Pharmacoinformatics Flashcards

Database management system
Terms Definitions
What is informatics?
The study of the collection, analysis, storage, retrieval, transferring, and dissemination of recorded knowledge, or data.
What is pharmacoinformatics?
informatics as it pertains to drugs and their use in medicine, as well as research aimed at the development of new drugs.
What are two types of knowledge?
empirical knowledge and knowledge obtained through reasoning
What are two types of data?
Primary data and secondary data
What are two methods for data analysis?
Induction and deduction
What are the goals of data collection?
propaganda, market research, decision support, and scientific research
What are the types of information storage and retrieval?
document retrieval systems, database systems, and reference retrieval systems
What are internet options for storage and retrieval of info?
HTTP, FTP, Telnet, E-mail, mailing lists, Usenet, electronic publishing, chat rooms, and videoconferences
What is telemedicine?
transferring medical examination data, including images, to clinical professionals at a distance from their patients
What is the John von Neumann model?
A model of computer design using a single storage structure to store both information and data. Separation of the storage from processing unit is critical. There are input and output devices back to the CPU, and program data and memory feeding into the CPU.
Describe the machine cycle on the microprocessor.
The data is fetched to the control unit, and decoded and sent to the arithmatic/ logic unit. The A/L unit processes the data, and the data is stored in memory. Memory may be Level 1, on the CPU, or level 2, off of the CPU
What are examples of input and output devices?
Input: keyboard, mouse, video camera, joystick, microphone, etc.Output: monitor, printer, speakers, film recorder
What is BIOS?
Basic Input Output System. A built-in program to set up the computer's hardware.
What is the CMOS and EEPROM? What do they have to do with BIOS?
CMOS: Complementary Metal Oxide Semiconductor. It is located on the Chipset or Real Time Clock Chip. Electrically Erasable Programmable Read Only Memory. Settings are saved on CMOS and EEPROM-- EEPROM provides a back up if CMOS loses data
Describe the BOOT Process.
BIOS checks the computer and system configuration. Then it loads the partition table from the hard disk and selects the bootable partition. The partition table can contain code to be executed. It then loads the "boot sector" of the oootable partition, which has a program that locates and loads system files for the OS, responsible for loading routines "device drivers" These initialize various system units and ensure the OS knows how to communicate with them. The last step is enabling the user to start the computer.
What is the purpose of the operating system?
It is software necessary for the computer to function. It maintains lists of files and folders, manages data inside the computer, recognizes inputs and sends outputs.
What are computer languages?
they allow a programmer to develop software for specific tasks
What are the levels of computer languages?
Machine level languages (binary only), assembly languages (names instead of numbers), high level languages (FORTRAN< Basic, C, C++, Java, COBOL, Pascal), and fourth generation languages (4GL), used mainly for database application, as they are closest to human languages
What is an application?
software developed to perform a specific task
What is a medical device? Can software be part of a medical device?
Any instrument ... used for diagnosis, treatment, or cure or prevention of disease or intended to affect the body. Yes, the FDA can regulate software used in medicine, such as in infusion pimps, MRIs, pacemakers, ventilators, etc.
What is analog processing and analog/digital conversion?
analog processing deals with a continuous signal, whereas analog/digital conversion chops it up into packets
What software is under FDA regulation?
software as a component of a medical device, software as an accessory, standalone software. Examples of software as an accessory is any software needed to calculate results from data or to analyze the data. Standalone software is anything not attached to a medical device, but still holds information relating to patients and diseases (such as software that aids in diagnosis)
What software is not under FDA regulation?
That which solely is used as a library function (such as storage, retrieval, and dissemination of information). Or that which is used for general accounting or communications or educational purposes. Also general purpase software or non-clinical research and teaching or that manufactured or altered by a practitioner for his own practice
What is a network?
a communications system for connecting users and devices such as computers, terminals, printers, and telephones. A network allows people to share information or data. Data transfer in the network must be fast, reliable, and efficient.
What are examples of computer networks?
LAN, WAN, and the internet
What is bandwidth in the analog sense?
The range of frequencies required to represent the information contained in the signal; expressed in hertz
What is bandwidth in the digital sense?
the information carrying capacity of the communications device or network; transmission speed/ bit rate... bps... bits per second. Compression speeds data transmission.
What are some local area network architectures?
Star, loop, and bus
What is the drawback of each type of LAN network architecture?
Star: central hub has to be reliable and efficientLoop: if a node fails, the ring is broken, and the addition of a new node requires the ring to be broken. Advantages: no routing is necessary and the ring system can notify the sender if the message was received; it's not as expensive as wellBus: Advantages: no routing necessary, and transmission is not affected by node failure; Dis: can be signal reflection leading to interference
What is an ethernet?
The implementation for networks with star or bus topology. The bus is made of several segments, or cables connecting computers. The computers are attached to the cable using network cards. Devices listen to the bus to determine when they can transmit. Collisions cannot occur, or both devices will have to stop transmitting and retransmit after a random amount of time. A main drawback is the time spent resolving collisions.
What is a token ring?
A token ring is implemented for loop topology. An empty token circulates continously, and a device has to seize an empty token and change a special bit. Then the device transmits the message. Other devices must wait until the token is empty. When the message is copied to the receiver, the bit in the token is changed back. If the network is busy it may take a while to get a hold of the token
What is the Internet?
a global network of computers
What is the WWW?
World Wide Web, a database or information and resources available on the internet
A program that contacts another computer to obtain data or service
A computer or software package providing service to clients
TCP: transmission control protocol; it breaks data into small chunks and wraps it into an electronic envelope containing both the sender and recipient computer addressesIP: Internet Protocol: determins the best route of delivery for each package
What are routers?
computers that are responsible for connections between networks; they determine the way the package travels
What is an IP address?
It is a four part number from 0 to 255. Each part is a byte (8 bits). IPv6 will have 6 parts to increase possible numbers from 2^32 to 2^48.
What allows virtual addressing use by computers?
Network Address Translation
What is ICANN?
Internet Corporation for Assigned Names and Numbers. It assigns IP address space, protocol parameters, domain name systems, and root server system management functions
What is a Domain Name?
The name of a computer or series of computers on the internet. Each one corresponds to one IP address. A DNS, domain name system, identifies a computer by the domain name
What is a URL?
A uniform resource locater. It locates a Web page location on the web server.
What is ISDN or DSL?
Integrated Services Digital Network and Digital Subscriber line. Ways of connecting to the internet through a digital phone line
What types of telemedicine platforms are there?
Communications systems and distributed telemedicine systems. Communications system have a bridge between the patient and providers platforms, while the distributed telemedicine system uses a BUS topology/ Internet to communicate information between multiple people.
What is a spreadsheet?
A table of values arranged in rows and columns. A spreadsheet application is computer software for creating and manipulating spreadsheets.
How are values in cells related to each other on a spreadsheet?
Through functions
What are multidimensional spreadsheets?
spreadsheets linked to one another
How may data be represented?
Text, tables, and graphics
How may statistical software/ functions be used with spreadsheets?
In Excel, one may perform ANOVA, correlation analysis, regression analysis, F-test, t-test, z-test and histogram analysis, among other things. SAS, STATA, RATS, MATHEMATICA, and MATLAB are statistical software examples.
What is computer modeling?
The process of developing a set of parameters and variables and mathematical relations between them to represent real world objects or phenomena, often a 3d object in a computer
What are examples of computer modeling?
Computer aided design/ computer aided manufacturing (CAD/CAM)Animation software
What is CADD?
Computer aided drug design; using computer modeling to develop new drugs. Includes Molecular Modeling software (sybyl), Docking software, protein alignment (EMBOSS), Quantum Chemistry Software, visualization software (RasMol), and biomolecular databases (PDB).
What is molecular modeling?
The generation, visualization, manipulation, and prediction of realistic molecular structures and associated with them physico-chemical properties.
What are the goals of molecular modeling?
graphical representation of structures and properties, construction of molecules and molecular complexes, calculation of molecular properties, and analysis of molecules and molecular complexes.
What are methods of molecular modeling?
molecular graphics (building and modifying structures), molecular mechanics (empirical approach using classical mechanics to optimize geometry), molecular dynamics (studies movements), and quantum mechanics (ab initio and semiempirical)
What is word processing?
Creating, editing, and printing documents using a computer. A word processor is a computer program enabling a user to create, modify, store, display, or print a document.
What are examples of word processors?
MS DOS Edit, pico, jot, nedit, MS Word, Corel WordPerfect, Lotus WordPro
What is desktop publishing? Examples?
Combining text and graphics into documents by using a computer system, special software, and high-resolution output devices; Adobe Pagemaker, MS Publisher
What is computer graphics?
displaying and manipulating pictural information using computers
What are presentation graphics?
software using plots, charts, graphs, and other images for slide shows and reports; includes functions for graphics and charts, text insertion, and importation of graphics
What are rules of presentations?
Define goal, objectives, audience, a plan, the number of slides. Use same design for all slides, with a title, make sure colors and text are clear.
What is image processing? What are uncompressed and compressed file formats?
importing an image, analyzing, and outputing the image;Uncompressed: bmp, tiff, pcxCompressed: jpeg, gif, png
What is multimedia?
text, graphics, animation, video, and sound used in an integrated way
What are audio formats? video formats?
au, wav, mp3, ram, vqfvideo:avi, mov, mpg, qt
What is a database? What are some examples?
a collection of data organized in some way, usually so that a computer program can quickly select desired pieces of data; examples: address book, telephone directory, cook book, etc
What is a hypertext database?
a set of objects so that each object can be linked to any other object
What is a data warehouse and a data mart>
A data mart is a subset of databases contained in a data warehouse. A data mart is used to make strategic business decisions. A data warehouse combines databases across an entire enterprise and is designed to support management decision making
What are the types of databases?
hierarchical databases, network databases, relational databases, and object oriented databases
What is the main problem with hierarchical databases?
Does not allow many-to-many relationships
What is the main difficulty with network databases?
They are very complex and difficult to manage since there is a lack of standards
What is DBMS?
Database management system: software for creating and maintaining databases; examples: ACCESS, ORACLE SYBASE< DB2
What is an example of each type of database?
hierarchical: IMSNetwork: CODASYLRelational: ACCESSObject oriented: Cache
What are the types of relationships in a database?
one to one, one to many, many to many
Describe a relational database.
A database where the info is stored in tables. Relationships between tables are defined by common information.
What is a field and a record in a table?
A field is a column, where a record is a row
What is a key?
A common field contained in two tables and is used to establish a link between them. A primary key is established in one table, and the foreign key is that field in another table.
What is normalization in a database?
Optimizing the tables in the database to avoid repetition
What are the steps to making a database?
1. Defining the purpose2. Making a list of all fields3. Adding keys4. Normalization5. Final product
What is referential integrity, nulls, and constraints?
Referential integrity: if a record is deleted, should all records with the entry be deleted?Nulls: absence of data, not zeroConstrains: limits on values, lengths, etc
What is SQL?
structured query language, a standard language for creating, accessing, and manipulating relational databases; statements include SELECT, CREATE, DECLARE, ALTER, etc
What are types of storage devices?
temporary storage (Random Access Memory), random access devices (Hard disks, floppy discs), sequential access devices (tapes)
What is storage access time? What is data transfer rate?
latency; thoroughput (MB/s), read rate/ write rate
Describe the levels of storage (primary, secondary, etc)
Primary is memory accessed by the CPU (RAM) through the memory bus. Secondary storage is not as quickly accessed-- it is the mass storage device, the hard drive. Tertiary storage may be removable and is even slower
What is a database server and a distributed database?
a program that runs on a server computer to set up, access, and maintain a databasea collection of data spread out over 2 or more servers
What is page rank?
The probability that a random surfer will visit a page. It is calculated for each page rank using an algorithm. Words in larger and bolder fonts are weighted larger. Text of a link is associated with both the page and its referring page
What are indexing languages?
Controlled Volcab or Assigned-Term Systems, Natural Language or Derived-Term Systems, and Free Term or Free Indexing Language
What are some search algorithms?
Boolean Searching, Searching by keywords, phrases, subject headings, author, title, truncation and string searcing
What is relevancy rating?
Search terms are given rates proportional to their inverse frequencies. A sum of these weights is calculated, the higher the sum, the higher the rank.
What are some bibliographical Databases?
Medline, ISI (Institute for Scientific Information), and OCLC (Online computer library center)
What is the OCLC accession number based on?
The Dewey Decimal system
What are US Government Document Numbers like?
They are SuDoc numbers arranging the collection by agency on the shelves; the stem is the portion of the number up to the colon, identifying agency, subagency, and series; the portion after the colon is unique for the document
What does the library of congress assign to bibliographic items?
control numbers; these numbers are part of the MARC: Machine Readable Cataloging Record
What is the MARC?
A bibliographic record containing the description of the item, the main entry and additional entries, the list of subject headings, and the call number
What is the ISBN and ISSN?
ISBN: International Standard Book NumberISSN: International Standard Serial NumberThese were developed by the International Organization for Standardization in Geneva. Other records include ISAN, ISRN, ISRC, etc
What are the parts of the ISBM?
Group identifier (Engish, French, etc), Publisher Identifier, Title Identifier, and Check digitBeginning 2007 ISBN will have 13 digits and will be prefixed by 978
What is an SICI?
Serial Item and Contribution Identifier, uses ISSN, adds Periodical Issue, volume Number, First Page, First letters of titpe words, code structure identifier, text publication version number, and check character
What is an ISMN?
International Standard Music numbers; begins with letter M, then publisher identifier, title identifier, and check digit.
What is an ISRC?
International Standard Recording Code
What is an ISWC?
International Standard Music Work Code... given to individual musical composition
What is an ISAN? ISRN? DOI? URN?
international standard audiovisual number, international standard technical report number, digital object identifier, and uniform resource name
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