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Posts Tagged ‘Geoinformatics’

Open Science in an Open World

December 21st, 2014

I began to think about a blog for this topic after I read a few papers about Open Codes and Open Data published in Nature and Nature Geoscience in November 2014. Later on I also noticed that the editorial office of Nature Geoscience made a cluster of articles themed on Transparency in Science (http://www.nature.com/ngeo/focus/transparency-in-science/index.html), which really created an excellent context for further discussion of Open Science.

A few weeks later I attended the American Geophysical Union (AGU) Fall Meeting at San Francisco, CA. That is used to be a giant meeting with more than 20,000 attendees. My personal focus is presentations, workshops and social activities in the group of Earth and Space Science Informatics. To summarize the seven-day meeting experience with a few keywords, I would choose: Data Rescue, Open Access, Gap between Geo and Info, Semantics, Community of Practice, Bottom-up, and Linking. Putting my AGU meeting experience together with thoughts after reading the Nature and Nature Geoscience papers, now it is time for me to finish a blog.

Besides incentives for data sharing and open source policies of scholarly journals, we can extend the discussion of software and data publication, reuse, citation and attribution by shedding more light on both technological and social aspects of an environment for open science.

Open science can be considered as a socio-technical system. One part of the system is a way to track where everything goes and another is a design of appropriate incentives. The emerging technological infrastructure for data publication adopts an approach analogous to paper publication and has been facilitated by community standards for dataset description and exchange, such as DataCite (http://www.datacite.org), Open Archives Initiative-Object Reuse and Exchange (http://www.openarchives.org/ore) and the Data Catalog Vocabulary (http://www.w3.org/TR/vocab-dcat). Software publication, in a simple way, may use a similar approach, which calls for community efforts on standards for code curation, description and exchange, such as the Working towards Sustainable Software for Science (http://wssspe.researchcomputing.org.uk). Simply minting Digital Object Identifiers to codes in a repository makes software publication no difference from data publication (See also: http://www.sciforge-project.org/2014/05/19/10-non-trivial-things-github-friends-can-do-for-science/) . Attention is required for code quality, metadata, license, version and derivation, as well as metrics to evaluate the value and/or impact of a software publication.

Metrics underpin the design of incentives for open science. An extended set of metrics – called altmetrics – was developed for evaluating research impact and has already been adopted by leading publishers such as Nature Publishing Group (http://www.nature.com/press_releases/article-metrics.html). Factors counted in altmetrics include how many times a publication has been viewed, discussed, saved and cited. It was very interesting to read some news about funders’ attention to altmetrics (http://www.nature.com/news/funders-drawn-to-alternative-metrics-1.16524) on my flight back from the AGU meeting – from the 12/11/2014 issue of Nature which I picked from the NPG booth at the AGU meeting exhibition hall. For a software publication the metrics might also count how often the code is run, the use of code fragments, and derivations from the code. A software citation indexing service – similar to the Data Citation Index (http://wokinfo.com//products_tools/multidisciplinary/dci/) of Thomson Reuters – can be developed to track citations among software, datasets and literature and to facilitate software search and access.

Open science would help everyone – including the authors – but it can be laborious and boring to give all the fiddly details. Fortunately fiddly details are what computers are good at. Advances in technology are enabling the categorization, identification and annotation of various entities, processes and agents in research as well as the linking and tracing among them. In our 06/2014 Nature Climate Change article we discussed the issue of provenance of global change research (http://www.nature.com/nclimate/journal/v4/n6/full/nclimate2141.html). Those works on provenance capture and tracing further extend the scope of metrics development. Yet, incorporating those metrics in incentive design requires the science community to find an appropriate way to use them in research assessment. A recent progress is that NSF renamed Publications section as Products in the biographical sketch of funding applicants and allowed datasets and software to be listed (http://www.nsf.gov/pubs/2013/nsf13004/nsf13004.jsp). To fully establish the technological infrastructure and incentive metrics for open science, more community efforts are still needed.

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Survival and thriving at AGU Fall Meeting 2012

December 11th, 2012

AGU Fall Meeting, if I am correct, is the biggest conference in the field of geosciences. For the year 2012 there were over 22000 people participated in the event. Yet, a conference is more than the number of attendees. AGU is not a single combination of a number of academic meeting sessions. There are various workshops, seminars, town halls, exhibitions and social activities together with it.
I once read an article written by the president of UNISCO (two years ago?), in which it is mentioned that the number of earth scientists across the world is about 440000. This is a tiny number comparing with the global population. While approaching San Francisco and Moscone Center, the city and venue of AGU, I could feel the number of earth scientists around me is increasing sharply. Especially along the 4th street to Moscone Center, what one can see during the AGU week should be called a deluge of earth scientists. Personally, I had an interesting feeling – am I driven by the deluge, or I am a part of it?
Back to the conference itself, it is a big conference so I (1) focused on sessions in the division of Earth and Space Science Informatics (ESSI), and prepared my personal schedule for posters and presentations I was interested. I also set (2) in-person meetings with people with whom we want to discuss some issues related to the research projects DCO-DS and GCIS-IMSAP at TW. There were (3) a number of other workshops and activities together with AGU, such as the workshop of Data Management 101 for Early Career Scientists, the workshop about NSF system, the ESSI reception, the Ignite Talk, etc. Some of them cannot be easily found on the AGU web site, but are informed through different channels. Many thanks to people in those email lists (e.g., AGU-ESSI, ESIP-SW) I joined for sending me the messages.
I gave two presentations on Friday: a poster for the modeling works in the GCIS-IMSAP project (Jin is first author), and an oral presentation on the exploratory visualization of earth science data with semantic web technologies. For the first one, David Arctur suggested that we may bring some geospatial components into the model framework. Stephan discussed that if we use GCMD keywords for GCIS, then in the GCMD keywords there is a part of it is for geospatial descriptions. While I was introducing the searching function in our plan for the GCIS-IMSAP project, Deana Pennington suggested we may also consider the user tag functions, that is, a reader can create tags in the NCA report for further use, while this may also be supported by some Semantic Web technologies. I also discussed the GCMD keywords with Tyler Stevens, a researcher in the GCMD keywords, on how to make GCMD keywords more open for use. He likes our feedback and already provided some information.
My oral presentation was based on some work originated from my PhD study. This work used datasets on the server of the British Geological Survey. I got some updates from Timothy McCormick, the Information Sector Manager (Geology) at BGS, on their Linked Data works of lithology. He suggested me to do some further work using their datasets and services. Luis Bermudez and David Arctur from Open Geospatial Consortium (OGC) suggested me to do more work on semantic web and Web Feature Service (WFS) and Sensor Web, and they suggested TW to obtain a membership at OGC to get fresh first-hand progress of OGC works.
AGU is a big event, a schedule is necessary, as those described above. And, there are also many other interesting side-events. Almost every day I crossed by some old friends, for some of them I had lost contact for more than seven years! The exhibit is great and I collected a bag of earth and space science cards, posters and toys for my son – is he going to be an earth scientist?
There is more to say about a seven-day conference with over 22000 participants. I have to stop here. For those issues related to specific research topics and projects at TW we will have further discussion in the separate groups soon.

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