Update on XplorMed: a web server for exploring scientific literature (original) (raw)

TPX: Biomedical literature search made easy

Bioinformation, 2012

TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features. These features include identification of relevant biomedical concepts from search results with linkouts to source databases, concept based article categorization, concept assisted search and filtering, query refinement. A distinguishing feature here is the ability to add user-defined concept names and/or concept types for named entity recognition. The tool allows contextual exploration of knowledge sources by providing concept association maps derived from the MEDLINE repository. It also has a full-text search mode that can be configured on request to access local text repositories, incorporating entity co-occurrence search at sentence/paragraph levels. Local text files can also be analyzed on-the-fly.

XplorMed: a tool for exploring MEDLINE abstracts

Trends in Biochemical Sciences, 2001

The most frequent access to the MEDLINE database of scientific abstracts is by keyword search. However, this is often not sufficient because although the user might find all the useful abstracts, these are buried in hundreds that are irrelevant. The exploratory tool XplorMed has been developed to analyse the result of any MEDLINE query. It suggests main groups of related topics and documents, sparing the user the need of reading all abstracts.

PubMed Assistant: a biologist-friendly interface for enhanced PubMed search

Bioinformatics/computer Applications in The Biosciences, 2006

MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations, and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar, and others which are lacking in PubMed.

Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

BMC Medical Informatics and Decision Making, 2006

The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results.

Semantic MEDLINE: a web application to manage the results of PubMed searches

We describe Semantic MEDLINE, a Web application that manages the results of PubMed searches by summarizing and visu-alizing semantic predications extracted from MEDLINE citations and linking them to several structured resources to provide an integrated environment. To demonstrate its utility, we present a scenario in which we use Semantic MEDLINE to gain insights into relaxin, a hormone whose function in humans has not been fully elucidated. We propose Semantic MEDLINE as an enabling information resource and exploration tool for biomedical scientists, health care profes-sionals, and consumers. (For access, send e-mail to trindflesch@mail.nih.gov).

Semantic MEDLINE: A Web Application for Managing the Results of PubMed Searches

2000

We describe Semantic MEDLINE, a Web application that manages the results of PubMed searches by summarizing and visu- alizing semantic predications extracted from MEDLINE citations and linking them to several structured resources to provide an integrated environment. To demonstrate its utility, we present a scenario in which we use Semantic MEDLINE to gain insights into relaxin, a hormone whose function

MedlineRanker: flexible ranking of biomedical literature

Nucleic Acids Research, 2009

The biomedical literature is represented by millions of abstracts available in the Medline database. These abstracts can be queried with the PubMed interface, which provides a keywordbased Boolean search engine. This approach shows limitations in the retrieval of abstracts related to very specific topics, as it is difficult for a nonexpert user to find all of the most relevant keywords related to a biomedical topic. Additionally, when searching for more general topics, the same approach may return hundreds of unranked references. To address these issues, text mining tools have been developed to help scientists focus on relevant abstracts. We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at

MEDLINE: A Guide to Effective Searching

1999

From the Book: The most remarkable thing about MEDLINE--other than its size--is the amount of human energy that has gone into indexing its contents. MEDLINE is the collective product of a small army of indexers, who have, for more than 30 years, characterized the contents of more than 4,200 journals that publish information about the causes, prevention, and treatment of disease and injury. Each of the more than ten million journal articles, letters, and editorials that are catalogued in MEDLINE has been read by a skilled indexer, who has assigned to it roughly a dozen subject headings, drawn from a controlled vocabulary of more than 19,000 Medical Subject Headings (MeSH). If you understand the elaborate indexing schemes that are embodied in MEDLINE, you can use this understanding to search it with a high degree of precision. Size is also important. Because its coverage is so broad, MEDLINE can be thought of as the index to the world's medical literature, the on-line catalogue of...

PubTree: A Hierarchical Search Tool for the MEDLINE Database

Keeping track of the ever-increasing body of scientific literature is an escalating challenge. We present PubTree a hierarchical search tool that efficiently searches the PubMed/MEDLINE dataset based upon a decision tree constructed using >26 million abstracts. The tool is implemented as a webpage, where users are asked a series of eighteen questions to locate pertinent articles. The implementation of this hierarchical search tool highlights issues endemic with document retrieval. However, the construction of this tree indicates that with future developments hierarchical search could become an effective tool (or adjunct) in the mining of biological literature.