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| are special types of software or web sites that are designed to help people find information stored in databases or web sites. |
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| they search the internet, they make an index of the words, they allow users to look for words or combinations of words found in that index. |
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| starting points are lists of heavily used servers and very popular pages, the spider will begin with a popular site, indexing the words on its pages and following every link found within the site, the spider quickly begins to travel, spreading out across the most widely used portions of the Web. |
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| 2 versions of Entrez System |
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| networked entrez (works locally on users workstations), web version of entrez (accessible through the web browser) |
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| advantages-faster disadvantages- data outside not available |
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| advantages- outside data available by clicking hyperlink disadvantages- slower |
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| sequence of words in non-quoted phrase is ignored and treated as Boolean, |
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| words must be in that order-limiting word order narrows search |
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| Boolean operators, date limits, author limits, language limits, file format limits, limit search to specific databases |
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| Evaluating the credibility of Search results |
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| author, objectivity, quality, and appearance |
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| search engines with advanced pattern-matching capabilities used when vocabulary may not be consistent |
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| search based on concept of key words-not just words themselves |
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| pre-linked gateways to databases selected by the portal designer |
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| used to extend the functionality of browsers- add to existing software |
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| enhance browser features, auto form-filling, searching within a document, dictionary tools, visual preview of web pages, favorites |
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| a way of displaying data that is visually simple and easy to interpret |
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| Areas in need of data visualization |
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| sequence visualization, user interface development, protein structure visualization, compliment to numeral analysis, statistical analysis. |
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| Primary activity of structural visualization |
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| visualizing 3-D structure of proteins |
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| hides intricacies of hardware and software, presents users with images, sounds and graphics, determines density of information that can be presented to a user, is a bandwidth-limiting element in delivery of data |
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| 4 basic components of User Interface |
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| physical user interface, graphical user interface, logical user interface, intelligent user interface |
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| concerned with physical input and physical output such as: monitors, haptic controls, speech synthesizers, complex mechanisms |
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| CRT or LCD have differing qualities for 3D effects |
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| mouse, joystick or other controller with computer-mediated tactile responses |
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| represents everything displayed on a computer monitor |
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| Rules, guidelines and standards of interface behavior, such as how an interface should display the image of a molecule |
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| Intelligent User Interface |
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| relies on a variety of pattern-recognition techniques to adapt to the users behavior |
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| Independent programs capable of completing complex assignments without intervention |
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| static graphics, animation, and simulation |
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| unchanging pictures-uses fixed data |
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| displays pre-computed data that can be accessed and analyzed as needed to illustrate certain findings or relationships-uses fixed data |
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| dynamic computational interaction of user with a program that reevaluates the underlying data and renders the results- uses dynamic data |
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| data processing using sophisticated data search capabilities and statistical algorithms to discover patterns and correlations in large preexisting databases |
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| Analysis of data in a database using tools which look for trends or anomalies without knowledge of the meaning of the data. Data mining was invented by IBM who hold some related parents |
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| hold enormous amounts of data, they are only useful when data is categorized |
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| Creator and user of database |
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| mush share an understanding of the organizational theme |
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| Iterative (repetitive) process |
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| in which processes are modified to support new hypotheses suggested by data |
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| one step in an overall knowledge-discovery process |
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| 1. Selection and sampling (Knowledge-Discovery) |
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| researchers generally rely on their knowledge of biology to identify valuable relationships and limit sampling accordingly |
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| 2. Preprocessing and Cleaning (Knowledge-Discovery) |
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| a) Data characterization b) consistency analysis c) Domain analysis d) Data enrichment e) frequency and distribution analysis f) Normalization g) Missing value analysis |
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| 3. Transformation and Reduction (Knowledge-Discovery) |
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| Data sets are reduced to minimum size through sampling or summary statistics |
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| 4. Data mining methods (Knowledge-Discovery) |
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| a) classification b) regression c) link analysis d) deviation detection e) segmentation |
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| 5. Evaluation (Knowledge-Discovery) |
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| patterns identified by data mining analysis are interpreted |
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| 6. Visualization (Knowledge-Discovery) |
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| converts tabular listing of data summaries to pie charts and graphics |
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| 7. Designing New Queries (Knowledge-Discovery) |
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| testing new hypothesis suggested by data returned by the data mining process, requires formulating new queries and returning to the selection and sampling stage |
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