DOI for geoscience data - how early practices shape present perceptions

The first minting of Digital Object Identifiers (DOI) for research data happened in 2004 in the context of the project “Publication and citation of primary scientific data” (STD-DOI). Some of the concepts and perceptions about DOI for data today have their roots in the way this project implemented DOI for research data and the decisions made in those early days still shape the discussion about the use of persistent identifiers for research data today. This project also laid the foundation for a tighter integration of journal publications and data. Promoted by early adopters, such as PANGAEA, DOI registration for data has reached a high level of maturity and has become an integral part of scientific publishing. This paper discusses the fundamental concepts applied in the identification of DOI for research data and how these can be interpreted for alternative and future applications of persistent identifiers for research data.

Klump, J., R. Huber, and M. Diepenbroek (2015), DOI for geoscience data - how early practices shape present perceptions, Earth Sci. Inform., doi:10.1007/s12145-015-0231-5.

The Anthropocene - an artist's rendition

We have already reported on the Anthropocene in this blog. The idea that we might be moving things in future deep time is inspiring and disturbing at the same time. The Haus der Kulturen der Welt has initiated a project working on cultural aspects of the Anthropocene, the "Anthropocene Project". The project is coming to a close now. The symposium of its working group will be broadcast live on Friday, 17 October 2014 starting from 0900 CET. The project put together an impressive lineup of speakers.

"Human Impacts and Their Consequences - A Forum on the Occasion of the First Meeting of the Anthropocene Working Group"

Friday, 17 October 2014 starting from 0900 CET


Programme and webcast can be accessed here.

Classification of igneous rocks revisited

Petrology, I must admit, was never my favourite subject even though I had to do quite a bit of it during my time as a student. Even my Honours project had a petrological component. An important tool for the classification of igneous rocks is the QAPF diagram which forms the basis of the IUGS classification of igneous rocks (Le Bas and Streckeisen, 1991). It was interesting to go back to this original publication to read about the considerations that led to the adoption of the classification schema. The general principles are solid science. In some of the finer points, however, it becomes apparent that this classification schema comes from the pre-digital age.

"One of the merits of the TAS system is that the boundaries are definitive although they could be criticized as over simplistic. Definitive boundaries remove the ambiguity in naming a rock which plots near a boundary between two adjacent rock types. The simple boundaries of the TAS system also enable the classification to be constructed in a few minutes by pencil and ruler"

Furthermore, the TAS classification system only takes into account the sum of Na₂O + K₂O over SiO₂ and does not account for any other major elements even though such classification systems had already been proposed (e.g. De La Roche et al. 1980).

"[It] was not adopted, partly because the two cation per mil parameters were difficult to calculate without electronic assistance"

Certainly, in the age before widespread use of spreadsheet calculation software, this might have been an argument. A bit more difficult to follow is the following argument:

"The most common interpretations made by geologists are petrogenetical, but there could also be aesthetic considerations."

Robert Huber, Jess Robertson and myself (JK) have started to look more closely at the classification of igneous rocks in the dawning age of data intensive research in the geosciences. Watch this blog for more on this subject.

Ackonwledgements

Thank you to Jess Robertson for pointing out this gem.

References

De la Roche, H., J. Leterrier, P. Grandclaude, and M. Marchal (1980), A classification of volcanic and plutonic rocks using R1R2-diagram and major-element analyses — Its relationships with current nomenclature, Chemical Geology, 29(1–4), 183–210, doi:10.1016/0009-2541(80)90020-0.

Le Bas, M. J., and A. L. Streckeisen (1991), The IUGS systematics of igneous rocks, J Geol Soc, 148(5), 825–833, doi:10.1144/gsjgs.148.5.0825. Online also available at https://www.utdallas.edu/~aiken/SHAKEBAKE/rockclassification.pdf

Australia Through Time - iPad App

On the weekend 11-13 July 2014 various Australian government institutions had invited to join GovHack 2014.

Governments collect and publish enormous amounts of data, but have limited resources to get it into the hands of their citizens in engaging ways. GovHack is an event to draw together people from government, industry, academia and of course, the general public to mashup, reuse, and remix government data. GovHack is about finding new ways to do great things and encouraging open government and open data.

Most projects targeted the obvious data, like census data or the national archives. Science data are not that attractive because the sources are normally not accessible through simple API and often domain knowledge is needed to understand the data. Not all entries have to be applications in the sense of an app, also interactive infographics are welcome. One entry this year made use of data from Geoscience Australia to make an interactive infographic of the development of the Australian continent through time.

The Australia Through Time iPad App is an interactive app that runs on iPad or in the browser, showing the geological, mineral and biological history of Australia from the Cambrian to the present. It is based on the Australia Through Time poster by Geoscience Australia.This app presents the data in a visually appealing format, condensing it into smaller, readable screens and includes an animated sea-level bar and continental-drift visualization which makes changes in the data more apparent. It uses an intuitive drag gesture to slide through the timeline and display varying content.

Webinars "iDigBio and Using schema.org and microdata for data discovery" 2014-04-15 at 1600 EDT

The topics for the next C4P Webinar are iDigBio (Gil Nelson, Florida State University) and Using schema.org and microdata for data discovery (Douglas Fils, Ocean Leadership Consortium).

The link to the webinar is

WebEx link for April 15, 4-5p ET (the date stated at the link updates weekly)

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

For plain text postings where the link did not show up: Any updated links or information as well as the updated webinar schedule and archived presentations will be posted at

http://workspace.earthcube.org/c4p/content/c4p-webinars

iDigBio (Gil Nelson, Florida State University)

http://www.idigbio.org

Integrated Digitized Biocollections (iDigBio) is NSF's national resource for facilitating and enabling the digitization of biological and paleobiological collection objects in non-federal, U.S. biodiversity collections. Through its portal it makes available data and images for millions of biological specimens in electronic format for the research community, government agencies, students, educators, and the general public.

Using schema.org and microdata for data discovery (Douglas Fils, Consortium for Ocean Leadership)

HTML5 developments in the area of microdata have provided methods for resource discovery based on structured data embedded into HTML pages.  Combined with the schema.org Dataset and other vocabularies this facilitates a means to bring structured data about scientific data resources to web pages.  This talk will demonstrate examples of these patterns applied to data.oceandrilling.org and other sites.  It will further provide live examples of these patterns and discuss methods that could be used to enhance domain specific data offerings.  

The format is 20 minutes per presenter, with two main parts: (a) 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.

More about C4P:

Website: http://workspace.earthcube.org/c4p

Technical information for webinars: cyber4paleo@gmail.com

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/

Lithologs sandbox

The sandbox is open now. It allows to test the lithologs editor without registration here.

Stones that look like chicken

Ok, not like a whole chicken, but this one has exactly the form and proportions of a good fried chicken drumstick. My son has found this stone somewhere in the bavarian alps this summer and it was worth to sample..

Who Shot the Sheriff?

Mass extinctions are among the most intriguing events in earth history and their cause a matter of heated and passionate debate. An article in EOS by Keller et al. reports on a recent workshop at the Natural History Museum in London.

Since the seminal paper by Alvarez et al. on the nature of the K-T boundary it had always been the argument mainly between the proponents of the impact hypothesis vs. the flood volcanism hypothesis. And both sides had good arguments to support their cause. At this recent workshop 150 scientists from different disciplines got together to discuss the cause of Phaenerozoic mass-extinctions in a multi-disciplinary approach.

It will be interesting to read the proceedings from this workshop. In preparation, Keller et al. have published an extensive summary of their view on the subject in Geoscientist.

We are still looking for the smoking gun.

The Mysteries of Deep Time

Originally published by by Randall Munroe on XKCD. http://xkcd.com/1194/

Introducing Lithologs

After some initial experiments with Psicat and SVG we can now offer a new, cool Snet tool: Lithologs. 

Lithologs is a tool which allows to create and plot lithological logs online. It is very inspired by Psicat and internally uses the Psicats XML to store litholog data. But unlike Psicat it plots lithological columns using SVG, which you can also embed in your blog, website etc. like this one (which you cannot see if your browser doesn't support SVG):

It further offers the possibility to store some basic metadata on these geological features.
The project is now in a very early alpha release phase.
More features are planned such as Psicat import and export, and the support of more standards such as OAI-PMH, Geo DC and in the future also GeoSciML..

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.

Don't build on external APIs

For one my older projects (agesearch) I needed access to search engine results which I used to 'calculate' a stratigraphic context of given keywords. The idea was to visit all pages the search engine returns and to use Ageparser to scan these pages for stratigraphic terms to estimate their chronostratigraphic context which should be representative also for the entire search phrase.

I started to use the YAHOO search API which nicely worked but after a while YAHOO decided to restrict free access and started to charge for the use of their API. So I switched to Google's Search API which also worked well and allowed me to access an even larger website index.
However, now also Google started to charge for API usage which again forced me to look for an alternative. So I came to Microsoft's BING API. This service also worked pretty good and now agesearch seems to work again. Microsoft still offers free access on this API but I could hardly believe to see that they recently placed it on their 'Windows Azure Marketplace' and offer several upgrade option.

So don't trust too much on external APIs even when offered by the big web elephants. Their strategy to introduce a new service for free and to restrict access and to charge for usage after a while truly can be a trap for your projects.

Termination of National Biological Information Infrastructure (NBII)

As earlier annouced at the whitehouse website, a major budget cut forced the USGS to terminate several initiatives. Among those, all services of the National Biological Information Infrastructure (NBII) will be shut down or transferred to yet unknown locations (maybe data.gov). This will happen at January 15, 2012 so if you have to work with the NBII services ... hurry up. These are really bad news, as I enjoyed the excellent web services of e.g. ITIS.

For those who want to know what will happen to all the tools, databases and services hosted at the NBII website, here are the FAQ: http://www.nbii.gov/portal/server.pt/community/termination_of_nbii_program/2057/termination_faqs/7650.

Most delicate, this termination will also be a shock for the WDC (now WDS system), as the NBII was also hosting the World Data Center for Biodiversity and Ecology!

UPDATE:

For those who want to know what will happen to ITIS:

"What will happen with related USGS Biological Informatics Programs such as the Integrated Taxonomic Information System (ITIS), USGS Gap Analysis Program (GAP), and USGS/NPS Vegetation Mapping Program?

The former USGS Biological Informatics Program (now part of the USGS Core Science Analysis and Synthesis Program) is the parent program to the NBII, ITIS, GAP, and the Vegetation Mapping Program. While the NBII Program has been terminated and its funding eliminated, ITIS, GAP, and the Vegetation Mapping Program remain funded activities and will continue to provide high quality data, services, and cyberinfrastructure to collaborators and users."

The taxonomy crisis: nothing left to discover?

In his post Taxonomy - crisis, what crisis? Rod Page reported on a new publication by Lucas et al (in press) which contains some really provocative findings:

• There is no decrease in the number of taxonomists, yet no 'taxonomy crisis'
• Instead there is an increase of taxonomists since 1900
  
• But there is a decline in the number of species descriptions per taxonomist

This is really interesting, especially when we remember the recently published estimates on the total number of species on Earth (ca. 8.7 Mio, Mora et. al 2011) which have also been used by the authors to illustrate the significance of taxonomists:

describing Earth's remaining species may take as long as 1,200 years and would require 303,000 taxonomists at an approximated cost of US$364 billion. With extinction rates now exceeding natural background rates by a factor of 100 to 1,000, our results also suggest that this slow advance in the description of species will lead to species becoming extinct before we know they even existed.

So what happened, are taxonomists getting lazy nowadays?

Lucas et. al. (in press) propose a different explanation:

[...] the currently decreasing numbers of species described per taxonomist over the past 50 years probably represents the effect of a declining pool of missing species.

Wait a moment.. are there too little species left to discover, thus the estimates above completely wrong?
Interesting, but the members of the TAXACOM list propose some other explanations, such as: 'we know hundreds of new species but publishing this is not funded anymore' etc.

Hard times for taxonomists...


References:

Lucas N. Joppa, David L. Roberts, Stuart L. Pimm The population ecology and social behaviour of taxonomists Trends in Ecology & Evolution doi:10.1016/j.tree.2011.07.010

Camilo Mora, Derek P. Tittensor, Sina Adl, Alastair G. B. Simpson, Boris Worm. How Many Species Are There on Earth and in the Ocean?. PLoS Biol 9(8): e1001127. doi:10.1371/journal.pbio.1001127

The state of the Geoblogosphere – geoscience communication in the social web

Science blogs are new and rapidly evolving media in the social web. In the last years, several hundred geoscience professionals and students have started their own Earth science blogs. Serious concerns exist about the credibility of scientific blogs but until now, no info has been published on the geoblogosphere’s motivation and the writer’s societal and scientific backgrounds. Here we present data from an online survey with 78 participants and from analysis of more than 200 Earth science blogs.

Full article here: http://www.geonetzwerk.org/2011/10/04/the-state-of-the-geoblogosphere-geoscience-communication-in-the-social-web/

Welcome to the Anthropocene

In its current issue, The Economist has published an interesting piece on "The Anthropocene - A man made world". In terms of public understanding of science it gives an interesting insight into how stratigraphy works, how palaeontology and geochemistry are used to define stratigraphical ages. It also looks at earth system science and on the interplay of human activity, climate and ocean chemistry.
Even though I do not agree with some of the suggestions on terraforming, it is the first time that I had the concept of "carbonate compensation depth" explained to me in a mainstream news magazine. I also found the example of the preservation of the ruins of a city on a fast sinking river delta highly original.

Paleontologists enter the web period

After James Landell circulated 'An Open Letter in Support of Digital Data Archiving' via the paleonet list server, a quite controversal discussion followed. This thread included almost any kind of paranoia you would expect to hear if someone asks a group of pre-web scientists to share their data.

Anyway, this letter apparantly had significant impact and NATURE editors now hope that 'Fossil data enter the web period'.. hopefully paleontologists will follow;)

Welcome in the post-taxonomic world

Rod Page reports on the growing number of unclassified and 'name less' GenBank entries in is new post 'Dark taxa: GenBank in a post-taxonomic world'.

European Research Ranking

Last friday I published the first public beta version of a new -and very different- project: European Research Ranking is an attempt to calculate the importance of research institutions based on the publicly available CORDIS database published by the European Commission.

This database contains some basic information on projects which have been funded by the European Commission such as project funding, duration and participating institutions.

As a first approach I have defined three basic categories of which I think one could estimate the performance of a research institution within the European research area: Funding and project participantion performance, Networking activity and alliances, Diversity of research areas.

For each of these categories I have defined one or more performance indicators and based on these indicators I calculated a total score for each institution based on project CORDIS data from the year 2010.

The first results are very promising, the Top 100 list for 2010 can be visited at http://www.researchranking.org/index.php?action=ranking. The clear winners of this ranking are french and german research organisations followed by well known top European universities such as the ETH, Cambridge, Leuven and Oxford.