1. Open Access Bibliographic Resources Anne Estreicher Swiss-Prot Group Swiss Institute of Bioinformatics Geneva – Switzerland Anne.Estreicher@isb-sib.ch Anne Estreicher Swiss-Prot Group Swiss Institute of Bioinformatics Geneva – Switzerland Anne.Estreicher@isb-sib.ch Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China August 17 - August 29, 2009 Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China August 17 - August 29, 2009

2. Open Access bibliographic resources: outline citations and abstracts Databases of citations and abstracts; full text Databases of full text articles; books Database of books; journals Open access journals; developing countries Initiatives for developing countries.

3. What do we mean by "Open access" ? Although access to the material is free, the use of the material still may still be subject to the copyright and/or related license terms of the respective authors or publishers.

4. PubMed www.ncbi.nlm.nih.gov/pubmed/ Established in 1950; citations and abstracts Database of citations and abstracts to biomedical and other life science journal literature; Encompasses MedLine; Gives access to:  > 18 millions papers  > 18 millions papers (dating back to the 1860s)

6. PubMed www.ncbi.nlm.nih.gov/pubmed/ Established in 1950; citations and abstractsbiomedical Database of citations and abstracts to biomedical and other life science journal literature; Encompasses MedLine; Gives access to:  > 18 millions papers  > 18 millions papers (dating back to the 1860s),  > 20’400 life science journals  > 20’400 life science journals, ~ 55 languages  ~ 55 languages (17’751 jounals in English, 2’000 in French, 372 in Chinese, 29 in Latin, 1 in Azerbaijani, etc…).

7. PubMed www.ncbi.nlm.nih.gov/pubmed/ Simple and advanced literature search with:  keywords,  author name(s),  MeSH (Medical Subject Heading) terms,  Journals,  single citation,  etc.

8. http://www.ncbi.nlm.nih.gov/pubmed/ Since April 2008, all final peer- reviewed manuscripts arising from research funded by NIH have to be free access.

10. http://www.ncbi.nlm.nih.gov/pubmed/

13. PubMed ‘Advanced Search’ combines Limits and Preview/Index

16. 5 related articles: computationally detected similarities using indexed MeSH (Medical Subject Heading) terms, text of titles and abstracts => detection of possible relationships Direct link to the journal Etc.

18. When the Entrez system comes on stage….

20. Access to a wide range of information and services beyond the Entrez system (MODs, UCSC genome browser, …)

21. Link to full text

22. PubMed Central (www.pubmedcentral.nih.gov) full-text articles Free digital archive of biomedical and life sciences full-text articles 2 aims: 1) permanently preserves digital journal literature in the life sciences (single repository, uniform and well-defined structured format -> better integration with related resources); 2) improves access to biomedical information to researchers. - Since 2000; 2 journals - In February 2000: 2 journals (PNAS and MBC); 685 journals - In May 2009:685 journals !

23. PubMed Central (www.pubmedcentral.nih.gov) full-text articles Free digital archive of biomedical and life sciences full-text articles - Free access to the literature, but use still subject to copyrights - Only peer-reviewed articles; - No promotional material (for the time being); - Almost all articles are in English.

25. PubMed Central (www.pubmedcentral.nih.gov) Free digital archive of biomedical and life sciences journal literature at the NIH (since 2000); 2 journals In February 2000: 2 journals (PNAS and MBC); 685 journals In May 2009:685 journals! Currency and age of material varies by journal (current -> 3 years !); Some material dates back to 1809;

26. PubMed Central (www.pubmedcentral.nih.gov) Completeness depends upon the journal: - Complete content for each issue, starting from the 1st (prior to late 1990s, scanned copies); - Complete issues and volumes only for recent years; - Only selection of articles (e.g. NIH funded research, or open access article) Over 1.5 millions articles, most have an entry in PubMed, but not all (book reviews, etc…)

27. Non-PMC journal

29. Books via the NCBI server (www.ncbi.nlm.nih.gov/sites/entrez?db=books)

30. Bookshelf Searchable collection of online biomedical textbooks and other literature. 1st book online: B. Alberts’ Molecular Biology of the Cell, 3rd ed; Currently > 150 books; Includes:  some classic biology and medical textbooks and monographs;  books and databases produced by the NLM and the NCBI. Access either directly (www.ncbi.nlm.nih.gov/sites/entrez?db=books) or from PubMed.

31. Searching the Bookshelf

32. Choose the book of interest

36. Access Bookshelf from PubMed

41. Agricola http://agricola.nal.usda.gov/ Catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information.

42. http://agricola.nal.usda.gov/

43. Agricola Agricola (http://agricola.nal.usda.gov/)

47. DOAJ Highwire Press Free Medical Journals CiteSeer Other initiatives

48. Directory of Open Access Journals (DOAJ) www.doaj.org Provides access to quality-controlled Open Access Journals; Open access without delay; Peer-review or editorial quality control, all languages, all subjects; Target group: researchers Users can "read, download, copy, distribute, print, search, or link to the full texts of these articles"; Hosted, maintained and partly funded by Lund University Libraries Head Office (Sweden).

49. www.doaj.org

50. A total of 223 journals in life sciences A total of 223 journals in life sciences (July 2009)

51. Acta Biochimica Polonica Acta Bioquímica Clínica Latinoamericana African Journal of Biochemistry Research American Journal of Biochemistry and Biotechnology Asian Journal of Biochemistry Biochemistry Insights Biokemistri Bioquímica y Patología Clínica BMB Reports BMC Biochemistry BMC Chemical Biology Bulgarian Journal of Plant physiology Chem-Bio Informatics Journal Computational Biology and Chemistry : Advances and Applications DNA Research European Cells and Materials (ECM) EXCLI Journal General and Applied Plant Physiology Indian Journal of Biochemistry & Biophysics International Journal of Biological Sciences Internet Electronic Journal of Molecular Design JBC Papers in Press Journal of Biochemistry and Molecular Biology Journal of Proteomics & Bioinformatics Molecular Medicine Nuclear Receptor Signaling Nutrition & Metabolism Open Biochemistry Journal Open Proteomics Journal Química Viva Research Letters in Biochemistry Türk Biyokimya Dergisi Open Access Biochemistry journals represented in DOAJ: All continents and some well-known journals

52. http://highwire.stanford.edu/

56. Etc.

59. http://citeseerx.ist.psu.edu/ Literature digital library and search engine that focus primarily on the literature in computer and information science.

60. http://citeseerx.ist.psu.edu/ Autonomous Citation Indexing (ACI): Creates citation indices; Locates articles on the web; Extracts citations; Identifies identical citations (occurring in different formats) Identifies the context of citations.

61. Etc.

62. Link to full text (not always up-to-date) Often incomplete or absent Not clearly indicated that it is a book (not a research article) When was the site updated ???

64. Instead of 10

65. List of articles cited in the paper ranked according to ACI

67. NAR paper 2004 ! The new NAR article of 2009 is not found -> too new to be cited enough ? => Currently (beta version?) CiteSeerX might not be the best place for "broad" bibliograpic searches.

68. Google scholar

69. Search by author name(s), keywords, titles… http://scholar.google.com/

70. Direct link to the journal

71. Might require a subscription !

72. Sometimes institution or author’s website => access to article difficult to find !

74. Full text from PubMed Central

76. Full text from the journal (might require a subscription!)

77. links to articles citing this article

78. Open Access bibliographic resources: outline citations and abstracts Databases of citations and abstracts; full text Databases of full text articles; books Database of books; journals Open access journals; developing countries Initiatives for developing countries.

79. Free access journals Authors pay to allow readers to get the papers free => problem of funding… The BMC initiative The Plos initiative

80. http://www.biomedcentral.com/

81. BioMed Central http://www.biomedcentral.com/  Science, Technology and Medicine publisher;  ~ 220 peer-reviewed journals ; Etc.

82. BioMed Central http://www.biomedcentral.com/  Science, Technology and Medicine publisher;  ~ 220 peer-reviewed journals ;  Free access to research articles in all journals published by BioMed Central, but subscription to view other content, such as reviews or paper reports;

83. http://www.plos.org/ 7 journals

84. Open Access bibliographic resources: outline citations and abstracts Databases of citations and abstracts; full text Databases of full text articles; books Database of books; journals Open access journals; developing countries Initiatives for developing countries.

85. The WHO HINARI Programme http://www.who.int/hinari/en/   The Access to Research Initiative (HINARI) provides free or ‘very low cost’ online access to the major journals in “ biomedical and related social sciences”.  Local, not-for-profit institutions in developing countries, such as national universities, research institutes, teaching hospitals, national medical libraries… 2002:  Launched in 2002: ~ 1’500 journals from 6 publishers;  2009  2009: > 6’200 journals from 150 publishers.  Participating institutions need computers connected to the Internet with a “high-speed (56kBd rate or higher) link” (WHO source).

86. The WHO HINARI Programme http://www.who.int/hinari/en/  2 groups of countries are considered, based on GNI per capita (World Bank figures): free access ; between $1’250-$3’500 -> fee of $ 1’000 / year / institution.

87. Eligible countries fee of $ 1’000

88. http://www.who.int/hinari/en/

89. The UN OARE Programme www.oaresciences.org/en/   Online Access to Research in the Environment (OARE), an international public-private consortium coordinated by the United Nations Environment Programme (UNEP), Yale University and publishers; 2006  Launched in 2006;  2009  2009: > 1’300 journals;  Public and non-governmental organizations performing environment- related work ;  Eligibility, technical requirements (high speed connection to internet) similar to HINARI Programme.

90. http://www.oaresciences.org/en/

91. The UN AGORA Programme www.oaresciences.org/en/   Online Access to Global Online Research in Agriculture, led by the Food and Agriculture Organization of the UN. 2003  Launched in 2003;  2009  2009: > 400 journals.  to major scientific journals in agriculture and related biological, environmental and social sciences to public institutions in developing countries;  Public and non-governmental organizations performing environment- related work ;  Eligibility, technical requirements (high speed connection to internet) similar to HINARI Programme.

92. http://www.aginternetwork.org/en/

93. Hands-on: o Test the search engine of the following sites (mostly PubMed): http://www.ncbi.nlm.nih.gov/pubmed/ http://www.doaj.org http://highwire.stanford.edu/ o Search with author names, keywords, publication dates; o From PubMed, follow the proposed links to other databases. Tutorials: http://www.nlm.nih.gov/bsd/disted/pubmed.html