Current Trends in Biomedical Publishing and Bioinformatics

Social networking sites reviewed...

2010-02-14T09:37:00.000-08:00

Here is a link to a blog item from Comprendia, the Biosciences Consulting Group. It is a good review of the some of the current social networking sites available to life scientists and the usage they get. As the authors says, these figures may not be totally accurate, but they do give an indication that some of these sites at least are gaining traction in the community.

Click here is see an earlier list of sites posted here last year.

On the reading habits of the digital generation...

2010-01-10T08:54:00.000-08:00

Read a nice summary by Martin Fenner on digital reading habits across formats. It will kindle your imagination...

Welcome to Jane...

2010-01-09T09:27:00.000-08:00

Jane stands for Journal/Author Name Estimator. None the wiser...?!

Have you recently written a paper, but you are not sure which journal to submit it to? Or maybe you want to find related articles so that you can identify a suitable referee.

Then just cut and paste the abstract of the paper into Jane and it (she?) will search Medline to find matching articles, journals and authors. It's like eTBlast - see earlier post.

Nice tools, but you should be able to do this with PubMed or Scopus.

Text mining with GeneIndexer

2010-01-02T08:02:00.000-08:00

GeneIndexer has been around now for a couple of years but seems too be getting some marketing dollars spent on it with a full page advertisement in the latest issue of Nature and a sale to the NIH Library. The tool enables researchers to reveal biological significance in a set of co-regulated or associated genes. Applications include:

Using keywords to identify and prioritize genes most relevant to any given research question. Keywords can be any string of words, e.g. disease names, molecular pathways, or Gene Ontology classifications.
Uncovering implicit, as well as explicit, functional relationships among genes--discover new genes and propose hypotheses above and beyond what is explicitly described in the literature.
Building hierarchical trees of genes in which gene subsets are clustered into functionally related groups. This allows researchers to navigate large gene collections easily and adds a new dimension to the analysis and discovery process.

Because GeneIndexer includes all of the genes contained in Entrez Gene and OMIM databases, and uses artificial intelligence and computational linguistic techniques, rather than human curators to identify conceptual gene relationships it is possibly the most up-to-date and accurate system of its kind.

eTBLAST 3.0: a similarity-based search engine

2010-01-02T07:41:00.000-08:00

I have only just come across eTBlast. Conceptually, it is a bit like NCBI's Blast utility wich assesses sequence similarites between geens or proteins. Here, you simply in put a paragraph of text and eTBLAST will return the abstracts of articles which use the same spectrum of terms. It works a little like PubMed's Related Article feature, except here you can supply your own text, which could be from an unpublished article or a research proposal. New features in version 3.0 include "Find an Expert" - identifies authors that are the most published in the topic of your query - and "Find a Journal" - identifies journals that published on your topic the most.

In this day and age of increasingly specialized science, it can often be a non-trivial task to identify an appropriate journal to submit to. And editors are forever trying to identify appropriate referees - so eTBLAST seems to fill a worthwhile niche.

Open access to federally funded research - a public debate

2010-01-02T07:11:00.000-08:00

Currently, the National Institutes of Health is the only federal body that requires that research funded by its grants be made available to the public online at no charge within 12 months of publication. The US Administration is seeking views as to whether this policy should be extended to other science agencies and, if so, how it should be implemented. You can follow the discussion at the OSTC Blog.

The discussion will occur in three major phases:

Implementation: Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release?
Features and Technology: In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change.
Management: What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

A wrap up of phase one is posted here. It provides an interesting overview of how the opportunities presented by Open Access are seen by different research communities.

Google Wave hits biology beach...

2009-12-18T09:41:00.000-08:00

If you want to see some interesting Google Wave applications being developed for the life sciences, visit this link! If you have time, take a look around, it is an interesting blog.

Impact Factors - the story goes on, and on...

2009-11-22T07:46:00.000-08:00

"I first mentioned the idea of an Impact Factor (IF) in Science in 1955. With support from the National Institutes of Health, the experimental Genetics Citation Index was published, and that led to the 1961 publication of the Science Citation Index." Little did Eugene Garfield realise that journal-based IF's would still be a sourse of heated debate in the second decade of the 21st Century.

In a recent article in PLoS One, Cameron Neylon and Shirley Wu examine the case for article-based metrics and find them wanting. In their concluding remarks, they state that:

"Indeed, the fundamental problem of which paper to read can also have different contexts. Which new papers are relevant to you? Which papers should you read if you are going to pursue research question X? Which papers do you need to read before submitting your paper?"

Quite so, but I suspect that the main influencers in each of these three circumstances are: the title of the article; the name of the author(s) and the aims and scope of the journal, respectively.

IF's matter for assessment purposes, but relevance is a personal thing, not something that can be measured by the wisdom of crowds.

Are informatics tools too difficult to use?

2009-11-18T05:56:00.000-08:00

A new RIN report, entitled "Patterns of information use and exchange: case studies of researchers in the life sciences" highlights that fact that, although different, all of the areas studied show very compex patterns of information use. Despite this, many of the groups studied used only a fraction of the information sources and tools available to them - one of the reasons given being that they just didn't have the time to learn how to use them effectively...!

Putting data on the page

2009-11-16T05:27:00.000-08:00

I was interested to see the article "Predicting new molecular targets for known drugs" in this weeks Nature. It is a good advertisement not only for "open data", but also on how additional functionality could be added to journal articles in the future. The idea that drugs can be "magic bullets", with incredible specificity in search out a unique target turns out not to be a biologically achievable goal. Chemicals inevitably interact with a variety of targets, producing desired, undesired and unexpected effects. Some of this information is buried in the literature, much has been mined and assembled into curated public and proprietary databases. There is much to be gained by linking this information and visualizing it as a network of interactions. There are some examples in the article, and there are companies such as Ingenuity and GeneGo who do this on a commercial basis, and also develop sophisticated viewing software. Others such as Symyx and Thomson Reuters Prous simply market the data. But wouldn't it be better if the abstraction and visualization of this type of information was an integral part of the publishing process?

NCBI's new user interface design for molecular biologists

2009-10-08T08:00:00.000-07:00

NCBI, home of PubMed, PubMed Central, BLAST, GenBank and many other databases cataloging sequence-specific and phenotypic information is gradually redesigning its user interface and updating its functionality. Take a preview tour...

Google Scholar vs. Scopus vs. Web of Science

2009-09-14T07:52:00.000-07:00

A recent study in the Journal of the American Medical Association shows that Web of Science, Scopus, and Google Scholarproduce quantitatively and qualitatively different citationcounts for articles published in 3 general medical journals.

The results would seem to indicate that Google Scholar and Scopus have a broader global range than Web of Science. Some of the other differences between the databases may be due to differences in article type classification.

The Physicians' Desk Reference morphs to PDR 2.0 ?

2009-09-14T06:42:00.000-07:00

The Physicians' Desk Reference (PDR) found in every US physician's office, clinic and hospital is merging with the Health Care Notification Network (HCNN), a network that delivers FDA-required drug alerts to physicians and other prescribers online. See link.

Thomson sold PDR to Lee Equity, a NY-based investment company. Thomson put PDR on the block in 2008, citing double digit fall in revenue as big pharmas focus shifted from print to online, allowing its more agile competitors, such as ePocrates and Medscape, to grab market share and surge ahead.

HCNN is run by the iHealth Alliance, a not-for-profit organization whose mission is to protect the interests of patients and providers, as healthcare increasingly moves online. The HCNN is funded by manufacturers that use the network to deliver patient safety alerts.

The new product offering will consist of an alerting service aimed at all prescribers and health care practitioners. This business model gives substantial opportunities for revenue development, compared to the relatively static web-presence of PDR and some of its European equivalents such as eMC.

Adding data to the open access mix

2009-09-10T07:07:00.000-07:00

An editorial in the current issue of Nature urges research funding agencies to recognize that preservation and access to digital data are central to their mission, and cites Genebank as an example of just how valuable legacy data sets can be. The article goes on to urge individual disciplines to support this activity be providing students with education programs which include information management, describing this as a discipline that encompasses the entire life cycle of data, from acquisition to storage. Data management, it says, is one of the "foundations of knowledge".

Ganesha Associates would agree whole-heartedly with this vision, but would argue for a selective approach when it comes to selecting priorities for data archiving. The curation of molecular data is a relatively simple task by comparison with other types of data, such as images and medical records. So the cost/benefit ratio will vary across data types.

The Nature article poses the question of responsibility for data storage and suggests that university libraries might be up to the task. But in many cases, we think, an international approach is required. Could this be a role for STM publishers?

Zen and the art of STM publishing (with apologies to Robert Pirsig - 1)

2009-07-11T09:04:00.000-07:00

If quality were a measurable parameter, it would not have a normal distribution (in the statistical sense). At best it would be nominal, i.e. categorical. In a recent PLoS ONE article by Liz Allen et al (2), the authors define a four point scale with the quality of a paper being assessed as “landmark”, “major addition to knowledge”, “useful step forward”, or just “for the record”. But this is, as Pirsig would describe, still a romantic view of reality. Allen et al are after all ranking the publications sourced by their own institute and all estimates of quality are very much in the eye of the beholder.

John Ioaniddis and colleagues (3) have argued, most current published research findings are false. For a research finding to be true, as Liz Allen and her colleagues define it, two things must be true. First, the hypothesis underpinning the study must be correct, and secondly the experimental methodology must be powerful enough to provide a conclusive result. Allen et als paper only reviews cases where they believe both of these test are positive. But there are three other possibilities: that the hypothesis is correct but the design is flawed and yields a negative result (“false negatives”), that the hypothesis is wrong but the statistical result is positive (“false positives”), or that neither is true (“noise”). It is likely that in terms of published articles, the “noise” category is the most numerous, followed by the “false positives”. By contrast, “false negatives” will be quite rare, and articles detailing real progress will be fewer still.

Peter Binfield, Managing Editor at PLos argues (4) that most journals make the peer review process unnecessarily complex and time-consuming by trying to assess whether a paper will have “substantial impact” or “significant advance”, rather than just focussing on methodological rigor., and allowing posterity to be the judge of significance. In other words, the classical STM peer-review process supports the view that quality is a continuous parameter, whereas, in reality, with the benefit of sufficient hindsight, the probabilities of either the design of the hypothesis being correct are either 0 or 1.

So article quality doesn’t end in a decimal point, and if it is deemed to be an important factor, then it should be measured from within the research program that funded the work. After all, as a tax payer, scientific progress means wealth, health and a better world for my grandchildren. Impact Factors, Eigenfactors, and Hirsch Indices aren’t really going to fire me up at the next Election…

Notes:
1. Zen and the art of motorcycle maintenance, Robert Pirsig.
http://en.wikipedia.org/wiki/Zen_and_the_Art_of_Motorcycle_Maintenance

2. Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs. PLoS ONE 4(6): e5910
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005910

3. Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8): e124.
http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124

4. PLoS ONE: Background, future, development and article-level metrics, Peter Binfield
http://conferences.aepic.it/index.php/elpub/elpub2009/paper/view/114/51

Measuring the quality of success

2009-07-08T12:17:00.000-07:00

In a recent article in PLoS ONE, Liz Allen, Ceri Jones, Kevin Dolby, David Lynn, Mark Walport, all from the Wellcome Trust, make a good case for believing that bibliometric indicators such as Impact Factors and number of citations are not good ways of assessing the quality of research outputs, as measured independently by experts.

Shortly after their publication in 2005, a team of referees assessed the importance of about 700 papers describing research funded by Wellcome. Four categories of descending quality were identified: landmark; major addition to knowledge; useful step forward; and for the record. Then in 2008 the group compared these gradings with the impact factors of the journals the papers appeared in, the number of citations each paper had received, and, where possible, an independent assessment made by Faculty of 1000.

Significant correlations were seen between the Wellcome Trust (WT) ratings and the Impact Factor of the journal the articles were published in, the number of citations each paper received, and the 2008 F1000 rating.

The correlation with journal impact factor is fairly convincing, but perhaps this does not tell us very much as you would expect authors to know if their research had a chance of being published in a highly cited journal or if it was only worth sending to an unspecialised journal. Which is the independent variable ?

The correlations between WT ratings and the number of citations and the later F1000 rating, however, are more contentious. You could argue that there is a correlation. But alternatively, the results could be skewed by a small number, perhaps a dozen, of truly excellent articles, which do well in any of the grading methods used, but that for the vast majority of papers the relationship between the various measures is random.

True impact is presumably a product of experimental design and the quality of the initial hypothesis. The former can be measured before publication, but the latter can only be assessed with the passage of time. It is a pity such a small proportion of the article cohort analysed went on to be featured in F1000, but perhaps the strongest message that the PLoS ONE article delivers is that progress comes from only a small fraction of the research performed.

Identifying reasons for failure in biomedical research and publishing

2009-07-07T01:28:00.000-07:00

The regular assessment of Brazilian scientific output means that individual university departments need to constantly improve the quantity and quality of their scientific output. A significant proportion of this output involves the work of Master’s and Doctoral students, but getting this work published in a suitable journal can often prove to be a challenge. Although students’ lack of fluency in English is a contributing factor, many of the problems observed have an early origin in the formulation of the research problem and its relevance to current research trends in the international literature. In short, more time needs to be spent in the library and less in the laboratory, and more effort needs to be made in teaching students basic research skills such as the effective use of bibliographic databases like PubMed, Web of Science and Scopus.

Follow this link to read the full length paper.

On the future of biomedical publishing…

2009-06-29T04:05:00.000-07:00

Commercial STM publishing came of age at the end of the Second World War when governments around the world realised that investment in scientific and technological innovation was essential for national economic competitiveness and for providing effective healthcare. The subsequent massive growth in scientific activity could not be absorbed by scientific societies alone and for-profit journal publishing rapidly moved to fill the gap.

Today, the digital information age is driving a second revolution in STM publishing. The volume of information generated by science has mushroomed and its structure become more complex, there is a compelling need for data sharing and re-use, and traditional methods of quality control such as peer-review are broken. The question is, “Are the conventional STM players up to this new challenge?”

Journals are just one of the peaks in the information mountain range confronting today’s researchers. Two recent reports sponsored by the JISC and RIN have highlighted the immense amount of time scientists spend searching for and using information. Not surprisingly, the information gathering activity of a single researcher will take them to several different data resources during the course of a working day, requiring the user to learn the intricacies of several different interfaces and systems of nomenclature.

Taking biomedicine as an example, a plethora of “-omic” databases such as Ensembl, Genbank and Uniprot must be regularly consulted. Centres such as NCBI, EBI and KEGG began life as sources of data consensus for the biomedical community, but now house interactive models of entire genomes (see for example the UCSC Genome Browser), while companies such as Genego and Ingenuity publish simulations of networks of protein and gene interactions. The scientific article increasingly becomes, at best, a simple annotation linked to these virtual models of how biological systems function, or how clinical decisions are made.

The public’s perception of scientific progress is of a sequence of “breakthroughs” reported by “vanity” journals such as Nature, Science and The Lancet. But the truth is that, if it could be sketched on a sheet of paper, progress would often look more like a random movement than a perfect straight line. Indeed, it has been argued that the results of most published biomedical research are wrong or biased, that not publishing original datasets, as well as negative or confirmatory findings, makes it impossible to weigh evidence effectively, and that the peer review process contributes little to the assessment of the true value of a piece of research.

So my point is that STM publishing has moved from being part of the solution to making content available, to being part of the problem of making it useful and realising its full value for the tax payer. And herein lies the commercial opportunity. There is a huge amount of work needed to reintegrate these huge volumes of data and information being created by modern research technologies.

We have plenty of technological tools, but what we lack is a blueprint of sufficient scale to inform us how these tools should be used and how development resources should be directed. To achieve this scale of vision, the process must be led by the payers (NIH, Wellcome, UK research councils, HHMI, and so on). Open Access could have provided a beginning to this process by shifting the publishing business model away from a subscription basis and towards a service-based one. But instead it has lurched into the green and gold ruts leading to even more “balkanisation” of information resources. Unless this changes, the next decade is going to be fairly boring for STM publishers, as Springer’s Derk Haank has predicted.

Viewed in this light, Elsevier’s development of navigational tools such as Scopus, and support for UK institutional repositories, even its ill-fated attempt to move into the electronic lab notebook market, could be seen as strategic moves. But to engage with the vision of the payers, the successful publishers will need to focus on a market vertical, as have non-trad players such as Lockheed Martin, SAIC and IMS, and to take a much broader view of “content” than is currently the case. From this perspective, Open Access seems like a serious distraction. Payers please take heed, your guidance is needed…

What would you say to Elsevier about Open Access?

2009-06-09T04:58:00.000-07:00

An excellent post from Cameron Neylon, who works at the Science and Technology Facilities Council, the UK’s major provider and supporter of large scale academic research facilities, including synchrotrons, neutron sources, and high powered lasers. He has been invited to speak at a forward planning exercise at Elsevier later this month. He says,

"My plan is to focus less on the arguments for making more research output Open Access and more on what happens as a greater proportion of those outputs become freely available, something that I see as increasingly inevitable. Where that proportion may finally be is anyone’s guess but it is going to be a much bigger proportion than it is now. What will authors and funders want and need from their publication infrastructure and what are the business opportunities that arise from those."

Focusing on the bigger picture is the way to go, I think, for commercial publishers. The easiest way to grow is to find new markets and to add new value - and its all there if you redefine the role of STM publishing in the way he suggests...

Google vs. Bing - at a split screen near you...

2009-06-04T08:00:00.000-07:00

Blackdog has created a split screen view so that you can compare and contrast search results using Google and the new Microsoft search engine, Bing.

The great thing about Google is that it does have some semantic capabilities, so when searching using terms such as "Ganesha" and "Associates", Google "knows" that the second term means I am probably not after references to the Hindu deity named in the first term. Bing doesn't have this sensitivity - yet.

Likewise, searches using the terms "drug" and "information" came up better on Google - a better quality of results, with a UK bias. Still , early days...

Some thoughts on Open Access publishing

2009-06-02T02:23:00.000-07:00

The JISC ‘Economic implications of alternative scholarly publishing models’ and the RIN ‘Activities, costs and funding flows in the scholarly communications system in the UK’ both set out to identify opportunities arising from the shifts towards online publishing and various open access business models.

Both reports could have made a better job at introducing the reader to their respective models . Both reports present a lot of data, but fail to deliver adequate executive summaries. As such it is impossible to reconcile the two descriptions completely without detailed study of the spreadsheet models.

Recommendation: JISC/RIN should together review the different modelling approaches taken and identify and agree basic common assumptions made.

As part of this accord it would be extremely helpful if the ‘dimensions’ for further investigations could be identified, e.g.

Overheads. RIN study appears in include ‘research costs’. The JISC study includes library ICT overheads. Which overhead costs should be in and which out ?
Overall scope. Are the JISC/RIN reports addressing identical library constituencies. Also RIN focuses mainly on journals, JISC on journals and books.
There seems to be a net shift of costs from the developing to the developed nations under both models. It would be worth making these benefits more explicit.
Disciplinary differences. The impact of these changes will be very different across the disciplines, due, for example, to the large differences in reading habits and the need for access to other linked sources of digital information. Compare for example economics, mathematics, biochemistry and oncology. It may be that the reports’ recommendations would differ significantly for different disciplines once this level of detail has been introduced.
Both studies identify the high costs associated with searching for information, reading and writing. This extends the definition of a scholarly publisher from one who processes article content to one who is tasked with the development of digital tools that enable a variety of different data resources to be used effectively. The JISC report includes an assessment of ‘research performance savings’. For example, in biomedicine, some of these will result from investments such as PMCUK and its links with the many molecular databases at NCBI and EBI. How will this be modeled ? What, in the future, is the JISC/RIN vision for the respective roles of commercial and governmental publishing resources in this area ?

Recommendation: As a next step compare and contrast two disciplinary areas using a broader definition of information needs which includes other database resources.

Impact of open access on publishing costs. The JISC report concentrates mostly on distribution and production cost savings - hence it shows a big reduction in costs for shifts to online, open access and self-archiving. However, the sales and marketing focus will need to shift away from institutions to authors (see for example, PLoS One) and this will probably cause a net increase in these costs. Some of the production savings on the publisher side may shift to the authors as they are expected to take more responsibility for the formatting of articles prior to publication.

Recommendation: The opportunity offered by OA may not be cost savings per se, but the opportunity for the payers to redefine the role of the commercial STM publisher, at least in certain disciplines such as biomedicine.

Impact of open access on libraries. JISC report seems to predict a much smaller impact on library costs and expenses. This is probably because the RIN model has a more sensitive approach of fixed and variable costs, and JISC covers a much broader academic constituency and includes books. While the self-archiving option appears to create the largest savings, where are the costs associated with the indexing this material and making it findable?

Recommendation: One of the objectives of the disciplinary studies suggested above would be to define the future roles and skill profiles of libraries and librarians.

PubGet - a step forward ?

2009-06-01T02:28:00.000-07:00

"Each year, scientists spend at least a quarter billion minutes searching for biomedical literature online. This is time they could better spend curing disease and building the future. Pubget's mission is to give them that time back." So the Mission Statement says...

But doesn't PubMed already have these features ? Less clearly signposted, perhaps, but researchers need fewer, better integrated interfaces if they are to become more efficient.

How the Semantic Web might improve cancer treatment

2009-06-01T01:48:00.000-07:00

This PriceWaterhouseCoopers interview with Lynn Vogel describes M D Anderson's semantic technology research and development from the perspective of healthcare. It offers, I think, a fairly complete overview of the opportunities and obstacles for semantic technologies in this area.

Semantic Web - Google's "Rich Snippets" launched

2009-05-16T01:10:00.000-07:00

Google announces "Rich Snippets". This requires content providers to extend their HTML mark up using RDFa and Microformats. The semantic enhancement can then be used by Google to present more information about page content in its search results.

Twitter - applications in STM

2009-05-14T01:41:00.000-07:00

Here's a neat little example of how publishers and educators are using Twitter.