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This section of the series introduces the topic of WWW search engines and directory sites; showing you how to find information using a search engine and a directory. It also covers other ways of searching for information on the internet.
PROBLEM: The Internet is not structured hierarchically and therefore it distinguishes from today's common knowledge sources. The rapidly growing number of medical websites offers comprehensive but not easy to find information resources and continuing education opportunities for ophthalmologists. METHODS AND RESULTS: The efficiency of an Internet search is related to knowledge about existing search strategies. Several search systems are described (search engines, catalogs, databases, indices, etc.). Additional advice about efficient usage (Meta-Search, use of Boolean operators, phrase search, etc.) is provided. The suggested search strategies are evaluated regarding their specific results, update status, and the usability of search engines used. New applications such as SemioMap and Intelligent Agents are described. CONCLUSION: Today the Internet provides practitioners and scientists who are able to use efficient search strategies with easy and fast to use information resources. The total number of scientific-medical documents on the Web is growing very quickly. More and more, their content is related to current problems in patient treatment and future trends in clinical research.
MOTIVATION: Protein search engines are essential for interpreting mass spectrometry data into biological insight. Current tools often face limitations in sensitivity when analyzing complex modern datasets, and lack a unified framework that effectively integrates deep learning features for both restricted and open searches, especially for scenarios aimed at discovering unknown modifications. RESULTS: We present pFind+, a high-performance search engine for data-dependent acquisition (DDA) proteomics, extending pFind. It introduces an enhanced raw scoring that delivers substantially improved pre-filtering ability, while recovering most of the computational overhead through a tailored acceleration strategy. Coupled with an enhanced rescoring framework that effectively integrates deep learning features, pFind+ uniquely supports high-sensitivity, DL-enhanced open search, enabling comprehensive PTM discovery while incorporating hardware-aware inference optimizations for practical deployment. Evaluations across diverse datasets demonstrate its superior sensitivity, with gains of 12.7%-29.3% (average 17.9%) in restricted search and 8.0%-38.4% (average 25.8%) in open search over the best existing tools.
Information on the World Wide Web is unstructured, distributed, multimedia and multilingual. Many tools have been developed to help users search for useful information: subject hierarchies, general search engines, browsers and search assistants. Although helpful, they present serious limitations, mainly in terms of precision, multilingual indexing and distribution. In this paper, we cover some on-line solutions to medical information discovery and present our own approach, the MARVIN (multi-agent retrieval vagabond on information network) project, which tackles medical information research with specialized cooperative retrieval agents. We also draw some outlines for future extensions.
Mastery of computer technology and the resources it brings to renal dietitians will be essential for future practice. The Internet, probably the most valuable resource computers bring to clinical practice, is a potential tool to fulfill goals of lifelong learning. A basic introduction to the Internet and a review of search engines and successful search strategies are provided. Major flaws of the Internet include uncertain quality and accuracy of many materials it provides. Guidelines to evaluate World Wide Web (WWW) materials are similar to guidelines dietitians use to assess written materials. The identification of certain anchor WWW sites with reliable information is a key to successful information retrieval on the Internet.
Part one of this series examined some Internet basics. Computer requirements and Internet connection options were covered, and Web addresses and search engines were reviewed. With this information in hand, you can determine if your current computer equipment is adequate or what type of computer and modern to purchase, and the type of Internet connection that will be right for you. Once online, remember to type web addresses exactly as they appear and to read the help sections of various search engines to learn how to perfect your search techniques. Part two of this series will cover practical issues of Internet use. Suggestions will be offered for dealing with e-mail file attachments, and how to avoid unsolicited e-mail and computer viruses. Techniques for reviewing and evaluating online health information will be discussed as well.
A great barrier to the use of Internet resources for patient education is the concern over the quality of information available. We conducted a study to determine what information was available in Web pages, both within text and metadata source code, that could be used in the assessment of information quality. Analysis of pages retrieved from 97 unique sites using a simple keyword search for "breast cancer treatment" on a generic and a health-specific search engine revealed that basic publishing elements were present in low frequency: authorship (20%), attribution/references (32%), disclosure (41%), and currency (35%). Only one page retrieved contained all four elements. Automated extraction of metadata elements from the source code of 822 pages retrieved from five popular generic search engines revealed even less information. We discuss the design of a metadata-based system for the evaluation of quality of medical content on the World Wide Web that addresses current limitations in ensuring quality.
Version 2.1 of ASDB (Alternative Splicing Data Base) contains 1922 protein and 2486 DNA sequences. The protein entries from SWISS-PROT are joined into clusters corresponding to alternatively spliced variants of one gene. The DNA division consists of complete genes with alternative splicing mentioned or annotated in GenBank. The search engine allows one to search over SWISS-PROT and GenBank fields and then follow the links to all variants. The database can be assessed at the URL http://cbcg.nersc.gov/asdb
The World Wide Web is an increasingly popular source for consumer health information, but many authors have expressed concerns about the quality of health information present on the Internet. We have developed a prototype system that responds to a consumer health query by returning a list of Web pages that are ranked according to the likely quality of the page contents. A computer program identifies some of the criteria that have been suggested for assessing the quality of health information on the Internet. It also identifies characteristics that may serve as proxies for desirable (or undesirable) qualities that are difficult to assess directly using an algorithm. Intervening in the search process and automatically analyzing the contents of each page returned by a general search engine may facilitate the search for high quality consumer health information on the Web.
The Internet is a rapidly growing information resource for rapid publication and access to information. While it has attracted a certain mystique and is undoubtedly attractive as an information source, its rapid and chaotic growth mitigates against ease of use for novices. The authors-all associated with health-care providers in the Dade/Broward market-offer the novice user their best assessment for initial Web sites to explore for health care information, and general guidance on using Internet search engines to direct effective searches.
MOTIVATION: To determine the most powerful artificial intelligence techniques for automated restriction mapping, and use them to create a powerful multiple-enzyme restriction mapping tool. RESULTS: The most effective search engine utilized model-driven exhaustive search and a form of binary logic pruning based on Pratt's separation theory. Additional experimentation led to the development of an input preprocessing module which significantly speeds up searches, and an output post-processing module which enables users to analyze large solution sets and reduce their apparent complexity. AVAILABILITY: An executable version of the resultant tool, Mapper, can be downloaded from our Web site (http://www.ai.eecs.uic.edu) by selecting the 'Software' option. CONTACT: nelson@eecs.uic.edu (http://www.ai.eecs.uic.edu/ñelson).
BACKGROUND: Health information on the Internet, with respect to common, self-limited childhood illnesses, has been found to be unreliable. Therefore, parents navigating on the Internet risk finding advice that is incomplete or, more importantly, not evidence-based. The importance that a resource such as the Internet as a source of quality health information for consumers should, however, be taken into consideration. For this reason, studies need to be performed regarding the quality of material provided. Various strategies have been proposed that would allow parents to distinguish trustworthy web documents from unreliable ones. One of these strategies is the use of a checklist for the appraisal of web pages based on their technical aspects. OBJECTIVE: The purpose of this study was to assess the quality of information present on the Internet regarding the home management of cough in children and to examine the applicability of a checklist strategy that would allow consumers to select more trustworthy web pages. METHODS: The Internet was searched for web pages regarding the home treatment of cough in children with the use of different search engines. Medline and the Cochrane database were searched for available evidence concerning the management of cough in children. Three checklists were created to assess different aspects of the web documents. The first checklist was designed to allow for a technical appraisal of the web pages and was based on components such as the name of the author and references used. The second was constructed to examine the completeness of the health information contained in the documents, such as causes and mechanism of cough, and pharmacological and nonpharmacological treatment. The third checklist assessed the quality of the information by measuring it against a gold standard document. This document was created by combining the policy statement issued by the American Academy of Pediatrics regarding the pharmacological treatment of cough in children with the guide of the World Health Organization on drugs for children. For each checklist, the web page contents were analyzed and quantitative measurements were assigned. RESULTS: Of the 19 web pages identified, 9 explained the purpose and/or mechanism of cough and 14 the causes. The most frequently mentioned pharmacological treatments were single-ingredient suppressant preparations, followed by single-ingredient expectorants. Dextromethorphan was the most commonly referred to suppressant and guaifenesin the most common expectorant. No documents discouraged the use of suppressants, although 4 of the 10 web documents that addressed expectorants discouraged their use. Sixteen web pages addressed nonpharmacological treatment, 14 of which suggested exposure to a humid environment and/or extra fluid. In most cases, the criteria in the technical appraisal checklist were not present in the web documents; moreover, 2 web pages did not provide any of the items. Regarding content completeness, 3 web pages satisfied all the requirements considered in the checklist and 2 documents did not meet any of the criteria. Of the 3 web pages that scored highest in technical aspect, 2 also supplied complete information. No relationship was found, however, between the technical aspect and the content completeness. Concerning the quality of the health information supplied, 10 pages received a negative score because they contained more incorrect than correct information, and 1 web page received a high score. This document was 1 of the 2 that also scored high in technical aspect and content completeness. No relationship was found, however, among quality of information, technical aspect, and content completeness. CONCLUSIONS: As the results of this study show, a parent navigating the Internet for information on the home management of cough in children will no doubt find incorrect advice among the search results. (ABSTRACT TRUNCATED)
As with most software, developers tend to create interfaces which seem logical and user-friendly. The only problem is that 'logical' to one person is confusing to another. The best approach is try out several search engines and spend enough time trying sample searches that you get a feel for the degree to which it satisfies your needs. All of these sites have adequate help areas and should be your first stop. Hopefully, these tools will help you to spend less time aimlessly surfing and more time realizing the potential of the Internet.
We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.
SUMMARY: The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently, there has been a significant increase in the size and complexity of ontologies due to new scales of biological knowledge, such as spatial transcriptomics, new ontology development methodologies, and curation on an increased scale. Existing Web-based tools for ontology browsing such as BioPortal and OntoBee do not support the full range of definitions used by today's ontologies. In order to support the community going forward, we have developed OLS4, implementing the complete OWL2 specification, internationalization support for multiple languages, and a new user interface with UX enhancements such as links out to external databases. OLS4 has replaced OLS3 in production at EMBL-EBI and has a backward compatible API supporting users of OLS3 to transition. AVAILABILITY AND IMPLEMENTATION: The source code of OLS is available at https://github.com/EBISPOT/ols4 and DOI 10.5281/zenodo.14960290 with Apache 2.0 License. A freely available implementation is accessible at https://www.ebi.ac.uk/ols4.
Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure and be able to use this information to infer structure-function properties. The goal of Entrez's 3D structure database is to make this information accessible and useful to molecular biologists. To this end, Entrez's search engine provides three powerful features: (i) Links between databases; one may search by term matching in Medline((R)), for example, and link to 3D structures reported in these articles. (ii) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view a combined molecular-graphic and alignment display, to infer approximate 3D structure. Entrez's MMDB (Molecular Modeling DataBase) may be accessed at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html
The internet has experienced tremendous growth over the past few years and has currently many resources in the field of medicine. However, many physicians remain unaware of how to gain access to this powerful tool. This article briefly describes the World Wide Web and its potential applications for physicians. The basics of web search engines and medical directories, as well as the use of advanced search with boolean operators are explained.
PROBLEM BEING ADDRESSED: The internet has experienced tremendous growth over the past few years and has many resources in the field of family medicine. However, many family physicians remain unaware of how the Internet can be used to enhance their practice and of how to gain access to this powerful tool. OBJECTIVE OF PROGRAM: To characterize components of the Internet, to explore how family physicians can use the Internet to enhance practice, and to increase awareness of how to gain access to Internet sites relevant to family medicine. MAIN COMPONENTS OF THE PROGRAM: An on-line search through the World Wide Web was conducted using multiple search engines including Lycos, WebCrawler, OpenText, and Yahoo as well as a conventional MEDLINE search of Internet publications for the past 5 years. A website containing an evolving selection of resources can be found at http:@dfcm 18.med.utoronto.ca/anthes/hpgdfcm1.htm. CONCLUSION: The Internet has useful applications and resources for family physicians including rapid communication between physicians, access to medical literature, continuing medical education programs, and lists of patient support and discussion groups.