Dataset Information

Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.

ABSTRACT:

Background

Receiving extraneous articles in response to a query submitted to MEDLINE/PubMed is common. When submitting a multi-word query (which is the majority of queries submitted), the presence of all query words within each article may be a necessary condition for retrieving relevant articles, but not sufficient. Ideally a relationship between the query words in the article is also required. We propose that if two words occur within an article, the probability that a relation between them is explained is higher when the words occur within adjacent sentences versus remote sentences. Therefore, sentence-level concurrence can be used as a surrogate for existence of the relationship between the words. In order to avoid the irrelevant articles, one solution would be to increase the search specificity. Another solution is to estimate a relevance score to sort the retrieved articles. However among the >30 retrieval services available for MEDLINE, only a few estimate a relevance score, and none detects and incorporates the relation between the query words as part of the relevance score.

Results

We have developed "Relemed", a search engine for MEDLINE. Relemed increases specificity and precision of retrieval by searching for query words within sentences rather than the whole article. It uses sentence-level concurrence as a statistical surrogate for the existence of relationship between the words. It also estimates a relevance score and sorts the results on this basis, thus shifting irrelevant articles lower down the list. In two case studies, we demonstrate that the most relevant articles appear at the top of the Relemed results, while this is not necessarily the case with a PubMed search. We have also shown that a Relemed search includes not only all the articles retrieved by PubMed, but potentially additional relevant articles, due to the extended 'automatic term mapping' and text-word searching features implemented in Relemed.

Conclusion

By using sentence-level matching, Relemed can deliver higher specificity, thus eliminating more false-positive articles. By introducing an appropriate relevance metric, the most relevant articles on which the user wishes to focus are listed first. Relemed also shrinks the displayed text, and hence the time spent scanning the articles.

SUBMITTER: Siadaty MS

PROVIDER: S-EPMC1780044 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.

Siadaty Mir S MS Shu Jianfen J Knaus William A WA

BMC medical informatics and decision making 20070110

<h4>Background</h4>Receiving extraneous articles in response to a query submitted to MEDLINE/PubMed is common. When submitting a multi-word query (which is the majority of queries submitted), the presence of all query words within each article may be a necessary condition for retrieving relevant articles, but not sufficient. Ideally a relationship between the query words in the article is also required. We propose that if two words occur within an article, the probability that a relation between ...[more]

PMID: 17214888

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Project description:BackgroundAnxiety disorders are the most prevalent mental disorders globally, with a substantial impact on quality of life. The prevalence of anxiety disorders has increased substantially following the COVID-19 pandemic, and it is likely to be further affected by a global economic recession. Understanding anxiety themes and how they change over time and across countries is crucial for preventive and treatment strategies.ObjectiveThe aim of this study was to track the trends in anxiety themes between 2004 and 2020 in the 50 most populous countries with high volumes of internet search data. This study extends previous research by using a novel search-based methodology and including a longer time span and more countries at different income levels.MethodsWe used a crowdsourced questionnaire, alongside Bing search query data and Google Trends search volume data, to identify themes associated with anxiety disorders across 50 countries from 2004 to 2020. We analyzed themes and their mutual interactions and investigated the associations between countries' socioeconomic attributes and anxiety themes using time-series linear models. This study was approved by the Microsoft Research Institutional Review Board.ResultsQuery volume for anxiety themes was highly stable in countries from 2004 to 2019 (Spearman r=0.89) and moderately correlated with geography (r=0.49 in 2019). Anxiety themes were predominantly long-term and personal, with "having kids," "pregnancy," and "job" the most voluminous themes in most countries and years. In 2020, "COVID-19" became a dominant theme in 27 countries. Countries with a constant volume of anxiety themes over time had lower fragile state indexes (P=.007) and higher individualism (P=.003). An increase in the volume of the most searched anxiety themes was associated with a reduction in the volume of the remaining themes in 13 countries and an increase in 17 countries, and these 30 countries had a lower prevalence of mental disorders (P<.001) than the countries where no correlations were found.ConclusionsInternet search data could be a potential source for predicting the country-level prevalence of anxiety disorders, especially in understudied populations or when an in-person survey is not viable.

Project description:BACKGROUND: Biologists may need to know the set of genes that are semantically related to a given set of genes. For instance, a biologist may need to know the set of genes related to another set of genes known to be involved in a specific disease. Some works use the concept of gene clustering in order to identify semantically related genes. Others propose tools that return the set of genes that are semantically related to a given set of genes. Most of these gene similarity measures determine the semantic similarities among the genes based solely on the proximity to each other of the GO terms annotating the genes, while overlook the structural dependencies among these GO terms, which may lead to low recall and precision of results. RESULTS: We propose in this paper a search engine called GRank, which overcomes the limitations of the current gene similarity measures outlined above as follows. It employs the concept of existence dependency to determine the structural dependencies among the GO terms annotating a given set of gene. After determining the set of genes that are semantically related to input genes, GRank would use microarray experiment to rank these genes based on their degree of relativity to the input genes. We evaluated GRank experimentally and compared it with a comparable gene prediction tool called DynGO, which retrieves the genes and gene products that are relatives of input genes. Results showed marked improvement. CONCLUSIONS: The experimental results demonstrated that GRank overcomes the limitations of current gene similarity measures. We attribute this performance to GRank's use of existence dependency concept for determining the semantic relationships among gene annotations. The recall and precision values for two benchmarking datasets showed that GRank outperforms DynGO tool, which does not employ the concept of existence dependency. The demo of GRank using 11000 KEGG yeast genes and a Gene Expression Omnibus (GEO) microarray file named "GSM34635.pad" is available at: http://ecesrvr.kustar.ac.ae:8080/ (click on the link labelled Gene Ontology 2).

Dataset Information

Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.

Background

Results

Conclusion

Publications

Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.

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