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Mining the Gene Wiki for functional genomic knowledge.

ABSTRACT: Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology.Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses.The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.

SUBMITTER: Good BM

PROVIDER: S-EPMC3271090 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Mining the Gene Wiki for functional genomic knowledge.

Good Benjamin M BM Howe Douglas G DG Lin Simon M SM Kibbe Warren A WA Su Andrew I AI

BMC genomics 20111213

<h4>Background</h4>Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translatin ...[more]

PMID: 22165947

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Project description:BackgroundClinical decision support systems are information technologies that assist clinicians in making better decisions. Their adoption has been limited because their content is difficult to adapt to local contexts and slow to adapt to emerging evidence. Collaborative writing applications such as wikis have the potential to increase access to existing and emerging evidence-based knowledge at the point of care, standardize emergency clinical decision making, and quickly adapt this knowledge to local contexts. However, little is known about the factors influencing health professionals' use of wiki-based knowledge tools.ObjectiveThis study aims to measure emergency physicians' (EPs) and other acute care health professionals' (ACHPs) intentions to use wiki-based knowledge tools in trauma care and identify determinants of this intention that can be used in future theory-based interventions for promoting the use of wiki-based knowledge tools in trauma care.MethodsIn total, 266 EPs and 907 ACHPs (nurses, respiratory therapists, and pharmacists) from 12 Quebec trauma centers were asked to answer a survey based on the theory of planned behavior (TPB). The TPB constructs were measured using a 7-point Likert scale. Descriptive statistics and Pearson correlations between the TPB constructs and intention were calculated. Multiple linear regression analysis was conducted to identify the salient beliefs.ResultsAmong the eligible participants, 57.1% (152/266) of EPs and 31.9% (290/907) of ACHPs completed the questionnaire. For EPs, we found that attitude, perceived behavioral control (PBC), and subjective norm (SN) were significant determinants of the intention to use wiki-based knowledge tools and explained 62% of its variance. None of the sociodemographic variables were related to EPs' intentions to use wiki-based knowledge tools. The regression model identified two normative beliefs ("approval by physicians" and "approval by patients") and two behavioral beliefs ("refreshes my memory" and "reduces errors"). For ACHPs, attitude, PBC, SN, and two sociodemographic variables (profession and the previous personal use of a wiki) were significantly related to the intention to use wiki-based knowledge tools and explained 60% of the variance in behavioral intention. The final regression model for ACHPs included two normative beliefs ("approval by the hospital trauma team" and "people less comfortable with information technology"), one control belief ("time constraints"), and one behavioral belief ("access to evidence").ConclusionsThe intentions of EPs and ACHPs to use wiki-based knowledge tools to promote best practices in trauma care can be predicted in part by attitude, SN, and PBC. We also identified salient beliefs that future theory-based interventions should promote for the use of wiki-based knowledge tools in trauma care. These interventions will address the barriers to using wiki-based knowledge tools, find ways to ensure the quality of their content, foster contributions, and support the exploration of wiki-based knowledge tools as potential effective knowledge translation tools in trauma care.

Project description:BackgroundGene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerged as the machine learning method of choice to solve this task, but its unsupervised nature makes result assessment problematic. This is often addressed by means of Gene Set Enrichment Analysis (GSEA).ResultsWe put forward a framework in which GED analysis is understood as an Exploratory Data Analysis (EDA) process where we provide support for continuous human interaction with data aiming at improving the step of hypothesis abduction and assessment. We focus on the adaptation to human cognition of data interpretation and visualization of the output of EDA. First, we give a proper theoretical background to bi-clustering using Lattice Theory and provide a set of analysis tools revolving around [Formula: see text]-Formal Concept Analysis ([Formula: see text]-FCA), a lattice-theoretic unsupervised learning technique for real-valued matrices. By using different kinds of cost structures to quantify expression we obtain different sequences of hierarchical bi-clusterings for gene under- and over-expression using thresholds. Consequently, we provide a method with interleaved analysis steps and visualization devices so that the sequences of lattices for a particular experiment summarize the researcher's vision of the data. This also allows us to define measures of persistence and robustness of biclusters to assess them. Second, the resulting biclusters are used to index external omics databases-for instance, Gene Ontology (GO)-thus offering a new way of accessing publicly available resources. This provides different flavors of gene set enrichment against which to assess the biclusters, by obtaining their p-values according to the terminology of those resources. We illustrate the exploration procedure on a real data example confirming results previously published.ConclusionsThe GED analysis problem gets transformed into the exploration of a sequence of lattices enabling the visualization of the hierarchical structure of the biclusters with a certain degree of granularity. The ability of FCA-based bi-clustering methods to index external databases such as GO allows us to obtain a quality measure of the biclusters, to observe the evolution of a gene throughout the different biclusters it appears in, to look for relevant biclusters-by observing their genes and what their persistence is-to infer, for instance, hypotheses on their function.

Project description:BackgroundToxicogenomics studies often profile gene expression from assays involving multiple doses and time points. The dose- and time-dependent pattern is of great importance to assess toxicity but computational approaches are lacking to effectively utilize this characteristic in toxicity assessment. Topic modeling is a text mining approach, but may be used analogously in toxicogenomics due to the similar data structures between text and gene dysregulation.ResultsTopic modeling was applied to a very large toxicogenomics dataset containing microarray gene expression data from >15,000 samples associated with 131 drugs tested in three different assay platforms (i.e., in vitro assay, in vivo repeated dose study and in vivo single dose experiment) with a design including multiple doses and time points. A set of "topics" which each consist of a set of genes was determined, by which the varying sensitivity of three assay systems was observed. We found that the drug-dependent effect was more pronounced in the two in vivo systems than the in vitro system, while the time-dependent effect was most strongly reflected in the in vitro system followed by the single dose study and lastly the repeated dose experiment. The dose-dependent effect was similar across three assay systems. Although the results indicated a challenge to extrapolate the in vitro results to the in vivo situation, we did notice that, for some drugs but not for all the drugs, the similarity in gene expression patterns was observed across all three assay systems, indicating a possibility of using in vitro systems with careful designs (such as the choice of dose and time point), to replace the in vivo testing strategy. Nonetheless, a potential to replace the repeated dose study by the single-dose short-term methodology was strongly implied.ConclusionsThe study demonstrated that text mining methodologies such as topic modeling provide an alternative method compared to traditional means for data reduction in toxicogenomics, enhancing researchers' capabilities to interpret biological information.

Project description:BackgroundThe highly dimensional data produced by functional genomic (FG) studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays). Although dimensionality reduction methods such as principal component analysis (PCA) have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies.ResultsThe proposed method (PM) is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data--a study of classification of human tissue samples and a study of E. coli cultures with different medium formulations.ConclusionWe have developed a PCA-based method that effectively identifies assay-specific signatures in ranked groups of genes from the full data set in a more efficient and simplistic procedure than current approaches. Although this work demonstrates the ability of the PM to identify assay-specific signatures in DNA microarray experiments, this approach could be useful in areas such as proteomics and metabolomics.

Dataset Information

Mining the Gene Wiki for functional genomic knowledge.

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Mining the Gene Wiki for functional genomic knowledge.

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