Transcript Diapositiva 1 - Institut Pasteur

Open Access
Bibliographic Resources
Anne Estreicher
Swiss-Prot Group
Swiss Institute of Bioinformatics
Geneva – Switzerland
[email protected]
Anne Estreicher
Swiss-Prot Group
Bioinformatic
and Comparative Genome Analysis Course
Swiss Institute
of Bioinformatics
HKU-Pasteur Research Centre - Hong Kong, China
Geneva – Switzerland
[email protected]
August 17 - August 29, 2009
Open Access
bibliographic resources:
outline
• Databases of citations and abstracts;
• Databases of full text articles;
• Database of books;
• Open access journals;
• Initiatives for developing countries.
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.
PubMed
www.ncbi.nlm.nih.gov/pubmed/
• Established in 1950;
• Database of citations and abstracts to biomedical and
other life science journal literature;
• Encompasses MedLine;
• Gives access to:
 > 18 millions papers (dating back to the 1860s)
PubMed
www.ncbi.nlm.nih.gov/pubmed/
• Established in 1950;
• Database of citations and abstracts to biomedical and
other life science journal literature;
• Encompasses MedLine;
• Gives access to:
 > 18 millions papers (dating back to the 1860s),
 > 20’400 life science journals,
 ~ 55 languages (17’751 jounals in English, 2’000 in
French, 372 in Chinese, 29 in Latin, 1 in Azerbaijani,
etc…).
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.
http://www.ncbi.nlm.nih.gov/pubmed/
Since April 2008, all final peerreviewed manuscripts arising from
research funded by NIH have to
be free access.
http://www.ncbi.nlm.nih.gov/pubmed/
PubMed ‘Advanced Search’
combines Limits and
Preview/Index
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.
When the Entrez system comes on stage….
Access to a wide range of
information and services beyond
the Entrez system (MODs, UCSC
genome browser, …)
Link to full text
PubMed Central
(www.pubmedcentral.nih.gov)
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;
- In February 2000: 2 journals (PNAS and MBC);
- In May 2009: 685 journals !
PubMed Central
(www.pubmedcentral.nih.gov)
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.
PubMed Central
(www.pubmedcentral.nih.gov)
Free digital archive of biomedical and life sciences journal literature at
the NIH (since 2000);
In February 2000: 2 journals (PNAS and MBC);
In May 2009: 685 journals!
Currency and age of material varies by journal (current -> 3 years !);
Some material dates back to 1809;
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…)
Non-PMC journal
Books via the NCBI server
(www.ncbi.nlm.nih.gov/sites/entrez?db=books)
Bookshelf
(www.ncbi.nlm.nih.gov/sites/entrez?db=books)
• 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.
Searching the Bookshelf
Searching the Bookshelf
Choose the book of interest
Access Bookshelf
from PubMed
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.
http://agricola.nal.usda.gov/
Agricola (http://agricola.nal.usda.gov/)
Agricola (http://agricola.nal.usda.gov/)
Agricola (http://agricola.nal.usda.gov/)
Other initiatives
DOAJ
Highwire Press
Free Medical Journals
CiteSeer
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).
www.doaj.org
A total of 223 journals in life sciences
(July 2009)
Open Access Biochemistry journals
represented in DOAJ:
All continents and some well-known journals
Acta Biochimica Polonica
Acta Bioquímica Clínica Latinoamericana
African Journal of Biochemistry Research
American Journal of Biochemistry and Biotechnology
Asian Journal of Biochemistry
Biochemistry Insights
European Cells and Materials (ECM)
Biokemistri
EXCLI Journal
Bioquímica y Patología Clínica
General and Applied Plant Physiology
BMB Reports
Indian Journal of Biochemistry & Biophysics
BMC Biochemistry
International Journal of Biological Sciences
BMC Chemical Biology
Internet Electronic Journal of Molecular Design
Bulgarian Journal of Plant physiology
JBC Papers in Press
Chem-Bio Informatics Journal
Journal of Biochemistry and Molecular Biology
Computational Biology and Chemistry :
Journal of Proteomics & Bioinformatics
Advances and Applications
Molecular Medicine
DNA Research
Nuclear Receptor Signaling
Nutrition & Metabolism
Open Biochemistry Journal
Open Proteomics Journal
Química Viva
Research Letters in Biochemistry
Türk Biyokimya Dergisi
http://highwire.stanford.edu/
Etc.
Etc.
Literature digital library and
search engine that focus primarily
on the literature in computer and
information science.
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.
http://citeseerx.ist.psu.edu/
Etc.
Often
Link to full text
(notNot
always
up-to-date)
clearly
indicated
that it
incomplete
is ora absent
book (not a research
article)
When was the site updated
???
Instead of 10
List of articles cited in the paper
ranked according to ACI
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.
Google scholar
http://scholar.google.com/
Search by author name(s),
keywords, titles…
Direct link to the journal
Might require a subscription !
Sometimes institution or author’s website
=> access to article difficult to find !
Full text
from
PubMed Central
Full text
from
the journal
(might require a subscription!)
links to articles citing this article
Open Access
bibliographic resources:
outline
• Databases of citations and abstracts;
• Databases of full text articles;
• Database of books;
• Open access journals;
• Initiatives for developing countries.
Free access journals
Authors pay to allow readers to get the papers free =>
problem of funding…
The BMC initiative
The Plos initiative
http://www.biomedcentral.com/
BioMed Central
http://www.biomedcentral.com/
 Science, Technology and Medicine publisher;
 ~ 220 peer-reviewed journals ;
Etc.
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;
http://www.plos.org/
7 journals
Open Access
bibliographic resources:
outline
• Databases of citations and abstracts;
• Databases of full text articles;
• Database of books;
• Open access journals;
• Initiatives for developing countries.
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…
 Launched in 2002: ~ 1’500 journals from 6 publishers;
 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).
The WHO HINARI Programme
http://www.who.int/hinari/en/
 2 groups of countries are considered, based on GNI per capita
(World Bank figures):
< $ 1’250 -> free access ;
between $1’250-$3’500 -> fee of $ 1’000 / year / institution.
Eligible countries
fee of $ 1’000
http://www.who.int/hinari/en/
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;
 Launched in 2006;
 2009: > 1’300 journals;
 Public and non-governmental organizations performing environmentrelated work;
 Eligibility, technical requirements (high speed connection to
internet) similar to HINARI Programme.
http://www.oaresciences.org/en/
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.
 Launched in 2003;
 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 environmentrelated work;
 Eligibility, technical requirements (high speed connection to
internet) similar to HINARI Programme.
http://www.aginternetwork.org/en/
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