gathered in any context, which permits the identification of the key biological processes involved in chronic sensitization to pain. (helsinki.fi)
  • On this basis, two groups of biological processes, the immune system and nitric oxide signalling, emerged as major players in sensitization to persisting pain, which is biologically highly plausible and in agreement with other lines of pain research. (helsinki.fi)
  • We show that knowledge discovery in genetic databases and contemporary machine-learned techniques can identify relevant biological processes involved in Persitent pain. (helsinki.fi)
  • In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. (biomedcentral.com)
  • Here we performed an integrative omics study investigating the biological processes of mRNAs and expressed miRNAs, as well as proteins in PDAC blood platelets, using benign disease as a refer-ence for inflammatory noise. (vumc.nl)
  • context": "http://obofoundry.github.io/registry/context.jsonld", "ontologies": [ { "activity_status": "active", "contact": { "email": "[email protected]", "github": "akodamullil", "label": "Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "dependencies": [ { "id": "bfo" } ], "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). (githubusercontent.com)
  • The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all infectious diseases. (bioontology.org)
  • This NCBO Workshop on the Infectious Disease Ontology is funded by the United States National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. (bioontology.org)
  • The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. (bioontology.org)
  • Please submit them on the issue tracker ( http://code.google.com/p/infectious-disease-ontology/ ), email the discussion list ( http://groups.google.com/group/ido-discuss ), or email them directly to Lindsay Cowell (lindsay DOT cowell AT utsouthwestern DOT edu). (bioontology.org)
  • Although some of these domains will probably always remain local to FlyBase, in time, community ontologies will be available for others (e.g. chemical compounds for mutagens) and FlyBase will then use these. (flybase.org)
  • The course will also include a practical introduction to community ontologies for biodiversity domain knowledge (anatomy, taxonomy, phenotypic quality). (phenoscape.org)
  • Requirement: semantic distance service(s) provided (i) within the annotation workflow and (ii) independently within NCBO ontology services. (bioontology.org)
  • For discussions on use cases and experiences with the NCBO Annotator, e.g. parameters, ontologies, semantic expansion, see the Annotator Users GoogleGroup and join in discussions with fellow users (group started March 2010). (bioontology.org)
  • It combines parts of several biological ontologies, covering domains such as anatomy, disease and chemical compounds. (nih.gov)
  • system": "git" }, "contact": { "email": "[email protected]", "github": "hescriva", "label": "Hector Escriva", "orcid": "0000-0001-7577-5028" }, "dependencies": [ { "id": "uberon" } ], "description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). (githubusercontent.com)
  • At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy ontologies for a variety of organisms. (bioontology.org)
  • are anatomy and development two separate or one single integrated ontology? (bioontology.org)
  • CARO will be embedded in a set of principles for constructing anatomy ontologies for different organisms at different developmental stages. (bioontology.org)
  • Listserv archives are available [http://listserv.buffalo.edu/archives/ontology-of-anatomy-list.html here]. (bioontology.org)
  • A ticket tracker is available [here]( https://github.com/FlyBase/drosophila-anatomy-developmental-ontology ). (flybase.org)
  • To functionally characterize the cyclic transcriptome in B. distachyon , we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. (biorxiv.org)
  • Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. (philpapers.org)
  • Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species. (bioontology.org)
  • Ontology is the solution, and this book is an excellent effort to evaluate a number of alternative ontology-exchange languages, and to recommend them for use within the larger bioinformatics community. (mit.edu)
  • However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. (biomedcentral.com)
  • The biological function of a chemical. (hmdb.ca)
  • Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. (biomedcentral.com)
  • Tools: Textpresso: an ontology-based information retrieval and extraction system for biological literature Muller HM, Kenny EE, Sternberg PW PLoS Biol. (boku.ac.at)
  • Researchers at the Jackson Lab are evaluating the utility of the Annotator Web service in triaging articles for curation based on the ontology terms recognized in their title and abstract. (bioontology.org)
  • The Gene Ontology (GO Terms) analysis component in geWorkbench is built around the Ontologizer 2.0 software product from Peter Robinson's group at the Charite Medical Institute of the Humboldt University in Berlin. (columbia.edu)
  • repository": "https://github.com/AgriculturalSemantics/agro", "tags": [ "agronomy" ], "title": "Agronomy Ontology", "tracker": "https://github.com/AgriculturalSemantics/agro/issues/", "usages": [ { "description": "AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. (githubusercontent.com)
  • IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. (bioontology.org)
  • Comments, changes to terms, or requests for new ontology terms can be made at GO issue tracker on GitHub . (planteome.org)
  • Functional annotation by gene ontology (GO) showed a biological signature of oogenesis, cell cycle regulation, epigenetic regulation and RNA maturation. (archives-ouvertes.fr)
  • For any other microarray platform type, the user must supply an alternate gene ontology annotation file directly in the Ontologizer setup. (columbia.edu)
  • Input the Gene Ontology OBO file and the desired organisms GOA annotation file. (paccanarolab.org)
  • This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining. (githubusercontent.com)
  • The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. (biomedcentral.com)
  • There has also been a move to automatically describe the provenance of computations (including the actual run of a workflow), and ontologies have been provided to support this recording [ 12 ]. (biomedcentral.com)
  • This thesis validates the usefulness of ontologies as semantic models in biomedicine enabling automated, computational processing of large datasets. (ubc.ca)
  • The first part of this dissertation demonstrates that ontologies can be used as common knowledge models, and details several use cases where they have been applied to existing information in the domain of biomedical investigations, clinical data and vaccine representation. (ubc.ca)
  • Jonathan Nowell, epub biological of Nielsen Book, long had the changes of finding the abstract ebook also in 2004, s that when rebuttal physics internationally took it, publishers across the Telephone conduced from 19 baby to 12 testing( Milliot 2004). (literary-liaisons.com)
  • The Software Ontology (SWO) is a description of software used to store, manage and analyze data. (biomedcentral.com)
  • An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. (biomedcentral.com)
  • As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. (biomedcentral.com)
  • The main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies. (bioontology.org)
  • In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. (biomedcentral.com)
  • Database : the journal of biological databases and curation , vol. 2018, 2018. (oregonstate.edu)
  • Important Note on Annotation Files - The Gene Ontology Term Analysis component will automatically make use of Affymetrix 3' Expression microarray annotation data if it was loaded along with the microarray dataset. (columbia.edu)
  • Ontologies as a critical framework for the vast amounts of data in the postgenomic era: an introduction to the basic concepts and applications of ontologies and ontology languages for the life sciences. (mit.edu)
  • Ontologies-computer-readable, precise formulations of concepts (and the relationship among them) in a given field-are a critical framework for coping with the exponential growth of valuable biological data generated by high-output technologies. (mit.edu)
  • They show how to construct and use ontologies, classifying uses into three categories: querying, viewing, and transforming data to serve diverse purposes. (mit.edu)
  • Given the current explosion of biological data in multiple dimensions, it is time to think systematically about strategies and techniques to not only store, but also integrate and represent them in knowledge-oriented ways. (mit.edu)
  • id": "agro.owl", "ontology_purl": "http://purl.obolibrary.org/obo/agro.owl", "title": "AgrO" } ], "publications": [ { "id": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf", "title": "Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics. (githubusercontent.com)
  • BookScan and BookNet are already remaindered for more many Societies publishing because they are publishers to serve which authors or presentations of data influence Integrating similarly, attract epub biological and environmental control of data and 1980s, type UPs, and assume part, discourse and chain presses. (literary-liaisons.com)
  • In: 3rd Annual Visualizing Biological Data Conference (VizBi2012), 6 - 8 March 2012, Heidelberg, Germany. (mdx.ac.uk)
  • The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. (biomedcentral.com)
  • The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. (biomedcentral.com)
  • However, there is a growing need for a framework to interpret biological data in an integrated manner and, further, to simulate and predict biological functions beyond simply storing and querying data. (biomedcentral.com)
  • OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies. (philpapers.org)
  • Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. (philpapers.org)
  • In conclusion, our data show that platelets change their biological repertoire in patients with PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can "educate" the platelet. (vumc.nl)
  • We demonstrated the performance of the proposed method using data from two complex biological responses: 1. (biomedcentral.com)
  • I encoded existing standard clinical guidelines from the Brighton Collaboration in Web Ontology Language (OWL) in the Adverse Events Reporting Ontology (AERO) I developed within the framework of the Open Biological and Biomedical Ontologies Foundry. (ubc.ca)
  • The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. (philpapers.org)
  • Where possible, metadata should be mapped to ontologies to maximise the FAIRness of any dataset. (elixir-europe.org)
  • We postulated that the direct incorporation of semantic similarity based on GO annotation could significantly enhance the construction of biologically meaningful gene modules which have strong associations with known biological functions. (biomedcentral.com)
  • Ontologies encode information about a domain of knowledge, such as how anatomical structures are related, which is crucial information for modeling character evolution. (phenoscape.org)
  • To train evolutionary biologists and developers of comparative analysis tools to adopt these new capabilities, the SCATE team held a short course on using ontologies in comparative analyses of integrated anatomical traits, in conjunction with iEvoBio and the Evolution Meetings, on June 26, 2019 in Providence, Rhode Island. (phenoscape.org)
  • Developing an application focused experimental factor ontology: embracing the OBO Community. (nih.gov)
  • Information about biological networks has been accumulated over many years, mainly through experimental analyses. (biomedcentral.com)
  • This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. (philpapers.org)
  • This recipe will suggest possible ontologies for metadata fields where these are available. (elixir-europe.org)
  • The following table contains a non-exhaustive list of suggested minimum metadata fields for biological samples. (elixir-europe.org)
  • You are using the Cyverse mirror of the Planteome Ontology Browser. (cyverse.org)
  • The authors first introduce the notion of an ontology, from hierarchically organized ontologies to more general network organizations, and survey the best-known ontologies in biology and medicine. (mit.edu)
  • We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. (philpapers.org)