Me doing stuff

Friday, 20 April 2018

2018 Vienna EGU and visiting University of Salzburg Z_GIS - some visual impressions

Wednesday, 18 April 2018

Making environmental research articles discoverable with OGC catalogue service

I am very happy to announce that our new article "Enhancing Location-related Hydrogeological Knowledge" has been published in the ISPRS International Jounral of Geo-information.

Kmoch, A.; Uuemaa, E.; Klug, H.; Cameron, S.G. (2018) Enhancing Location-Related Hydrogeological Knowledge. ISPRS Int. J. Geo-Inf. , 7, 132, http://www.mdpi.com/2220-9964/7/4/132

In a joint study by the University of Tartu (Estonia), the Institute of Geological and Nuclear Sciences (New Zealand) and the University of Salzburg (Austria) more than 5,800 scientific articles from three environmental research journals were digitised and analysed. In addition, a geographical search method was developed to identify the location of a studied area.

We use Georeferencing of scientific journal articles and text-mining in order to provide spatial search capabilities for environmental research. Journal articles are made discoverable through spatial queries. We propose that journal publishers should provide these capabilities on their platforms. This would allow everyone to search for journal articles for their desired regions of interest and it would really well complement existing search functionalities with keywords etc.

The press release from Tartu University explains really nicely how our results enable geographic search for scientific papers through text mining and geocoding; and how to better find environmental research articles via location.

http://researchinestonia.eu/2018/04/17/enabling-geographic-search-for-scientific-papers-through-text-mining-and-geocoding-how-to-better-find-environmental-research-articles-via-location/

Estonian version of the press release: https://novaator.err.ee/821096/kuidas-otsida-teadustoid-geograafilise-piirkonna-jargi

(This article belongs to the Special Issue Place-Based Research in GIScience and Geoinformatics)
MDPI OpenAccess: http://www.mdpi.com/2220-9964/7/4/132

ResearchGate: https://www.researchgate.net/publication/323990934_Enhancing_Location-Related_Hydrogeological_Knowledge

Monday, 26 March 2018

Interoperable exchange of groundwater data with OGC GroundWaterML2

WaterML2 has become a well-known synonym for internationally standardised hydrological data exchange, in particular for government agencies and research institutes across North America, Europe, Australia and New Zealand. Technically, WaterML2 is becoming a suite of standards actively promoted and endorsed by the World Meteorological Organisation (WMO), more details: http://www.whycos.org/wordpress/?page_id=929)

- WaterML 2.0: Part 1 - Time series of Observations

- WaterML 2.0: Part 2 - Ratings, Gaugings and Sections

- WaterML 2.0: Part 3 - Surface Hydrology Features (aka HY_Features)

- WaterML 2.0: Part 4 - aka GroundWaterML 2 (GWML2) Data Exchange for Groundwater Features (including wells, springs, borelogs and well constructions)

Now there is a scientific publication that explains the GWML2 standard, its development and application in hydrogeology in detail:

"GWML2 is an international standard for the online exchange of groundwater data that addresses the problem of data heterogeneity. This problem makes groundwater data hard to find and use because the data are diversely structured and fragmented into numerous data silos. Overcoming data heterogeneity requires a common data format; however, until the development of GWML2, an appropriate international standard has been lacking. GWML2 represents key hydrogeological entities such as aquifers and water wells, as well as related measurements and groundwater flows. It is developed and tested by an international consortium of groundwater data providers from North America, Europe, and Australasia, and facilitates many forms of data exchange, information representation, and the development of online web portals and tools."

Brodaric, B., Boisvert, E., Chery, L. et al. (2018) Enabling global exchange of groundwater data: GroundWaterML2 (GWML2). Hydrogeology Journal. https://doi.org/10.1007/s10040-018-1747-9

Related links and information:

https://link.springer.com/article/10.1007%2Fs10040-018-1747-9

https://www.researchgate.net/publication/323914313_Enabling_global_exchange_of_groundwater_data_GroundWaterML2_GWML2

WaterML2 Part 4: GroundWaterML2 (GWML2) http://www.opengeospatial.org/standards/gwml2

Groundwater SWG http://www.opengeospatial.org/projects/groups/groundwaterswg

OGC GroundWaterML 2 – GW2IE FINAL REPORT https://portal.opengeospatial.org/files/?artifact_id=64688

Wednesday, 28 February 2018

Publishing Datasets on Zenodo and Citing them with Mendeley

Open access dataset citing is becoming more important. Funders do not only increasingly demand open access publishing of funded research articles, but also the underlying datasets. This is good practice as it also supports reproducability of studies and thus supports credibility of research results reported in articles.

Zenodo is a very popular repository for this type of making datasets available. As a matter of fact, you can publish all sorts of "data" and "supplemental materials" on Zenodo and back them with a forever persistent unique digital object identifier: a DOI, that thing that you also have for all your articles that a published in respectable journals. The very thing that is the reference when Reuters is counting your citations :-) So, you basically just create an account, upload your datasets, reserve a DOI and fill out the metadata, like title etc.

Furthermore, Zenodo allows you for example to link your GitHub repositories, your ORCID
But you also want that the citation looks good in your manuscript, or at least in the references sections. I had a few tries and read a few articles on the web about citing datasets with Mendeley in particular, but I didn't really get to the point where I could reproduce something like following reference:

Kmoch, A. & Uuemaa, E. Geo-referencing of journal articles and platform design for spatial query capabilities. Dataset on Zenodo (2018). doi:10.5281/zenodo.1153887

Several articles suggested to create a Bibtex entry with the "misc" type (instead of "journal" as seen below), because you want to indicate that it is actually a dataset and not an article (or book section). Similar issues happen when you want to cite a software program that is not described by a scientific article which in turn is what you would cite in your work.

Thus, in Mendeley, the free online citation manager, for Linux, Windows and Mac, with Bibtex, Endnote and RIS Import/Export support, I ended up creating a journal article entry, where the journal name is "Dataset on Zenodo". And most citation styles, such as MDPI IJGI, or Nature if you like, will nicely list your data this way (see above) in your references section :-)

For example, in our recent article "Enhancing Location-Related Hydrogeological Knowledge" on MDPI IJGI (http://www.mdpi.com/2220-9964/7/4/132) we added the Zenodo repository as supplementary material (https://zenodo.org/record/1153887), and it is nicely visible directly on the journal article's landing page.

"""
@article{Kmoch2018,
abstract = {We analyzed the corpus of three geoscientific journals to investigate if there are enough locational references in research articles to apply a geographical search method, on the example of New Zealand. We counted place name occurrences that match records from the official Land Information New Zealand (LINZ) gazetteer in the titles, abstracts and full texts of freely available papers of the New Zealand Journal of Geology and Geophysics, the New Zealand Journal of Marine and Freshwater Research, and the Journal of Hydrology, New Zealand, for the years 1958 to 2015. We generated ISO standard compliant metadata records for each article including the spatial references and make them available in a public catalogue service.},
address = {Tartu},
author = {Kmoch, Alexander and Uuemaa, Evelyn},
doi = {10.5281/zenodo.1153887},
journal = {Dataset on Zenodo},
mendeley-groups = {my datasets},
publisher = {Dataset on Zenodo},
title = {{Geo-referencing of journal articles and platform design for spatial query capabilities}},
url = {https://zenodo.org/record/1153887},
year = {2018}
}
"""

Wednesday, 7 February 2018

Info Session for MSc programme in Geoinformatics for Urbanised Society

Today we broadcast a webinar info session about the new MSc programme in Geoinformatics for Urbanised Society at the University of Tartu.

One of the recurring core topics in this new MSc curriculum is Data and GIS use in Urban Planning.

Until just a decade ago spatial planning and analytics projects had problems with getting enough data. But nowadays there is so much data available, that it is increasingly hard to make sense of it – because of the 3 V’s of big data - volume, variety, velocity. The open data movement, government agencies, research institutes and citizen scientists alike make more and more data available publicly, mobile phones, sensor networks and satellites generate a multitude of datasets every day

In order solve the Interdisciplinary challenges of urban planning we want to empower you with skills and knowledge to analyse, visualise and understand processes and data. For that we teach the Full cycle of spatial data management, from the various methods of data acquisition, followed by efficient and practical processing techniques, to subsequent meaningful analysis and visualisation; in order to consequently make successful planning decisions for a sustainable future.

So what does it mean to study Geoinformatics for Urbanised Society with us in Tartu?

You will learn how to combine geography and IT in the age of BIG data. This is essentially what we believe modern Geoinformatics is representing. Mastering Geoinformatics will provide you with tools to analyse social and natural processes in space for interdisciplinary decision- and policy-making.

Watch the whole recorded session for more info:

Links:

Wednesday, 31 January 2018

A call to science and technology to work on standards for environmental data sharing

Which recent Geoscience related journal article has most influenced your work?

For me it was Laniak et al. (2013) "Integrated Environmental Modeling: A Vision and Roadmap for the Future". With a BSc in Computer Science I had worked in the IT industry before I started in academia. When I read Laniak et al. (2013) my Geography Master’s I knew that that was exactly how I would want to apply my computational background. Laniak et al. presented a vison for the future of integrated environmental modelling. They called to science and technology to work on standards for data sharing, and envisioned web-based platforms for transdisciplinary community interactions. I knew that science is not only about observations and theory. But it was then when I deeply understood how the capabilities of modern computers support research, make it reproducible and, thus, can accelerate research. The potential of linking people and knowledge from different disciplines in order to jointly understand natural processes and to make decisions together overwhelmed me. This landmark paper has since influenced me throughout my PhD and beyond.

Reference:

Laniak, Gerard F, Gabriel Olchin, Jonathan Goodall, Alexey Voinov, Mary Hill, Pierre Glynn, Gene Whelan, et al. 2013. “Integrated Environmental Modeling: A Vision and Roadmap for the Future.” Environmental Modelling & Software 39 (0):3–23. https://dx.doi.org/10.1016/j.envsoft.2012.09.006

Monday, 15 January 2018

Staying informed with Literature Review on the smartphone

As a scientist / researcher you have to stay informed about the latest research findings in your field. Typically, this means that you should follow the publications of the most important journals in your research domain. I found that many researchers (including myself so far) only conduct proper literature reviews when they work on a specific problem, when writing articles and grant applications. Often they wouldn't find the time to go to all the journal websites and scroll through the article lists etc.

I recently discovered the Feedly RSS reader. RSS is long-known internet feed syndication protocol that is used to subscribe to updates on websites and blogs. I found that many, if not all journals, more or less provide RSS feeds for their latest articles, often with an abstract provided. Feedly is a website application that helps you to organise RSS feeds and read them online. There is also an Android and an iPhone app. With these you can then read and manage your feeds on the phone. Now I quickly scroll through the latest articles every day via my mobile phone. This way it is just like scrolling through Facebook, Twitter or Instagram, but for journals. And the very few articles that you find relevant or that are of interest for you, you can save them in your Feedly backlog in order to read them later when you are in your office and take reading time :-)

Update: Inoreader is another very similar application to read your RRS feeds, and there are also the respective smartphone apps available.

One advantage of Feedly is that you can export and import lists of your RSS feed sources with so called OPML files. OPML is available in many RSS reader web sites and applications, so you can both import and export OPML files of RSS subscriptions.

I prepared an OPML Export file for you, a standard list format for your feed URLs, so you don't have to aggregate all the RSS URLs again. Happy reading and feel confident that you are not missing out on latest papers in your field.

Link to my export.opml file: https://www.dropbox.com/s/li0yjvwyt8cezsc/export.opml?dl=0

It includes links and feeds to the following resources:

Information systems and information technology : nature.com subject feeds - rss url and webpage url
Google Cloud Big Data and Machine Learning Blog - Google Cloud Big Data and Machine Learning Blog - rss url
Research Participant Portal - Funding Opportunities - Recently published Calls - rss url - webpage url