1 27 February 2011 [email protected]Bioinformatički centri i baze podataka Željko Jeričević, Ph.D. www.riteh.uniri.hr/~zeljkoj/Zeljko_Jericevic.html [email protected]27 February 2011 [email protected]2 What Is Bioinformatics? “Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. …” from NCBI web site
What Is Bioinformatics?“Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. …”from NCBI web site
Što je bioinformatika?“Bioinformatika je multidisciplinarna znanostu kojoj se biologija, računalna znanost i informacijska tehnologija sjedinjuju u jednudisciplinu. Konačni cilj je omogućiti otkrićanovih bioloških uvida i stvoriti globalnuperspektivu iz koje se mogu razaznati biološkiprincipi objedinjena (unifying principles).”
Zašto biološke baze podataka• Razvoj molekularne biologije i genomskih
tehnologija doveo je do eksplozivnog rastabioloških podataka
• Poplava bioloških podataka nužno zahtjevaračunarske baze podataka i metode zapohranu, pronalaženje, organizaciju, obradu i vizualizaciju podataka
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What Is a Biological Database?“A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. A simple database might be a single file containing many records, each of which includes the same set of information. For example, a record associated with a nucleotide sequence database typically contains information such as contact name, the input sequence with a description of the type of molecule, the scientific name of the source organism from which it was isolated, and often, literature citations associated with the sequence.”from NCBI web site
NAR DB Issue 2011 editorial“The current 18th Database Issue of Nucleic Acids Researchfeatures descriptions of 96 new and 83 updated online databases covering various areas of molecular biology. It includes two editorials, one that discusses COMBREX, a new exciting project aimed at figuring out the functions of the ‘conserved hypothetical’ proteins, and one concerning BioDBcore, a proposed description of the ‘minimal information about a biological database’. …The Nucleic Acids Research online Database Collection, available at: http://www.oxfordjournals.org/nar/database/a/, now lists 1330 carefully selected molecular biology databases. Nucleic Acids Research web site http://nar.oxfordjournals.org/
NAR WS Issue 2010 editorial“This year’s special emphasis is on next-generation sequencing data analysis, molecular network and pathway analysis, and biological text mining. A total of 15 papers deal with these topics. A large number of papers cover two common tasks, alignment for DNA, RNA or proteins (10 papers), and various forms of gene set enrichment analysis (9 papers). A large number of papers cover DNA and RNA sequence and structure analysis (23 papers) and protein analysis, primarily of protein structure (35 papers). “
NCBI Pocket BookshelfHandheld computer versions ready for downloading:•Blood Groups and Red Cell Antigens•Clinical Methods•Genes and Disease•Health Services/Technology Assessment Text (HSTAT)•Inflammatory Atherosclerosis: Characteristics of the
Injurious Agent•Medical Microbiology
AHRQ is Agency for Healthcare Research and Quality
U.S. National Library of Medicine MeSH jepomoćna baza podataka koja sadržikontrolirani rječnik termina upotrebljenih zaindeksiranje publikacija u MEDLINE/PubMed. MeSH terminologijaomogućuje pronalaženje izvora informacijakoji koriste različita imena za isti koncept.
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MeSH (Medical Subject Heading)Primjer: Ptičja groznica → bird AND flu•Influenza in Bird•Avian Flu•Flu, Avian•Avian Influenza•Fowl Plague•Plague, Fowl•Influenza, Avian•Avian Influenzas•Influenzas, Avian
• Može li informacija biti vlasništvo?• Što možemo naučiti iz povijesti
(usporedba kemije i biologije)?• Može li se poslovati s profitom bez
prava vlasništva nad informacijama?
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The Federal Research Public Access Act of 2006 (Cornyn-Lieberman)
>>the policy would require that agencies with research budgets of more than $100 million enact policy to ensure that articles generated through research funded by that agency are made available online within 6 months of publication.<<(from article by Robin Peek, Newsbreaks, October 31, 2006)
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The Federal Research Public Access Act of 2006
>>“Public access to research expands shared knowledge across scientific fields and is the best path for accelerating multi-disciplinary breakthroughs in research,” said Richard J. Roberts, a Nobel Prize laureate and research director at New England Biolabs. “As a scientist and a taxpayer, I support this bill because it lifts barriers that hinder, delay, or block the spread of scientific knowledge supported by federal tax dollars.”<< (from article by Robin Peek, Newsbreaks,
October 31, 2006)
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The Federal Research Public Access Act of 2006
>>In an article in The Washington Post, Patricia S. Schroeder, president and chief executive of the Association of American Publishers, promised a fight (not surprisingly). “It is frustrating that we can’t seem to get across to people how expensive it is to do the peer review, edit these articles, and put them into a form everyone can understand”Schroeder said.<<
(from article by Robin Peek, Newsbreaks, October 31, 2006)
Open AccessWelcome to the Directory of Open Access Journals.
This service covers free, full text, quality controlled scientific and scholarly journals. We aim to cover all subjects and languages. There are now 3881 journals in the directory. Currently 5999 journals are searchable at article level. As of today 259860 articles are included in the DOAJ service.
Ultimate Open Source & Open Access Application: Wikipedia
“Since Wikipedia was launched online in 2001 as "the free encyclopedia that anyone can edit," it has blossomed to more than a billion words spread over 10 million articles in 250 languages, including 2.5 million articles in English, according to Wikipedia cofounder Wales”
