Semantic relations for interpreting DNA microarray data.
Ontology highlight
ABSTRACT:
SUBMITTER: Hristovski D
PROVIDER: S-EPMC2815475 | biostudies-literature | 2009 Nov
REPOSITORIES: biostudies-literature
Publications
Semantic relations for interpreting DNA microarray data.
Hristovski Dimitar D Kastrin Andrej A Peterlin Borut B Rindflesch Thomas C TC
AMIA ... Annual Symposium proceedings. AMIA Symposium 20091114
The results from microarray experiments, in the form of lists of over- and under-expressed genes, have great potential to support progress in biomedical research. However, results are not easy to interpret. Information about the function of the genes and their relation to other genes is needed, and this information is usually present in vast amounts of biomedical literature. Considerable effort is required to find, read and extract relevant information from the literature. A potential solution i ...[more]
Similar Datasets
Project description:Public repositories of large-scale biological data currently contain hundreds of thousands of experiments, including high-throughput sequencing and microarray data. The potential of using these resources to assemble data sets combining samples previously not associated is vastly unexplored. This requires the ability to associate samples with clear annotations and to relate experiments matched with different annotation terms. In this study, we illustrate the semantic annotation of Gene Expression Omnibus samples metadata using concepts from biomedical ontologies, focusing on the association of thousands of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) samples with a given target, tissue and disease state. Next, we demonstrate the feasibility of quantitatively measuring the semantic similarity between different samples, with the aim of combining experiments associated with the same or similar semantic annotations, thus allowing the generation of large data sets without the need of additional experiments. We compared tools based on Unified Medical Language System with tools that use topic-specific ontologies, showing that the second approach outperforms the first both in the annotation process and in the computation of semantic similarity measures. Finally, we demonstrated the potential of this approach by identifying semantically homogeneous groups of ChIP-seq samples targeting the Myc transcription factor, and expanding this data set with semantically coherent epigenetic samples. The semantic information of these data sets proved to be coherent with the ChIP-seq signal and with the current knowledge about this transcription factor.
| S-EPMC5429001 | biostudies-literature
Project description:ADGO 2.0 is a web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate composite annotations solely for interpreting lists of genes but usually provide highly redundant information. This new version has the following additional features: first, it provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. Second, it screens redundant composite annotations when generating and prioritizing them. Third, it incorporates union and subtracted sets as well as intersection sets. Lastly, users can upload their own gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. The first two features are unique to ADGO 2.0. Using our tool, we demonstrate analyses of a microarray dataset and a list of genes for T-cell differentiation. The new ADGO is available at http://www.btool.org/ADGO2.
| S-EPMC3125784 | biostudies-literature
Project description:BackgroundThe proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved. Classical IR systems usually return a list of documents that have to be read by the user to extract relevant information. This tedious and time-consuming work can be lessened with automatic Question Answering (QA) systems, which aim to provide users with direct and precise answers to their questions. In this work we propose a novel methodology for QA based on semantic relations extracted from the biomedical literature.ResultsWe extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which came from 21,014,382 MEDLINE citations (i.e., the complete MEDLINE distribution up to the end of 2012). A total of 58,879,300 semantic relation instances were extracted and organized in a relational database. The QA process is implemented as a search in this database, which is accessed through a Web-based application, called SemBT (available at http://sembt.mf.uni-lj.si ). We conducted an extensive evaluation of the proposed methodology in order to estimate the accuracy of extracting a particular semantic relation from a particular sentence. Evaluation was performed by 80 domain experts. In total 7,510 semantic relation instances belonging to 2,675 distinct relations were evaluated 12,083 times. The instances were evaluated as correct 8,228 times (68%).ConclusionsIn this work we propose an innovative methodology for biomedical QA. The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions. A typical question is answered within a few seconds. The tool has some extensions that make it especially useful for interpretation of DNA microarray results.
| S-EPMC4307891 | biostudies-literature
Project description:BackgroundThe aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.ResultsSeveral conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached.ConclusionIt is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experiment.
| S-EPMC2712748 | biostudies-literature
Project description:This paper presents a new method of analysis by which structural similarities between brain data and linguistic data can be assessed at the semantic level. It shows how to measure the strength of these structural similarities and so determine the relatively better fit of the brain data with one semantic model over another. The first model is derived from WordNet, a lexical database of English compiled by language experts. The second is given by the corpus-based statistical technique of latent semantic analysis (LSA), which detects relations between words that are latent or hidden in text. The brain data are drawn from experiments in which statements about the geography of Europe were presented auditorily to participants who were asked to determine their truth or falsity while electroencephalographic (EEG) recordings were made. The theoretical framework for the analysis of the brain and semantic data derives from axiomatizations of theories such as the theory of differences in utility preference. Using brain-data samples from individual trials time-locked to the presentation of each word, ordinal relations of similarity differences are computed for the brain data and for the linguistic data. In each case those relations that are invariant with respect to the brain and linguistic data, and are correlated with sufficient statistical strength, amount to structural similarities between the brain and linguistic data. Results show that many more statistically significant structural similarities can be found between the brain data and the WordNet-derived data than the LSA-derived data. The work reported here is placed within the context of other recent studies of semantics and the brain. The main contribution of this paper is the new method it presents for the study of semantics and the brain and the focus it permits on networks of relations detected in brain data and represented by a semantic model.
| S-EPMC3682999 | biostudies-literature
Project description:When applied to Image-to-text models, explainability methods have two challenges. First, they often provide token-by-token explanations namely, they compute a visual explanation for each token of the generated sequence. This makes explanations expensive to compute and unable to comprehensively explain the model's output. Second, for models with visual inputs, explainability methods such as SHAP typically consider superpixels as features. Since superpixels do not correspond to semantically meaningful regions of an image, this makes explanations harder to interpret. We develop a framework based on SHAP, that allows for generating comprehensive, meaningful explanations leveraging the meaning representation of the output sequence as a whole. Moreover, by exploiting semantic priors in the visual backbone, we extract an arbitrary number of features that allows the efficient computation of Shapley values on large-scale models, generating at the same time highly meaningful visual explanations. We demonstrate that our method generates semantically more expressive explanations than traditional methods at a lower compute cost and that it can be generalized to a large family of vision-language models.
| S-EPMC10561255 | biostudies-literature
Project description:Two experiments examined the size of the typicality effect for true items in a category verification task as a function of the type of false item used. In Experiment 1, compared to the case where false items paired unrelated concepts ("carrot-vehicle"), the typicality effect was much larger when false items paired an exemplar with a category coordinate to its proper category ("carrot-fruit"). In contrast, when false items paired coordinate concepts ("carrot-pea") or reversed the ordering of subject and predicate terms ("All vegetables are carrots"), the typicality effect did not change in size. Further, the time to verify true sentences did not increase monotonically with the semantic similarity of the two terms used in false sentences. Experiment 2 showed that the pattern of results for coordinate items reflected semantic processing, not simply task difficulty. A combined analysis examined data across multiple experiments, increasing the power of the statistical analysis. The size of the typicality effect when coordinate false items were used was again the same as when false items paired unrelated concepts. The most straightforward explanation of this pattern of results seems to be in terms of a sparse semantic network model of lexical semantic memory, in which labeled links are used to indicate the semantic relation that exists between pairs of words.
| S-EPMC7026369 | biostudies-literature
Project description:GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with a specification of the data. The server performs normalization, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user.
| S-EPMC169191 | biostudies-literature
Project description:The purpose of this study was to examine automatic language processing among Spanish-speaking language-minority children. A sample of 73 children (mean age?=?90.4?months) completed two measures of semantic priming: an auditory lexical decision task and a looking-while-listening task. It was hypothesized that within- and cross-language semantic priming effects would occur but that translation priming effects would not occur. Results from vocabulary assessments indicated that language-minority children in this study were more proficient in English than they were in Spanish. Limited evidence for semantic priming effects within English and from English to Spanish emerged. In addition, substantial evidence for translation priming from Spanish to English and from English to Spanish emerged. Given the lack of within-Spanish semantic priming effects and the presence of translation priming effects from Spanish to English, the results of this study indicated that Spanish-speaking language-minority children rely on translation from their less proficient language to their more proficient language to access meaning. There was partial evidence that language-minority children's two languages are active simultaneously, indicating that early in life children develop semantic knowledge that is associated with words known in both languages.
| S-EPMC5750065 | biostudies-literature
Project description:Semantic technology plays a key role in various domains, from conversation understanding to algorithm analysis. As the most efficient semantic tool, ontology can represent, process and manage the widespread knowledge. Nowadays, many researchers use ontology to collect and organize data's semantic information in order to maximize research productivity. In this paper, we firstly describe our work on the development of a remote sensing data ontology, with a primary focus on semantic fusion-driven research for big data. Our ontology is made up of 1,264 concepts and 2,030 semantic relationships. However, the growth of big data is straining the capacities of current semantic fusion and reasoning practices. Considering the massive parallelism of DNA strands, we propose a novel DNA-based semantic fusion model. In this model, a parallel strategy is developed to encode the semantic information in DNA for a large volume of remote sensing data. The semantic information is read in a parallel and bit-wise manner and an individual bit is converted to a base. By doing so, a considerable amount of conversion time can be saved, i.e., the cluster-based multi-processes program can reduce the conversion time from 81,536 seconds to 4,937 seconds for 4.34 GB source data files. Moreover, the size of result file recording DNA sequences is 54.51 GB for parallel C program compared with 57.89 GB for sequential Perl. This shows that our parallel method can also reduce the DNA synthesis cost. In addition, data types are encoded in our model, which is a basis for building type system in our future DNA computer. Finally, we describe theoretically an algorithm for DNA-based semantic fusion. This algorithm enables the process of integration of the knowledge from disparate remote sensing data sources into a consistent, accurate, and complete representation. This process depends solely on ligation reaction and screening operations instead of the ontology.
| S-EPMC3792926 | biostudies-literature