Dataset Information

MeSH indexing based on automatically generated summaries.

ABSTRACT: BACKGROUND:MEDLINE citations are manually indexed at the U.S. National Library of Medicine (NLM) using as reference the Medical Subject Headings (MeSH) controlled vocabulary. For this task, the human indexers read the full text of the article. Due to the growth of MEDLINE, the NLM Indexing Initiative explores indexing methodologies that can support the task of the indexers. Medical Text Indexer (MTI) is a tool developed by the NLM Indexing Initiative to provide MeSH indexing recommendations to indexers. Currently, the input to MTI is MEDLINE citations, title and abstract only. Previous work has shown that using full text as input to MTI increases recall, but decreases precision sharply. We propose using summaries generated automatically from the full text for the input to MTI to use in the task of suggesting MeSH headings to indexers. Summaries distill the most salient information from the full text, which might increase the coverage of automatic indexing approaches based on MEDLINE. We hypothesize that if the results were good enough, manual indexers could possibly use automatic summaries instead of the full texts, along with the recommendations of MTI, to speed up the process while maintaining high quality of indexing results. RESULTS:We have generated summaries of different lengths using two different summarizers, and evaluated the MTI indexing on the summaries using different algorithms: MTI, individual MTI components, and machine learning. The results are compared to those of full text articles and MEDLINE citations. Our results show that automatically generated summaries achieve similar recall but higher precision compared to full text articles. Compared to MEDLINE citations, summaries achieve higher recall but lower precision. CONCLUSIONS:Our results show that automatic summaries produce better indexing than full text articles. Summaries produce similar recall to full text but much better precision, which seems to indicate that automatic summaries can efficiently capture the most important contents within the original articles. The combination of MEDLINE citations and automatically generated summaries could improve the recommendations suggested by MTI. On the other hand, indexing performance might be dependent on the MeSH heading being indexed. Summarization techniques could thus be considered as a feature selection algorithm that might have to be tuned individually for each MeSH heading.

SUBMITTER: Jimeno-Yepes AJ

PROVIDER: S-EPMC3706357 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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MeSH indexing based on automatically generated summaries.

Jimeno-Yepes Antonio J AJ Plaza Laura L Mork James G JG Aronson Alan R AR Díaz Alberto A

BMC bioinformatics 20130626

<h4>Background</h4>MEDLINE citations are manually indexed at the U.S. National Library of Medicine (NLM) using as reference the Medical Subject Headings (MeSH) controlled vocabulary. For this task, the human indexers read the full text of the article. Due to the growth of MEDLINE, the NLM Indexing Initiative explores indexing methodologies that can support the task of the indexers. Medical Text Indexer (MTI) is a tool developed by the NLM Indexing Initiative to provide MeSH indexing recommendati ...[more]

PMID: 23802936

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Project description:BackgroundEvaluation of Word Sense Disambiguation (WSD) methods in the biomedical domain is difficult because the available resources are either too small or too focused on specific types of entities (e.g. diseases or genes). We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE. We demonstrate the use of this method by developing such a data set, called MSH WSD.MethodsIn our method, the Metathesaurus is first screened to identify ambiguous terms whose possible senses consist of two or more MeSH headings. We then use each ambiguous term and its corresponding MeSH heading to extract MEDLINE citations where the term and only one of the MeSH headings co-occur. The term found in the MEDLINE citation is automatically assigned the UMLS CUI linked to the MeSH heading. Each instance has been assigned a UMLS Concept Unique Identifier (CUI). We compare the characteristics of the MSH WSD data set to the previously existing NLM WSD data set.ResultsThe resulting MSH WSD data set consists of 106 ambiguous abbreviations, 88 ambiguous terms and 9 which are a combination of both, for a total of 203 ambiguous entities. For each ambiguous term/abbreviation, the data set contains a maximum of 100 instances per sense obtained from MEDLINE.We evaluated the reliability of the MSH WSD data set using existing knowledge-based methods and compared their performance to that of the results previously obtained by these algorithms on the pre-existing data set, NLM WSD. We show that the knowledge-based methods achieve different results but keep their relative performance except for the Journal Descriptor Indexing (JDI) method, whose performance is below the other methods.ConclusionsThe MSH WSD data set allows the evaluation of WSD algorithms in the biomedical domain. Compared to previously existing data sets, MSH WSD contains a larger number of biomedical terms/abbreviations and covers the largest set of UMLS Semantic Types. Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions.

Project description:BackgroundPsychiatric disorders often have an onset at an early age, and early identification and intervention help improve prognosis. A fine-grained, unobtrusive, and effective way to monitor symptoms and level of function could help distinguish severe psychiatric health problems from normal behavior and potentially lead to a more efficient use of clinical resources in the current health care system. The use of smartphones to monitor and treat children, adolescents, and young adults with psychiatric disorders has been widely investigated. However, no systematic review concerning smartphone-based monitoring and treatment in this population has been published.ObjectiveThis systematic review aims at describing the following 4 features of the eligible studies: (1) monitoring features such as self-assessment and automatically generated data, (2) treatment delivered by the app, (3) adherence to self-monitoring, and (4) results of the individual studies.MethodsWe conducted a systematic literature search of the PubMed, Embase, and PsycInfo databases. We searched for studies that (1) included a smartphone app to collect self-monitoring data, a smartphone app to collect automatically generated smartphone-based data, or a smartphone-based system for treatment; (2) had participants who were diagnosed with psychiatric disorders or received treatment for a psychiatric disorder, which was verified by an external clinician; (3) had participants who were younger than 25 years; and (4) were published in a peer-reviewed journal. This systematic review was reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The risk of bias in each individual study was systematically assessed.ResultsA total of 2546 unique studies were identified through literature search; 15 of these fulfilled the criteria for inclusion. These studies covered 8 different diagnostic groups: psychosis, eating disorders, depression, autism, self-harm, anxiety, substance abuse, and suicidal behavior. Smartphone-based self-monitoring was used in all but 1 study, and 11 of them reported on the participants' adherence to self-monitoring. Most studies were feasibility/pilot studies, and all studies on feasibility reported positive attitudes toward the use of smartphones for self-monitoring. In 2 studies, automatically generated data were collected. Three studies were randomized controlled trials investigating the effectiveness of smartphone-based monitoring and treatment, with 2 of these showing a positive treatment effect. In 2 randomized controlled trials, the researchers were blinded for randomization, but the participants were not blinded in any of the studies. All studies were determined to be at high risk of bias in several areas.ConclusionsSmartphones hold great potential as a modern, widely available technology platform to help diagnose, monitor, and treat psychiatric disorders in children and adolescents. However, a higher level of homogeneity and rigor among studies regarding their methodology and reporting of adherence would facilitate future reviews and meta-analyses.

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MeSH indexing based on automatically generated summaries.

Publications

MeSH indexing based on automatically generated summaries.

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