Archive for category Journals Publishing
Docbook is the older of the two specifications and created specifically for technical documentation. DITA, is a younger specification which grew out of IBM, and is referred to as having its own architecture and was designed to provide structure to more than just a book. Both specifications are OASIS standards.
As with XML schemas, both specifications can be extended to include bespoke features. However, Docbook is based more on a book structure with Sections and subsections, where as DITA is built around topics that can be built up in any arrangement based on a document map. A DITA topic is open to specialisation itself, however, a topic has only three required elements
- An id attribute
- A title
- A body
A topic can exist as a single XML file which can be composed into any arrangement for publication through the use of a document map. A DITA structure would present a more flexible architecture where the same “topic”, i.e a journal article section, such as an abstract, materials and methods, or results, could be included with ease more than one publication, correctly referenced. In this respect DITA is more like an object-oriented document schema, and can be more easily repurposed (in terms of structure) for any output format (i.e pdf, HTML). In the same respect, Docbook can be configured with some work to behave on a more topic by topic basis and DITA can support a book based methodology. They are after all both XML schemas and are equally extensible or open to specialisation.
As its a standard, whole ecosystems have emerged which makes use of the DITA architecture. For example, DITA for publishers provides libraries to convert DITA markup into HTML, PDF, EPUB, and Kindle rendering support. This allows content structures in DITA to be repurposed for different audiences or different devices with relative ease.
I have recently started using DITA as an architecture to represent content, primarily designed for books. However, with new demands appearing for different delivery mechanisms of the traditional textbook, such as Web delivery and ebooks, DITA is proving to be immensely powerful to deliver the same content through different mediums with relative ease and speed. In using it, it seems obvious that a DITA architecture would benefit the representation of content within a journal article, allowing references re-purposing and multiple format delivery. Maybe a topic for discussion through the Beyond the PDF forum.
In the end, it’s just XML, so I wont repeat the virtues of content markup through XML. However, for me its main advantage is the object oriented -like topic structure as a working architecture.
- Using RDFa with DITA and DocBook (devx.com)
- Dita Educational Use cases (docs.oasis-open.org)
- Converting documents between a wiki and Word, XML, FrameMaker or other help formats (ffeathers.wordpress.com)
- Future-proofing e-books with XML (teleread.com)
- The PDF Landscape for DITA Content (tc.eserver.org)
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.
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.
I was trying to work out a suitable journal to where I could submit a paper on sepCV, the PSI ontology for sample preparation and separation techniques. I found my self drawing up a table, so I thought I would blog it. My initial remit is that is should be in a proteomics relevant journal as well as bioinformatics, as we are trying to encourage a greater community contribution for term collection. In this respect it has to be open access. I would also prefer the journal to accept LateX instead on proprietary formats such as word. I was really disappointed with the number of journals that only accept word documents, even PlosOne refuses anything other than word or rft, tut, tut.
Based on this loose criteria, Proteome science comes top closely followed by Journal of Proteomics and Bioinformatics (if I sacrifice using word for open access). BMC Bioinformatics also ticks all the boxes but it misses out on the proteomics audience. The table below also includes Impact factor, but I did not really take that into consideration. Wouldn’t it be nice is there was an app that you could just enter in criteria like this, target audience, submission format, copyright, etc and get back the journals that meet these requirements. Something like this would save me an afternoon trawling through the web building spreadsheets.
How do you select your journal?