Archive for August, 2008

What is your data sharing statement?

More and more funding bodies asking to make the findings of publicly funded scientific research freely available. However typically they provide limited infrastructure or recommendations as to how this should actually happen. I was wondering what type of data sharing statement researchers are (or should) be including within their grant proposals? Below is an example of how this could look. However, it provides no indication of how this could actually take place, for example via wikis, hosting on sourceforge, google code etc. It also does not imply timing, for example, this happens live, or when the grant is finished. Should the infrastructure and timing also be included?

  1. The protocols, methods and algorithms developed will be made available under the Creative Commons Attribution 3.0 License
  2. The data produced will be made available via the Science Commons, Protocol for Implementing Open Access Data.
  3. All source code developed will be made available under an open source license.

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Is a knol a scientific publishing platform?

Image representing Knol as depicted in CrunchBaseImage via CrunchBase, source unknown

Google has recently released knol, which most people are calling Google’s version of Wikipedia. The main difference between a knol and a wikipedia article is that a knol has associated authorship or ownership against an article. This factor has caused some issues an outcries focusing on the merits of the wisdom of crowds verses the merits of single individuals and the whole ethos if information dissemination on the Web. (There are too many to cite but some discussion can be found on FriendFeed+knol)

However, on looking at knol and having a snoop around I was not drawn into thinking about competing with Wikipedia or advertising revenue, rather what struck me is that a knol, with owner authorship looks incredibly like a scientific journal publication platform…

According to the Introduction to knol (or instructions for authors)  you to can write about anything you like, so disseminiation of science must fall under that. You can collaborate on a unit of knowledge (or manuscript) with other authors and they are listed – I assume the contribution to the text will also be stored in the revision history, makes the authors contribution section a little easier to write. It is not limited to one article per subject, so this allows all manner of opinions or scientific findings to be reported contrasted and compared with each other. You can select your copyright and license for your article (rather than handing it over). You can request a (peer-) review of the article, However more important the article is available for continuous peer-review in the form of comments on the article.

So is a knol a Google Wikipedia or is it a scientific publishing platform? What would prevent publishiing a knol and getting credit (hyperlinks), citations (analytics) impact factors (page ranks) in the same way you do for the traditional scientific publishers? You would of course not have to pay for the privilage of trying to diseminate your findings, loosing copyright and then asking your institution to pay for a subscription so you and your lab members can read your own articles. In fact you, as an author (lab, institution) can even share revenue for your article via adsense.

Some traditional publishers are trying to embrace new mechanisms of disseminating scientific knowledge. Only today Nature Reviews Genetics (as described by Nacsent) published the paper Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges by Lincoln Stein and published the supplementary material as a community editable wiki.

With knol as a scientific publishing platform, what can the traditional scientific publishing houses now offer for the publishing fees? Faster turn around? revenue sharing? Are they really still the gatekeepers of scientific knowledge? Or in the Web 2.0 era has that mantle passed to Google? Certainly, in the first instance it would make a nice preceedings platform.

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MIAPE: Gel Informatics is now available for Public Comment

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The MIAPE: Gel Informatics module formalised by the Proteomics Standards Initiative (PSI) now available for Public Comment on the PSI Web site. Typically alot of this information will be contained in the image analysis software, so we would especially encourage software vendors to review the document. The public
comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.

This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.

If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI.

If you have comments that you would like to make but would prefer not to make public, please email the PSI editor Norman Paton.

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PEFF:A Common Sequence Database Format in Proteomics

Robotic preparation of MALDI mass spectrometry...Image via Wikipedia

PEFF:A Common Sequence Database Format in Proteomics is now available for Public Comment on the PSI Web site (http://psidev.info/index.php?q=node/363). The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.

This document presents a unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools (spectra library search tools, sequence alignment software, data repositories, etc). This format enables consistent extraction, display and processing of information such as protein/nucleotide sequence database entry identifier, description, taxonomy, etc. across software platforms. It also allows the representation of structural annotations such as post-translational modifications, mutations and other processing events. The proposed format has the form of a flat file that extends the formalism of the individual sequence entries as presented in a FASTA format and that includes a header of meta data to describe relevant information about the database(s) from which the sequence has been obtained (i.e., name, version, etc). The format is named PEFF (PSI Extended FASTA Format). Sequence database providers are encouraged to generate this format as part of their release policy or to provide appropriate converters that can be incorporated into processing tools.

This is an announcement to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.

If you do not feel well placed to comment on this document, but know someone who may be, please consider alerting them towards this information. There is no requirement that people commenting should have had any prior contact with the PSI

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Double standards in Nature biotechnology

OK, So that is a relatively inflammatory and controversial headline, edging on the side of tabloid sensationalism. What is refers to is probably a situation that I may never find myself in again, which is in this months edition of Nature Biotechnology I am an author on two, biological standards related publications.

The first is a letter advertising the PSI’s MIAPE Guidelines for reporting the use of gel electrophoresis in proteomics. This letter is also accompanied by letters referring to the  MIAPE guidelines for Mass Spectrometry, Mass Spectrometry Informatics and protein modification data.

The second is a paper on the Minimum Information about a Biomedical or Biological Investigations (MIBBI) registry entitled Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

The following press release describes this paper in more detail.

More than 20 grass-roots standardisation groups, led by scientists at the European Bioinformatics Institute (EMBL-EBI) and the Centre for Ecology & Hydrology (CEH), have combined forces to form the “Minimum Information about a Biomedical or Biological Investigation” (MIBBI) initiative. Their aim is to harmonise standards for high-throughput biology, and their methodology is described in a Commentary article, published today in the journal Nature Biotechnology.

Data standards are increasingly vital to scientific progress, as groups from around the world look to share their data and mine it more effectively. But the proliferation of projects to build “Minimum Information” checklists that describe experimental procedures was beginning to create problems. “There was no way of even finding all the current checklist projects without days of googling,” says the EMBL-EBI’s Chris Taylor, who shares first authorship of the paper with Dawn Field (CEH) and Susanna-Assunta Sansone (EMBL-EBI). “As a result, much of the great work that’s going into developing community standards was being overlooked, and different communities were at risk of developing mutually incompatible standards. MIBBI will help to prevent them from reinventing the wheel.

The MIBBI Portal already offers a one-stop shop for researchers, funders, journals and reviewers searching for a comprehensive list of minimum information checklists. The next step will be to build the MIBBI Foundry, which will bring together diverse communities to rationalise and streamline standardisation efforts. “Communities working together through MIBBI will produce non-overlapping minimal information modules,” says CEH’s Dawn Field. “The idea is that each checklist will fit neatly into a jigsaw, with each community being able to take the pieces that are relevant to them.” Some, such as checklists describing the nature of a biological sample used for an experiment, will be relevant to many communities, whereas others, such as standards for describing a flow cytometry experiment, may be developed and used by a subset of communities.

“MIBBI represents the first new effort taking the Open Biomedical Ontologies (OBO) as its role model”, says Susanna-Assunta Sansone. “The MIBBI Portal operates in a manner analogous to OBO as an open information resource, while the MIBBI Foundry fosters collaborative development and integration of checklists into self-contained modules just like the OBO Foundry does for the ontologies”.

There is a growing understanding of the value of such minimal information standards among biologists and an increased willingness to work together across disciplinary boundaries. The benefits include making experimental data more reproducible and allowing more powerful analyses over diverse sets of data. New checklist communities are encouraged to register with MIBBI and consider joining the MIBBI Foundry.

Press release issued by the EMBL-European Bioinformatics Institute and the Centre for Ecology and Hydrology, UK.
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