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1.
Background
Web-based, free-text documents on science and technology have been increasing growing on the web. However, most of these documents are not immediately processable by computers slowing down the acquisition of useful information. Computational ontologies might represent a possible solution by enabling semantically machine readable data sets. But, the process of ontology creation, instantiation and maintenance is still based on manual methodologies and thus time and cost intensive.Method
We focused on a large corpus containing information on researchers, research fields, and institutions. We based our strategy on traditional entity recognition, social computing and correlation. We devised a semi automatic approach for the recognition, correlation and extraction of named entities and relations from textual documents which are then used to create, instantiate, and maintain an ontology.Results
We present a prototype demonstrating the applicability of the proposed strategy, along with a case study describing how direct and indirect relations can be extracted from academic and professional activities registered in a database of curriculum vitae in free-text format. We present evidence that this system can identify entities to assist in the process of knowledge extraction and representation to support ontology maintenance. We also demonstrate the extraction of relationships among ontology classes and their instances.Conclusion
We have demonstrated that our system can be used for the conversion of research information in free text format into database with a semantic structure. Future studies should test this system using the growing number of free-text information available at the institutional and national levels. 相似文献2.
Pablo Moreno Stephan Beisken Bhavana Harsha Venkatesh Muthukrishnan Ilinca Tudose Adriano Dekker Stefanie Dornfeldt Franziska Taruttis Ivo Grosse Janna Hastings Steffen Neumann Christoph Steinbeck 《BMC bioinformatics》2015,16(1)
Background
Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.Results
We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.Conclusions
BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0486-3) contains supplementary material, which is available to authorized users. 相似文献3.
Background
Evidence about relevant outcomes is required in the evaluation of clinical interventions for children with autism spectrum disorders (ASD). However, to date, the variety of outcome measurement tools being used, and lack of knowledge about the measurement properties of some, compromise conclusions regarding the most effective interventions.Objectives
This two-stage systematic review aimed to identify the tools used in studies evaluating interventions for anxiety for high-functioning children with ASD in middle childhood, and then to evaluate the tools for their appropriateness and measurement properties.Methods
Electronic databases including Medline, PsychInfo, Embase, and the Cochrane database and registers were searched for anxiety intervention studies for children with ASD in middle childhood. Articles examining the measurement properties of the tools used were then searched for using a methodological filter in PubMed, and the quality of the papers evaluated using the COSMIN checklist.Results
Ten intervention studies were identified in which six tools measuring anxiety and one of overall symptom change were used as primary outcomes. One further tool was included as it is recommended for standard use in UK children''s mental health services. Sixty three articles on the properties of the tools were evaluated for the quality of evidence, and the quality of the measurement properties of each tool was summarised.Conclusions
Overall three questionnaires were found robust in their measurement properties, the Spence Children''s Anxiety Scale, its revised version – the Revised Children''s Anxiety and Depression Scale, and also the Screen for Child Anxiety Related Emotional Disorders. Crucially the articles on measurement properties provided almost no evidence on responsiveness to change, nor on the validity of use of the tools for evaluation of interventions for children with ASD.PROSPERO Registration number
CRD42012002684. 相似文献4.
Chante Karimkhani Lindsay N. Boyers David J. Margolis Mohsen Naghavi Roderick J. Hay Hywel C. Williams Luigi Naldi Luc E. Coffeng Martin A. Weinstock Cory A. Dunnick Hannah Pederson Theo Vos Christopher J. L. Murray Robert P. Dellavalle 《PloS one》2014,9(7)
Importance
Disease burden data helps guide research prioritization.Objective
To determine the extent to which grants issued by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) reflect disease burden, measured by disability-adjusted life years (DALYs) from Global Burden of Disease (GBD) 2010 project.Design
Two investigators independently assessed 15 skin conditions studied by GBD 2010 in the NIAMS database for grants issued in 2013. The 15 skin diseases were matched to their respective DALYs from GBD 2010.Setting
The United States NIAMS database and GBD 2010 skin condition disability data.Main Outcome(s) and Measure(s)
Relationship of NIAMS grant database topic funding with percent total GBD 2010 DALY and DALY rank for 15 skin conditions.Results
During fiscal year 2013, 1,443 NIAMS grants were issued at a total value of $424 million. Of these grants, 17.7% covered skin topics. Of the total skin disease funding, 82% (91 grants) were categorized as “general cutaneous research.” Psoriasis, leprosy, and “other skin and subcutaneous diseases” (ie; immunobullous disorders, vitiligo, and hidradenitis suppurativa) were over-represented when funding was compared with disability. Conversely, cellulitis, decubitus ulcer, urticaria, acne vulgaris, viral skin diseases, fungal skin diseases, scabies, and melanoma were under-represented. Conditions for which disability and funding appeared well-matched were dermatitis, squamous and basal cell carcinoma, pruritus, bacterial skin diseases, and alopecia areata.Conclusions and Relevance
Degree of representation in NIAMS is partly correlated with DALY metrics. Grant funding was well-matched with disability metrics for five of the 15 studied skin diseases, while two skin diseases were over-represented and seven were under-represented. Global burden estimates provide increasingly transparent and important information for investigating and prioritizing national research funding allocations. 相似文献5.
Astrid Duque-Ramos Martin Boeker Ludger Jansen Stefan Schulz Miguela Iniesta Jesualdo Tomás Fernández-Breis 《PloS one》2014,9(8)
Objective
To (1) evaluate the GoodOD guideline for ontology development by applying the OQuaRE evaluation method and metrics to the ontology artefacts that were produced by students in a randomized controlled trial, and (2) informally compare the OQuaRE evaluation method with gold standard and competency questions based evaluation methods, respectively.Background
In the last decades many methods for ontology construction and ontology evaluation have been proposed. However, none of them has become a standard and there is no empirical evidence of comparative evaluation of such methods. This paper brings together GoodOD and OQuaRE. GoodOD is a guideline for developing robust ontologies. It was previously evaluated in a randomized controlled trial employing metrics based on gold standard ontologies and competency questions as outcome parameters. OQuaRE is a method for ontology quality evaluation which adapts the SQuaRE standard for software product quality to ontologies and has been successfully used for evaluating the quality of ontologies.Methods
In this paper, we evaluate the effect of training in ontology construction based on the GoodOD guideline within the OQuaRE quality evaluation framework and compare the results with those obtained for the previous studies based on the same data.Results
Our results show a significant effect of the GoodOD training over developed ontologies by topics: (a) a highly significant effect was detected in three topics from the analysis of the ontologies of untrained and trained students; (b) both positive and negative training effects with respect to the gold standard were found for five topics.Conclusion
The GoodOD guideline had a significant effect over the quality of the ontologies developed. Our results show that GoodOD ontologies can be effectively evaluated using OQuaRE and that OQuaRE is able to provide additional useful information about the quality of the GoodOD ontologies. 相似文献6.
Background
A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data.Methodology
To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy.Conclusions
A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. 相似文献7.
Fengqiong Huang James A Macklin Hong Cui Heather A Cole Lorena Endara 《BMC bioinformatics》2015,16(1)
Background
The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software.Methods
OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java.Results
Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts’ opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available.Conclusion
OTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains. 相似文献8.
9.
Background
In general, the definite determination of bacterial species is a tedious process and requires extensive manual labour. Novel technologies for bacterial detection and analysis can therefore help microbiologists in minimising their efforts in developing a number of microbiological applications.Methodology
We present a robust, standardized procedure for automated bacterial analysis that is based on the detection of patterns of protein masses by MALDI mass spectrometry. We particularly applied the approach for classifying and identifying strains in species of the genus Erwinia. Many species of this genus are associated with disastrous plant diseases such as fire blight. Using our experimental procedure, we created a general bacterial mass spectra database that currently contains 2800 entries of bacteria of different genera. This database will be steadily expanded. To support users with a feasible analytical method, we developed and tested comprehensive software tools that are demonstrated herein. Furthermore, to gain additional analytical accuracy and reliability in the analysis we used genotyping of single nucleotide polymorphisms by mass spectrometry to unambiguously determine closely related strains that are difficult to distinguish by only relying on protein mass pattern detection.Conclusions
With the method for bacterial analysis, we could identify fire blight pathogens from a variety of biological sources. The method can be used for a number of additional bacterial genera. Moreover, the mass spectrometry approach presented allows the integration of data from different biological levels such as the genome and the proteome. 相似文献10.
Background
Little is known about colorectal cancer or colon and rectal cancer. Are they the same disease or different diseases?Objectives
The aim of this epidemiology study was to compare the features of colon and rectal cancer by using recent national cancer surveillance data.Design and setting
Data included colorectal cancer (1995–2008) from the Surveillance, Epidemiology, and End Results Program (SEER) database. Only adenocarcinoma was included for analysis.Patients
A total of 372,130 patients with a median follow-up of 32 months were analyzed.Main outcome measures
Mean survival of patients with the same stage of colon and rectal cancer was evaluated.Results
Around 35% of patients had stage information. Among them, colon cancer patients had better survival than those with rectal cancer, by a margin of 4 months in stage IIB. In stage IIIC and stage IV, rectal cancer patients had better survival than colon cancer patients, by about 3 months. Stage IIB colorectal cancer patients had a poorer prognosis than those with stage IIIA and IIIB colorectal cancer. After adjustment of age, sex and race, colon cancer patients had better survival than rectal cancer of stage IIB, but in stage IIIC and IV, rectal cancer patients had better survival than colon cancer.Limitations
The study is limited by its retrospective nature.Conclusion
This was a population-based study. The prognosis of rectal cancer was not worse than that of colon cancer. Local advanced colorectal cancer had a poorer prognosis than local regional lymph node metastasis. Stage IIB might require more aggressive chemotherapy, and no less than that for stage III. 相似文献11.
Background
The emerging market of mobile phone technology and its use in the health sector is rapidly expanding and connecting even the most remote areas of world. Distributing diagnostic images over the mobile network for knowledge sharing, feedback or quality control is a logical innovation.Objective
To determine the feasibility of using mobile phones for capturing microscopy images and transferring these to a central database for assessment, feedback and educational purposes.Methods
A feasibility study was carried out in Uganda. Images of microscopy samples were taken using a prototype connector that could fix a variety of mobile phones to a microscope. An Information Technology (IT) platform was set up for data transfer from a mobile phone to a website, including feedback by text messaging to the end user.Results
Clear images were captured using mobile phone cameras of 2 megapixels (MP) up to 5MP. Images were sent by mobile Internet to a website where they were visualized and feedback could be provided to the sender by means of text message.Conclusion
The process of capturing microscopy images on mobile phones, relaying them to a central review website and feeding back to the sender is feasible and of potential benefit in resource poor settings. Even though the system needs further optimization, it became evident from discussions with stakeholders that there is a demand for this type of technology. 相似文献12.
13.
Charles P. Mercado Stephanie Byrum Marjorie L. Beggs Endrit Ziu Preeti Singh Vinay R. Raj Randy S. Haun Fusun Kilic 《PloS one》2013,8(8)
Background
Serotonin (5-HT) is a biogenic amine that also acts as a mitogen and a developmental signal early in rodent embryogenesis. Genetic and pharmacological disruption of 5-HT signaling causes various diseases and disorders via mediating central nervous system, cardiovascular system, and serious abnormalities on a growing embryo. Today, neither the effective modulators on 5-HT signaling pathways nor the genes affected by 5-HT signal are well known yet.Methodology/Principal Findings
In an attempt to identify the genes altered by 5-HT signaling pathways, we analyzed the global gene expression via the Illumina array platform using the mouse WG-6 v2.0 Expression BeadChip containing 45,281 probe sets representing 30,854 genes in megakaryocytes isolated from mice infused with 5-HT or saline. We identified 723 differentially expressed genes of which 706 were induced and 17 were repressed by elevated plasma 5-HT.Conclusions/Significance
Hierarchical gene clustering analysis was utilized to represent relations between groups and clusters. Using gene ontology mining tools and canonical pathway analyses, we identified multiple biological pathways that are regulated by 5-HT: (i) cytoskeletal remodeling, (ii) G-protein signaling, (iii) vesicular transport, and (iv) apoptosis and survival. Our data encompass the first extensive genome-wide based profiling in the progenitors of platelets in response to 5-HT elevation in vivo. 相似文献14.
Martijn AH Oude Voshaar Peter M ten Klooster Erik Taal Eswar Krishnan Mart AFJ van de Laar 《Arthritis research & therapy》2012,14(2):R47-7
Introduction
Patient-reported physical function is an established outcome domain in clinical studies in rheumatology. To overcome the limitations of the current generation of questionnaires, the Patient-Reported Outcomes Measurement Information System (PROMIS®) project in the USA has developed calibrated item banks for measuring several domains of health status in people with a wide range of chronic diseases. The aim of this study was to translate and cross-culturally adapt the PROMIS physical function item bank to the Dutch language and to pretest it in a sample of patients with arthritis.Methods
The items of the PROMIS physical function item bank were translated using rigorous forward-backward protocols and the translated version was subsequently cognitively pretested in a sample of Dutch patients with rheumatoid arthritis.Results
Few issues were encountered in the forward-backward translation. Only 5 of the 124 items to be translated had to be rewritten because of culturally inappropriate content. Subsequent pretesting showed that overall, questions of the Dutch version were understood as they were intended, while only one item required rewriting.Conclusions
Results suggest that the translated version of the PROMIS physical function item bank is semantically and conceptually equivalent to the original. Future work will be directed at creating a Dutch-Flemish final version of the item bank to be used in research with Dutch speaking populations. 相似文献15.
Background
Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult.Principal Findings
We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell.Conclusions
For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases.Availability
The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download. 相似文献16.
Background
Water plays an important role in the transmission of many infectious diseases, which pose a great burden on global public health. However, the global distribution of these water-associated infectious diseases and underlying factors remain largely unexplored.Methods and Findings
Based on the Global Infectious Disease and Epidemiology Network (GIDEON), a global database including water-associated pathogens and diseases was developed. In this study, reported outbreak events associated with corresponding water-associated infectious diseases from 1991 to 2008 were extracted from the database. The location of each reported outbreak event was identified and geocoded into a GIS database. Also collected in the GIS database included geo-referenced socio-environmental information including population density (2000), annual accumulated temperature, surface water area, and average annual precipitation. Poisson models with Bayesian inference were developed to explore the association between these socio-environmental factors and distribution of the reported outbreak events. Based on model predictions a global relative risk map was generated. A total of 1,428 reported outbreak events were retrieved from the database. The analysis suggested that outbreaks of water-associated diseases are significantly correlated with socio-environmental factors. Population density is a significant risk factor for all categories of reported outbreaks of water-associated diseases; water-related diseases (e.g., vector-borne diseases) are associated with accumulated temperature; water-washed diseases (e.g., conjunctivitis) are inversely related to surface water area; both water-borne and water-related diseases are inversely related to average annual rainfall. Based on the model predictions, “hotspots” of risks for all categories of water-associated diseases were explored.Conclusions
At the global scale, water-associated infectious diseases are significantly correlated with socio-environmental factors, impacting all regions which are affected disproportionately by different categories of water-associated infectious diseases. 相似文献17.
Background
In Germany, surveillance for infectious disease outbreaks is integrated into an electronic surveillance system. For 2007, the national surveillance database contains case-based information on 201,224 norovirus cases, three-quarters of which are linked to outbreaks. We evaluated the data quality of the national database in reflecting nosocomial norovirus outbreak (NNO) data available in 19 Hessian local public health authorities (LPHAs) and the influence of differences between LPHA''s follow-up procedures for laboratory notifications of Norovirus positive stool samples on outbreak underascertainment.Methods
Data on NNO beginning in 2007 and notified to the 19 LPHAs were extracted from the national database, investigated regarding internal validity and compared to data collected from LPHAs for a study on NNO control. LPHAs were questioned whether they routinely contacted all persons for whom a laboratory diagnosis of norovirus infection was notified. The number of outbreaks per 1,000 hospital beds and the number of cases within NNOs for acute care and rehabilitation hospitals were compared between counties with and without complete follow-up.Results
The national database contained information on 155 NNOs, including 3,115 cases. Cases were missed in the national database in 58 (37%) of the outbreaks. Information on hospitalisation was incorrect for an estimated 47% of NNO cases. Information on county of infection was incorrect for 24% (199/820) of cases being forwarded between LPHAs for data entry. Reported NNO incidence and number of NNO cases in acute care hospitals was higher in counties with complete follow-up (incidence-rate ratio (IRR) 2.7, 95% CI 1.4–5.7, p-value 0.002 and IRR 2.1, 95% CI 1.9–2.4, p-value 0.001, respectively).Conclusions
Many NNOs are not notified by hospitals and differences in LPHA procedures have an impact on the number of outbreaks captured in the surveillance system. Forwarding of case-by-case data on Norovirus outbreak cases from the local to the state and national level should not be required. 相似文献18.
Yu-Tao Xiang Robert W. Buchanan Gabor S. Ungvari Helen F. K. Chiu Kelly Y. C. Lai You-Hong Li Tian-Mei Si Chuan-Yue Wang Edwin H. M. Lee Yan-Ling He Shu-Yu Yang Mian-Yoon Chong Ee-Heok Kua Senta Fujii Kang Sim Michael K. H. Yong Jitendra K. Trivedi Eun-Kee Chung Pichet Udomratn Kok-Yoon Chee Norman Sartorius Chay-Hoon Tan Naotaka Shinfuku 《PloS one》2013,8(6)
19.
20.
Philippe Nizard Frédéric Ezan Dominique Bonnier Nolwenn Le Meur Sophie Langou?t Georges Baffet Yannick Arlot-Bonnemains Nathalie Théret 《BMC genomics》2014,15(1)