Interactive and fuzzy search: a dynamic way to explore MEDLINE

Wang, Jiannan; Cetindil, Inci; Ji, Shengyue; Li, Chen; Xie, Xiaohui; Li, Guoliang; Feng, Jianhua

doi:10.1093/bioinformatics/btq414

Cited by 24 publications

(15 citation statements)

References 4 publications

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“…They feature novel search/retrieval functions that are currently not available through PubMed, which may be preferred by some users in practice. iPubMed (42) provides an interactive search interface: search as you type. When a user types several characters into the search box, the system will instantly show any citations containing that text so that users may narrow their searches.…”

Section: Other Tools Comparable To Pubmedmentioning

confidence: 99%

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PubMed and beyond: a survey of web tools for searching biomedical literature

2011

Database

412

346

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The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field.Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search

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Section: Other Tools Comparable To Pubmedmentioning

confidence: 99%

“…iPubMed (42) provides an interactive search interface: search as you type. When a user types several characters into the search box, the system will instantly show any citations containing that text so that users may narrow their searches.…”

Section: Other Tools Comparable To Pubmedmentioning

confidence: 99%

PubMed and beyond: a survey of web tools for searching biomedical literature

2011

Database

412

346

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show abstract

“…As for the first category, let us recall here RefMed [34], MedlineRanker [35], and iPubMed [36]. RefMed (http://dm.postech.ac.kr/refmed/) is a search engine for PubMed that provides relevance ranking.…”

Section: State Of the Artmentioning

confidence: 99%

Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges

Manconi

Vargiu

Armano

et al. 2012

Advances in Bioinformatics

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The world has widely changed in terms of communicating, acquiring, and storing information. Hundreds of millions of people are involved in information retrieval tasks on a daily basis, in particular while using a Web search engine or searching their e-mail, making such field the dominant form of information access, overtaking traditional database-style searching. How to handle this huge amount of information has now become a challenging issue. In this paper, after recalling the main topics concerning information retrieval, we present a survey on the main works on literature retrieval and mining in bioinformatics. While claiming that information retrieval approaches are useful in bioinformatics tasks, we discuss some challenges aimed at showing the effectiveness of these approaches applied therein.

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“…Another promising system is iPubmed [31]. The iPubmed system focuses on providing high performance and interactive search interface to MEDLINE data, through a "search-as-you-type" feature.…”

Section: Related Workmentioning

confidence: 99%

Supporting BioMedical Information Retrieval: The BioTracer Approach

Ramampiaro

2011

Transactions on Large-Scale Data- And Knowledge-Centered Systems IV

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Abstract. The large amount and diversity of available biomedical information has put a high demand on existing search systems. Such a tool should be able to not only retrieve the sought information, but also filter out irrelevant documents, while giving the relevant ones the highest ranking. Focusing on biomedical information, this work investigates how to improve the ability for a system to find and rank relevant documents. To achieve this goal, we apply a series of information retrieval techniques to search in biomedical information and combine them in an optimal manner. These techniques include extending and using well-established information retrieval (IR) similarity models such as the Vector Space Model (VSM) and BM25 and their underlying scoring schemes. The techniques also allow users to affect the ranking according to their view of relevance. The techniques have been implemented and tested in a proofof-concept prototype called BioTracer, which extends a Java-based open source search engine library. The results from our experiments using the TREC 2004 Genomic Track collection are promising. Our investigation have also revealed that involving the user in the search process will indeed have positive effects on the ranking of search results, and that the approaches used in BioTracer can be used to meet the user's information needs.Keywords: Biomedical Information Retrieval, Evaluation, BioTracer. Background and MotivationThe continuous increase in the amount of available biomedical information has resulted in a higher demand on biomedical information retrieval (IR) systems. While their use has helped researchers in the field to stay updated on recent literature, many of the existing search systems tend to be either too restrictive (returning results with a low recall) or too broad (finding results with a This article is a revised and an extended version of the ITBAM 2010 paper [1].

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Interactive and fuzzy search: a dynamic way to explore MEDLINE

Abstract: Interactive and fuzzy searching algorithms for exploring MEDLINE are implemented in a system called iPubMed, freely accessible over the web at http://ipubmed.ics.uci.edu/ and http://tastier.cs.tsinghua.edu.cn/ipubmed.

Cited by 24 publications

References 4 publications

PubMed and beyond: a survey of web tools for searching biomedical literature

PubMed and beyond: a survey of web tools for searching biomedical literature

Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges

Supporting BioMedical Information Retrieval: The BioTracer Approach

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