EarthCube webinar series "Advances And Emergent Needs in Paleogeoscience Cyberinfrastructure"

The steering committee of the Collaboration and Cyberinfrastructure for Paleogeosciences (C4P) project announced a new webinar series "Advances And Emergent Needs in Paleogeoscience Cyberinfrastructure".

The first webinar will be held on Tuesday, 04 February 2014 at 1600h Eastern Time (2200h CET, 2000h UTC).

The topics on 04 February 2014 are "Community Inventory of EarthCube Resources for Geosciences Interoperability (CINERGI)" and the "Neotoma Database".

The link to the webinar is https://earthcube.webex.com/earthcube/j.php?ED=260505727&UID=1743065277&PW=NOGRjZmUzMDVl&RT=MiMxMQ%3D%3D%20 for 04 FEB 2014. The date stated at the link is updated weekly.

If a password is required, enter the Meeting Password: 73131647.

The format is 20 minutes per presenter, with two main parts:

• a show-and-tell presentation of the science and the resource
• (b) discussion of the key informatics needs that the resource is facing.

The intended audience for this webinar is professional paleogeoscientists and cyber/computer scientists.  All webinars will be recorded and publicly archived at http://workspace.earthcube.org/c4p/content/c4p-webinars. 

CINERGI EarthCube project (Ilya Zaslavsky)

Community Inventory of EarthCube Resources for Geosciences Interoperability. This Building Blocks project focuses on constructing a community inventory and knowledge base on geoscience information resources to meet the challenge of finding resources across disciplines, assessing their fitness for use in specific research scenarios, and providing tools for integrating and re-using data from multiple domains. The project team envisions a comprehensive system linking geoscience resources, users, publications, usage information, and cyberinfrastructure components. This system would serve geoscientists across all domains to efficiently use existing and emerging resources for productive and transformative research.

http://workspace.earthcube.org/cinergi

Neotoma Database (Eric Grimm)

Neotoma Paleoecology Database and Community is an online hub for data, research, education, and discussion about paleoenvironments. Anyone with an Internet connection can access Neotoma. The primary philosophy behind Neotoma is data sharing so that users can easily: Discover: find information efficiently by searching the database on spatial, temporal, and metadata criteria; Explore: interactively browse and visualize live data and metadata; Share: get data and information in a variety of useful formats (e.g., downloads, reports, graphics).


http://www.neotomadb.org/

Biodiversity Data Journal - archiving or self archiving?

Another interesting development in the world of research data management: Pensoft announced that the Biodiversity Data Journal (BDJ) will start accepting submissions in December 2012. The BDJ is a new data journal similar to the Earth System Science Data Journal (ESSD) which pioneered in publishing research data.

Biodiversity Data Journal (BDJ) is a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, morphological descriptions, occurrences, data tables, etc. – will be treated and stored as DATA.

So far this sounds very good. But IMHO not so good is the data archive policy of BDJ, which is a bit vague.

The BDJ journal homepage only provides a link to the general pensoft data publishing guidelines which offers many options how one should archive data. Of course they mention Dryad and PANGAEA etc. which are suitable data archives. But it is hard to understand why GBIF's Integrated Publishers Tookit (IPT) and scratchpads are also included as an option.

GBIF is not an archive and both, scratchpads and the IPT are software solutions which can be used for archiving purposes but need to be hosted by a reliable organisation - but these are not named. Therefore, in its current form, pensofts data archiving policy could be understood as an invitation to self archiving ... or does BDJ e.g. mean IPT in the sense of "pensoft IPT"?. This should be fixed until December.

Elsevier's 'article of the future' vision

Elsevier has presented their vision of the 'article of the future' at the CELL website where a short video introduces some new features for future web journals.

The first striking detail is a tabbed menu on top of the article which allows to navigate between the main sections of an article such as abstract, results, discussion etc. as well as data, figures and references. This is nothing revolutionary but a progress - currently you can only navigate between the article, the figures and the references.

Most interesting are their attempts to link as many information as possible to allow a quick overview on the essence of an article. Surely a result of Elsevier's journal XML (however they call it), which precisely describes the structure of an article and allows to mark elements such as figures or citations within the text. This linking allows interactive navigation within the article. You can immediately take a look a figure by clicking on a link within the results section. And vice versa, by clicking on the data or figures you can immediately highlight the secions in which this figure is mentioned.

However, what was intended to support 'fast reading' seems a bit confusing to me. The text, figures and figure captions are all shown at one page. As a result the area in which the text is shown is reduced to a very narrow column which makes it hard to read. Further, sometimes the figure captions seem to be shown below the figure and sometimes beneath, very confusing.

And Elsevier's idea of a graphic abstract seems really ridiculous to me. This just perverts scientific reading: Mouse eats fatty diet -> Tumor grows -> Mouse dead. Come on guys!!

I was also a bit disappointed by the way Elsevier treats data and external information sources. Elsevier's seems to regard figures as data. But figures are of course highly interpretative visualisations - based on data! It would therefore be great to be able to click on a figure and see the data on which it is based on.

Today a growing amount of such data is stored in specialised data centers such as GeneBank or PANGAEA. But from the impression the demo gave to me, linking to such external sources seems not to be the part of their vision. This is astonishing, as some very exciting and successful cooperation already exist. Just think of the already existing links to GeneBank or the recently announced cooperation with PANGAEA for geoscientific supplementary data. Instead they included some poor Excel files in their data section.

But anyway Elsevier surely heads to the right direction and most of the issues above can easily be fixed. But honestly, if presented to the audience in it's present state Elsevier's vision would offer little advantages to scientist. Most researchers would still prefer to read the abstract online to get a quick overview and print the pdfs to study the details. Or expressed as 'graphical abstract' ... see above.

Vertebrates and their vertebrae

Looking at modern vertebrates, their number of vertebrae varies remarkably. While some snakes have of the order of 300 vertebrae (all thoracic vertebrae), some turtles only have 18 vertebrae in total - from neck to tail. Then, in mammals the number of vertebrae and their functional division is remarkably constant.

In a recent study Johannes Müller (Berlin Natural History Museum) and co-workers surveyed 436 recent and extant amniote taxa to study the development of vertebrae in response to environmental pressure, body mass and genetic factors.

The key findings were:

• Early mammals (synapsids) had six cervical vertebrae and in total twenty thoracic plus lumbar vertebrae.
• The number of vertebrae is determined by somite formation and Hox-gene expression during embrional development. This also determines the position of the limbs along the spinal column.
  
• Early synapsids already showed the same number of vertebrae as recent mammals, while basal reptiles already showed a great variation in their number of vertebrae.

The paper is available on-line at PNAS:

Müller J., Scheyer T.M., Head J.J., Barrett P., Werneburg I., Ericson P.G.P., Pol D., Sánchez-Villagra M.R: Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes. In: Proceedings of the National Academy of Sciences (PNAS), doi: 10.1073/pnas.0912622107

The paper comes with substantial amounts of supporting information. Unfortunately, the direct link from the article "splash page" does not work. This, again, shows the importance of using persistent identifiers like DOI for the publication of supplementary data.