Biological Ontologies: Structured vocabularies describing concepts from the fields of biology and relationships between concepts.Vocabulary, Controlled: 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)Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Gene Ontology: 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.Terminology as Topic: The terms, expressions, designations, or symbols used in a particular science, discipline, or specialized subject area.Computational Biology: 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.Anatomy: A branch of biology dealing with the structure of organisms.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Natural Language Processing: Computer processing of a language with rules that reflect and describe current usage rather than prescribed usage.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Semantics: The relationships between symbols and their meanings.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Internet: 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.Databases, Factual: 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.Systems Integration: 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)Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Programming Languages: Specific languages used to prepare computer programs.Oligonucleotide Array Sequence Analysis: 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.Knowledge Bases: 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).Models, Biological: 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, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Documentation: 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.Data Mining: Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Information Science: 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.Artificial Intelligence: 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.Unified Medical Language System: 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.Cluster Analysis: 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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Systematized Nomenclature of Medicine: Controlled vocabulary of clinical terms produced by the International Health Terminology Standards Development Organisation (IHTSDO).Proteins: 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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Computer Graphics: 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.Gene Regulatory Networks: 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 Processes: Biological activities and function of the whole organism in human, animal, microorgansims, and plants, and of the biosphere.Biology: One of the BIOLOGICAL SCIENCE DISCIPLINES concerned with the origin, structure, development, growth, function, genetics, and reproduction of animals, plants, and microorganisms.PubMed: 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.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.National Center for Health Statistics (U.S.): A center in the PUBLIC HEALTH SERVICE which is primarily concerned with the collection, analysis, and dissemination of health statistics on vital events and health activities to reflect the health status of people, health needs, and health resources.Arterioles: The smallest divisions of the arteries located between the muscular arteries and the capillaries.Dictionaries, ChemicalAgrochemicals: Chemicals used in agriculture. These include pesticides, fumigants, fertilizers, plant hormones, steroids, antibiotics, mycotoxins, etc.Aphorisms and Proverbs as Topic: Short popular sayings effectively expressing or astutely professing general truths or useful thoughts. (From Random House Unabridged Dictionary, 2d ed, p97, p1556)Quality of Life: A generic concept reflecting concern with the modification and enhancement of life attributes, e.g., physical, political, moral and social environment; the overall condition of a human life.Quality Control: A system for verifying and maintaining a desired level of quality in a product or process by careful planning, use of proper equipment, continued inspection, and corrective action as required. (Random House Unabridged Dictionary, 2d ed)Quality of Health Care: The levels of excellence which characterize the health service or health care provided based on accepted standards of quality.Ethers, Cyclic: Compounds of the general formula R-O-R arranged in a ring or crown formation.Formates: Derivatives of formic acids. Included under this heading are a broad variety of acid forms, salts, esters, and amides that are formed with a single carbon carboxy group.

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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Based on automated MP annotations supported by experiments on knockout mouse models. Click on icons to go to all Timp3 data for that phenotype. ...
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. ...
0.37% of tested genes with null mutations on a B6N genetic background have a phenotype association to abnormal femur morphology (14/3757) 0.16% females (6/3733) 0.37% males (14/3751) ...
Human Phenotype Ontology:HP:0000212,MedGen:C0017567,Human Phenotype Ontology:HP:0000316,MedGen:CN000296,Human Phenotype Ontology:HP:0000821,MedGen:C0020676,Human Phenotype Ontology:HP:0001382,MedGen:C1844820,Human Phenotype Ontology:HP:0001636,MedGen:CN001489,Human Phenotype Ontology:HP:0002019,MedGen:C0009806,Human Phenotype Ontology:HP:0004322,MedGen:C0349588,Human Phenotype Ontology:HP:0012471,MedGen:C1836543,MeSH:C536914,MedGen:C0238462,Orphanet:ORPHA1332,SNOMED CT:255032005,MeSH:D013964,MedGen:C0040136,MeSH:D018761,MedGen:C0025267,OMIM:131100,Orphanet:ORPHA652,SNOMED CT:30664006,MeSH:D018813,MedGen:C0025268,OMIM:171400,Orphanet:ORPHA247698,SNOMED CT:61808009,MeSH:D018814,MedGen:C0025269,OMIM:162300,Orphanet:ORPHA247709,SNOMED CT:6153000,SNOMED CT:61530001,MedGen:C0031511,OMIM:171300,MedGen:C1833929,MedGen:C1970712,OMIM:610755,Orphanet:ORPHA276152,MedGen:CN073359,Orphanet:ORPHA653,SNOMED CT:61808009,MedGen:CN169374,MedGen: ...
FYPO is a formal ontology of phenotypes observed in fission yeast. FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the new online fission yeast resource (www.pombaes.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions ...
Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) The Infectious Disease Ontology Workshop and Meeting (see link below under "Past Meetings") were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the Burroughs Wellcome Fund. September 21, 2007 ...
At the 2007 Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. More recent files and information about the email list can be found via the link above. ...
The achievements and ongoing efforts of C-Paths Critical Path to TB Drug Regimens (CPTR) initiatives work on the Hollow Fiber System Model for Tuberculosis (HFS-TB) are detailed in a new supplement published in the Clinical Infectious Diseases journal. The supplement includes an editorial by the European Medicines Agency (EMA) on its qualification of this tool to reliably assess the potential efficacy of new drugs and combination regimens, an editorial by U.S. Food and Drug Administration (FDA) supporting the use of this tool in drug development, and articles co-authored by members of CPTRs Preclinical and Clinical Sciences Workgroup. Read it online at http://cid.oxfordjournals.org/content/61/suppl_1.toc.. The HFS-TB provides a deep understanding of how drugs move through the body and exert their pharmacokinetic and pharmacodynamic effect on mycobacterium tuberculosis (MTB). Recognition of this tool as a significant advancement in the development of effective treatments for MTB led to an ...
GLIMP Investigators, Di Pasquale, M. F., Sotgiu, G., Gramegna, A., Radovanovic, D., Terraneo, S., Reyes, L. F., Rupp, J., del Castillo, J. G., Blasi, F., Aliberti, S. & Restrepo, M. I., 1-May-2019, In : Clinical Infectious Diseases. 68, 9, p. 1482-1493 12 p.. Research output: Contribution to journal › Article › Academic › peer-review ...
Clinical Infectious Diseases 2006 free download. Get the latest version now. A medical reference text with detailed step-by-step procedures, work-ups and treatments.
The 1st Area Medical Laboratory (1st AML) recently hosted a three-day course in Operational Clinical Infectious Disease (OCID) management.
J:228563 Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H, The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res. 2014 Jan;42(Database issue):D802-9 ...
J:228563 Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H, The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res. 2014 Jan;42(Database issue):D802-9 ...
There is an increasing accumulation of data on disease-related mutations and associated phenotypes in a wide variety of databases worldwide. Exploiting these data in the context of whole genome sequencing is inhibited because the phenotype information in these databases is often difficult to search meaningfully or relate between data sets, and automated computational integration is not possible. Key to this integration is the development of ontology-based methods for describing diseases in terms of their component phenotypes. This would allow analysis of variation in disease manifestation, relationships between diseases and phenotypes in model organisms, and linking diseases to gene mutations, pathways, and phenotypes. Building a systematic link to phenotypes manifested in model organisms will be of particular importance with the advent of new, large-scale phenotyping projects such as the International Mouse Phenotyping Consortium. In addition to improved semantic description, funding and ...
Identifying genes that are important for embryo development is a crucial first step towards understanding their many functions in driving the ordered growth, differentiation and organogenesis of embryos. It can also shed light on the origins of developmental disease and congenital abnormalities. Current international efforts to examine gene function in the mouse provide a unique opportunity to pinpoint genes that are involved in embryogenesis, owing to the emergence of embryonic lethal knockout mutants. Through internationally coordinated efforts, the International Knockout Mouse Consortium (IKMC) has generated a public resource of mouse knockout strains and, in April 2012, the International Mouse Phenotyping Consortium (IMPC), supported by the EU InfraCoMP programme, convened a workshop to discuss developing a phenotyping pipeline for the investigation of embryonic lethal knockout lines. This workshop brought together over 100 scientists, from 13 countries, who are working in the academic and
Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in
Flow cytometry (FCM) bioinformatics is a sub-field of bioinformatics, aimed at developing effective and efficient computational tools to store, organize, and analyze high-throughput/dimensional FCM data. Flow cytometers are capable of analyzing thousands of cells per second for up to 40 features. These features primarily signal the presence of different proteins on cells in the bloodstream. Hence contributing large amounts of data towards the big biological data paradigm. The data that a flow cytometer outputs from a biological sample, is called a FCS file.The International Mouse Phenotyping Consortium (IMPC) is a collaboration between 23 international institutions and funding organizations. Its aim is to decipher the function of 20,000 mouse genes. IMPC is doing so by breeding mice with a certain gene knocked out (KO), cancelling the function of that gene. In turn, FCM is used to measure the immunological changes correlated to this knockout. Many tools exist to classify FCS files. However, ...
Fifty-two newly discovered genes that are critical for hearing have been found by testing gene-modified knockout mice. The newly identifed genes will provide insights into the causes of hearing loss in humans. The study published Oct. 12 in Nature Communications was carried out by the International Mouse Phenotyping Consortium (IMPC), which includes the Mouse Biology Program at the University of California, Davis.. ...
Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed in text. There are many recognizers for specific ontologies, but a general approach for concept recognition is an open problem. Three dictionary-based systems (MetaMap, NCBO Annotator, and ConceptMapper) are evaluated on eight biomedical ontologies in the Colorado Richly Annotated Full-Text (CRAFT) Corpus. Over 1,000 parameter combinations are examined, and best-performing parameters for each system-ontology pair are presented. Baselines for concept recognition by three systems on eight biomedical ontologies are established (F-measures range from 0.14-0.83). Out of the three systems we tested, ConceptMapper is generally the best-performing system; it produces the highest F-measure of seven out of eight ontologies. Default parameters are not ideal for most systems on most ontologies; by changing
... , a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
... , a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
TY - JOUR. T1 - The human phenotype ontology in 2017. AU - Köhler, Sebastian. AU - Vasilevsky, Nicole A.. AU - Engelstad, Mark. AU - Foster, Erin. AU - McMurry, Julie. AU - Aymé, Ségolène. AU - Baynam, Gareth. AU - Bello, Susan M.. AU - Boerkoel, Cornelius F.. AU - Boycott, Kym M.. AU - Brudno, Michael. AU - Buske, Orion J.. AU - Chinnery, Patrick F.. AU - Cipriani, Valentina. AU - Connell, Laureen E.. AU - Dawkins, Hugh J.S.. AU - DeMare, Laura E.. AU - Devereau, Andrew D.. AU - De Vries, Bert B.A.. AU - Firth, Helen V.. AU - Freson, Kathleen. AU - Greene, Daniel. AU - Hamosh, Ada. AU - Helbig, Ingo. AU - Hum, Courtney. AU - Jähn, Johanna A.. AU - James, Roger. AU - Krause, Roland. AU - Laulederkind, Stanley J.F.. AU - Lochmüller, Hanns. AU - Lyon, Gholson J.. AU - Ogishima, Soichi. AU - Olry, Annie. AU - Ouwehand, Willem H.. AU - Pontikos, Nikolas. AU - Rath, Ana. AU - Schaefer, Franz. AU - Scott, Richard H.. AU - Segal, Michael. AU - Sergouniotis, Panagiotis I.. AU - Sever, ...
Apologies for multiple copies.] **** FOIS 2008 CALL FOR PAPERS **** **** The 5th International Conference **** on Formal Ontology in Information Systems **** **** http://fois08.dfki.de **** **** October 31st November 3rd, 2008 **** Saarbr cken, Germany **** DFKI, Competence Center Semantic Web Conference Description ---------------------- Since its inception ten years ago, the International Conference on Formal Ontology in Information Systems has explored the multiple perspectives on the notion of ontology that have arisen from such diverse research communities as philosophy, logic, computer science, cognitive science, linguistics, and various scientific domains. As ontologies have been applied in new and exciting domains such as the World Wide Web, bioinformatics, and geographical information systems, it has become evident that there is a need for ontologies that have been developed with solid theoretical foundations based on philosophical, linguistic, and logical analysis. Similarly, there is ...
Chye, J.K.; Lim, C.T.; Ng, K.B.; Lim, J.M.; George, R.; Lam, S.K. (1997) Vertical transmission of dengue. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 25 (6). pp. 1374-7. ISSN 1058-4838. Cox-Singh, J.; Davis, T.M.E.; Lee, K.; Shamsul, S.S.G.; Matusop, A.; Ratnam, S.; Rahman, H.A.; Conway, D.J.; Singh, B. (2008) Plasmodium knowlesi malaria in humans is widely distributed and potentially life threatening. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 46 (2). pp. 165-71. ISSN 1537-6591. Lam, Sai Kit; Chua, Kaw Bing (2002) Nipah virus encephalitis outbreak in Malaysia. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 34 Sup. S48-51. ISSN 1537-6591. ...
TY - JOUR. T1 - Measurement of human immunodeficiency virus (HIV) type 1 RNA load distinguishes progressive infection from nonprogressive HIV-1 infection in men and women. AU - Burger, Harold. AU - Fang, Guowei. AU - Siegal, Frederick P.. AU - Weiser, Barbara. AU - Grimson, Roger. AU - Anastos, Kathryn. AU - Back, Sara. PY - 1997. Y1 - 1997. UR - http://www.scopus.com/inward/record.url?scp=16944367451&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=16944367451&partnerID=8YFLogxK. M3 - Article. C2 - 9332540. AN - SCOPUS:16944367451. VL - 25. SP - 332. EP - 333. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 2. ER - ...
TY - JOUR. T1 - A man with AIDS and gastric ulcers. AU - Brown, Jennifer. AU - Brown, William R.. AU - Storfa, Amy H.. AU - Tayal, Shalini. PY - 2012/8/15. Y1 - 2012/8/15. UR - http://www.scopus.com/inward/record.url?scp=84864463375&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=84864463375&partnerID=8YFLogxK. U2 - 10.1093/cid/cis416. DO - 10.1093/cid/cis416. M3 - Comment/debate. C2 - 22821572. AN - SCOPUS:84864463375. VL - 55. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 4. ER - ...
TY - JOUR. T1 - IDSA/AASLD Response to Cochrane Review on Direct-Acting Antivirals for Hepatitis C. AU - Powderly, William G.. AU - Naggie, Susanna. AU - Kim, Arthur Y.. AU - Vargas, Hugo E. AU - Chung, Raymond T.. AU - Lok, Anna S.. PY - 2017/12/1. Y1 - 2017/12/1. KW - antivirals. KW - hepatitis C. KW - treatment. UR - http://www.scopus.com/inward/record.url?scp=85034833455&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=85034833455&partnerID=8YFLogxK. U2 - 10.1093/cid/cix620. DO - 10.1093/cid/cix620. M3 - Comment/debate. C2 - 29020156. AN - SCOPUS:85034833455. VL - 65. SP - 1773. EP - 1775. JO - Clinical Infectious Diseases. JF - Clinical Infectious Diseases. SN - 1058-4838. IS - 11. ER - ...
Background. Although a considerable amount of research has gone into the study of the role of bactericidal versus bacteriostatic antimicrobial agents in the treatment of different infectious diseases, there is no accepted standard of practice.. Methods. A panel of infectious diseases specialists reviewed the available literature to try to define specific recommendations for clinical practice.. Results. In infections of the central nervous system, the rapidity with which the organism is killed may be an important determinant, because of the serious damage that may occur during these clinical situations. The failure of bacteriostatic antibiotics to adequately treat endocarditis is well documented, both in human studies and in animal models.. Conclusion. The bulk of the evidence supports the concept that, in treating endocarditis and meningitis, it is important to use antibacterial agents with in vitro bactericidal activity. This conclusion is based on both human and animal data. The data to ...
Toll-like receptor 2 (TLR2)is a member of the TLR family, which plays a central role in the innate immune response to a wide variety of microorganisms. Animal studies have shown thatTLR2-knockout mice are more susceptible to septicemia due to Staphylococcus sure us and Listeria monocyto genes,meningitis due to Streptococcus pneumoniae,and infection with Mycobacterium tuberculosis,suggesting that functional TLR2polymorphisms may impair host response to a certain spectrum of microbial pathogens. In humans, 2 polymorphisms in the exon part of TLR2, which attenuatereceptor signaling, enhance the risk of acute severe infections, tuberculosis, and leprosy. Because gram-positive bacteria have became the first cause of severe infections, including septic shock, knowledge of the role that alteration or lack of TLR2function plays in the pathogenesis of infectious diseases could contribute to the design of new the rapeuticstrategies, including prevention, pharmacologicalintervention, and vaccine ...
2. Simon DW, Da Silva YS, Zuccoli G, Clark RSB. Acute encephalitis. Crit Care Clin 2013;29:259-77. 1 Keratitis is the clinical term describing inflammation of the cornea and one of its causes includes infectious pathogens. Corneal infections often occur when there is a breach in the integrity of the corneal epithelium due to contact lenses, trauma, surgery, or existing ulcerations from other etiologies (ie, nutritional, lagophtalmos associated with leprosy). 1). However, some of the herpes viruses may also affect the cornea leading to viral keratitis. Anatomy and physiology of cerebrospinal fluid. Eur Ann Otorhinolaryn Head Neck Dis 2011;128:309-16. 2. Simon DW, Da Silva YS, Zuccoli G, Clark RSB. Acute encephalitis. Crit Care Clin 2013;29:259-77. 1 Keratitis is the clinical term describing inflammation of the cornea and one of its causes includes infectious pathogens. Corneal infections often occur when there is a breach in the integrity of the corneal epithelium due to contact lenses, trauma, ...
Wei Wang, MD, PhD, Associate Professor, Doctor, (E-mail: [email protected]) Jiangsu Institute of Parasitic Diseases, Key Laboratory on Technology for Parasitic Disease Prevention and Control, National Health and Family Planning Commission, Jiangsu Provincial Key Laboratory on Molecular Biology of Parasites, Wuxi 214064, Jiangsu Province, China. ...
The most important educational exercise for the fellows, beyond the vast amount of bedside teaching in the inpatient and outpatient settings, is the weekly ID Case Conference. Fellows are responsible for organization of this conference, where an unknown case is presented to the attending physicians who then discuss differential diagnosis, diagnostic evaluation, and initial treatment recommendations. Following this discussion, the findings and outcome are presented by the fellow, after which he/she presents an in-depth review of the literature pertaining to the case.
With the improvement of hygiene and income level, the prevalence of TB is decreasing in developed countries although it still considers a challenge in developing countries such as Iran. The peak age of disseminated TB were children, frequently affected under the age of three, nevertheless this trend has changed over the last decade (5). Therefore, increase in the rate of HIV infection and the number of adults with impairment in cellular immunity have led to an additional peak of TB among young adults (6) Hepatic granulomas are present in more than 90% of patients with TB, approximately 70% of them have extra-pulmonary TB and about 25% of them again have isolated pulmonary infections (7)., It should be borne in mind that chest radiograph allows the possibility of identifying 59 to 69% of miliary tuberculosis with high specificity and good interobserver agreement (8). In our patient there was no sign of other organs involvement and also her chest x-ray had non-specific findings. Liver involvement ...
Results: There was no significant difference between the two groups in terms of age distribution and clinical signs/symptoms during the baseline visit. There was no significant difference between clinical or bacteriological responses between the two groups. Three-day regimen of ciprofloxacin showed high microbiological eradication rate for E. coli (66.7%) which was similar to the eradication rate observed for 7-day regimen (64.8%). No statistically significant difference was found in adverse effects between the groups, except for nausea (p=0.041). ...
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they - and only they - are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called specializations in [81. Entity doesnt have a closure axiom because the subclasses dont necessarily exhaust all possibilites. For example Werner Ceusters portions of reality ...
TTY = "ET" is assigned to the value of tag = "synonym" where the scope identifier is "BROAD," "NARROW," or "RELATED" in records where there is no "is_obsolete" tag ...
In this paper we introduce various vocabularies and definitions used for defining Protein Ontology. Protein Ontology provides the technical and scientific infrastructure and knowledge to allow description and analysis of relationships between various proteins. Protein Ontology uses relevant protein data sources of information like PDB, SCOP, and OMIM. Protein Ontology describes: Protein Sequence and Structure Information, Protein Folding Process, Cellular Functions of Proteins, Molecular Bindings internal and external to Proteins, and Constraints affecting the Final Protein Conformation.. ...
Institutions: National Center for Biotechnology Information. Genomic resources for the mouse genome have increased greatly. A Whole Genome Shotgun (WGS) assembly generated by the Mouse Genome Sequencing Consortium (MGSC) was released and published. During the past year, sequencing resources for mouse have shifted towards clone based (HTGS) sequence. As of July 25, 2003, 1.03 Gb of non-redundant finished sequence and 2.28 Gb of redundant draft sequence were available. Greater than 95% of the HTGS sequence generated is from the reference strain (C57BL/6J). To leverage all available sequence data, NCBI has been performing composite assemblies that integrate HTGS sequence from C57BL/6J into the MGSCv3. NCBI Build 30 (based on data from Jan. 27, 2003) integrated 0.736 Gb of HTGS phase 3 (finished) sequence. It is anticipated that future builds will utilize all C57BL/6J HTGS. In addition to producing the reference assembly, NCBI has been producing alternate assemblies in a strain specific manner. In ...
Institutions: Medical Research Council Mammalaian Genetics Unit. FESA provides a secure and economical means of storing the enormous number of new mutations and genetically manipulated lines generated during contemporary genetic and ENU mutagenesis programmes. This explosion of new lines necessitates the provision of central, securely funded archives to ensure these resources are not lost to future researchers.. At Harwell, FESA already contains ,300,000 frozen embryos from ,1000 stocks. We offer a free service for cryopreservation, storage and promotion of mouse embryos and spermatozoa. Charges are levied for withdrawals from the archive.. FESA is one of six nodes that constitute EMMA (European Mouse Mutant Archive) and acts as the central UK repository for deposition and distribution of mouse mutants and stocks that are essential to todays research.. Contact [email protected] The MGU Harwell web site can be accessed at: http://www.mgu.har.mrc.ac.uk. ...
first in the germ cell lineage sharing many features with the embryonic stem cells Unlike differentiated somatic cells the PGCs possess ability to erase epigenetic modifications on the genome accumulated during development Thus PGCs can be regarded as the cells programmed to rejuvenate the genomic status Despite of this biological importance molecular nature of the PGCs remains largely unknown We have established systematic methodologies to analyze PGCs and related embryonic cells PGCs were purified from transgenic mouse embryos in which the PGCs were marked by GFP reporter expression and cDNA libraries were made with the purified PGCs transcriptome of the PGCs were explored by EST analyses and microarray ESTs were classified according to the NIA Mouse Gene Index the analyzed 18 293 ESTs were clustered into 6 159 transcripts and 4 833 genes of which 435 were unknown genes Analysis of EST frequency suggested expression level of each gene and identified signature genes for PGCs Principal component ...
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they - and only they - are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called specializations in [81. Entity doesnt have a closure axiom because the subclasses dont necessarily exhaust all possibilites. For example Werner Ceusters portions of reality ...
It is a challenge to perform artificial intelligence without Matlab tools ? Yes it is possible if we understand correctly what we do. Do we use determinic mathematical link to do this ? Yes and … not. Why ? Because in fact we lay the « logical » or rules as « prolog » can do. That is we have to find some algorithms to find bad and right solutions after passing through rules. Then there are not parallelism nor so much « codelets » [HOFSTADTER-MITCHELL-1995] to perform our 256 possibilities. We just choose to run randomly them and to stop after 10, 20 100 tries. There we have a small « Coderack » as somebody can memorize and visualize in subconscient some inputs with eyes. Then we construct as a « prolog » heart ! Is it a good exercice for scientist ? « Who can do more can do less !« ...
1999 US Public Health Service (USPHS)/Infectious Diseases Society of America (IDSA) Guidelines for Preventing Opportunistic Infections (OIs) in Persons Infected with HIV, published in this issue of Clinical Infectious Diseases [1], provide disease-specific recommendations for the prevention of the most common serious OIs in HIV-infected persons in the United States [2]. This article synthesizes these recommendations and offers health care providers an organized approach for preventing OIs in patients infected with HIV. We recognize that preservation or reconstitution of immune function by instituting highly active antiretroviral therapy (HAART) can now provide the most potent protection against OIs in persons with advanced HIV disease, including many OIs for which specific prevention measures are not available [3, 4]. However, HAART is effective only for persons who have access to therapy, who are willing to accept therapy, who are able to adhere to it, and in whom viral suppression is achieved ...
Chow EPF; Callander D; Fairley CK; Zhang L; Donovan B; Guy R; Lewis DA; Hellard M; Read P; Ward A, 2017, Increased Syphilis Testing of Men Who Have Sex With Men: Greater Detection of Asymptomatic Early Syphilis and Relative Reduction in Secondary Syphilis, Clinical Infectious Diseases, vol. 65, pp. 389 - 395, http://dx.doi.org/10.1093/cid/cix326. Stoové M; Asselin J; Pedrana A; Lea T; Hellard M; Wilson D; Prestage G; de Wit J; Holt M, 2017, Declining prevalence of undiagnosed HIV in Melbourne: Results from community-based bio-behavioural studies of gay and bisexual men, Australian and New Zealand Journal of Public Health, http://dx.doi.org/10.1111/1753-6405.12708. Quinn B; Seed C; Keller A; Maher L; Wilson D; Farrell M; Caris S; Williams J; Madden A; Thompson A, 2017, Re-examining blood donor deferral criteria relating to injecting drug use, International Journal of Drug Policy, vol. 48, pp. 9 - 17, http://dx.doi.org/10.1016/j.drugpo.2017.05.058. Taaffe JE; Longosz AF; Wilson D, 2017, ...
Vekemans, J., Gouvea-Reis, F., Kim, J. H., Excler, J. L., Smeesters, P. R., Obrien, K. L., Van Beneden, C. A., Steer, A. C., Carapetis, J. R. & Kaslow, D. C., 1 Sep 2019, In : Clinical Infectious Diseases. 69, 5, p. 877-883 7 p., ciy1143.. Research output: Contribution to journal › Review article ...
Stockdale AJ; Saunders MJ; Boyd MA; Bonnett LJ; Johnston V; Wandeler G; Schoffelen AF; Ciaffi L; Stafford K; Collier AC, 2018, Effectiveness of Protease Inhibitor/Nucleos(t)ide Reverse Transcriptase Inhibitor-Based Second-line Antiretroviral Therapy for the Treatment of Human Immunodeficiency Virus Type 1 Infection in Sub-Sah, Clinical Infectious Diseases, vol. 66, pp. 1846 - 1857, http://dx.doi.org/10.1093/cid/cix1108. Yao AH; Moore CL; Lim PL; Molina JM; Madero JS; Kerr S; Mallon PWG; Emery S; Cooper DA; Boyd MA, 2018, Metabolic profiles of individuals switched to second-line antiretroviral therapy after failing standard first-line therapy for treatment of HIV-1 infection in a randomized, controlled trial, Antiviral Therapy, vol. 23, pp. 21 - 32, http://dx.doi.org/10.3851/IMP3171. Mwasakifwa GE; Moore C; Carey D; Amin J; Penteado P; Losso M; Lim PL; Mohapi L; Molina JM; Gazzard B, 2018, Relationship between untimed plasma lopinavir concentrations and virological outcome on second-line ...
Mandell, L., Wunderink, R., Anzueto, A., Bartlett, J., Campbell, D., Dean, N., Dowell, S., File, T., Musher, D., Niederman, M., Torres, A., Whitney, C. (2007). Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults. Clinical Infectious Diseases, 44(2), s27-72. doi:10.1086/511159. Retrieved March 22, 2018, from: https://www.thoracic.org/statements/resources/mtpi/idsaats-cap. ...
Kalsdorf, Barbara, Division of Clinical Infectious Diseases, Medical Clinic Research Center Borstel, Borstel, Germany; Germany German Center for Infection Research (DZIF), Clinical Tuberculosis Center, Borstel, Germany; International Health/Infectious Diseases, University o (Germany ...
Salim S. Abdool Karim is a clinical infectious diseases epidemiologist who is widely recognised for his research contributions in HIV prevention and treatment. He is CAPRISA Professor for Global Health in the Department of Epidemiology at the Mailman School of Public Health at Columbia University. He is also Director of the Centre for the AIDS Program of Research in South Africa (CAPRISA), Pro Vice-Chancellor (Research) at the University of KwaZulu-Natal in Durban, South Africa and Adjunct Professor of Medicine at Weill Medical College of Cornell University. His contributions to microbicides for HIV prevention spans two decades and culminated in the CAPRISA 004 tenofovir gel trial which provided proof-of-concept that antiretroviral drugs can prevent sexually transmitted HIV infection and herpes simplex virus type 2 in women. He is co-inventor on patents which have been used in several HIV vaccine candidates and his clinical research on TB-HIV treatment has shaped international guidelines on the clinical
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, May 1, 2010, Vol.50(9), pp.1300- ...
A three-year study by Yale School of Medicine researchers has found that vaccinating pregnant women against influenza is over 90 percent effective in preventing their infants from being hospitalized with influenza in the first six months of life. Published in the December 15 issue of Clinical Infectious Diseases, the study builds on preliminary data the research team presented last year at the Infectious Disease Society of America in Philadelphia.. Influenza is a major cause of serious respiratory disease in pregnant women and of hospitalization in infants. Although the flu vaccine is recommended for all pregnant women and children, no vaccine is approved for infants under six months of age. Preventive strategies for this age group include general infection control and vaccination of those coming in close contact with them.. First author Isaac Benowitz, a Yale medical student, senior author Marietta Vazquez, M.D., and their colleagues examined the effectiveness of flu vaccine during pregnancy in ...
Stevens, E. R., Nucifora, K. A., Hagan, H., Jordan, A. E., Uyei, J., Khan, B., Dombrowski, K., des Jarlais, D. & Braithwaite, R. S., Jun 10 2020, In : Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 70, 12, p. 2652-2662 11 p.. Research output: Contribution to journal › Article ...
Because ongoing pain is a significant problem that affects 39 to 85 percent of people living with HIV, everyone with the infection should be assessed for chronic pain, recommend guidelines released by the HIV Medicine Association of the Infectious Diseases Society of America and published in the journal Clinical Infectious Diseases.
Despite an increased urgency for new antibiotics to fight increasingly drug-resistant, deadly bacteria, the US Food and Drug Administration (FDA) has approved only one new systemic antibiotic since 2010, and that was more than 2 years ago, the Infectious Diseases Society of America (IDSA) said in a report today in Clinical Infectious Diseases. The IDSA launched its "10 X 20" initiative in 2010, which "calls for development and regulatory approval of 10 novel, efficacious, and safe systemically administered antibiotics by 2020" to combat resistant pathogens, the IDSA said in todays report. The group identified seven new drugs in development for combating multidrug-resistant Gram-negative bacilli (GNB), which the US Centers for Disease Control and Prevention (CDC) last month called "nightmare bacteria." None of them, however, will work against the most resistant bacteria strains, the IDSA said. "Were losing ground because we are not developing new drugs in pace with superbugs ability to ...
Apr 11, 2013 By David Douglas. NEW YORK (Reuters Health) Apr 11 - In a study of men with HIV, antiretroviral therapy (ART) with lamivudine or tenofovir disoproxil fumarate (TDF) appeared to protect against infection with hepatitis B virus (HBV), Japanese researchers say.. Dr. Hiroyuki Gatanaga of the National Center for Global Health and Medicine, Tokyo and colleagues evaluated stocked serum samples from HIV-infected men who have sex with men.. They found a lower frequency of incident HBV infection under lamivudine- and TDF-containing ART than under ART without lamivudine and TDF, or without ART at all, Dr. Gatanaga told Reuters Health by email, adding that HBV-active ART seems to work as a pre-exposure prophylaxis against HBV.. As reported March 13th online in Clinical Infectious Diseases, the research team had access to first stocked blood samples from 1,434 HIV-infected men who hadnt been vaccinated against HBV; 354 were negative for all analyzed HBV serological markers.. During ...
(2005) Mutsch et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. BACKGROUND: Influenza outbreaks have been reported among travelers, but attack rates and incidence are unknown.\n\nMETHODS: A cohort study was conducted. Travelers to subtropical and tropical count...
Oldenburg, Catherine E.; Bärnighausen, Till; Tanser, Frank; Iwuji, Collins C.; De Gruttola, Victor; Seage, George R.; Mimiaga, Matthew J. et al. (Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 2016) Link to Published Version ...
Randolph, A. G., Xu, R., Novak, T., Newhams, M. M., Wardenburg, J. B., Weiss, S. L., Sanders, R. C., Thomas, N. J., Hall, M. W., Tarquinio, K. M., Cvijanovich, N., Gedeit, R. G., Truemper, E. J., Markovitz, B., Hartman, M. E., Ackerman, K. G., Giuliano, J. S., Shein, S. L. & Moffitt, K. L., 2019, In : Clinical Infectious Diseases. 68, 3, p. 365-372 8 p.. Research output: Contribution to journal › Article ...
Nasal drops of harmless bacteria can inhibit a related bug that sometimes causes meningococcal disease, according to new findings published online in Clinical Infectious Diseases. The study--conducted among college students, a group at higher risk for this often serious illness--suggests a new approach that could help suppress outbreaks of the disease, if supported by future research.. ...
Arroyo, G., Rodriguez, S., Lescano, A. G., Alroy, K. A., Bustos, J. A., Santivañez, S., Pretell, E. J., Garcia, H. H., Gilman, R. H., Gonzalez, A., Tsang, V. C. W., Gonzalez, I., Saavedra, H., Martinez, M., Alvarado, M., Verastegui, M., Zimic, M., Mayta, H., Guerra, C., Castillo, Y. & 13 others, Castro, Y., Lopez, M. T., Gavidia, C. M., Gomez, L., Moyano, L. M., Gamboa, R., Muro, C., Vilchez, P., Nash, T. E., Mahanty, S., Noh, J., Handali, S. & Friedland, J., Jan 15 2018, In : Clinical Infectious Diseases. 66, 2, p. 282-288 7 p.. Research output: Contribution to journal › Article ...
Woods, C. W., Brasslar, A. M., LiPuma, J. J., Alexander, B. D., Clements, D. A., Weber, D. J., Moore, C. M., Reller, L. B. & Kaye, K. S., May 1 2004, In : Clinical Infectious Diseases. 38, 9, p. 1243-1250 8 p.. Research output: Contribution to journal › Review article ...
ORCID: https://orcid.org/0000-0001-7680-2200 and White, N. J. (2002) A randomized, double-blind, placebo-controlled trial of acetazolamide for the treatment of elevated intracranial pressure in cryptococcal meningitis. Clinical Infectious Diseases, Vol 35, Issue 6, pp. 769-772. Norheim, G., Rosenqvist, E., Aseffa, A., Yassin, Mohammed A., Mengistu, G., Kassu, A., Fikremariam, D., Tamire, W., Hoiby, E. A., Alebel, T., Berhanu, D., Merid, Y., Harboe, M. and Caugant, D. A. (2006) Characterization of Neisseria meningitidis isolates from recent outbreaks in Ethiopia and comparison with those recovered during the epidemic of 1988 to 1989. Journal of Clinical Microbiology, Vol 44, Issue 3, pp. 861-871. Norheim, G., Aseffa, A., Yassin, Mohammed A., Mengistu, G., Kassu, A., Fikremariam, D., Tamire, W., Merid, Y., Hoiby, E. A., Caugant, D. A., Fritzsonn, E., Tangen, T., Melak, B., Berhanu, D., Harboe, M., Kolberg, J. and Rosenqvist, E. (2008) Specificity of subcapsular antibody responses in Ethiopian ...
Patients diagnosed with HIV who started antiretroviral treatment within 30 days had significantly lower rates of dropping out of treatment, and higher rates successful treatment, than those who started later, particularly those who started more than three months after their diagnosis, a study in China has found.. Researchers, led by Yan Zhao and Zunyou Wu of the Chinese Center for Disease Control and Prevention reported their findings, gathered from nationwide patient records spanning three years, in Clinical Infectious Diseases.. The findings on the benefits of immediate treatment upon diagnosis, are important, the authors note, at a time when too few patients gain the benefits of "early" treatment, which depends on being diagnosed early in the progression of infection. The message implicit in immediate treatment initiation, they write, counters misleading perceptions about HIV treatment and care that accompany postponing the start of treatment for months after diagnosis.. Acting on the ...
Taking antibiotics for diarrhea may put travelers visiting developing parts of the world at higher risk for contracting superbugs and spreading these daunting drug-resistant bacteria to their home countries, according to a new study published in Clinical Infectious Diseases and now available online. The study authors call for greater caution in using antibiotics for travelers diarrhea, except in severe cases, as part of broader efforts to fight the growing public health crisis of antibiotic resistance and the spread of highly resistant bacteria worldwide.
Making flu shots mandatory in 2008 dramatically increased the vaccination rate among St. Louis-based BJC HealthCares nearly 26,000 employees to more than 98 percent, according to a report now online in the journal Clinical Infectious Diseases.
The Population Council announces the appointment of leading South African AIDS researcher, Salim S. Abdool Karim, to the Council Board of Trustees. Dr. Karim, a clinical infectious diseases epidemiologist is the Director of the Centre for the AIDS Programme of Research in South Africa (CAPRISA), CAPRISA Professor of Global health at Columbia University in New York and Honorary Pro Vice-Chancellor (Research) at the University of KwaZulu-Natal. ...
NaturalHealth365) Makers of the flu vaccine claim receiving it decreases the risk of getting sick due to the triggering of antibody development in the body. However, a Chinese study reveals quite the opposite.. Researchers in Hong Kong have found that in addition to actually increasing the risk of flu, receiving the flu vaccine also raises the risk of getting a respiratory infection by 5.5 times. The study was published in the journal Clinical Infectious Diseases.. Stringent double-blind study shows disturbing side effects of flu vaccine. While research on the side effects of the flu vaccine have been lacking in the U.S., Chinese researchers have been more active about looking into the possible side effects of flu shot. This recent study conducted in Hong Kong looked at vaccinated versus unvaccinated subjects and how they fared health-wise.. In the study, the seasonal trivalent flu vaccine was tested for side effects of flu shot. What makes this effort particularly noteworthy is the fact that it ...
The two-drug antiretroviral combination dolutegravir and lamivudine is virologically effective and safe in people starting HIV therapy for the first time, according to US research published in the online edition of Clinical Infectious Diseases.. The phase 2 pilot study recruited 120 antiretroviral-naïve adults. After 24 weeks of treatment, 90% of participants had viral suppression and none of the participants discontinued therapy because of side-effects. There were few virological failures, and these were linked to poor adherence. Modern antiretroviral therapy usually consists of three separate drugs and is highly effective. Safety and cost considerations mean there is interest in identifying effective two drug combinations. Dolutegravir and lamivudine performed well in a small study with high rates of virological suppression over 96 weeks.. Investigators in the US wanted to build on this research. They therefore designed a pilot, phase 2, open-label study (ACTG A5353) involving adults with a ...
Many hospitals are now utilizing motion sensors, hand-washing coaches and video cameras in their facilities to monitor whether nurses and doctors are washing their hands, the New York Times reported. Hand-washing, or basic hand hygiene, is essential in the hospital industry, especially in the wake of a recent report from  the Centers for Disease Control and Prevention (CDC) indicating that drug-resistant superbugs are on the rise. Infections acquired in hospitals cost $30 billion a year and lead to approximately 100,000 patient deaths annually. As a result, hospitals are going to great lengths to ensure proper hand-washing and sanitation. In a study published in the journal Clinical Infectious Diseases, North Shore University Hospital in Long Island, N.Y., installed motion sensors designed to power on whenever someone entered an intensive care room in the hospital. The sensors activated a video camera, which transmitted images to workers in India who monitored whether nurses and ...
by Daniel J. Cameron, MD MPH. According to a 2017 study published in Clinical Infectious Disease, a pronounced TH17 cytokine response may be beneficial in the early stages of Lyme disease. "In these patients, the levels of inflammatory mediators, particularly TH17-associated cytokines, correlated directly with B. burgdorferi IgG antibodies (P,0.02), suggesting a beneficial role for these responses in control of early infection," states Strle et al. from the Center for Immunology and Inflammatory Diseases and Massachusetts General Hospital.. The authors describes a subset of patients with increased TH17 cytokine levels in response to Lyme arthritis. "The levels of TH17-associated mediators were more variable, but correlated strongly with autoantibodies to ECGF, MMP-10, and apoB-100 in joints of patients with antibiotic-refractory LA, implying a shift in TH17 responses towards an autoimmune phenotype.". The endothelial cell growth factor (ECGF), apolipoprotein B-100 (apoB-100), and matrix- ...
by Christine M. Kukka. Experts Say Breastfeeding While Taking Antivirals Is Safe Women infected with the hepatitis B virus (HBV) face a medical conundrum. If they have high viral loads they are encouraged to take antivirals during pregnancy to reduce their HBV DNA levels to avoid infecting their newborns-but then theyre told not to take antivirals if they want to breastfeed.. A fetus is exposed to far higher levels of an antiviral in utero if the mother takes a daily antiviral pill than through breast milk. And to date, no medical studies have found any harm to babies from exposure to the miniscule amounts of antivirals found in breast milk, according to a provocative study published in the October issue of the journal of Clinical Infectious Diseases.. In fact, the World Health Organization recommends that HIV-infected women continue antiviral treatment (which includes some of the same drugs used to suppress viral load in HBV-infected women) while breastfeeding.. According to the international ...
Large sample randomization inference of causal effects in the presence of interference. Liu, L., Hudgens, M.G. (2014). Journal of the American Statistical Association, 109(505), 288-301.. Sharpening bounds on principal effects with covariates. DM Long, MG Hudgens (2013). Biometrics, 69(4), 812-819.. Sensitivity Analysis of Per-Protocol Time-to-Event Treatment Efficacy in Randomized Clinical Trials. PB Gilbert, BE Shepherd, MG Hudgens (2013). Journal of the American Statistical Association, 108(503), 789-800.. Pooled individual data analysis of 5 randomized trials of infant nevirapine prophylaxis to prevent breast-milk HIV-1 transmission. MG Hudgens, TE Taha, SB Omer, DJ Jamieson, H Lee, LM Mofenson, et al (2012). Clinical Infectious Diseases, 56(1), 131-139.. Maternal and infant antiretroviral regimens to prevent postnatal HIV-1 transmission: 48-week follow-up of the BAN randomised controlled trial. DJ Jamieson, CS Chasela, MG Hudgens, CC King, AP Kourtis, D Kayira, et al (2012). The Lancet, ...
Much of the contentious debate over the abuse of antibiotics in farming boils down to a couple of simple questions: whether resistant organisms that arise on farms because of antibiotic use leave the farm, and whether, once they do, they reach human beings.. A piece of research (PDF) released Friday morning in the journal Clinical Infectious Diseases helps answer both those questions.. A team of researchers from Arizona bought meat and poultry in five cities across the United States, tested them for bacteria, and found this: 47 percent of the samples contained the very common pathogen Staphylococcus aureus, and 96 percent of those isolates were resistant to at least one antibiotic. Of more concern: 52 percent of those staph isolates were resistant to at least three antibiotics that are commonly used in both veterinary and human medicine.. That is, roughly one in four packages of meat and poultry from across the United States contained multidrug resistant staph.. Here are the details: A team from ...
Chow, A., Lim, V. W., Khan, A., Pettigrew, K., Lye, D. C. B., Kanagasabai, K., Phua, K., Krishnan, P., Ang, B., Marimuthu, K., Hon, P-Y., Koh, J., Leong, I., Parkhill, J., Hsu, L-Y. & Holden, M. T. G. 15 May 2017 In : Clinical Infectious Diseases. 64, suppl_2, p. S76-S81 6 p.. Research output: Contribution to journal › Article ...
Nasal drops of harmless bacteria can inhibit a related bug that sometimes causes meningococcal disease, according to new findings published online in Clinical Infectious Diseases. The study--conducted among college students, a group at higher risk for this often serious illness--suggests a new approach that could help suppress outbreaks of the disease, if supported by future research ...
li,Mohan A.K., Coté T.R., Block J.A, Manadan A.M., Siegel J.N., Braun M. Tuberculosis following the use of Etanercept: a tumor necrosis factor inhibitor. ,em,Clinical Infectious Disease. ,/em,2004:39:295-299,/li ...
People over 65 are often offered a standard vaccine or a high-dose version. But a new study has found that the higher dosage is effective only for people 85 and older.. A new study from the U.S. Department of Veterans Affairs found that for those between age 65 and 84, the standard vaccine works just as well.. The finding was published in the journal Clinical Infectious Diseases.. The investigators looked at more than 165,000 VA patients who got either the regular or high-dose vaccine during the 2010 - 2011 flu season. The study tracked hospitalizations and deaths- indicators of the flus more severe impacts.. About 25,000 of the veterans had gotten the high dose, and the rest the standard vaccine.. "The main overall outcome was that we didnt find a difference between the groups," says study author Dr. Darren Linkin, with the CDC Prevention Epicenter Program. "But in a secondary analysis, there appeared to be a strong effect for those 85 and older.". The new findings contrast with those from ...
Founder of LFM Healthcare Solutions LLC, Lawrence F. Muscarella, PhD, has researched and authored more than 200 articles on the topics of disinfection, sterilization, instrument reprocessing, risk management, infection control and prevention, modes of disease transmission, and factors that pose an increased risk of healthcare-acquired infections (HAIs), with a focus in the fields of gastrointestinal endoscopy and critical care.. His articles have been published in such peer-reviewed medical journals as: The Journal of Hospital Infection, The American Journal of Infection Control, Gastrointestinal Endoscopy, Chest, Infection Control and Hospital Epidemiology, Endoscopy, and the World Journal of Clinical Infectious Diseases.. ...
Thinking of grilling a steak this weekend? Well, dont read this, then: a disturbing new study revealed that about a quarter of all meat and poultry sampled from around the United States have drug-resitant strains of Staphylococcus aureus.About half — 47% of the samples — contained S. aureus, the researchers reported Friday in Clinical Infectious Diseases. Of those bacteria, 52% were resistant to at least three classes of antibiotics. DNA testing suggested the animals were the source of conta...
The annual seasonal flu shots effectiveness continues to be debated. Discover more about the troubling findings published by the Clinical Infectious Diseases Journal in February 2013 at the National Vaccine Information Centers March 2013 blog post.
Short courses of antibiotics appear just as effective as longer ones - and a great deal safer - in treating respiratory infections that might cause pneumonia in children on temporary breathing devices, according to a Johns Hopkins Childrens Center study published online May 3 in Clinical Infectious Diseases.. In the studys analysis of 150 children treated with antibiotics for respiratory infections while on a ventilator, longer antibiotic courses did not only fail to confer extra protection against full-blown pneumonia when compared with shorter therapy, but also considerably increased a childs risk for developing drug-resistant infections within a month.. To rein in the spread of bacterial drug resistance, the researchers advise clinicians to carefully evaluate the need for antibiotics in the first place and to use antibiotics for the shortest time needed to achieve clinical effect.. "Our study underscores the old physician maxim to first do no harm," said lead investigator Pranita Tamma, M. ...
A study by UK investigators published in Clinical Infectious Diseases provides further evidence that patient-to-patient S. aureus transmission is a relatively uncommon event, even as an explanation for S. aureus "acquisition" events in the ICU. Using whole genome sequencing (WGS), the investigators found that only 7 of 37 ICU patients who "newly acquired" S. aureus were colonized with strains that were closely related to other patients who had an overlapping ICU stay. There are several limitations to the work, most of which are outlined by the authors in their discussion and by the excellent accompanying editorial by David and Daum. The limitation most concerning to me is the assumption that a single nares + perineum culture plated directly to solid agar media (chromogenic agar and Columbia CNA) is a sensitive method for detection of S. aureus carriers. It isnt. Failure to perform a throat culture or to use broth enrichment probably reduced sensitivity by 30-50% (explaining their overall ...
In addition to these two studies, there was also a clinical study conducted in Hong Kong in in 2012 comparing vaccinated with unvaccinated children in regards to the flu vaccine. Researchers conducted a double-blind placebo-controlled trial on children with the trivalent inactivated influenza vaccine. Their results were published in the journal Clinical Infectious Diseases in 2012, and they found that the seasonal trivalent flu vaccine resulted in 5.5 times more incidents of respiratory illness than the placebo group. Read more about the study here ...
Anagnostopoulos, Alexia; Ledergerber, Bruno; Kuster, Stefan P; Scherrer, Alexandra U; Näf, Bettina; Greiner, Michael A; Rancic, Zoran; Kobe, Adrian; Bettex, Dominique; Hasse, Barbara (2019). Inadequate perioperative prophylaxis and postsurgical complications after graft implantation are important risk factors for subsequent vascular graft infections - prospective results from the VASGRA Cohort Study. Clinical Infectious Diseases, 69(4):621-630.. Osinga, Rik; Steiger, Peter; Giovanoli, Pietro; Plock, Jan A; Mannil, Lijo (2019). Enzymatisches Débridement zur Behandlung von Brandverletzungen: Erste Erfahrungen in der Schweiz. Handchirurgie, Mikrochirurgie, Plastische Chirurgie, 51(02):80-85.. Willms, J F; Boss, O; Keller, E (2019). Safety, Feasibility, and Efficiency of a New Cooling Device Using Intravenous Cold Infusions for Fever Control. Neurocritical Care, 30(1):149-156.. Boettger, Soenke; Meyer, Rafael; Richter, André; Fernandez, Susana Franco; Rudiger, Alain; Schubert, Maria; Jenewein, ...
Clinical Infectious Diseases. 36(10):1266-1267, MAY 15TH, 2003. DOI: 10.1086/374360 , Issn Print: 1058-4838. Publication Date: May 15th, 2003. ...
A new study, published inthe journal Clinical Infectious Diseases, shows that people with vitamin A deficiency may be 10 times more likely to develop tuberculosis (TB).
Clinical Infectious Diseases. 30(1):234, JANUARY 2000. DOI: 10.1086/313575 , PMID: 10619777. Issn Print: 1058-4838. Publication Date: January 2000. ...
Giamarellos-Bourboulis, E.J., Grecka, P., Poulakou, G., et al. (2001) Assessment of procalcitonin as a diagnostic marker of underlying infection in patients with febrile neutropenia. Clinical Infectious Diseases, 32, 1718-1725. doi10.1086/320744
Staph (Staphylococcus) likes to hang around, and it can contaminate a nonporous surface for longer than you may expect. Methicillin-resistant Staphylococcus aureus (MRSA), for example, can live on a toilet seat -- and any nonporous part of a toilet -- for more than two months. And it only takes as few as three seconds for it to transmit from a seat to your skin [source: Clinical Infectious Diseases]. However, despite the bad news about its longevity, the truth about staph on toilet seats is this: Youre more likely to expose yourself to it by using your cell phone than you are by sitting on toilet seat. More than half of all our phones carry the bacteria [source: Cohen].. Still not convinced that the toilets safe? Then heres what you need to do: Skip those paper seat covers and carry antiseptic alcohol wipes with you. Wipe the seat before you sit. Its the only effective way to be sure youve killed staph, as well as other bacteria that may cause boils or skin infections.. ...
Followers of professional teams often wonder why so many top athletes, people who should be in prime physical condition, fall ill during their playing seasons. A new study in the journal Clinical Infectious Diseases helps explain things and provides a lesson for not only other professionals, but college, scholastic and...
2. Marra C. Infections associated with myelopathy, radiculopathy and neuropathy. In: Root RK, Waldvogel F, Corey L, Stamm WE, editors. Clinical infectious diseases: a practical approach. New York: Oxford University Press, 1999: 715-722 ...
The prevalence of multimorbidity rose from 8.2% to 22.4% in the United States between 2000 and 2009 among people living with HIV who received treatment, according to data published in Clinical Infectious Diseases.“In the context of HIV infection, multimorbidity may have far-reaching implications given the increases in numbers of [persons living with HIV (PLWH)] aged 50 years or older, the
A study recently published in the journal, Clinical Infectious Diseases, discovered azole-resistance markers in 75% of a small group of aspergillosis patients who had not previously been treated with...
Stekler, Joanne D.; Swenson, Paul D.; Coombs, Robert W.; Dragavon, Joan; Thomas, Katherine K.; Brennan, Catherine A.; Devare, Sushil G.; Wood, Robert W.; Golden, Matthew R.; Clinical Infectious Diseases, 2009, vol. 49, issue 3, p 444, ISSN 10584838. ISBN 15376591. ...
The N meningitidis bacteria causing a recent cluster of sexually transmitted infections in Columbus, Ohio and other US cities have adapted to the urogenital environment, an analysis of their DNA shows.. Update: May 2016 Clinical Infectious Diseases paper on the same urethritis cluster.. Genetic changes make this clade look more like relatives that are known to cause gonorrhea. Some good news is that these guys are less likely to cause meningitis because they have lost their outer capsule. They have also gained enzymes that help them live in low oxygen.. The DNA analysis helps doctors track the spread of this type of bacteria and anticipate which vaccines might be protective against it. Thankfully, no alarming antibiotic resistance markers are present (yet) and currently available vaccines may be helpful. Full press release here, and information about meningococcal disease from the CDC here.. This looks like a well-worn path in bacterial evolution, since N. gonorrhoeae is thought to have evolved ...
1 - The Burden of Group B Streptococcus Worldwide for Pregnant Women, Stillbirths, and Children - Clinical Infectious Diseases Supplement (free arti
The Young Sick Bacchus (Italian: Bacchino Malato), also known as the Sick Bacchus or the Self-Portrait as Bacchus, is an early self-portrait by the Baroque artist Michelangelo Merisi da Caravaggio, dated between 1593 and 1594. It now hangs in the Galleria Borghese in Rome. According to Caravaggios first biographer, Giovanni Baglione, it was a cabinet piece painted by the artist using a mirror. The painting dates from Caravaggios first years in Rome following his arrival from his native Milan in mid-1592. Sources for this period are inconclusive and probably inaccurate, but they agree that at one point the artist fell extremely ill and spent six months in the hospital of Santa Maria della Consolazione.[citation needed] According to a 2009 article in the American medical publication Clinical Infectious Diseases, the painting indicates that Caravaggios physical ailment likely involved malaria, as the jaundiced appearance of the skin and the icterus in the eyes are indications of some active ...
Young children are more likely to become infected by respiratory viruses and experience severe symptoms and longer duration of illness than other age-groups, according to a study yesterday in Clinical Infectious Diseases.. The University of Utahs Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) study analyzed symptom reports and nasal swabs from 26 households comprising 108 individuals over 52 weeks (4,166 person-weeks). Participants ranged in age from 1 day to 57 years, and 85% of households had at least one child.. Researchers used polymerase chain reaction (PCR) testing to detect 16 respiratory viruses from 2009 to 2010, a period that included the second wave of the 2009 H1N1 pandemic.. Respiratory viruses were detected 783 times in participants over the year, and 440 (56%) of those infections were symptomatic. Individuals had an average of five respiratory viruses per year.. Children under age 5 tested positive for respiratory viruses in 50% of person-weeks, ...
A Better Grip: T Cells Strengthen Our Hand against Influenza Clinical Infectious Diseases, 52 (1), 8-9 DOI: 10.1093/cid/ciq018Flu vaccines are important and useful, but also relatively ineffective compared to many other vaccines. Immunity is imperfect, there are many strains of influenza in a given year only some of which are addressed by the available vaccine (though often the most common ones) and one years vaccine does not provide immunity to subsequent years influenza because the virus changes so much. Well, actually thats not exactly true: The influenza virus has various different parts, and the parts that the traditional flu vaccine uses to induce an antigenic reaction in the potential hose is highly variable. Other parts of the flu virus are not as variable. If only a vaccine could be developed that uses the less variable part of the influenza virus, then perhaps it would be a universal, long-lasting vaccine that you take once, and become pretty much immune to all future influenza ...
Won, Sarah Y.; Munoz-Price, L. Silvia; Lolans, Karen; Hota, Bala; Weinstein, Robert A.; Hayden, Mary K.; Clinical Infectious Diseases, 2011, vol. 53, issue 6, p 532, ISSN 10584838. ISBN 15376591. ...
"Finto: MeSH: Streptomyces antibioticus". finto: Finnish Thesaurus and Ontology Service. Retrieved 10 August 2015. Atta, Houssam ... Atta, Houssam M. (2010). "Production, Purification, Physico-Chemical Characteristics and Biological Activities of Antifungal ... isolation and biological properties". Journal of Saudi Chemical Society. 19 (1): 12-22. doi:10.1016/j.jscs.2011.12.011. Oh, ...
These parasites have been used in successful biological control against pest sawflies, including Cephus cinctus throughout the ... Rasnitsyn, A.P. (2006). "Ontology of evolution and methodology of taxonomy". Paleontological Journal. 40 (S6): S679-S737. doi: ... Biological Journal of the Linnean Society. 83 (2): 219-227. doi:10.1111/j.1095-8312.2004.00383.x. Krokene, Paal (6 December ... Biological Journal of the Linnean Society. 79: 245-275. doi:10.1046/j.1095-8312.2003.00233.x. Schulmeister, S. "'Symphyta'". ...
GeorgeTown.edu - Protein Ontology Chicco, Davide; Masseroli, Marco (25 November 2017). "Biological and Medical Ontologies: ... Protein Ontology (PRO)". Reference Module in Life Sciences. Elsevier. doi:10.1016/B978-0-12-809633-8.20396-8 - via ... The Protein Ontology (PRO) is another popular database released by the Protein Information Resource. http://pir.georgetown.edu ...
1] Bourlard, H.; Kamp, Y. (1988). "Auto-association by multilayer perceptrons and singular value decomposition". Biological ... Chicco, Davide; Sadowski, Peter; Baldi, Pierre (25 October 2014). "Deep Autoencoder Neural Networks for Gene Ontology ...
See also: Jesús Mosterín (1994). "Mereology, Set Theory, and Biological Ontology". In D. Prawitz and D. Westerståhl (eds.): ... Mosterín has also tackled issues like the definition of life itself or the ontology of biological organisms and species. ... which combines the ontology of animals as paradigmatic individuals with the insights and results of biological research. This ... Concerning the ontological thesis of Michael Ghiselin and David Hull on the individuality of biological species, Mosterín shows ...
Illinois University Biological Computer Laboratory BCL Report 3.0. Urbana: Biological Computer Laboratory, University of ... In 1962, he published Cybernetic ontology and transjunctional operations. Later he lectured at the University of Hamburg until ... ISBN 3-7873-1033-9. 1962, Cybernetic Ontology and Transjunctional Operations. University of Illinois, Engineering Experiment ...
Dybkaer, René (2004). "An ontology on property for physical, chemical, and biological systems". APMIS Suppl. (117): 1-210. PMID ...
"carbamoyl group (CHEBI:23004)". ChEBI: The database and ontology of Chemical Entities of Biological Interest. European ... Shaw WV, Tsai L, Stadtman ER (Feb 1966). "The enzymatic synthesis of N-methylglutamic acid". The Journal of Biological ... Identification of p35 as a novel regulatory subunit". The Journal of Biological Chemistry. 271 (1): 471-7. PMID 8550604. Lewis ... "EC 2.9.1". School of Biological & Chemical Sciences at Queen Mary, University of London. Nomenclature Committee of the ...
A database and ontology for chemical entities of biological interest". Nucleic Acids Research. 36 (Database issue): D344-D350. ... and is responsible for leading the team working on Chemical Entities of Biological Interest (ChEBI). He headed the ... "The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013". Nucleic Acids Research. ...
ISBN 0-231-02427-4. Stamos, D.N. (2003). The species problem : biological species, ontology, and the metaphysics of biology. ... Biological Journal of the Linnean Society. 94: 217. doi:10.1111/j.1095-8312.2008.00984.x. Ashlock, Peter D. (March 1971). " ...
Stamos, David N. (2003). The Species Problem: Biological Species, Ontology, and the Metaphysics of Biology. Lexington Books. p ... Unlike the Biological Species Concept, a cladistic species does not rely on reproductive isolation, so it is independent of ... In biology, a species is the basic unit of biological classification and a taxonomic rank, as well as a unit of biodiversity, ... Pimentel, David (2014). Biological Invasions: Economic and Environmental Costs of Alien Plant, Animal, and Microbe Species. CRC ...
A database and ontology for chemical entities of biological interest". Nucleic Acids Research. 36 (Database issue): D344-50. ... Sackmann, W.; Kern, H., Wiesmann, E.; Studies on the biological effects of solanine and tomatine.; Schweiz. Z. Allg. Pathol. ... Journal of Biological Chemistry. 289 (21): 14913-14924. doi:10.1074/jbc.M114.556241. PMC 4031541 . PMID 24719321. Ebert, S. M ... Journal of Biological Chemistry. 290 (42): 25497-25511. doi:10.1074/jbc.M115.681445. PMC 4646196 . PMID 26338703. Fujiwara, Y; ...
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 ...
He has also worked on species concept, evolutionary ontology and biological nomenclature. The standard author abbreviation ...
"The database and ontology of Chemical Entities of Biological Interest". EMBL-EBI, European Molecular Biology Laboratory, ...
Kloepper, J. W (1993). "Plant growth-promoting rhizobacteria as biological control agents". In Metting, F. B. Jr. Soil ... described by the Gene Ontology". BMC Microbiology. 9(Suppl 1): S6. doi:10.1186/1471-2180-9-S1-S6. ... Journal of Biological Chemistry. 286 (10): 7737-7743. doi:10.1074/jbc.C110.209288. PMC 3048661 . PMID 21257745. Maron, PA; ...
Chemical Entities of Biological Interest, also known as ChEBI, is a database and ontology of molecular entities focused on ' ... a database and ontology for chemical entities of biological interest". Nucleic Acids Research. 36 (Database issue): D344-50. ... "Chemical Entities of Biological Interest: an update". Nucleic Acids Research. 38 (Database issue): D249-54. doi:10.1093/nar/ ... small' chemical compounds, that is part of the Open Biomedical Ontologies effort. The term "molecular entity" refers to any " ...
A database and ontology for chemical entities of biological interest". Nucleic Acids Research. 36 (Database issue): D344-D350. ... Reference Genome Group of the Gene Ontology Consortium (2009). Bourne, Philip E., ed. "The Gene Ontology's Reference Genome ... "Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics. 25 (1): 25-29. doi:10.1038/ ... Wroe, C. J.; Stevens, R.; Goble, C. A.; Ashburner, M. (2003). "A methodology to migrate the gene ontology to a description ...
Stamos, DN (2003). The species problem: Biological species, ontology, and the metaphysics of biology. Lanham: Lexington Books. ... The term species was just used as a term for a sort or kind of organism, until in 1686 John Ray introduced the biological ... He argued for what came to be called the Biological Species Concept (BSC), that a species consists of populations of organisms ... This notion has been heavily criticized as essentialist, but modern realists have argued that while biological natural kinds ...
Gene ontology analysis provides a standard way to define these relationships. Gene ontologies start with very broad categories ... Finally, it takes a great amount of effort to discuss the biological significance of each regulated gene, so scientists often ... Breitling R (2006). "Biological microarray interpretation: the rules of engagement". Biochim. Biophys. Acta. 1759 (7): 319-27. ... Commonly used gene sets include those derived from KEGG pathways, Gene Ontology terms, gene groups that share some other ...
ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, pp. 17-24. Wikidata ...
"The Gene Ontology". Retrieved 31 May 2017. Tweedie, Susan; et al. (2009). "FlyBase: Enhancing Drosophila Gene Ontology ... GO annotation comprises at least three components: a GO term that describes molecular function, biological role or subcellular ... The Gene Ontology Project is a major bioinformatics initiative with the aim of standardizing the representation of gene and ... The Gene Ontology project was established 13 years ago in order to summarize this data consistently across different databases ...
... s are most often selected for study based on a priori knowledge of the gene's biological functional impact on the ... When examining functionality between genes in pathways, the Gene Ontology Consortium can help map these relationships. The GO ... The origins of complex disease involve many biological pathways, some of which may differ between disease phenotypes. Most ... Suitable candidate genes are generally selected based on known biological, physiological, or functional relevance to the ...
ISBN 0-7914-6938-7 The Species Problem: Biological Species, Ontology, and the Metaphysics of Biology. Lexington Books. 2004. ...
Maere, S (2005). "BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks". ... Ashburner, M (2000). "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium". Nat. Genet. 25: 25-29 ... ontology. In addition, DAVID tools can be used to analyze the roles of genes in metabolic pathways and show the biological ... TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched gene ontology terms ...
Gene ontology. Molecular function. • transcription factor activity, sequence-specific DNA binding. • RNA polymerase II ... Biological process. • anterior/posterior pattern specification. • multicellular organism development. • anterior/posterior axis ...
In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology ... Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The ... We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. ... association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or ...
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products ...
... Hang Yin,1 ShaoPeng Wang,2 Yu- ... M. A. Harris, J. I. Deegan, J. Lomax et al., "The gene ontology project in 2008," Nucleic Acids Research, vol. 36, pp. D440- ... L. Chen, C. Chu, J. Lu, X. Kong, T. Huang, and Y.-D. Cai, "Gene ontology and KEGG pathway enrichment analysis of a drug target- ... J. Yang, L. Chen, X. Kong, T. Huang, and Y.-D. Cai, "Analysis of tumor suppressor genes based on gene ontology and the KEGG ...
Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry ... we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and ... These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to ... We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of ...
bp_form_complete-{ontology_id_list}-{value}. * For example, bp_form_complete-NCIT-uri. will use NCI Thesaurus (ontology id is ... var BP_ontology_id = "NCIt,SNOMEDCT"; * You can set the variable to all to search all ontologies in BioPortal: var BP_ ... Note: If you would like to use Quick Jump across multiple ontologies: * You can enter a comma-separated list of ontology ids: ... The autocomplete widget accesses ontology content from the latest version of the ontology. ...
Ontology of Biological and Clinical Statistics LOOM http://purl.obolibrary.org/obo/PR_000000001 Ontology of Biological and ... Chemical Entities of Biological Interest Ontology LOOM http://purl.obolibrary.org/obo/CHEBI_36080 Ontology of Biological ... www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#Protein Cell Line Ontology [by Mahadevan] LOOM ... www.imgt.org/download/IMGT-ONTOLOGY/IMGT-ONTOLOGY-v1-0-2.owl#protein Immunogenetics Ontology LOOM ...
http://purl.obolibrary.org/obo/ODGI.owl#Biological_Process OGDI LOOM http://www.semanticweb.org/ontologies/2010/5/22/ ... http://www.co-ode.org/ontologies/galen#BiologicalProcess GALEN LOOM http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_ ... http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Biological_process GFO-BIO LOOM ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ...
... www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#Dermis MCCL LOOM ... http://purl.bioontology.org/ontology/SNMI/T-01200 SNMI LOOM http://phenomebrowser.net/ontologies/mesh/mesh.owl#D020405 RH-MESH ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://phenomebrowser.net/ontologies/mesh/mesh.owl#A17.815.180 RH-MESH LOOM ...
The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ...
... www.imgt.org/download/IMGT-ONTOLOGY/IMGT-ONTOLOGY-v1-0-2.owl#protein IMGT-ONTOLOGY LOOM ... www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#Protein MCCL LOOM ... http://purl.bioontology.org/ontology/LNC/LP32142-9 LOINC LOOM http://glycomics.ccrc.uga.edu/ontologies/GlycO#protein GLYCO LOOM ... http://jermontology.org/ontology/JERMOntology#Protein JERM LOOM http://bioontology.org/projects/ontologies/birnlex#birnlex_23 ...
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... http://purl.obolibrary.org/obo/ODGI.owl#Biological_Process OGDI LOOM http://www.semanticweb.org/ontologies/2010/5/22/ ... http://www.co-ode.org/ontologies/galen#BiologicalProcess GALEN LOOM http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_ ... http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Biological_process GFO-BIO LOOM ...
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division ... Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division ...
The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://purl.bioontology.org/ontology/CSP/0581-3156 CRISP LOOM http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Arteriole SYN ...
http://www.limics.fr/ontologies/ontoparonnoy#Objet ONTOPARON LOOM http://www.limics.fr/ontologies/ontoparonnoy#Objet ONTOPARON_ ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://www.owl-ontologies.com/Ontology1184060740.owl#OWLClass_fede789e_08ff_4d4a_bf4a_cd6f393a670d EXACT LOOM ... http://bioportal/bioontology.org/ontologies/HIVO0004#OWLClass_697c460c_224e_4301_900f_29e232403462 HIVO004 LOOM ...
http://purl.bioontology.org/ontology/CSP/2483-1217 CRISP LOOM http://www.cognitiveatlas.org/ontology/cogat.owl#CAO_00212 NIFSTD ... http://purl.bioontology.org/ontology/SNMI/C-D2235 SNMI LOOM http://www.onto-med.de/ontologies/gfo-persian-medicine-diseases.owl ... http://www.cognitiveatlas.org/ontology/cogat.owl#CAO_00205 CHEAR LOOM http://www.cognitiveatlas.org/ontology/cogat.owl#CAO_ ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ...
The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://purl.bioontology.org/ontology/SNOMEDCT/34582008 SNOMEDCT LOOM http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C88516 ...
The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are ... BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.. Maere S1, Heymans K ... BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in ...
http://phenomebrowser.net/ontologies/mesh/mesh.owl#D014859 RH-MESH LOOM http://purl.bioontology.org/ontology/SNMI/C-A6530 SNMI ... www.semanticweb.org/席婷/ontologies/2019/3/untitled-ontology-62#Warfarin PCALION LOOM ... www.semanticweb.org/席婷/ontologies/2019/3/untitled-ontology-62#Warfarin PCALION LOOM ... http://purl.bioontology.org/ontology/SNOMEDCT/372756006 SNOMEDCT LOOM http://purl.bioontology.org/ontology/LNC/LP16309-4 LOINC ...
The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://purl.bioontology.org/ontology/SNOMEDCT/34641002 SNOMEDCT LOOM http://data.bnf.fr/ark:/12148/cb12216776m FAST-TOPICAL ...
http://www.semanticweb.org/ontologies/epo.owl#Levonorgestrel EPO LOOM http://purl.bioontology.org/ontology/NDDF/001304 NDDF ... http://www.co-ode.org/ontologies/galen#Levonorgestrel GALEN LOOM http://phenomebrowser.net/ontologies/mesh/mesh.owl#D04.808. ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://phenomebrowser.net/ontologies/mesh/mesh.owl#D016912 RH-MESH LOOM http://purl.obolibrary.org/obo/DDO.owl#DDO_0004734 DDO ...
http://www.owl-ontologies.com/OntologyXCT.owl#Stable CTX LOOM http://www.limics.fr/ontologies/menelastop/stable ONTOPSYCHIA ... http://www.limics.fr/ontologies/ontopsychiasoc#Stable ONTOPSYCHIA LOOM http://www.co-ode.org/ontologies/galen#stable GALEN LOOM ... http://www.semanticweb.org/ontologies/epo.owl#Stable EPO LOOM http://doe-generated-ontology.com/OntoPneumo#Stable ONTOPNEUMO ... http://www.limics.fr/ontologies/ontoparonnoy#Stable ONTOPARON_SOCIAL LOOM http://www.limics.fr/ontologies/ontoparonnoy#Stable ...
... www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#NervousSystem MCCL LOOM ... http://phenomebrowser.net/ontologies/mesh/mesh.owl#D009420 RH-MESH LOOM http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl# ... http://bioportal.bioontology.org/ontologies/FISHO#FISHO_0000221 FISHO LOOM http://purl.bioontology.org/ontology/CST/NER COSTART ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ...
http://phenomebrowser.net/ontologies/mesh/mesh.owl#C008281 RH-MESH LOOM http://sbmi.uth.tmc.edu/ontology/ochv#C0064992 OCHV ... http://purl.bioontology.org/ontology/PDQ/CDR0000664042 PDQ LOOM http://purl.bioontology.org/ontology/SNOMEDCT/11038000 SNOMEDCT ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://purl.bioontology.org/ontology/RXNORM/1426476 RXNORM LOOM http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C61714 NCIT ...
http://swrl.stanford.edu/ontologies/3.3/swrla.owl#Entity OGDI LOOM http://swrl.stanford.edu/ontologies/3.3/swrla.owl#Entity OF ... http://swrl.stanford.edu/ontologies/3.3/swrla.owl#Entity BOF LOOM http://swrl.stanford.edu/ontologies/3.3/swrla.owl#Entity CTX ... www.semanticweb.org/abed/ontologies/2015/2/untitled-ontology-346#Entity FALL LOOM ... http://swrl.stanford.edu/ontologies/3.3/swrla.owl#Entity SITBAC LOOM http://swrl.stanford.edu/ontologies/3.3/swrla.owl#Entity ...
  • The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-HG004028. (bioontology.org)
  • As of 2006, OBO forms part of the resources of the U.S. National Center for Biomedical Ontology where it will form a central element of the NCBO's BioPortal. (wikipedia.org)
  • Databases, such as Ontology Lookup Service or ses, such as MIRIAM Registry or of the EBI-EMBL, the TissueDistributionDB, including the Tissue Synonym Library of the German Cancer Research Center (DKFZ) in Heidelberg or the Bioportal plattform of the National Center for Biomedical Ontology (Stanford, USA) rely on the BTO and implement the encyclopedia as an essential repository of information into their respective plattform. (wikipedia.org)
  • The National Center for Biomedical Ontology (www.bioontology.org) develops tools for automated annotation of database records based on the textual descriptions of those records. (wikipedia.org)
  • Overall, this study suggests that epigenetic mechanisms may be important to maintaining appropriate patterns of gene regulation in biological systems that differ in genome copy number. (royalsocietypublishing.org)
  • Tools and techniques for biological inference problems at scales ranging from genome-wide to pathway-specific. (mit.edu)
  • The Ancestry Ontology (Ancestro) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. (ebi.ac.uk)
  • By combining gene function, ontology, pathways and statistical analysis tools, PANTHER enables biologists to analyze large-scale, genome-wide data obtained from the current advance technology including: sequencing, proteomics or gene expression experiments. (wikipedia.org)
  • Since PANTHER is part of the GO reference genome project, the Gene Ontology (GO) terms are used for gene function. (wikipedia.org)
  • BRENDA links to some further databases and repositories such as: BRENDA tissue ontology ExPASy NCBI databases (Protein, nucleotide, structure, genome, OMIM, Domains IUBMB enzyme nomenclature KEGG PDB database (3D information) PROSITE SCOP CATH InterPro ChEBI Uniprot Chang A, Scheer M, Grote A, Schomburg I, Schomburg D (2008). (wikipedia.org)
  • PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and its features, together with a wide range of associated biological data and references to supporting literature. (wikipedia.org)
  • When the first draft of the human genome was completed in the early 2000s, TBI continued to grow and demonstrate prominence as a means to bridge biological findings with clinical informatics, impacting the opportunities for both industries of biology and healthcare. (wikipedia.org)
  • identifying portions of the genome that do not code for proteins identifying elements on the genome, a process called gene prediction, and attaching biological information to these elements. (wikipedia.org)
  • WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about other related nematodes. (wikipedia.org)
  • In the fields of metabolic engineering and systems biology, fluxomic methods are considered a key enabling technology due to their unique position in the ontology of biological processes, allowing genome scale stoichiometric models to act as a framework for the integration of diverse biological datasets. (wikipedia.org)
  • 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)
  • description of the main biological concepts and the new data-driven algorithms. (mit.edu)
  • Gruber introduced the term to mean a specification of a conceptualization: An ontology is a description (like a formal specification of a program) of the concepts and relationships that can formally exist for an agent or a community of agents. (wikipedia.org)
  • Relational database concepts of computer science and Information retrieval concepts of digital libraries are important for understanding biological databases. (wikipedia.org)
  • There are two common concepts of biological databases: Primary Databases and Secondary Databases. (wikipedia.org)
  • Computationally, semantic similarity can be estimated by defining a topological similarity, by using ontologies to define the distance between terms/concepts. (wikipedia.org)
  • Similarity is also applied to find similar geographic features or feature types: SIM-DL similarity server can be used to compute similarities between concepts stored in geographic feature type ontologies. (wikipedia.org)
  • Similarity Calculator can be used to compute how well related two geographic concepts are in the Geo-Net-PT ontology. (wikipedia.org)
  • Such ontologies must therefore consist of terms expressing very general concepts, but such concepts are so basic to our understanding that there is no way in which they can be defined, since the very process of definition implies that a less basic (and less well understood) concept is defined in terms of concepts that are more basic and so (ideally) more well understood. (wikipedia.org)
  • There is no self-evident way of dividing the world up into concepts, and certainly no non-controversial one There is no neutral ground that can serve as a means of translating between specialized (or "lower" or "application-specific") ontologies Human language itself is already an arbitrary approximation of just one among many possible conceptual maps. (wikipedia.org)
  • To draw any necessary correlation between English words and any number of intellectual concepts we might like to represent in our ontologies is just asking for trouble. (wikipedia.org)
  • To make this search more effective, the NIF is constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g. stating that a neuron is a cell. (wikipedia.org)
  • To fix this, we need mechanisms for specifying and sharing design patterns as a way of standardising logical definitions both within and between phenotype ontologies. (oregonstate.edu)
  • We introduce the phenotype ontology community to the idea and benefits of pattern-based ontology development and present two suites of tools, one for analysing the state of alignment between phenotype ontologies and prioritising design pattern changes and another for implementing these changes. (oregonstate.edu)
  • This will start with an introduction to pattern-based ontology development emphasising its benefits and importance, illustrated using the dead simple OWL design pattern (DOSDP framework) and examples from phenotype ontologies. (oregonstate.edu)
  • A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. (ku.edu)
  • We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (ku.edu)
  • Cui H, Macklin J, Sachs J, Reznicek A, Starr J, Ford B, Penev L, Chen H (2018) Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production. (pensoft.net)
  • When added to the massive amount of phenotype data sitting in older publications, these free-text character descriptions represent a major, under-utilised resource for integrating phenotypic data into modern, large-scale biological research projects that typically involve genomic, climatic and habitat data. (pensoft.net)
  • Concomitant with an increasing number of omic experiments now being carried out, the quantity of associated experimental meta-data has reached unprecedented levels and traditional approaches to biological meta-data management are no longer adequate. (springer.com)
  • In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. (biomedcentral.com)
  • OBCS is a timely ontology that represents statistics-related terms and their relations in a rigorous fashion, facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (biomedcentral.com)
  • To facilitate discovery and usability of these data to external users, and also to address the goal of reproducibility, ImmPort is seeking wherever possible to draw on publicly available ontologies such as the Cell Ontology (CL) [ 5 ] and the Protein Ontology (PRO) [ 6 ] as sources for the terms used in these templates. (biomedcentral.com)
  • http://www.environmentontology.org ) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. (biomedcentral.com)
  • ENVO is comprised of classes (terms) referring to key environment-types that may be used to facilitate the retrieval and integration of a broad range of biological data. (biomedcentral.com)
  • The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. (ebi.ac.uk)
  • Therefore, it is important to have a consistent terminology metadata model and a resource for discovering appropriate ontologies or other resource for use in annotating data. (oregonstate.edu)
  • The EFO data is available through a public web interface, BioPortal Web Service hosted at the National Centre for Biomedical Ontology (NCBO) and downloads. (wikipedia.org)
  • Advantages of this approach include the general increased quality of the data returned in searches and with proper tagging, ontologies finding entries that may not explicitly state the search term but are still relevant. (wikipedia.org)
  • Another use of ontologies is within databases such as SwissProt, Ensembl and TrEMBL, which use this technology to search through the stores of human proteome-related data for tags related to the search term. (wikipedia.org)
  • the result was a data-warehouse like effect, with easy access to multiple databases through the use of ontologies. (wikipedia.org)
  • The MGED Ontology was originally identified in the transcriptomics domain by the FGED Society and was developed to address the needs of data integration. (wikipedia.org)
  • Most biological databases are available through web sites that organise data such that users can browse through the data online. (wikipedia.org)
  • Biological data comes in many formats. (wikipedia.org)
  • Query tools allow navigation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. (wikipedia.org)
  • Most of the interoperable behaviours seen in Moby are achieved through the Object (data-format) and Namespace (data-type) ontologies. (wikipedia.org)
  • The MOBY Object Ontology is an ontology consisting of IS-A, HAS-A, and HAS relationships between data formats. (wikipedia.org)
  • MOBY Central is aware of the Object, Namespace and Service ontologies, and thus can match consumers who have in-hand Moby data, with service providers who claim to consume that data-type (or some compatible ontological data-type) or to perform a particular operation on it. (wikipedia.org)
  • The BioMOBY Object Ontology controls the valid data structures in exactly the same way as an OWL ontology defines an RDF data instance. (wikipedia.org)
  • Before analyzing data for biological variation, QC steps must be performed to determine whether the data is fit for statistical testing. (wikipedia.org)
  • The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. (wikipedia.org)
  • The existing core modules of Chado are: sequence - for sequences/features cv - for controlled-vocabs/ontologies general - currently just dbxrefs organism - taxonomic data pub - publication and references companalysis - augments sequence module with computational analysis data map - non-sequence maps genetic - genetic and phenotypic data expression - gene expression natural diversity - population data The full list of GMOD software components is found on the GMOD Components page. (wikipedia.org)
  • Fig. 1-2) a reference layer of individual metabolite compounds and their reference spectra including additional information on their biological roles, locations, concentrations and raw data from metabolomic experiments. (wikipedia.org)
  • Official website MetaboLights Tutorial-MetaboLights Train On-Line Biological Magnetic Resonance Data Bank- A repository for NMR spectroscopy http://www.isa-tools.org/-[permanent dead link] The Investigation/Study/Assay format for reporting metadata Metabolites Standard Initiative- (Correspondence) Nature Biotechnology 25: 2007. (wikipedia.org)
  • It plays a role in the text mining of biological literature and the development of biological and gene ontologies to organize and query biological data. (wikipedia.org)
  • To study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. (wikipedia.org)
  • Model organism databases (MODs) are biological databases dedicated to the provision of in-depth biological data for intensively studied model organisms. (wikipedia.org)
  • Ontologies such as the Gene Ontology are being used to annotate the results of biological experiments in a variety of model organisms in order to create logically tractable bodies of data available for reasoning and search. (wikipedia.org)
  • There are several computational methods of protein function prediction that can infer protein function using a variety of biological and evolutionary data, but there is significant room for improvement. (wikipedia.org)
  • Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. (wikipedia.org)
  • ZFIN consists of two principal parts: a website of community news and announcements, as well as biological resources such as laboratory protocols, a gene nomenclature guide, and anatomy information a relational database containing biological data that are curated from the scientific literature and that are directly submitted by zebrafish research laboratories (e.g. (wikipedia.org)
  • GenMAPP allows users to visualize and analyze their data in the context of pathway collections and the Gene Ontology. (wikipedia.org)
  • InterMine is used to create databases of biological data accessed by sophisticated web query tools. (wikipedia.org)
  • Support is provided for several common biological formats and there is a framework for adding other data. (wikipedia.org)
  • Initially, the focus of TBI was on ontology and vocabulary designs for searching the mass data stores. (wikipedia.org)
  • Expression profiling, text mining for trends analysis, population-based data mining providing biomedical insights, and ontology development has been explored, defined and established as important contributions to TBI. (wikipedia.org)
  • EMAGE (e-Mouse Atlas of Gene Expression) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. (wikipedia.org)
  • However, with the burgeoning volume of biological data and increasingly diverse densely informative published literatures, expert curation becomes more and more laborious and time-consuming, increasingly lagging behind knowledge creation. (wikipedia.org)
  • Another community based approach to analyze biological data is called Systems Biology Verification (SBV) IMPROVER. (wikipedia.org)
  • In 2012, Poldrack undertook a project to collect brain imaging, behavior, and biological data on himself for an extended period of time. (wikipedia.org)
  • Poldrack's lab also develops informatics tools to help make sense of the growing body of neuroimaging data (including the OpenfMRI.org and neurovault.org data sharing projects and the Cognitive Atlas ontology) as well as tools to help improve the reproducibility of neuroimaging research (including the Brain Imaging Data Structure and BIDS-Apps projects). (wikipedia.org)
  • An important resource for finding biological databases is a special yearly issue of the journal Nucleic Acids Research (NAR). (wikipedia.org)
  • however, such approaches are not focused on, or do not include, the conceptual part of complexity related to organization and topological attributes or algebraic topology, such as network connectivity of genomes, interactomes and biological organisms that are very important. (wikipedia.org)
  • Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. (wikipedia.org)
  • Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. (wikipedia.org)
  • Biological knowledge is distributed among many different general and specialized databases. (wikipedia.org)
  • One solution is how biological databases cross-reference to other databases with accession numbers to link their related knowledge together. (wikipedia.org)
  • ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, pp. 17-24. (wikipedia.org)
  • Furthermore, cross-references to external information resources such as sequence and 3D-structure databases, as well as biomedical ontologies, are provided. (wikipedia.org)
  • 0.1867361 The EMBL-EBI hosts a number of publicly open, free to use life science resources, including biomedical databases, analysis tools and bio-ontologies. (wikipedia.org)
  • GenMAPP builds and maintains gene databases for a variety of key model organisms: human - Homo sapiens mouse - Mus musculus rat - Rattus norvegicus yeast - Saccharomyces cerevisiae zebrafish - Danio rerio worm - Caenorhabditis elegans fruit fly - Drosophila melanogaster dog - Canis familiaris cow - Bos taurus mosquito - Anopheles gambiae E.coli - Escherichia coli GenMAPP provides tools to create, edit and annotate biological pathway maps. (wikipedia.org)
  • A biocurator is a professional scientist who curates, collects, annotates, and validates information that is disseminated by biological and model Organism Databases. (wikipedia.org)
  • For example, Genbank has "gi" identifiers that are used to enumerate all of their sequence records - this is defined as "NCBI_gi" in the Namespace Ontology. (wikipedia.org)
  • TErminology for the Description of DYnamics (TEDDY) aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. (wikipedia.org)
  • It was the need for consistent description of the environmental origins of tissue, pathogen, and metagenomics samples, together with a parallel need in the labeling of samples and artifacts in museum collections that precipitated the creation of the Environment Ontology (ENVO). (biomedcentral.com)
  • By this way, if a lower level ontologies want to realign its relations to another high-level ontology, a new profile can be created to associate them. (w3.org)
  • To solve this problem some genuinely top level ontologies have been developed, which are deliberately designed to have minimal overlap with any domain ontologies. (wikipedia.org)
  • The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format. (wikipedia.org)
  • Robert Arp (born March 20, 1970 in Chicago, Illinois, United States) is an American philosopher known for his work in ethics, modern philosophy, ontology (information science), philosophy of biology, cognitive science, evolutionary psychology, and philosophy and popular culture. (wikipedia.org)
  • Concerning biological function (biology), Arp has put forward a middle position between the two viable accounts of function today-namely, the organizational account of function (usually attributed to Robert Cummins) and the modern history account of function (usually attributed to Paul Griffiths and Peter Godfrey-Smith)-and his position has been called "reconciliatory" and "pluralist. (wikipedia.org)
  • The philosophy of biology is a subfield of philosophy of science, which deals with epistemological, metaphysical, and ethical issues in the biological and biomedical sciences. (wikipedia.org)
  • An updated list of publications of theoretical biologist Robert Rosen Theory of Biological Anthropology (Documents No. 9 and 10 in English) Drawing the Line Between Theoretical and Basic Biology, a forum article by Isidro A. T. Savillo Synthesis and Analysis of a Biological System[permanent dead link], by Hiroyuki Kurata, 1999. (wikipedia.org)
  • Systems biology recognizes the complexity of biological systems and has the broader goal of explaining and predicting this complex behavior. (wikipedia.org)
  • 2012) Stepping Beyond the Newtonian Paradigm in Biology: Towards an Integrable Model of Life - Accelerating Discovery in the Biological Foundations of Science INBIOSA White Paper. (wikipedia.org)
  • In the early 1990s, the widely cited Web page and paper "Toward Principles for the Design of Ontologies Used for Knowledge Sharing" by Tom Gruber is credited with a deliberate definition of ontology as a technical term in computer science. (wikipedia.org)
  • Metabolomic technologies are increasingly being applied to study biological questions in a range of different settings from clinical through to environmental. (springer.com)
  • Increasingly these ontologies are being used to govern the behaviour of all BioMOBY functions using DL reasoners. (wikipedia.org)
  • A biological process represents a specific objective that the organism is genetically programmed to achieve. (bioontology.org)
  • 2006a ), we define here a 'biological sample' as a discrete entity comprised of one or more organism(s), or parts thereof. (springer.com)
  • Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. (ebi.ac.uk)
  • Nevertheless, this approach has its supporters which define humans as a biological organism and asserts the proposition that a psychological relation is not necessary for personal continuity. (wikipedia.org)
  • The BTO is one of the first tissue-specific ontologies in life sciences, not restricted to a specific organism or a specific organism group providing a user-friendly access to the wide range of tissue and cell-type information. (wikipedia.org)