Basic reading, writing and informatics skills for biomedical research

1. Basic reading, writing and informatics skills for biomedical research Segment 2. Introduction to the virtual library Ganesha Associates

2. A brief history of scientific publishing • Scientific societies first began to form the seventeenth century and grew out of informal meetings held by people interested in the new experimental science • The Royal Society began in this way in 1645 • At that time, the act of publishing academic inquiry was controversial, and widely ridiculed. It was not at all unusual for a new discovery to be announced as an anagram, reserving priority for the discoverer, but indecipherable for anyone not in on the secret: both Newton and Leibniz used this approach • As the Royal Society grew there came a point where it became easier to exchange their ideas as written notes and letters. The journal Philosophical Transactions of the Royal Society was first published in 1665. Ganesha Associates

3. A brief history of scientific publishing • According to Bishop Sprat's History of the Royal Society (1667), society members sought to reject "amplifications, digressions, and swellings of style...bringing all things as near the Mathematical plainness, as they can: and preferring the language of Artizans, Countrymen, and Merchants, before that, of Wits and Scholars." Ganesha Associates

4. A brief history of the format of scientific publishing • The rapid growth in volume and types of scientific research after the second world war meant that many new journals were launched by commercial publishers • The process of peer review became widespread at this time as editors became more selective, and the volume and complexity of scientific information has increased • The emergence of the internet allows new forms of scientific publishing to evolve • The technology underlying publishing is becoming increasingly involved in the management and accessibility of huge amounts of complex information – hence linking to bioinformatics Ganesha Associates

5. The structure of a scientific article • A scientific article is a written report describing original research results whose format has been defined by centuries of developing tradition, editorial practice, scientific ethics and the interplay with printing and publishing services. • The result of this process is that virtually every scientific paper has a title, abstract, introduction, materials and methods, results and discussion – the so-called IMRD structure. • However, most journals have slightly different formats: So read the Journal’s Instructions for Authors before starting to write! Ganesha Associates

6. Structure of a scientific article • Abstract • Short summary • Introduction • What you studied and why it is important • Methods • How you studied it • Results • What you saw, measured, calculated • Discussion • What is your interpretation of what you saw and why is this important Ganesha Associates

7. A brief history of the growth of scientific publishing Ganesha Associates

8. Main types of print journal • Primary journal • Abstract & Indexing (A&I or secondary) Journal • Review (or tertiary) journal Ganesha Associates

9. The structure of an A&I journal record • Journal name, ISSN • Date of publication, volume, page numbers • Title • Authors names • Address, affiliation, contact details • Keywords • Abstract • …and more… Ganesha Associates

10. From print… Ganesha Associates

11. …to online Ganesha Associates

12. …to online (view source) Ganesha Associates

13. …to online (metadata) Define: Metadata is structured data about data. It may include information about the author, title and subject of web resources. It is available for searching but is not displayed on the page. </rdf:RDF> --><span class="articletype">Methodology article</span><h1>Exon level integration of proteomics and microarray data</h1><div class="multipleins"><p class="authors"><strong>Danny A Bitton</strong>^*¹ <a href="/logon/logon.asp?msg=ce"><imgsrc="/graphics/article/email.gif" alt="email" title="Email"></a>, <strong>Micha&#322; J Okoniewski</strong>^*¹ <a href="/logon/logon.asp?msg=ce"><imgsrc="/graphics/article/email.gif" alt="email" title="Email"></a>, <strong>Yvonne Connolly</strong>² <a href="/logon/logon.asp?msg=ce"><imgsrc="/graphics/article/email.gif" alt="email" title="Email"></a> Ganesha Associates

14. From metadata to databases Ganesha Associates

15. Gene ontology • There is no universal standard terminology in biology and related domains, and term usages may be specific to a species, research area or even a particular research group. • This makes communication and sharing of data more difficult. • The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: • cellular component, the parts of a cell or its extracellular environment • molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis • biological process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. Ganesha Associates

16. Ganesha Associates

17. 60 50 40 30 20 10 0 ER plastid cytosol cell wall nucleus ribosome chloroplast extracellular mitochondria other binding kinase activity protein binding golgi apparatus hydrolase activity other membranes nucleotide binding transporter activity transferase activity plasma membrane protein metabolism nucleic acid binding DNA or RNA binding other enzyme activity other cellular processes other molecular function DNA or RNA metabolism developmental processes other cellular components transcription factor activity receptor binding or activity other biological processes structural molecule activity other metabolic processes unknown molecular function cellular component unknown other intracellular components other cytoplasmic components cell organization and biogenesis response to abiotic or biotic stimulus electron transport or energy pathways CC Canker CC Healthy stem transport transcription response to stress signal transduction unknown biological processes Molecular Function Cellular Component Biological Process Ganesha Associates

18. The opportunity – semantic applications Ganesha Associates

19. Finding stuff should be so easy… Ganesha Associates

20. Sources of scientific information • Primary research journals, e.g. Nature • Abstract & indexing databases (A&I), e.g. Scopus, Web of Science, PubMed, SciELO (sometimes called ‘Secondary sources’ • Review journals, e.g. Nature Reviews in…, Trends in…, Current Opinion in…, Annual Reviews in… (sometimes called ‘Tertiary journals’) • Books • Conference proceedings Ganesha Associates

21. Where do I access articles online ? • Direct – Electronic journal portal • See examples in next slides • Direct – Dedicated electronic journal site • Indirect – Abstract & indexing service • See examples in next slides • Indirect - Web search engine • Google • Google Scholar • Scirus Ganesha Associates

22. Open access • Open access (OA) is the practice of providing unrestricted access via the Internet to peer-reviewed scholarly journal articles. • OA is also increasingly being provided to theses, scholarly monographs and book chapters. • Open access comes in two main forms: Green and Gold Ganesha Associates

23. Where do I access electronic articles? • Via an electronic journal • Government portal - subscriptions • CAPES Periodicals • Publisher’s portal – subscriptions and open access • ScienceDirect • Highwire Press • SpringerLink/ BioMed Central • Other publishers • Open access portal or publisher • PubMed Central • SciELO • Biblioteca Virtual emSaude Ganesha Associates

24. Where do I access electronic articles? • Via an Abstract & Indexing database • PubMed (NLM) • Scopus (Elsevier) • Web of Science (WoS) • Ovid • Via an internet search engine • Google Scholar • Google, Bing Ganesha Associates

25. On and off campus access • IP ADDRESS:  Every computer or device on the Internet has what is known as an IP address, which uniquely defines that device and enables devices to find each other on the Internet. • The IP address format is a string of four numbers, each from 0 to 255, separated by periods, for example, 192.168.15.1. Ganesha Associates

26. On and off campus access • CAPES circulates valid on-campus IPs to publishers • So subscribed-to content can be accessed anywhere on campus • You may be able to get off-campus access by using the personalisation features which come with Scopus and WoS • Open access content is available anywhere Ganesha Associates

27. You can get access if… • The journal is subscribed to by CAPES • You have a personal subscription • The journal is of the ‘Open Access’ type • Note: some journals only make their content ‘Open Access after 6 or longer months. Some journals contain a mixture of OA and non-OA articles. • Journals in the ‘red’ categories are available anywhere • CAPES journals are only available from computers within the University network • Most CAPES journals will be available from more than one source Ganesha Associates

28. Go to… http://www.pubmedcentral.nih.gov/fprender.fcgi to find out more about the availability of OA journals Ganesha Associates

29. Go to… http://library.buffalo.edu/hsl/biomed/ http://www.science.co.il/Biomedical-Databases.asp To find more information about biological and biomedical databases. There are many other sources of information… Ganesha Associates

30. Which sources should I use ? • No single source contains all of the articles relevant to your research • Google has the broadest coverage, but not all of the documents you find will be peer-reviewed articles • Scopus, WoS and PubMed give you the best balance between quality and quantity, and, in theory, should link to all the content subscribed to by CAPES, plus OA content. Ganesha Associates

31. Which sources should I use ? • But, using a journal portal such as Science Direct or CAPES Periodicals lets you browse individual journals more easily • Since every source has a different way of selecting and sorting the results of a search • So it is good to use several sources on a regular basis Ganesha Associates

32. So, which sources should I use ? • Recommendations: • Pubmed, Scopus and/or Web of Science for a broad coverage of the science in your field • Google for information other than what is published in the primary literature, such as technologies, conferences, etc • ScienceDirect, CAPES Portal for browsing specific journals • Avoid books, Scielo Ganesha Associates