Best Match: New relevance search for PubMed.
Ontology highlight
ABSTRACT:
SUBMITTER: Fiorini N
PROVIDER: S-EPMC6112631 | biostudies-literature | 2018 Aug
REPOSITORIES: biostudies-literature
Publications
Best Match: New relevance search for PubMed.
Fiorini Nicolas N Canese Kathi K Starchenko Grisha G Kireev Evgeny E Kim Won W Miller Vadim V Osipov Maxim M Kholodov Michael M Ismagilov Rafis R Mohan Sunil S Ostell James J Lu Zhiyong Z
PLoS biology 20180828 8
PubMed is a free search engine for biomedical literature accessed by millions of users from around the world each day. With the rapid growth of biomedical literature-about two articles are added every minute on average-finding and retrieving the most relevant papers for a given query is increasingly challenging. We present Best Match, a new relevance search algorithm for PubMed that leverages the intelligence of our users and cutting-edge machine-learning technology as an alternative to the trad ...[more]
Similar Datasets
Project description:Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ?21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/.
| S-EPMC3394277 | biostudies-literature
Project description:BackgroundVisual search declines with aging, dementia, and brain injury and is linked to limitations in everyday activities. Recent studies suggest that visual search can be improved with practice using computerized visual search tasks and puzzle video games. For practical use, it is important that visual search ability can be assessed and practiced in a controlled and adaptive way. However, commercial puzzle video games make it hard to control task difficulty, and there are little means to collect performance data.ObjectiveThe aim of this study was to develop and initially validate the search and match task (SMT) that combines an enjoyable tile-matching match-3 puzzle video game with features of the visual search paradigm (taskified game). The SMT was designed as a single-target visual search task that allows control over task difficulty variables and collection of performance data.MethodsThe SMT is played on a grid-based (width × height) puzzle board, filled with different types of colored polygons. A wide range of difficulty levels was generated by combinations of 3 task variables over a range from 4 to 8 including height and width of the puzzle board (set size) and the numbers of tile types (distractor heterogeneity). For each difficulty level, large numbers of playable trials were pregenerated using Python. Each trial consists of 4 consecutive puzzle boards, where the goal of the task is to find a target tile configuration (search) on the puzzle board and swap 2 adjacent tiles to create a line of 3 identical tiles (match). For each puzzle board, there is exactly 1 possible match (single target search). In a user study with 28 young adults (aged 18 to 31 years), 13 older (aged 64 to 79 years) and 11 oldest (aged 86 to 98 years) adults played the long (young and older adults) or short version (oldest adults) of the difficulty levels of the SMT. Participants rated their perception and the usability of the task and completed neuropsychological tests that measure cognitive domains engaged by the puzzle game.ResultsResults from the user study indicate that the target search time is associated with set size, distractor heterogeneity, and age. Results further indicate that search performance is associated with general cognitive ability, selective and divided attention, visual search, and visuospatial and pattern recognition ability.ConclusionsOverall, this study shows that an everyday puzzle game-based task can be experimentally controlled, is enjoyable and user-friendly, and permits data collection to assess visual search and cognitive abilities. Further research is needed to evaluate the potential of the SMT game to assess and practice visual search ability in an enjoyable and adaptive way. A PsychoPy version of the SMT is freely available for researchers.
| S-EPMC6532342 | biostudies-literature
Project description:Background and objectivesPhysicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase.Design, setting, participants, & measurementsA diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated.ResultsThe high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles.ConclusionsThese empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.
| S-EPMC3463205 | biostudies-literature
Project description:MotivationFinding protein-protein interaction (PPI) information from literature is challenging but an important issue. However, keyword search in PubMed(®) is often time consuming because it requires a series of actions that refine keywords and browse search results until it reaches a goal. Due to the rapid growth of biomedical literature, it has become more difficult for biologists and curators to locate PPI information quickly. Therefore, a tool for prioritizing PPI informative articles can be a useful assistant for finding this PPI-relevant information.ResultsPIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques. For easy user access, PIE the search provides a PubMed-like search environment, but the output is the list of articles prioritized by PPI confidence scores. By obtaining PPI-related articles at high rank, researchers can more easily find the up-to-date PPI information, which cannot be found in manually curated PPI databases.Availabilityhttp://www.ncbi.nlm.nih.gov/IRET/PIE/.
| S-EPMC3278758 | biostudies-literature
Project description:A new search-match procedure has been developed and tested which, in contrast to previously existing methods, does not use a set of lines identified from a diffraction pattern, but an optimized Rietveld fitting on the raw data. Modern computers with multicore processors allow the routine to be fast enough to perform the entire search in a reasonable time using quite large databases of crystal structures. The search-match is done using the crystal structures for all phases and the instrumental geometry, and as such can be applied to every kind of diffraction experiment, including X-rays, thermal/time-of-flight neutrons and electrons. The methodology can also be applied to nanocrystalline samples for which peak identification may be a problem. A web interface has been developed to permit easy testing and evaluation of the procedure. The quality of the results mainly depends on the availability of the sought phase in the structure database. The method permits not only phase identification but also a rapid quantification of the phases and their gross microstructural features, provided the instrumental function is known.
| S-EPMC6557175 | biostudies-literature
Project description:BACKGROUND:With the continuous expansion of available biomedical data, efficient and effective information retrieval has become of utmost importance. Semantic expansion of queries using synonyms may improve information retrieval. OBJECTIVE:The aim of this study was to automatically construct and evaluate expanded PubMed queries of the form "preferred term"[MH] OR "preferred term"[TIAB] OR "synonym 1"[TIAB] OR "synonym 2"[TIAB] OR …, for each of the 28,313 Medical Subject Heading (MeSH) descriptors, by using different semantic expansion strategies. We sought to propose an innovative method that could automatically evaluate these strategies, based on the three main metrics used in information science (precision, recall, and F-measure). METHODS:Three semantic expansion strategies were assessed. They differed by the synonyms used to build the queries as follows: MeSH synonyms, Unified Medical Language System (UMLS) mappings, and custom mappings (Catalogue et Index des Sites Médicaux de langue Française [CISMeF]). The precision, recall, and F-measure metrics were automatically computed for the three strategies and for the standard automatic term mapping (ATM) of PubMed. The method to automatically compute the metrics involved computing the number of all relevant citations (A), using National Library of Medicine indexing as the gold standard ("preferred term"[MH]), the number of citations retrieved by the added terms ("synonym 1"[TIAB] OR "synonym 2"[TIAB] OR …) (B), and the number of relevant citations retrieved by the added terms (combining the previous two queries with an "AND" operator) (C). It was possible to programmatically compute the metrics for each strategy using each of the 28,313 MeSH descriptors as a "preferred term," corresponding to 239,724 different queries built and sent to the PubMed application program interface. The four search strategies were ranked and compared for each metric. RESULTS:ATM had the worst performance for all three metrics among the four strategies. The MeSH strategy had the best mean precision (51%, SD 23%). The UMLS strategy had the best recall and F-measure (41%, SD 31% and 36%, SD 24%, respectively). CISMeF had the second best recall and F-measure (40%, SD 31% and 35%, SD 24%, respectively). However, considering a cutoff of 5%, CISMeF had better precision than UMLS for 1180 descriptors, better recall for 793 descriptors, and better F-measure for 678 descriptors. CONCLUSIONS:This study highlights the importance of using semantic expansion strategies to improve information retrieval. However, the performances of a given strategy, relatively to another, varied greatly depending on the MeSH descriptor. These results confirm there is no ideal search strategy for all descriptors. Different semantic expansions should be used depending on the descriptor and the user's objectives. Thus, we developed an interface that allows users to input a descriptor and then proposes the best semantic expansion to maximize the three main metrics (precision, recall, and F-measure).
| S-EPMC7303830 | biostudies-literature
Project description:Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians.We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries "therapy") and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles.The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were relevant (corrected) (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55).The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.
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| S-EPMC5330033 | biostudies-literature
Project description:BACKGROUND:Integrated care is an increasingly important principle for organising healthcare. Integrated care models show promise in reducing resource wastage and service fragmentation whilst improving the accessibility, patient-centredness and quality of care for patients. Those needing reliable access to the growing research evidence base for integrated care can be frustrated by search challenges reflective of the topic's complexity. The aim of this study is to report the empirical development and validation of two search filters for rapid and effective retrieval of integrated care evidence in PubMed. One filter is optimised for recall and the other for precision. METHODS:An Expert Advisory Group comprising international integrated care experts guided the study. A gold standard test set of citations was formed from screening Handbook Integrated Care chapter references for relevance. This set was divided into a Term Identification Set (20%) for determining candidate terms using frequency analysis; a Filter Development Set (40%) for testing performance of term combinations; and a Filter Validation Set (40%) reserved for confirming final filter performance. In developing the high recall filter, recall was steadily increased while maintaining precision at ?50%. Similarly, the high precision filter sought to maximise precision while keeping recall ?50%. For each term combination tested, an approximation of precision was obtained by reviewing the first 100 citations retrieved in Medline for relevance. RESULTS:The gold standard set comprised 534 citations. The search filter optimised for recall ('Broad Integrated Care Search') achieved 86.0-88.3% recall with corresponding low precision (47-53%). The search filter optimised for precise searching ('Narrow Integrated Care Search') demonstrated precision of 73-95% with recall reduced to between 55.9 and 59.8%. These filters are now available as one-click URL hyperlinks in the website of International Foundation for Integrated Care. CONCLUSIONS:The Broad and Narrow Integrated Care Search filters provide potential users, such as policy makers and researchers, seamless, reliable and ongoing access to integrated care evidence for decision making. These filters were developed according to a rigorous and transparent methodology designed to circumvent the challenges of information retrieval posed by this complex, multifaceted topic.
| S-EPMC6971984 | biostudies-literature
Project description:A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.
| S-EPMC7052050 | biostudies-literature