IN SILICO ANALYSIS TECHNIQUES (BIOINFORMATICS) - LITERATURE RESEARCHES
Reading a newspaper on a personal digital assistant (PDA) rather than as traditional newsprint reduces the amount of CO₂ pumped into the atmosphere by a factor of between 32 and 140, and cuts emissions of oxides of nitrogen and sulphur by several orders of magnitude. And business delegates can reduce all 3 emissions by up to 1,000-folds if they teleconference instead of travelling to overseas meetings^ref.

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medical writing

• the standard format of original research prevails of :
• abstract
• introduction
• materials and methods
• results
• discussion
• acknowledgements : who is Olivier Danvy? He is the most thanked person in computer science, according to an automated analysis of 335,000 acknowledgements within the lab's CiteSeer archive of computer-science papers. The technique, which relies on text-mining software, offers a new way to investigate the influence of individuals, research agencies and companies within different areas of science. Until now, research on acknowledgements has been hampered by the lack of a data repository to study. In contrast, citation statistics (which track which papers are referenced by others) have been manually compiled over the past 4 decades by the company Thomson ISI in Philadelphia. Acknowledgement analysis could allow this type of inspirational or motivational person to be more routinely appreciated. Experts are divided over the significance of the new approach. Acknowledgements are more slippery than citations - there are many reasons to acknowledge somebody, different countries and fields have different traditions of who they acknowledge, and there is no requirement to mention everyone who deserves recognition. Peer review requires you to incorporate the latest and relevant citations. However no one is checking whether all contributors are referenced in the acknowledgements. Social scientists have already tackled some of these problems. They have divided acknowledgements into 6 main types, including support from funders, and the, perhaps more tantalizing, Danvy-type 'conceptual' support of individuals. This type of categorization is essential in any analysis of acknowledgements, otherwise you'll get a mishmash. This would identify connections between groups of collaborators who might otherwise appear isolated.

Web resources :

• European Medical Writers Association (EMWA)
• American Medical Writers Association (AMWA)
• Medical Writing - Writers Write(R)
• style manuals
• University of Fordham Style Manual
• The University of Madison Writing Center
• The Chicago Manual of Style
• The Columbia Guide to Online Style

Publication ethics:

• salami slicing : a redundant publication is one which duplicates previous, simultaneous, or future publications by the same author or group or, alternatively, could have been combined with the latter into one paper. As there is no information about the extent of this problem in the surgical literature, we set out to assess the incidence, spectrum, and salient characteristics of redundant publications in 3 leading surgical journals
• almost 1 in every 6 original articles published in leading surgical journals represents some form of redundancy^ref
• a 2003 survey of opthalmology journals estimated that at least 1.5% of all papers are duplicates^ref. Some researchers seem to have perfected the art: a study released last month identified two papers that had each been published 5 times^ref ! While most scientists agree on what constitutes scientific chicanery and malfeasance^ref and an Office of Research Integrity (ORI) has existed since 1992, plagiarism remains a serious threat to scientific integrity, with no tangible remedies on offer^ref. Despite this, US institutions are permitted to conduct inquiries under a veil of secrecy (cleverly disguised as privacy), and leniency in interpretation of the guidelines ensures that inquiries can be handled without compulsory disclosure to ORI^ref. University compliance documents are replete with inconsistencies, misinformation, and a tendency to obscure the true scope of the misconduct problem, making independent assessments difficult. Allegations of misconduct are on the rise according to ORI records. PubMed keyword searching on 'scientific misconduct' returns an average of 163 citations per year since 1992 (when ORI was set up) and 64 per year in the decade prior to 1992. Before 1992, an average of seven articles on scientific plagiarism were published annually, rising to 24 articles per annum since 1992. In fact, the number of articles in both categories started to rise in 1990-1991, so the increase is not directly attributable to the setting up of ORI. Further compounding the problem is the ineffectiveness of guidelines in clear-cut instances of misconduct. Universities can apparently comply with ORI guidelines yet fail to reprimand professors who steal ideas from junior researchers without apportioning credit. This is effectively the sanctioning of plagiarism, and measures to prevent it will be ineffective for as long as the authority to enforce them is vested in the offending institution. Protection for junior researchers is woefully inadequate, despite much-needed reform being tabled. Unfavorable outcomes coupled with a fear of retaliation dissuades most junior whistleblowers from ever making allegations, and legal options are limited for resource-restricted students contemplating litigation against attorney-laden universities.


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• simultaneous submission of articles to more than one journal : most medical journals do not allow it. The need for sequential submission is an important factor in delaying the publication of research. We propose that journals should allow authors to submit to two or more journals at the same time. This would lead to greater competition among journals and shorten publication delay, which would benefit both patients and authors. Timely publication of research findings is crucial because delays will have a harmful effect on patients' health. In a review of AIDS trials, Ioannidis found a delay of between 1.7 and 3 years between study completion and publication, with negative trials taking significantly longer to be published^ref. Furthermore, a study looking at economic evaluations found that on average the economic results were published two years after the clinical results^ref. Morally, as well as ethically, all those involved in the research process have a duty to report their findings as quickly as possible. An important barrier to early publication and dissemination is often the researcher. Many researchers take too long to write up their findings. However, another big factor is sequential submission, whereby authors are allowed to submit to only one journal at a time. Authors intending to submit a manuscript that they consider to be of high quality and general appeal may consider a general medical journal (BMJ, JAMA, Lancet, New England Journal of Medicine, etc). These journals have a fairly rapid turnaround. Even so, unless the journal considers the paper for its "rapid" publication section, a decision usually takes six to eight weeks. If the decision is positive (usually subject to amendment), the study is then published within a few months of the final manuscript being received. However, many papers are not accepted by the first journal and resubmission to a second or third journal is required. Ironically, in our experience, the most interesting and methodologically sound papers are often delayed the most as these are usually more likely to be sent to highly cited and competitive journals. On the other hand, many authors overestimate the value of their work and aim too high and therefore contribute to the delay in publication. Nevertheless, it is not uncommon for a paper to be rejected 2 or 3 times before it is finally accepted. Indeed, major general journals reject most of the papers they receive. Because our anecdotal experience was that such delays were widespread we undertook a small survey of corresponding authors of randomised controlled trials. We searched Web of Science with the phrase "randomised controlled trial" for a single month (January 2004). We emailed 95 corresponding authors asking how many times they had submitted their manuscript before it was accepted. Of the 40 who replied, about half (18/40) had submitted the paper to two or more journals, and for a quarter of those the time to publication was 20 months or more (compared with about 12 months for those who published in their first journal). This delay will not be entirely the fault of journals: some of the authors will have been inefficient in resubmitting their manuscripts. Nevertheless, a large proportion will be due to the requirement of journals that papers are submitted to one journal at a time. Journals require sequential submission for several reasons, one of which may be to reduce competitive forces between journals. Altman described various methods journals have used to maintain an advantage in order to increase circulation and profits^{ref1, ref2}. Sequential submission can be seen in this context. During the time an article is under submission to a journal it cannot be sent elsewhere for possible publication; in effect, the journal is holding a temporary monopoly on the paper. If the paper is rejected, the journal will suffer some loss in terms of the time and costs of peer and editorial review. Researchers and research consumers also lose from rejection. Delays in publication can adversely affect researchers' careers ("publish or perish") and their institutions' financial status, as distribution of public research funding in the United Kingdom is partly decided by a research assessment exercise. Research consumers (patients, doctors, and policy makers) lose out because the results of effective or ineffective treatments remain unknown. One method suggested some years ago that could address this problem is multiple submission^ref. Multiple submission is different from duplicate publication in that if the same manuscript were sent to two different journals and was accepted by one, the submission would then be withdrawn from the other. Multiple submission has a potential benefit of reducing the delay incurred by sequential submission. For example, an author might submit a paper to a general journal and a specialist publication. If the general journal accepted the paper for publication, it could be withdrawn from the specialist journal. To avoid encouraging duplicate publication, journals adopting a multiple submission policy could insist that authors inform them of the other journals that the article has been sent to. Acceptance or rejection letters could be sent not only to the authors but also to the other journals. This would prevent duplicate publication and also stop authors from waiting until they received a better offer from another journal. As well as speeding up publication of important findings, such a system would also lead to competition between journals for the best articles. Awareness that competing journals were also looking at the paper would provide a strong incentive to rapidly peer review the manuscript and make a final decision. This effect could increase the speed of peer review and publication. Indeed, early entrants to such a competition would, in our view, benefit from receiving higher quality submissions. For example, if the Lancet and BMJ were the only general journals to allow multiple submission, many authors would be tempted to prioritise those two journals before other general journals. Although journals could compete in such a system, they might also collaborate. For example, the BMJ might collaborate with the British Journal of Obstetrics and Gynaecology. Authors with a manuscript on obstetrics that could appeal to a general medical readership would submit the paper to both journals simultaneously. If the BMJ thought that the paper was not of sufficient interest to a general audience then no time would be lost in the paper being considered by a prestigious specialist journal. Multiple or simultaneous submission could introduce valuable competitive forces among journals for the best manuscripts. Multiple submission is allowed in some specialties. Piron compared his experience of writing and submitting papers to economics, finance, maths, and psychology journals, which do not allow multiple submissions, with law review journals, which do^ref. He noted that law review journals in the United States had the "fastest turnaround times of any set of journals on the planet." Journals may have other reasons than preventing competition for not allowing multiple submission. Multiple submission would increase the workload of journal staff through the increased flow of manuscripts. For some journals, the extra administrative burden would not be worth while as it may slow down their decision making processes and allow a competitor to "scoop" the article. This would leave them with the sunk costs of mailing the paper to reviewers etc, without having had the chance of publishing the paper. Workload would also increase for researchers as they will be asked to review more papers. This is a burden some of us would bear to increase turnaround. Indeed, as a condition of allowing multiple submission, journals could set the condition that one or more of the authors of the submitted paper would agree to review one of the journal's other recent submissions. Workload for both journals and reviewers would fall, however, if a collaborative model of multiple submission was adopted. In this model, a journal would allow multiple submission on the condition that the paper went to a partner journal. Both journals could then share the reviewer's reports and one journal's staff could handle the administration. Some journals use an author pays system—for example, BioMed Central journals. It is feasible that journals could have a single (free) submission policy or a multiple (pay) approach. This would allow the journal to offset some of its increased costs from losing an article to a rival but it would also depress the demand for the service. However, this approach might be less than ideal given that some organisations can better afford to pay than others. Additionally, authors may be more likely to pay if they have positive findings than negative results. Allowing papers with negative findings to be submitted at no charge might offset this problem. Several models of multiple submission exist. Journals could adopt any of these, and they might even experiment with different models using a randomised trial.
• International Committee of Medical Journal Editors (ICMJE) : journal editors will require companies to register a clinical trial in a public database before it starts if they hope to publish its final results. Trial leaders will need to describe the condition the trial aims to treat, which drug will be tested and how the trial will measure the success or failure of the drug. The policy is intended to solve a problem that has long plagued medical research: if a drug fails in a clinical trial, a company gains little from publishing that result. So the published articles as a whole include many articles about a drug's success, but few about its failures. As a result, doctors get an unbalanced picture about the true effectiveness of drugs. A study in 2003 looking at 500 cancer clinical trials found that 26% failed to be fully published 5 years after preliminary data was first presented at a leading cancer conference. If only positive results are published this can distort medical literature and leave doctors thinking a treatment is more effective than it actually is : this in turn can affect the validity and findings of subsequent reviews, treatment decisions and clinical practice guidelines. 12 international journals, including the New England Journal of Medicine, The Lancet, and the Journal of the American Medical Association, published the statement online
• The Journal of Interferon & Cytokine Research (a 1900-subscriber publication with 225 manuscripts per year, 25 to 30% of which ask for the guarantee) started making the offer in 1997 out of frustration of waiting months to get your latest research manuscript peer reviewed : send in $125 with your paper, and you'll get your review in just 14 days, guaranteed, or your money back. Both peer reviewers receive $50 if they meet the 2-week deadline. The other $25 goes to pay for extra overnight shipping charges. If there are lots of competing research teams that are working in similar areas, those folks have special incentives to publish first : in some fields, the citation half-life can be as short as a year or two. Some authors may pay the $125 because it's not their money they're spending; it's their grant money. If people were paying it out of pocket, I think they'd think a little different. If you choose not to pay the fee, your manuscript will probably get reviewed within 30 days. That's relatively fast; most journals try to get the author a decision within about 3 months. If revisions are necessary, most can decide within 6 months
• The editors in chief, deputy editors, managing editors, and editorial advisory boards who control scientific publication – collectively known as gatekeepers – exert a special influence on the orchestration of international research activity. The selection of journal gatekeepers is a self-organizing process that science has developed over the last three centuries. An invitation to serve as a gatekeeper is both a distinction and reward. But the process has skewed gatekeeper demographics, as we found when we built and evaluated a database of international core journal gatekeepers in 2003.  We were trying to figure out whether counting such gatekeepers would be correlated with the trends in counts of journal papers and citations. In our database, science journals were defined as "international" if their editorial boards included scientists from at least eight countries, regardless of the journal title used. The "international" label in the title of some journals may hide what is really only a national one. On the other hand, for example, the editorial board of the American Heart Journal includes not only US-based scientists but also others, mostly from ten European countries. The current database contains data for 240 core journals from 12 science fields, chosen by the Glänzel and Schubert classification system^ref, and includes the top 20 ranked by ISI's journal impact factor in each of the fields. The total number of analyzed gatekeepers can be considered as statistically significant when they are compared to indicators based on papers and/or citations. Results for 2003 and includes the number and percentage of gatekeepers for 10 countries. It also shows the number of papers in 12 science fields published and their citations, from 2000 to 2002, of papers published in 2000. The top 10 countries account for about 86 % of the gatekeepers. With few exceptions the number of US gatekeepers dominates the world of science to an extent that is considerably higher than their share of publications and citations.


The prevailing dominance of the USA in all fields is also clearly visible in the number of editors-in-chiefs of the investigated core journals in science and in 12 science fields

The dominance of the US gatekeepers, as demonstrated by our measurements, is not a conspiracy with some hidden intentions, but a consequence of the self organizing nature of science. Nothing needs to be done. However, it is an important reflection of the self-organizing mechanism which has allowed US gatekeepers to have a decisive influence on what, when and where worldwide research is published.
• frauds : faked data / data fabrication / fabricated data-sets (making up data values) and falsification (changing data values).
• John Darsee : in 1983, an investigation at Emory University, before he was appointed a fellow at the Harvard Medical School's Cardiac Research Laboratoryl, has revealed fabrication of data, unauthorized use of co-authors' names, and fictitious collaborators. The Emory investigation was undertaken after Harvard notified Emory of its suspicion of Darsee's Harvard research. Emory's investigative report focused only on the extent of Darsee's data fabrication. A copy of the report was sent immediately to the NIH, but the university was reluctant to send it to medical licensing boards or to the hospital where Darsee is currently employed^ref. Rather than prescribe action for Emory alone, the panel recommended seven procedural steps that should be taken by all NIH-supported research centers to guard against similar occurrences. These recommendations are being reviewed by NIH^ref. The NIH recommended that Darsee be denied federal research funds for the next 10 years^ref
• Luk van Parijs, 35, a rising star at the Massachusetts Institute of Technology (MIT) in the hot field of RNA interference (RNAi) was dismissed last week after admitting that he had fabricated and falsified data in grant applications, submitted manuscripts, and one published paper, the university reported in a statement. The California Institute of Technology (Caltech) in Pasadena has now begun reviewing two papers published by the researcher, when he was a postdoc there. Harvard Medical School and Brigham and Women's Hospital, where Van Parijs was a graduate student, is also scrutinizing his early work^ref.
• Kazunari Taira, a 53 years old professor of biochemistry engineering at the University of Tokyo faked data in an overseas scientific journal in February 2003 in which he stated that his research team had succeeded in having E. coli bacteria produce a human enzyme called Dicer -- so called as it dices RNA -- by implanting a Dicer gene in a plasmid. It was discovered in Jan 2006^ref
• Jon Sudbo, a Norwegian doctor specialised in mouth cancer at Oslo hospital, fabricated the database of a study describing the association between mouth cancer and the use of anti-inflammatory drugs that was published in The Lancet in October 2005. Sudbo published 2 other articles in 2001 and 2004 in the New England Journal of Medecine. The US National Cancer Institute gave him a grant of 70 million Norwegian krona (10.5 million dollars, 8.7 million euros) for his research. It was discovered in Jan 2006^ref
Statistical methods for the detection of data fabrication in clinical trials^{ref1, ref2, ref3}
many journals contribute to the prevalence of bad science, because, when the fundamental observation that led to the original publication cannot be reproduced, it is nearly impossible to publish a paper documenting this. Hence, controversies persist in the literature over many years, simply because the corrected story either is never published, or is not published as prominently as the initial paper. True, there is an extensive specialist literature where ambiguous or conflicting results can be addressed in detail, but the readership is limited. Some journals, such as Nature, have mechanisms for publishing technical comments on published research (Brief Communications Arising: online only), but these are few in number and must adhere to strict criteria. Reviewers of contradictory results often ask that the authors explain how the original authors could have obtained their results. To quote a recent rejection letter, "an adequate explanation for the apparent contradictory findings is not provided". Certainly, speculative explanations can be offered for some kinds of experimental differences. But it is never possible to prove how another lab obtained data that cannot be reproduced. One can only be certain of one's own data. This demand for explanation creates serious problems in the case of scientific fraud. In a minor case, the original authors may have fudged one small set of data to 'prove' their theory. In a more serious case, fundamental observations cannot be reproduced. Whether this irreproducibility is due to outright fraud, scientific incompetence or some combination cannot be determined by the authors who try to reproduce the result and fail. Another often-made request of reviewers is that the original experiments be reproduced exactly. This sounds reasonable but, in fact, can become an absurd burden. Even if the methods section were complete and accurate, one can never say with certainty that one has reproduced the experimental conditions precisely. Instead, the appropriate approach is to design experiments to test the conclusions of the original paper. If these conclusions are disproved, then the details of how they were arrived at are not relevant. Of course, a contradictory paper should be held to a higher standard than was the paper it refutes. But all journals must endeavour to correct errors, or those who perpetrate scientific misconduct (not necessarily outright fraud) will be rewarded, and those who try to correct wrong hypotheses in the proper hegelian manner — thesis, antithesis, synthesis — will be punished^ref.
Research subject to data audit could include studies presenting possible risks to public health, or those questioned by a whistleblower or by peer review. Others could be subject to random audits. Up to 1% of all studies could be audited every 3-5 years, at < 1% of the cost of the original study (Accountability Res. 1, 77–83, 1989). Auditing could be done by an independent body that would certify the validity of published results. Sponsoring institutions could choose to publish a transparent analysis of selected papers on the web. Although these processes might not eliminate all fraud or misconduct, they could substantially reduce such unethical practices^{ref1, ref2}.
Image manipulation : the Journal of Cell Biology (JCB) examines all digital images in all accepted manuscripts for evidence of manipulation. For black and white images this involves simple adjustments of brightness and contrast in Photoshop (see figure, part A). For color images, they use the "Levels" adjustment in Photoshop to compress the tonal range and visualize dim pixels (see figure part B). They have created standards for acceptable manipulation^ref, and they perform an initial investigation with the authors if they believe those standards may have been violated. To do so, they request that they submit the original data to the journal for comparison to the prepared figure(s) in question. Editors of some high-profile biomedical journals have recently voiced the opinion that journals cannot be investigative bodies^ref (L.K. Altman, W.J. Broad, "Global trend: More science, more fraud," The New York Times, Dec. 20, 2005). Clearly, journal editors cannot get access to authors' lab notebooks, but they certainly have a right to examine the raw data corresponding to any information presented in a manuscript, especially when it is possible to determine empirically whether the raw data have been manipulated. This adds another layer to the review process beyond traditional peer review. During their 3.5 years of screening experience at the JCB, they have had to revoke the acceptance of 1% of papers that passed peer review because they detected fraudulent image manipulation that affected interpretation of the data. They do not take such cases lightly. Four editors must agree on a determination of fraudulent manipulation: the managing editor and three academic editors, including the monitoring editor, a senior editor, and the editor in chief. They do not consider the element of intent; acceptance is revoked if any conclusion in a paper is called into question by the manipulation. 25% of all their accepted manuscripts have at least one figure that must be remade because they detect "inappropriate" manipulation, that is, the manipulation does not affect the interpretation of the data, but it violates their guidelines for presenting image data. This indicates a widespread misunderstanding of the line between appropriate and inappropriate manipulation, which will have to be addressed during the training of students in the responsible conduct of research. In almost all cases, they have been able to resolve incidents of image manipulation themselves; only on very rare occasions have they needed to request the help of an institutional investigative body. One of the supplemental figures that Hwang and colleagues published in the now infamous stem cell cloning paper^ref contained manipulated images. The image in the figure, part B is from the third row of Supplemental Figure S1B in that paper. It purports to show negative staining for a particular cell-surface marker in 4 different cell lines. A simple adjustment of tonal range clearly shows that the 2 middle images are identical. The minor differences in pixel structure are due to image compression. It is likely that they would have identified this duplication with their routine screen. It is important to note, however, that this would only have led us to request the original data from the authors, who could have dishonestly claimed to have made a clerical error and provided different images. This illustrates a potential limitation of their investigative capabilities, but editors will be surprised at how easily a deception can unravel if they start asking questions. What about other types of data besides image data? It is clearly more difficult to determine whether numerical data have been misrepresented, fabricated, or falsified. There are, however, clues to potential problems with these data that should raise red flags with peer reviewers and editors. These include exceedingly small data sets, exceedingly narrow and/or uniform error bars on a graph, or the presentation of data from a "representative experiment."

A) For black and white images, brightness and contrast adjustments can reveal background inconsistencies that are clues to manipulation. In the top panel, the intensity of the band in lane 4 has been adjusted. In the bottom panel, lane 5 is a duplicate of lane 2. Note the rectangular boxes around the manipulated bands. B) For color images, tonal-range adjustments can reveal manipulations. The original shows what appears to be negative staining in four separate cell lines. In the adjusted image, the two middle panels are clearly duplicates. The minor differences in pixel structure are due to image compression. One possible way to address problems with numerical data would be to require authors to submit all their raw data for comparison to the prepared figures. However, doing this comparison would be much more time consuming than image screening. At a minimum, journals should set guidelines for presentation of numerical data that promote accurate graphing practices. JCB advocates that journal editors take a proactive approach to detect potential misconduct and resolve it before publication. It is not enough to respond to allegations of misconduct made by others, and it is certainly not necessary to pass on all such suspicions to an investigative body, as others have advocated^ref. Despite the additional safeguards we have put in place, if someone is determined to publish fraudulent data, they may well succeed. It is important to keep in mind that our screening can pick up manipulations done to image files after they have been acquired, but it will not pick up adjustments to the data made during acquisition (e.g., using settings on a microscope). Even with these limitations, it is a cop-out for an editor to say that the review process can never be perfect, when the publication of fraudulent work comes to light (BBC News, "Cancer study patients made up'," Jan. 16, 2006). Editors have a responsibility to do what they can to protect the published record, and they can now do something beyond peer review. To editors who argue that they do not have the time or funds to do this kind of screening, think about the effort expended in dealing with a high-profile case of fraudulent research. The vast majority of biomedical journals are owned by commercial publishers, who make considerable profits from them. These companies should bear the cost of improving manuscript review as part of the responsibility of participating in scholarly publishing. Such enhanced review has the potential to save considerable time and public funds wasted by scientists forced to debunk published fraudulent research, when they could have been used instead to make real progress.

Web resources :

• Campaign Against Fraudulent Medical Research (CAFMR)
• Commitee on Publication Ethics (COPE)
• Danish Council on Scientific Dishonesty

Scientific and engineering publications between 1997 and 2001 :

• 1,265,000 from the USA : 4.3 papers per 1,000 inhabitants (293,800,204 people)
• 342,000 from the United Kingdom : 5.8 papers (35% more) per 1,000 inhabitants (59,050,800 people)

Online periodic journals on general medicine (specialistic journals are listed under respective sections; journals regarding immunology are listed in Journals on basic immunology; see also Publishers section)

• Complete list of all journal names
• Institute for scientific information (ISI), Inc. :
• impact factor (IF) is calculated by dividing the number of current citations to articles published in the 2 previous years by the total number of articles published in the 2 previous years^ref; impact factors 2005 (will be published in June 2006), 2004, 2003, 2002, 2001, 2000, 1999, 1998, compared 1992-2001; copied citations give impact factors a boost ; Science journal ranking by average impact factors  ; Submithelp.de (journals listed by IF for each topic)

The scientific community has come to regard impact factors, calculated by the Institute for Scientific Information (ISI), as providing a quantitative and largely objective guide to which journals publish the best research. Although many problems can result from naïve reliance on journal impact factors as a quality metric (especially when attempting to compare different fields)^ref, the perception of many scientists is that, to get recognition and career advancement, they must publish in a journal with a good impact factor. This presents a major obstacle to publishers of new journals, since even the best journal won't have a proper impact factor for 3 years. But this situation is even worse than it sounds, as the clock only starts ticking when ISI starts "tracking" the journal.  When does ISI start tracking the journal? It depends… According to ISI, the factors it uses to decide when to start tracking a journal include:
• how many articles the journal publishes
• how many competing journals ISI already tracks in the same discipline
• the previous citation record of the journal's editorial board
• the previous citation record of the authors who publish in the journal
• the number of times the journal has been cited in journals that are already tracked by ISI
Unfortunately, despite good intentions, this selectivity on ISI's part has the unintended consequence of concealing the success of new journals. A case in point is BMC Bioinformatics. Since it published its first article in 2000, this journal has rapidly established itself as one of the most active and successful in its field :

However, since ISI only began tracking BMC Bioinformatics in 2002, this will not translate into an official impact factor until June 2005, when the 2004 impact factors are released. All is not lost, however. It is possible to calculate an unofficial impact factor for any journal, even if it is not officially tracked by ISI, by making use of the information in ISI's cited reference database which includes the entire reference list of all tracked journal articles, and therefore includes citations of journals which are not themselves tracked^ref. Using this method, the 2003 impact factor for BMC Bioinformatics can be estimated as follows:
• BMC Bioinformatics articles published in 2001-2
• 48   (one 'Correction' article ignored for citation analysis purposes)
• 2003 citations of these BMC Bioinformatics articles
• 235   (according to ISI Web of Science cited reference database)
• Unofficial 2003 impact factor for BMC Bioinformatics
• Impact factor = 235/48 = 4.896
This "unofficial" 2003 impact factor for BMC Bioinformatics already compares very favourably with that of more established journals.
A comparison of 2003 journal impact factors

Journal	2003 impact factor
Genome Research	9.635
Bioinformatics	6.701
Nucleic Acids Research	6.575
Molecular Biology and Evolution	6.050
BMC Bioinformatics	4.896 (estimated)
Journal of Computational Biology	4.600
Genetics	4.276
Molecular Ecology	3.870
Evolution	3.833
Protein Science	3.787
Genomics	3.488
Journal of Molecular Evolution	3.114
Molecular Phylogenetics and Evolution	2.826
Gene	2.754
Genome	1.861

The journals listed are a selection of the journals that most frequently publish and/or cite bioinformatics-related articles. Note that the figure listed for BMC Bioinformatics is not an official impact factor, but an estimate, based on ISI's data, of what the impact factor would be, if it were calculated.  This estimated impact factor places BMC Bioinformatics in the top 5% of all journals covered by ISI. Yet an author reviewing the 2003 Journal Citation Report from ISI would have no idea that the journal BMC Bioinformatics was so highly cited. The number of articles on which this calculation is based is relatively small. The official impact factor, which is expected to arrive in mid-2005, may be significantly higher or lower, but it seems clear that it will be respectable. BMC Bioinformatics is not alone in facing this problem: there are many other recently launched journals, both from BioMed Central and from other publishers, whose impressive citation record is not currently captured by the impact factors listed in ISI's Journal Citation Report. It is an unfortunate fact that this may needlessly dissuade many authors from publishing in these new journals, and thus may serve to hold back innovation in science publishing. After many years of having the field of citation analysis largely to itself, ISI is finally facing the prospect of serious competition. The increasing use of standard XML formats by publishers mean that citation analysis is no longer a daunting logistical challenge. It is simply a question of number crunching. Citation tracking data for Open Access content is already available through Citebase, and the usefulness of this free service will grow as the amount of Open Access content increases. Meanwhile, CrossRef (the full text linking service) is also now collecting article reference lists from publishers for 'forward linking' purposes^ref, and these could in future potentially also be used to calculate impact-factor-like metrics. In addition Elsevier is now working on Scopus, a bibliographic database/citation analysis service that the publisher claims will offer broader journal coverage than ISI. With luck, this competition may give ISI just the spur it needs. BioMed Central's recommendation is that ISI should reconsider its policy on citation tracking, and should introduce a policy of immediately tracking any peer-reviewed journal that meets basic quality standards and which can provide reference list data in an appropriate form to allow automated analysis. By doing this, ISI would provide a valuable impartial service to the scientific community.
Emphasis on where research is published—relying on impact factors to reward academic work with funding or promotion—is ripping the soul out of academia. Publications become more important than teaching and the actual research itself.  In South Asia, job promotion often depends largely on the number of research papers published, and some doctors go to unreasonable lengths to "persuade" editors to publish their work. The quality of clinical work or even of the research itself is less important than the length of a citation list on a curriculum vitae. China, too, offers promotion according to the number of research papers. There are other systems. Germany, for example, has an intense hierarchy, where the chief specialist is one notch below God—or one notch above—with junior staff promoted on a whim or shunted to a dead end post in a flash of irritation. What value research or academic excellence in such an environment? Japan has managed to marry these arbitrary approaches. In the country's fierce hierarchy, promotion is aided by applicants listing journal impact factors beside references in their citation list. Candidates boast individual impact factors of, for example, over 100, somewhere in the 30s, or a miserable 0.3. Japan's fascination with genomics and impact factors is hindering advancement in academia for good clinicians with little basic science research experience. Although a correlation existed in the likelihood of papers from high impact factor journals being cited in US evidence based guidelines, journals with low impact factors were also cited frequently as providing important evidence^ref. Effect on readers' knowledge or clinical practice remains unmeasured, they conclude, and clinical and preventive research is undervalued. Impact factors have much to answer for, as do deans, sponsors, government agencies, and employment panels who use them as a convenient—but flawed—performance measure. How can a score count for so much when it is understood by so few and its value is so uncertain? In defence, worshippers of impact factors say we have no better alternative. Isn't it time for the scientific community to find one?^ref
• International Digital Electronic Access Library (IDEAL) : search article
• Science Direct : online Journals service from Elsevier
• Instructions to authors for journals in the health sciences : A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
• The Hirsch number (h) is a newly proposed measure of scientific productivity that attempts to go beyond simple publication-counting. The concept was invented by Jorge E. Hirsch of University of California San Diego in 2005. Hirsch proposed that an individual's Hirsch number is the largest integer h such that he or she has at least h publications with at least h citations in the refereed literature. The Hirsch number is calculable using free Internet databases and serves as an alternative to more traditional impact factor metrics which are available for a fee. Because only the most highly cited articles contribute to the Hirsch number, its determination is a speedy process. Hirsch has demonstrated that h has high predictive value for whether or not a scientist has won honors like National Academy membership or the Nobel Prize. In physics, a moderately productive scientist should have an h equal to the number of years of service while biomedical scientists tending to have higher values^{ref1, ref2}.

• open-access (OA) journals (OAJ) : in Britain, an inquiry by the House of Commons Science and Technology Committee concluded in July 2004 that open access seems viable but requires further experimentation. The committee advised the government to require UK-based authors to publish articles on their institutions' websites, but the government largely rejected the advice on 8 November. In August, 25 Nobel laureates signed a letter calling on the US government to provide public access to government-funded research. As a result, the US National Institutes of Health in September invited comments on a proposal to make the results of all federally funded research freely available shortly after publication. And in October, the German government gave 6.1 million to the Max Planck Society to develop an open-access system for publications from the society's institutes. Meanwhile, 48 biomedical societies united to oppose open access. On 16 March, they launched a series of Principles for Free Access to Science, which backs open access but reserves the right of publishers to charge for several months after publication. Society editors argued that it would be impossible to generate income for other society activities if they only raised money through payments from authors. The impact factors of nearly 200 open-access journals are similar to those of traditional journals in the same fields, according to a recent Thomson ISI report. The 58 open-access medical journals that receive impact factors fell, on average, at the 40^th percentile of all medical journals, with all but 11 ranking higher than the 10^th percentile. For life sciences journals, the 37 open-access journals were ranked, on average, at the 39^th percentile. It is clear that at an overall macro-economic level, a switch to Open Access publishing would not negatively impact research funding. The cost of the present system of biomedical research publishing, with all its inefficiencies and overly generous profit margins, still only amounts to about 1-2% of the overall funding for biomedical research (estimate from the Wellcome Trust, cited by Public Library of Science in their submission to the House of Commons inquiry). There is no reason why the cost of Open Access publishing should exceed the cost of the current system, since the fundamental process is the same. In fact, Open Access publishers are leading the way in using web technology to reduce costs further, so the cost of Open Access publishing to the scientific community will be significantly less than the cost of the system that it replaces. Meanwhile, the vastly increased access to research that is delivered by Open Access will greatly increase the effectiveness of the research money that is spent, since all research builds on what has gone before it, and is needlessly handicapped if access to previous research is inconvenient, slow, or impossible. In short, funders will get more "bang for their buck". At the micro-economic level, there will certainly be transitions that need to be carefully managed as the Open Access publishing model grows in economic significance. e.g. since the total cost of publishing scientific articles is roughly proportional to the amount of research to be published, it may well make sense for the costs of publishing to be incorporated into research funding grants, rather than being covered by library budgets. These are important issues, which deserve attention. But these transitional challenges should not be allowed to obscure the overall picture which is that with the Open Access publishing model the scientific community will pay significantly less, yet receive vastly more (in terms of access and usability). On 29th April 2004 the Wellcome Trust published a report on the economic implications of Open Access publishing. The report (Costs and Business Models in Scientific Research Publishing) indicates that Open Access publishing could offer savings of up to 30%, compared to traditional publishing models, whilst also vastly increasing the accessibility of research. Elsevier's figure of 97% of researchers in the UK having access to Elsevier content is misleading. As explained in the small print of their written submission, this refers to researchers at UK Higher Education institutions only, many of which have indeed taken out ScienceDirect subscriptions as a part of JISC's "big deal" agreement. However, these researchers do not have access to all ScienceDirect content by any means - the subset of journals that is accessible varies widely from institution to institution, meaning that access barriers are frequently a problem, even for researchers. The access situation at institutions which focus primarily on teaching rather than research is particularly bad, but Elsevier disguises this by weighting each institution according to the number of 'researchers' employed, to come up with the 97% figure. More fundamentally, the Higher Education sector is only one of several sectors carrying out biomedical research in the UK. Much medical research in the UK goes on within the NHS. Lack of online access to subscription-only research content within the NHS is a major problem, as detailed in a separate report. Similarly, Elsevier's figures conveniently omit researchers employed at institutes funded by charities such as the Wellcome Trust and Cancer Research UK, and in industry. To say that being able to go to the library and request an interlibrary loan is a substitute for having Open Access to research articles online is rather like saying that carrier pigeon is a substitute for the Internet. Yes - both can convey information, but attempting to watch a live video stream with data delivered by carrier pigeon would be a frustrating business.
• Practically, the obstacles to obtaining an article via the interlibrary loan route are so huge that all but the most determined members of the public are put off. For those who persist, after a time lag that will typically be several weeks, their article may (if they are lucky) finally arrive in the form of a photocopy. What the user can do with that photocopy is extremely restricted compared to what they can do with an Open Access article.
• With an online Open Access online article, you can cut and paste information from the article into an email. With a photocopy you cannot.
With an Open Access online article, the license agreement explicitly allows you to print out as many copies as you like and distribute them as you see fit. But if you copy and distribute the article you received by Interlibrary Loan without seeking appropriate permission from the publisher, you may well be in violation of copyright law. It is also worth noting that an increasing fraction of public libraries now offer free or low-cost Internet access, making it even more convenient for the public to view Open Access research. There is already a vast amount of material on medical topics available on the Internet, much of which is junk. Can it really be beneficial for society as a whole that patients should have access to all the dubious medical information on the web, but should be denied access to the scientifically sound, peer-reviewed research articles? In some cases, to be sure, comprehending a medical research study can be a demanding task, requiring additional background reading. But patients suffering from diseases are understandably motivated to put in the effort to learn more about their conditions, as the success of patient advocacy groups in the USA has shown. Patients absolutely should have the right to see the results of the medical research that their taxes have paid for. It is peculiar to hear large commercial publishers saying that Open Access would be a very good thing for the pharmaceutical and other industries, and then claiming that this is a problem with the Open Access model. The chemical, biotech and pharmaceutical industries play a major role in the UK economy, and so this argues strongly for Open Access.
To say that they do not contribute significantly in terms of publishing research is inaccurate. Industry publishes a significant amount of research itself, and also funds much research within the academic community that then goes on to be published. It is certainly possible that under an Open Access model, institutions (and countries) that publish a lot of research would pay a somewhat higher proportion of the cost of publishing than they do currently. Since it is the process of publishing the research that incurs the lion's share of the costs (with Internet distribution being very cheap in comparison), this is the most logical, sustainable way to fund the publication process. In contrast, the current situation, in which small universities effectively subsidize the cost of publishing the research carried out at relatively wealthy research centres, is far more inequitable and unsustainable. But in any case, the absolute amount of money expended by the research institutions will fall, due to the far greater efficiency of Open Access publishing. Furthermore, research institutions that support Open Access will benefit greatly in terms of kudos and influence, due to the greater accessibility and visibility of their research. These institutions would therefore be cutting off their nose to spite their face to oppose Open Access on the grounds given above. The assertion being made is, essentially, that Open Access publishers have an incentive to publish dubious material, in order to increase their revenue from Article Processing Charges. This is a very peculiar accusation for a traditional publisher to make given that in the same evidence session, Elsevier's hefty annual subscription price increases was justified as follows: "On pricing, we have put our prices up over the last five years by between 6.2 per cent and 7.5 per cent a year, so between six and seven and a half per cent has been the average price increase. During that period the number of new research articles we have published each year has increased by an average of three to five per cent a year. [...] Against those kinds of increases we think that the price rises of six to seven and a half per cent are justified." [Oral evidence to Inquiry, March 1st 2004, Crispin Davis (CEO, Reed Elsevier)] i.e. Elsevier's primary justification for increasing their subscription charges (and profits) is that each year they are publishing more articles. In which case, if their own argument is to be believed, they face the exactly the same conflict of interest as Open Access publishers. Fortunately, however, no such conflict of interest exists, for either Open Access or traditional publishers. Any scientific journal's success depends on authors choosing to submit their research to it for publication. Authors publish research in order for the value of their findings to be recognized. The kudos granted by a solid publication record is crucial for scientific career progression. Authors submit their research to journals with a reputation for publishing good science. If a journal had a reputation for publishing poor science, it would not receive submissions. Thus the system is inherently self-correcting. It should also be noted that many leading journals (both commercial and not-for-profit) already have page charges and colour figure charges for authors, in order to defray expenses and to keep subscription costs down. Just 2 examples (of many hundreds) are the Proceedings of the National Academy of Sciences (USA), and Genes & Development. So author charges are hardly an unprecedented experiment. It is true that commercial publishers have tended in some cases to remove author charges, and to commensurately increase subscription fees, since this suits their commercial interests in maximizing profits. But it is clear that author charges pose no fundamental problem to effective peer review. Health InterNetwork Access to Research Initiative (HINARI), and its sister initiative, Access to Global Online Research in Agriculture (AGORA), are commendable initiatives and are undoubtedly warmly welcomed by researchers working in the eligible countries.
Via these schemes, publishers give some of the poorest countries free access to some of their journals. In HINARI, twenty-eight publishers participate, making a total of more than 2000 journals available for free to some of the poorest countries (defined as having a per capita annual income of less than $1000); and at a deep discount for some slightly less disadvantaged countries (per capita annual income between $1000 and $3000). Unfortunately these schemes offer only a partial solution to the access problems of the developing world. The list of eligible countries has many notable omissions. It excludes large low-income countries such as India, Pakistan and Indonesia, even though these countries have per capita annual incomes of $735 or less, and are therefore "low-income" countries according to World Bank criteria. Countries such as Brazil and China (which are "lower-middle income" according to the World Bank) are also excluded from the eligibility list, even for discounts. There is an obvious explanation for these omissions. These larger countries have significant research programs, so publishers can generate substantial income by selling subscriptions to them. It appears that traditional publishers will only offer Open Access to the developing world when they can be sure it won't affect their profits. It is therefore clear that researchers in developing countries have a huge amount to gain from greatly expanded access to the global scientific literature that Open Access publishing will offer. Certainly, there are challenges that need to be faced to ensure that authors in developing countries can publish in Open Access journals, but these challenges are by no means insurmountable. Indeed, many low-income countries have already started their own Open Access journals. Meanwhile, BioMed Central currently offers a full waiver of the article processing charge to authors in low and low-middle income countries. Long term, the scientific community will certainly find ways to ensure that scientists in developing countries get the full benefit of Open Access, both as readers and as authors. Firstly, sending out printed copies of journals to subscribers who pay for them is in no way in conflict with the goals of Open Access. Many Open Access journals (such as PLoS Biology, Journal of Biology and Genome Biology) have print editions. Wherever there is a demand for print (from libraries or from individuals) then print editions are available to those who wish to pay to receive them, just as with a traditional journal. But, far more importantly, by Elsevier's own estimate some 30 million people in the UK (and more than half a billion people worldwide) use the Internet. The wonderful thing about Open Access is that any one of those hundreds of millions of people can print out copies of any Open Access article, and distribute them to whomever they want. If you want to get hold of an Open Access article, there are literally hundreds of millions potential sources. We already see the power of this mechanism in action. In the poorest countries in Africa, those scientists who are lucky enough to have access to the Internet are downloading Open Access articles from BioMed Central's journals (e.g. Malaria Journal), printing them out in large numbers, and distributing them to their colleagues in areas the Internet does not yet reach. They confirm to us that this makes the research vastly more accessible than research published in traditional print-only journals. In contrast, many traditional journals are received in print by only a few hundred libraries worldwide. Not only that, the libraries that hold these print copies are bound by strict rules governing what is and is not permissible in terms of copying and redistribution. To argue that these few hundred printed copies provide greater access to research than making articles openly accessible online is, frankly, ludicrous. A high quality journal such as Nature would need to charge authors £10,000-£30,000 in order to move to an Open Access model. But even for Nature, the figure of £10,000-£30,000 is wildly off the mark. The calculation used by Macmillan was as follows: "Very crudely, £30 million of sales: we get income of £30 million and we publish 1,000 papers a year. That is your [£30,000]." [Oral evidence to Inquiry, March 1st 2004, Richard Charkin (CEO, Macmillan)]. £30,000 is indeed a lot of money. But Nature clearly spends nothing like that on each research article that it publishes. There are several major problems with the calculation that was used: A significant fraction of Nature's £30m revenue is spent to commission and produce the non-research-article content of the journal (e.g. News & Views articles, book reviews, commentaries, editorials etc.) This non-research content would continue to drive healthy print and online subscription revenue, even if the research articles were made freely accessible online. Since the non-research content (the front-matter) is far more widely read than the research articles themselves, it is far from clear whether making the research articles Open Access would have any negative impact on subscription revenue. In fact, the opposite can be argued. For the same reason, there is no reason to believe that Nature's impressive advertising revenue would suffer dramatically as a result of Open Access, yet they are assumed to fall to zero in Nature's calculation. Part of the argument used to justify the high cost per published article is that Nature rejects more than 90% of papers submitted, and so has to review more than 10 papers for every one it publishes, and has to bear the entire cost of this. "[Nature] publishes fewer than 10% of the research articles submitted. Economics dictates that high quality journals like Nature have a high unit cost per paper published, because for every article published more than ten have been reviewed and de-selected."
Letter to Inquiry, January 13th 2004, Richard Charkin (CEO, Macmillan) This would indeed be expensive, and it is true that the repeated peer-reviewing of rejected papers as they trickle down the journal pyramid is one of the worst inefficiencies of the present system. In fact, however, Nature is not that profligate and had already taken steps to address this issue: "If a paper cannot be accepted by Nature, the authors are welcome to resubmit to Nature Cell Biology. Nature will then release referees' comments to the editors of Nature Cell Biology with the permission of the authors, allowing a rapid editorial decision. In cases where the work was felt to be of high quality, papers can sometimes be accepted without further review" From the HoC website : Thus, if a paper is scientifically sound, but is not exceptional or fashionable enough to appear in Nature, it may well be submitted and accepted into one of the next tier of journals in the Nature stable (Nature Cell Biology, Nature Medicine, Nature Genetics etc.) without requiring significant additional editorial work or costs. This is a very sensible system, and is one that is already in use at BioMed Central. If an article is rejected for publication in BioMed Central's top-tier journal, Journal of Biology, but is judged by the reviewers and editors to be scientifically sound, the authors may be offered publication in one of our more specialist journals. Public Library of Science plans to operate a similar mechanism as it launches new journals. This trickle-down approach benefits authors by avoiding the delays caused by repeated rounds of peer-review, and benefits science as a whole by reducing the cost of the publication process while maintaining quality. Taken together, the above factors make it clear that the actual figure that would be necessary as an author charge for Nature would most likely be vastly lower than the suggested figure of £10,000-£30,000. It is even possible that Nature could operate at a profit while offering Open Access to research content and making no author charge whatsoever. Elsevier cannot realistically claim to have led the transition of scientific publishers from print to online – that was done by smaller, more nimble operators such as HighWire Press (which launched the Journal of Biological Chemistry in 1995) and BioMedNet (which made the Current Opinion series of journals available online in full text form back in 1994). Of the large commercial publishers, Academic Press started IDEAL in 1995, years before ScienceDirect. Similarly, Elsevier's figure of £200 million for the development costs of ScienceDirect is more an indication of corporate inefficiency than of innovation. Huge investment by a large corporation is not the best driver of innovation, especially in the modern connected world. The explosion of the Internet has shown that open platforms are the real spur for innovation. The open standards of the Internet mean that anyone can create a website and offer any imaginable online service, and it will be instantly accessible by all Internet users world-wide. The result has been an unparalleled wealth of innovation, which goes far beyond what proprietary online services had previously achieved. Open Access to the scientific literature holds the promise of the same benefits for science. Once the majority of the scientific literature is Open Access, in the full sense of being openly re-distributable and re-usable, the entire scientific community will be free to develop and improve techniques to mine and explore that literature. They will not be constrained by any one corporate budget or policy, nor by the barriers inherent in the current fragmentation of the literature. At this point in time we can only imagine what is possible, but it is certain that it will dwarf what any one company might achieve. Scientific integrity is protected not by copyright law, but by the norms, standards and processes of the scientific community. An article is only "stolen" from an author if it is mis-attributed. This is fraud, and laws other than copyright deal with fraud. It is exceptionally rare for a scientific publisher to use copyright law to defend the integrity of a scientific paper on behalf of an author. In fact BioMed Central knows of no situation where this has happened. The "scientific integrity" argument simply provides a convenient excuse, which is used by traditional publishers to attempt to justify their requirement for transfer of copyright. Meanwhile, the real reason for copyright transfer is clear. Publishers regularly use copyright law to protect the profits they derive by controlling access to the literature. For example, in ongoing litigation, Elsevier and Wiley are suing various US photocopying firms for, amongst other things, including copies of research articles in student course-packs without paying royalties to the publisher.
The new National Institutes of Health (NIH) policy, which comes into effect on 2 May 2005, requests that authors whose research was funded by the NIH submit copies of their papers to the agency's National Library of Medicine (NLM) after they are accepted for publication. The papers will then be placed in an online archive. Authors can decide when the papers are made available to the public, but the NIH would like this to happen as soon as possible, and in any case within 12 months of publication. Advocates of full open access to scientific literature are unhappy that the policy relies on voluntary participation from authors, and that it does not require public access within 6 months of publication. It would put researchers in the difficult position of having to negotiate between the NIH, which wants researchers to make their work available as soon as possible, and journals, which may want researchers to wait. Publishers and societies that draw income from publishing have also criticized some aspects of the policy. They object to the NIH's plan to archive papers on its own site, instead of simply directing the public to journal websites, branding it a waste of public money. NIH officials estimate that the archive will cost between $2 million and $4 million a year to run. Types of open access to scientific literature :

type	description	examples
home page	faculty research paper hosted on personal or department home page	home page of Ted Bergstrom
e-print repository	open-access repository where authors deposit preprints, postprints, or both	open-access archive of Cornell University Library DSpace at Cornell University
unqualified access	immediate and full open-access publication of journal	D-Lib Magazine
dual-mode access	both print subscription and open-access journal editions offered	British Medical Journal
delayed access	open-access edition available some months after initial publication	Most HighWire Journals New England Journal of Medicine
author fee	fee paid by authors or their institutions to support open-access publication	BioMedCentral PLoS Biology
partial access	open access to some articles in an issue	format used by many publishers for advertisement or promotion of an article to a wider audience
low-income access	open access made available to particular countries on the basis of per-capita income	Health InternNetwork Access to Research Initiative (HINARI)
indexing access	open access to bibliographic information and abstracts with links to full-text articles	PubMed ScienceDirect CiteSeer.IST OAlster
cooperative access	support of open-access journals and the development of publishing resources contributed by member institutions	German Academic Publishers Project

The subscription cost of commercial journals rose by 224% from 1988 to 1998, according to the Association of Research Libraries — although nonprofit publishers have also contributed^ref. One could also argue that the crisis is due in part to the failure of institutions to increase their acquisition budgets at a time of substantial growth in the number and size of journals. For example, in 1960, the field of economics was served by some 30 journals, almost all of which were nonprofit ventures; by 2000, there were 300 economics journals, 2/3 of them from commercial presses^ref. Growth within the academy and pressure on faculty members to publish have led to the expansion of journal offerings, which, in turn, has sparked demands for libraries to purchase them. It has been estimated that the average scientific article costs $3,000 to publish (Frank M, Reich M, Ra'anan A. A not-for-profit publisher's perspective on open access. Serials Rev 2004;30:281-7). Higher costs are associated with greater rigor and selectivity of the peer-review process, as well as with higher levels of technical review and copy editing. Such costs are traditionally recovered through institutional subscriptions, as well as from advertising, fees for author submissions and color figures, and reprint sales. The more extreme advocates of open access believe that the scientific literature should be free to the reader, but there is a cost associated with publishing. The question thus becomes how to recover this cost in a way that satisfies the need for access. PLoS Biology, an open-access journal published by the Public Library of Science, has solved this problem. Its authors pay a $1,500 fee to have an article published, but this charge is a fraction of the real cost of publication. The remainder is covered by foundation grants from supporters of open access and by institutional membership fees (similar to subscription fees). It is unlikely, however, that sufficient philanthropy exists to make up the difference between $1,500 and the true cost of publication for the > 5000 journals indexed by PubMed. Consequently, in a world in which authors pay to publish, most journals will have to ask authors to contribute the full cost of publication, which for many will be > $3,000.On May 2, 2005, the National Institutes of Health (NIH) initiated a program to provide the public with access to the research of the investigators it supports. The agency asked NIH-funded authors to deposit their peer-reviewed manuscripts voluntarily into PubMed Central (a full-text repository) within 12 months after journal publication. The original plan required that published articles be deposited after only 6 months, but it was modified in response to public comments and the recognition that this requirement could have a deleterious effect on niche journals and quarterly publications. The NIH asserted that its policy would avert the need for journals to move from subscriptions to "author-pays" publishing. Efforts are now under way, however, to make deposit mandatory within 6 months and require that grantees deposit the final published copy of their articles. Although these changes would limit the confusion caused by the existence on PubMed Central of clinically relevant manuscripts that have not undergone copy editing and technical review, they would also negatively affect journals whose articles report predominantly NIH-funded research and those that serve niche fields and are published quarterly, limiting their ability to recover costs through subscription revenue. The ready availability of content on PubMed Central could lead to subscription cancellations and accelerate the transition to an author-pays publishing model, the economic implications of which are not adequately evaluated by John Willinsky, the principal investigator of the Public Knowledge Project at the University of British Columbia (Willinsky J. The access principle: the case for open access to research and scholarship. Cambridge, Mass.: MIT Press, 2006). A study at Cornell University estimated that author-pays publishing would increase that institution's expenses by $1.5 million annually^ref. If, in order to survive, journals had to ask authors to pay the full cost of publication, a portion of NIH grant funds would have to be diverted each year to cover the cost of making grantees' 65,000 articles free to readers. Spending some $200 million in support of open access should give Congress pause, particularly since the NIH budget has been cut this year for the first time in 36 years. At a time of shrinking budgets for biomedical research, does it make sense to spend scarce dollars on publication costs instead of on research to develop treatments and cures for disease? Willinsky makes the case for access to research literature as a public good, but the advancement of medical knowledge through research is also a public good. When there is not enough money to go around, the question facing us is this: How should we decide which public good is preferable?
• Annual Reviews Collection at NCBI BookShelf
• BioMed Central : Open Access now
• Directory of Open Access Journals (DOAJ)
• FindArticles.com
• Frontiers in Bioscience (FBS)
• Journal of Medical Internet Research (JMIR)
• Molecular Biology Today
• Public Library of Science (PLoS)
• PLoS Biology
• PLoS Medicine
• PubMed Central (PMC)
• Medical Subject Headings (MeSH) : a thesaurus published by the National Library of Medicine for use in MEDLARS
• BMC Titles [complete list]
• British Medical Journal [archive starts with Vol. 316(7131); 1998]
• Bulletin of the Medical Library Association [archive starts with Vol. 88(1); 2000]
• Canadian Medical Association Journal (CMAJ) [archive starts with Vol. 163(2); 2000]
• Critical Care
• Genome Biology
• Journal of the American Medical Informatics Association [archive starts with Vol. 4(1); 1997]
• Journal of the Medical Library Association [archive starts with Vol. 90(1); 2002]
• Molecular Biology of the Cell [archive starts with Vol. 8(10); 1997]
• Proceedings of the National Academy of Sciences of the USA (PNAS) [archive starts with Vol. 87(23); 1990]
• ...
• OAIster
• The Scientist [free registration required !]
• BioTechniques
• upon payment
• Annual Reviews of Genetics
• Biochemical Journal
• Biochemistry, molecular and cellular biology journals online
• Blood
• Cell
• Current Biology
• Developmental Cell
• Expert Reviews in Molecular Medicine
• Functional & Integrative Genomics
• Genomics Bibliography (last update Dec. 2000)
• Genome Research
• Glycobiology
• International Archives of Bioscience
• Journal of Biological Chemistry (JBC)
• Journal of Cell Biology
• Journal of Experimental Medicine
• Microbiology and Molecular Biology Reviews
• Molecular and Cellular Biology
• Molecular Cell
• Nature Publishing Group Reference
• Nature (weekly) [free registration required !]
• Nature primary research titles (monthly)
• Nature Biotechnology
• Nature Cell Biology
• Nature Genetics
• Nature Medicine
• Nature Structural Biology
• ...
• Nature Reviews (monthly)
• Nature Reviews Genetics
• Nature Reviews Molecular Cell Biology
• ...
• Nature Publishing Group Specialists Journals list
• New England Journal of Medicine
• New Scientist
• Nucleic Acid Research (NAR)
• Postgraduate Medicine
• Protein Engineering
• Science Magazine
• Scientific American Magazine : archive
• Structure
• The EMBO Journal
• The Lancet (search archive)
• Trends & Current Opinion at BioMedNet (BMN)
• Wiley Interscience

Search-engines for official medical literature

• AGRICultural OnLine Access (AGRICOLA) by National Agricultural Library (NAL)
• arXiv.org : e-Print archive
• Quantitative Biology archive (q-bio)
• BIOSIS
• Budapest Open Access Initiative
• Cambridge Scientific Abstracts (CSA)
• Cochrane Collaboration
• Computer Retrieval of Information on Scientific Projects (CRISP) at NIH
• CrossRef Search pilot project : 29-publisher pilot for full-text scholarly research 
• Database of Abstract of Reviews of Effectiveness (DARE)
• D-Lib Magazine
• Excerpta Medica database (EMBASE)
• Faculty of 1000
• Gateway
• Health Answers
• Health Finder from the US Department of Health and Human Services (HHS)
• Highwire : library of the sciences and medicine from Stanford University
• Medical Matrix
• Medscape
• MedMiner (combines GeneCards and PubMed searchengines based on a gene, gene-gene or gene-drug queries)
• Medscout
• National Electronic Library for Health (NELH) at NHS
• PubMed at NCBI (search in MEDLINE database) 
• HubMed : pubmed rewired (RSS feeds of literature queries - updated daily)
The PubMed Text Version will work with your handheld, but try PubMed for Handhelds which in addition to PubMed searching, offers PubMed?s Systematic Reviews subset and the Clinical Queries filters. The URL for mobile phones with WAP browsers is: http://pubmedhh.nlm.nih.gov/indexw.html. Another interface for handhelds, PubMed on Tap, is a product being evaluated and runs on the Palm and PocketPC operating systems. Both of these products are free to use. User feedback is encouraged.
• Pub re-miner
• Index Medicus : a monthly publication of the National Library of Medicine in which the world's leading biomedical literature is indexed by author and subject
• Quarterly Cumulative Index Medicus : a former publication of the American Medical Association, in which was indexed most of the medical literature in the world; replaced by ...
• Cumulated Index Medicus : an annual publication of the National Library of Medicine, comprising the twelve monthly issues of the Index Medicus.
• Internet Grateful Med (IGM) at NLM
• Arctic Health
• Bioethics
• Biotechnology Information
• Cancer Information
• Chemical Information
• Clinical Alerts
• Consumer Information
• DIRLINE^® (Directory of Health Organizations)
• DOCLINE^®
• Drug Information
• Health Service Research & Health Care Technology (includes HSTAT)
• History of Medicine
• HIV/AIDS Resources
• Interlibrary Loan
• LOCATORplus
• Medical Subject Headings (MeSH^®) (includes MeSH Browser)
• MEDLINEplus
• MEDLINE^®
• MIMCom Malaria Research Resources
• Multiple Congenital Anomaly/Mental Retardation (MCA/MR) Syndromes
• NLM Gateway
• NLM Online Exhibitions
• OLDMEDLINE
• Population Information
• Profiles in Science
• Space Life Sciences
• Toxicology and Environmental Health Information (TOXNET^®)
• Unified Medical Language System (UMLS^®)
• Visible Human Project^®
• Sequence analysis bibliographic references (SeqAnalRef) at Genomics and Bioinformatics Group, NCI
• The Scientific World
• Usenet bionet.journals
• Textpresso is a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's 2 major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate 2 objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text^ref
• Vivisimo Velocity for Life Sciences

Free online medical books

• BookShelf
• Science - Books et al.
• International Amedeo Literature Program by Bernd Sebastian Kamps : all services are free of charge. This policy was made possible thanks to generous unrestricted educational grants provided by AMGEN, AstraZeneca, Berlex, Boehringer Ingelheim, Novartis, Pfizer, Roche, Schering AG.
• Flying Publisher
• Free Books for Doctors (FB4D)
• Free Medical Information (Doctor = Publisher)
• The free medical journals site
• GoldenLinks4Doctors
• Medicine on Earth

Online book-sellers

• Amazon : USA, United Kingdom, France, Germany and Japan
• Barnes&Noble.com
• BookSense.com
• Froogle
• MedTech.com

Search-engines for non-official medical literature

• Google's web search manages to make the most useful references appear at the top of the page using algorithms that exploit the structure of the links between web pages. Pages with many links pointing to them are considered 'authorities', and ranked highest in search returns. The ranking is refined by taking into account the importance of the origins of links to a paper.
• Google Scholar uses the citations at the end of each paper, rather than web links. It automatically identifies the format and content of scientific texts from around the web, extracts the references and builds automatic citation analyses for all the papers indexed. This approach has been pioneered in computer science by ResearchIndex, software produced by the information technology company NEC. Much of the peer-reviewed material has been made available to Google by publishers, including Nature Publishing Group, the Association for Computing Machinery and the Institute of Electrical and Electronics Engineers, through a pilot cross-publisher search engine called CrossRef Search. Publishers have arranged for Google robots to scan the full texts of their articles. Users clicking on a hit returned by Google Scholar are directed to the article on the publisher's site, where subscribers can access full text and non-subscribers get an abstract or information on how to buy an article. Google Scholar has a subversive feature, however. Each hit also links to all the free versions of the article it has found saved on other sites, for example on personal home pages, elsewhere on the Internet.

Image archives

• Bristol BioMed Image Archive : a collection of medical, dental and veterinary images for use in teaching
• Digital Morphology (DigiMorph)
• Free biomedical images
• The Braunwald ImageBank, edited by Eugene Braunwald, MD, is a collection of thousands of high-quality clinical images covering a variety of cardiovascular topics
• Biodidac : > 6,000 images available [free registration required]
• NetterArt.com - Frank H.Netter MD
• The Netter Collection of Medical Illustrations Licensing Program

Softwares for literature gestion

• Librarian 1.1  is a free tool powered by PHP, Apache and MySQL, for self-creation of virtual annotated library of PDF articles, designed for small trusted groups, e.g. science labs. Once a PDF file is put into the program, Librarian links up with the PubMed database and automatically annotates keywords from the abstract and citation references. It allows a user to establish a network quickly, and then the home PC acts as a server available to any member of the laboratory. Librarian works on any Windows, Macintosh, or Unix-based computer.

the digital object identifier (DOI) system is an identification system for intellectual property in the digital environment. Developed by the International DOI Foundation on behalf of the publishing industry, its goals are to provide a framework for managing intellectual content, link customers with publishers, facilitate electronic commerce, and enable automated copyright management. Publishing on the Internet requires new tools for managing content. Where traditional printed texts such as books and journals provided a title page or a cover for specific identifying information, digital content needs its own form of unique identifier. This is important for both internal management of content within a publishing house and for dissemination on electronic networks. In the fast-changing world of electronic publishing, there is the added problem that ownership of information changes, and location of electronic files changes frequently over the life of a work. Technology is needed that permits an identifier to remain persistent although the links to rights holders may vary with time and place. The network environment creates an expectation among users that resources can be linked and that these links should be stable. The DOI system provides a way to identify related materials and to link the reader or user of content to them. DOI has wide applicability to all forms of intellectual content and can therefore be applied to all forms of related materials, such as articles, books, classroom exercises, supporting data, videos, electronic files, and so on. DOI provides a basis for work now in progress to develop automated means of processing routine transactions such as document retrieval, clearinghouse payments, and licensing. Publishers and users are being encouraged to experiment with DOI usage, and to commonly develop guidelines for DOI scope and rules for usage. The DOI system has 2 main parts (the identifier, and a directory system) and a third logical component, a database.

• the identifier: the DOI, is made up of 2 components.
• the first element -- the prefix -- is assigned to the publisher by a registration agency. Eventually, there may be multiple registration agencies to serve separate geographical regions or for each intellectual property sector (such as text publishing, photographs, music, software, etc.). However, at this stage there is only one registration agency and Directory Manager. Prefixes all begin with 10 to designate the DOI directory manager, followed by a number designating the publisher who will be depositing the individual DOIs, which ensures that a publisher can designate its own DOIs without fear of creating duplicate numbers. Publishers may choose to request a prefix for each imprint or product line, or may use a single prefix.
• the second element, following a slash mark, is the suffix. This is the designation assigned by the publisher to the specific content being identified. Many publishers have elected to use recognized existing international standards for their suffixes when such a standard applies to the object being identified (e.g., ISBN for a book), but may alternatively choose to use an internal code. In use, the DOI identifier is an opaque string without intelligent meaning other than as an identifier. The suffix can follow any system of the publisher's choosing, and be assigned to objects of any size -- book, article, abstract, chart -- or any file type -- text, audio, video, image or software. An object (book) may have one DOI, and a component within that object (chapter) may have another DOI. The publisher decides the level or "granularity" of identification based on the nature of objects sold and distributed over the Internet. The suffix can be as simple as a sequential number or a publisher's own internal numbering system.
• the directory: the power of the DOI system is its function as a routing or "resolution" system. Because digital content may change ownership or location over the course of its useful life, the DOI system uses a central directory. When a user clicks on a DOI, a message is sent to the central directory where the current web address associated with that DOI appears. This location is sent back to the user's Internet browser with a special message telling the system to "go to this particular Internet address." In a split second the user sees a "response screen" -- a Web page -- on which the publisher offers the reader either the content itself, or, if not, then further information about the object, and information on how to obtain it. When the object is moved to a new server or the copyright holder sells the product line to another company, one change