Enabling knowledge creation in data-driven science
Today, many scientific fields can be described as data-intensive disciplines, which turn raw data into information and then knowledge. If this sounds familiar it’s because this represents the late and influential computer scientist Jim Gray’s vision of the fourth research paradigm. Gray divided up the evolution of science into four periods or paradigms. One thousand years ago, science was experimental in nature, a few hundred years ago it became theoretical, a few decades ago it moved to a computational discipline, and today it’s data driven. Researchers are reliant on e-science tools to enable collaboration, federation, analysis, and exploration to address this data deluge, equal to about 1.2 zettabytes each year. If 11 ounces of coffee equaled one gigabyte, a zettabyte would be the same volume as the Great Wall of China.
The amount of data is so much that journals such as Neuroscience have stopped accepting supplementary files along with research manuscripts in order to better handle the peer review process. To answer this problem, some are creating infrastructures and software that are set to radically transform the way scientific publishing is done, which has been little changed for centuries.
Research publishing 2.0
While a number of scientific institutes, European Commission-funded projects, and research communities work on establishing common data policies and open-access infrastructures to make research data more searchable, shareable, and citable, the life sciences are looking at data analysis and publishing approaches that move the compute to the data rather than moving the data to the computers.
The GigaSciencejournal is creating an open-access data platform that combines software workflows, databases, and cloud computing to make all stages of scientific research computable - a first for genomics and biomedical data. The journal, a collaboration with BGI, in Shenzhen China and the journal BioMed Central, aims to turn research papers into executable data objects. With this, for example, a researcher could, in theory, create a separate methods publication from a research paper, with its own Digital Object Identifier (DOI) that can be indexed and cited.
Scott Edmunds, an editor of the GigaScience journal says, “You don’t need methods sections in a paper anymore as methods can be computed, making it easier for reviewers to check data.” To enable this new journal platform, GigaScience is using an open-source workflow system called Galaxy, which is run by a team at Penn State University, Pennsylvania, US. For those in the know, this is the same team that was involved in the data release of the ENCODE project in September 2012. ENCODE published 30 research papers about the function of the human genome simultaneously. Peer review of the project’s findings were made easier with virtual machines, which contained terabytes of input data, code, scripts, processing steps, and outputs.
“ENCODE is state of the art,” says Edmunds. “They set everything up in the Amazon cloud. James Taylor of Penn State University who set up their virtual peer-review environment paid for the Amazon charges himself. They came to $5,000, which, considering the size of the data and the number of people is quite cheap.”
If we build it, will they come?
Last year, the GigaScience journal launched their first citable DOI dataset on the nasty E. coli genome. The information was released on Twitter with a creative commons license and in a pre-publication citable format. Upon release, researchers around the world started producing their own assemblies and annotations, sharing data on Twitter, with some dubbing it as the first ‘Tweenome’.
Currently, the journal stores about 20 terabytes of public data on its servers and another 5-10 terabytes are being prepared for release. They have already released a number of peer-reviewed papers and are hard at work finalizing their data platform, enabling analysis and recreation of experiments on Galaxy in the next few months.
“When we’re confident it’s shiny and ready for prime time we’ll publish something. I’d like to say our platform will answer everything, but it’s really just another step in the right direction,” says Edmunds. “We have to see if people actually use the infrastructure. People have been used to publishing research papers in a certain way for three centuries. Some people will get our platform and use it immediately. But, I think it will take a while for the rest of the community to get used to it.”
Flipping publishing on its head
Another group of researchers have decided to invert the publishing model, making all research data computer-readable. This would make data mining facts and linking information for knowledge discovery easier.
Data can be represented as a nanopublication, discussed in a 2011 Nature article. This is the smallest unit of publication of a single assertion associating two concepts based on a foundation in machine-readable form, with associated metadata and its own open-source universally unique identification ID or UUID. GigaScience’s data may be included in this approach.
“Converting data from classical relational databases or spreadsheets into nanopublications is relatively easy, while harvesting them from classical narrative is the main issue,” says Barend Mons, scientific director of the Netherlands Bioinformatics Centre.
There are dozens of projects converting major datasets globally, creating new semantic software and new terminology. These projects include nanopub.org, which helps researchers create nanopublications of their data. The Phortos Group is a collaboration of companies and researchers providing services to big data owners. They aim to develop applications to find associations or semantic relationships in nanopublications too difficult for any one human brain to analyze alone.
Mons says research in his biosemantics group has already inferred new discoveries from what they refer to as the 'explicitome' or all explicit assertions they can find. They estimate that the explictome of the biomedical life sciences currently consists of 100 trillion nanopublications.
By grouping similar assertions under a summarized or cardinal assertion, 100 trillion nanopublications can be reduced to 200 billion unique assertions, reduced further to less than two million concepts, a manageable amount of data, says Mons.
“From the explictome we can infer novel protein-protein interactions for example and there is more to come. Our work may go beyond just dealing with big data, as we advance e-science publishing (or publishing 2.0) and also evidence-aware computer reasoning. We’re moving into studies on the very nature of human knowledge discovery and this will give some very exciting insights,” says Mons.
A distributed community of communities
A bigger question is could a software approach that serves one research community be transferable to another community? The ScienceSoft project is trying to address this question. It’s building a catalogue of software products for all research communities. But, it’s also much more than that says Alberto Di Meglio, project director of the European Middleware Initiative.
ScienceSoft aims to be a distributed community of communities that use scientific software, addressing issues such as software identification, the long-term preservation of software information, and relationships between software, publications, and data sets.
Information that’s uniquely identifiable can be used as a knowledge base across different research areas and advance reliability of peer-review.
“We’re not the only ones thinking of unique identifiers for digital objects, but as far as we know, most of this research has been done in individual categories of objects,” says Di Meglio. “Today, the way data sets and software are referred to in research papers do not yet allow other people to reproduce the results in a consistent and easily accessible way. Creating links across knowledge is essential. Science today is distributed and the advantages of cross-disciplinary research are becoming apparent,” says Di Meglio.
In one example, Mike Conlon, principal investigator of the VIVO project gave a keynote speech about new scientific results that were made possible by linking two completely different research areas at the 8th IEEE International Conference on eScience 2012 .
Di Meglio says the vision is to create a semantic system that will help researchers find information quickly, spot similarities across disciplines, avoid errors, and increase collaboration. “It’s also important for decision makers too because they can understand what areas require more attention and funding, maybe creating a more measurable relationship between research projects and funding agencies.”
The ScienceSoft project is looking to include various science disciplines in this discussion and it’s organizing a workshop in January 2013 on the topic of unique identifiers for software digital objects.
About the Author
Adrian Giordani is the Science Journalist of iSGTW, based at CERN, in Geneva. He has a Bachelor of Arts (B.A) degree in Software Systems and a Master of Science (M.Sc) degree in Science Communication.
Digital Stream
Comments
GOOD article
I'm impressed. I don't think I've met anyone who knows as much about this subject as you do. You're truly informed and very intelligent
www.thenoblerelocation.in
great post
Hello,I love reading through your blog, I wanted to leave a little comment to support you and wish you a good continuation.
http://removalists.blogspot.in/2013/04/various-kinds-of-shifting-service...
nice blog
Hi. I'll bookmark your site because your posts are very informative. We appreciate your posts and look forward to coming back
citypackersandmoversbangalore.com
interesting article
Thank you for another essential article. Where else could anyone get that kind of information in such a complete way of writing ?
www.stplogiic.com
Good Information!
At a wedding, there are most likely many guests, and the speaker probably does not know all or even most of them Meme
Really good article
I wanted to thank you for this unique read. I definitely savored all bits and pieces of it including all the comments and I have added you to my bookmark list to check out new articles you post.
https://twitter.com/AnupamaChauhan4/status/308537028587433984
Best post ever read
I wanted to say that it's so nice to know that finally someone else also mentioned this as I had trouble finding the same info elsewhere. This was the first place that told me the answer. Thank you very much.
drchandrasekharnaidu
Informative post
I wanted to thank you for this unique read. I definitely savored all bits and pieces of it including all the comments and I have added you to my bookmark list to check out new articles you post.
Dr.Y.V. Rao
You might write about the
You might write about the uniqueness on the blog. You should formulate it's necessary. Your blog explanation might grow your co-ops. logo design service
law firm
I really enjoy simply reading all of your weblogs. Simply wanted to inform you that you have people like me who appreciate your work. Definitely a great post.
www.lawfirmbangalore.in
Good post
I want to visit again, Look forward for more interesting updates. I'd certainly say this blog is a brilliant
lawparkassociates.co.in
Good Information
I'm thoroughly enjoying and appreciate the smart way you write articles in this blog
www.rajendradesailawfirm.in
Yakenzu
Excellent post i must say. Your article touches a lot of urgent issues in our society. by Agen Bola Ligabet88 Promo Bonus 100% IBCBET SBOBET 368BET
This is quite wonderful post.
This is quite wonderful post. Your article affects a lot of urgent problems in our minds. We can not be indifferent to these problems. Your article gives good ideas and concepts. Keep it up.
pinworm treatment
Excellent article. The post
Excellent article. The post touches a lot of urgent issues in our society. We can not be untouched to these issues. This post gives a lot of awesome information and inspiration. I appreciate the information and the effort you put into your article.
Albenza
Fantastic blog post. It
Fantastic blog post. It touches a lot of urgent challenges in our society. We can not be untouched to these challenges. Your post gives a lot of fantastic information and inspiration. This was very interesting to read. norvasc
Definitely excellent post.
Definitely excellent post. Your post touches a lot of urgent challenges of our society. We can not be uninvolved to these problems. This article gives the light in which we can observe the real life. I really enjoyed simply reading.
amlodipine 5
Asian Packers
Thanks We are really grateful for your blog post. You will find a lot of approaches after visiting your post. I was exactly searching for this
http://digitalinberlin.com/packers-and-movers-bangalore/
Awesome post
Well, the article is actually the sweetest topic on this related issue. I fit in with your conclusions and will thirstily look forward to your forthcoming updates.
http://digitalinberlin.com/liposuction-in-hyderabad/
Wonderful site
Awesome blog. I enjoyed reading your articles. This is truly a great read for me. I have bookmarked it and I am looking forward to reading new articles. Keep up the good work!
https://twitter.com/AnupamaChauhan4
knowledge creation data
Buying a hot tub is something that many homeowners have considered over time. The appeal of having a spa or jacuzzi in the home is that it provides a source of relaxation without having to go to a pricey health club. It is also appealing to some buyers as they are looking for a home to purchase. Spas can be enjoyed by adults and children if they are old enough and can provide some real health benefits if they are not over used. When a family is thinking about purchasing a tub, it is essential to read several portable hot tubs before making a purchase. Reading these reviews can provide insight into the type of tub that should be purchased and the amount of money that can be expected to be spent on the purchase.
These splat hair dye may be great, but the women who are wearing these styles are definitely more than just cute. With delicate feminine features such as the neck, nape and face boldly revealed, there is no doubting that the wearers of these cuts are beautiful, confident women
Purple hair can be achieved one of two ways: 1) with purple hair dye or 2) with black hair styles. If you're going for a lilac or lavender color, you need only a little bit of purple dye (or red & blue hair dye) mixed in with white conditioner. But whether you see a professional or dye your hair yourself, either way, you will need to bleach your hair to a platinum blonde or white first before attempting to dye it yellow (especially if you have dark hair), otherwise the color will not show up very well. Any leftover brassiness will mess with the purple. Do some research to see how to get the best, longest-lasting color possible. Below are several videos to help you get started.
Adam smith
Hello There. I found your blog very knowledgeable. That is a really well written article. I'll make sure to bookmark it and come back to read extra of your helpful info. Thanks for the post. I'll certainly comeback.
http://removalists.blogspot.in/2013/03/high-quality-is-primary-concern-f...
Vishnu priya
I am really enjoying this blog post. It has many amazing tips.Provide me with any new updates about your blog. Thanks for the nice blog
http://removalists.blogspot.in/2013/03/dispatch-of-goods-punctually-ever...
City Packers
Hello there, just became aware of your blog through Google, and found that it is truly informative. I’ll appreciate if you continue this in future. Many people will be benefited from your writing. Cheers!
http://removalists.blogspot.in/2013/03/the-procedure-of-furniture-moving...
science driven data
Buying a hot tub is something that many homeowners have considered over time. The appeal of having a spa or jacuzzi in the home is that it provides a source of relaxation without having to go to a pricey health club. It is also appealing to some buyers as they are looking for a home to purchase. Spas can be enjoyed by adults and children if they are old enough and can provide some real health benefits if they are not over used. When a family is thinking about purchasing a tub, it is essential to read several used hot tubs before making a purchase. Reading these reviews can provide insight into the type of tub that should be purchased and the amount of money that can be expected to be spent on the purchase.
These short haircuts for round faces may be great, but the women who are wearing these styles are definitely more than just cute. With delicate feminine features such as the neck, nape and face boldly revealed, there is no doubting that the wearers of these cuts are beautiful, confident women
Purple hair can be achieved one of two ways: 1) with purple hair dye or 2) with short layered haircuts. If you're going for a lilac or lavender color, you need only a little bit of purple dye (or red & blue hair dye) mixed in with white conditioner. But whether you see a professional or dye your hair yourself, either way, you will need to bleach your hair to a platinum blonde or white first before attempting to dye it yellow (especially if you have dark hair), otherwise the color will not show up very well. Any leftover brassiness will mess with the purple. Do some research to see how to get the best, longest-lasting color possible. Below are several videos to help you get started.
science here, science there
Buying a hot tub is something that many homeowners have considered over time. The appeal of having a spa or jacuzzi in the home is that it provides a source of relaxation without having to go to a pricey health club. It is also appealing to some buyers as they are looking for a home to purchase. Spas can be enjoyed by adults and children if they are old enough and can provide some real health benefits if they are not over used. When a family is thinking about purchasing a tub, it is essential to read several hot tub chemicals before making a purchase. Reading these reviews can provide insight into the type of tub that should be purchased and the amount of money that can be expected to be spent on the purchase.
These blonde hair colors may be great, but the women who are wearing these styles are definitely more than just cute. With delicate feminine features such as the neck, nape and face boldly revealed, there is no doubting that the wearers of these cuts are beautiful, confident women
Purple hair can be achieved one of two ways: 1) with purple hair dye or 2) with red hair dye. If you're going for a lilac or lavender color, you need only a little bit of purple dye (or red & blue hair dye) mixed in with white conditioner. But whether you see a professional or dye your hair yourself, either way, you will need to bleach your hair to a platinum blonde or white first before attempting to dye it yellow (especially if you have dark hair), otherwise the color will not show up very well. Any leftover brassiness will mess with the purple. Do some research to see how to get the best, longest-lasting color possible. Below are several videos to help you get started.
knowledge creation
Buying a hot tub is something that many homeowners have considered over time. The appeal of having a spa or jacuzzi in the home is that it provides a source of relaxation without having to go to a pricey health club. It is also appealing to some buyers as they are looking for a home to purchase. Spas can be enjoyed by adults and children if they are old enough and can provide some real health benefits if they are not over used. When a family is thinking about purchasing a tub, it is essential to read several hot tub repair before making a purchase. Reading these reviews can provide insight into the type of tub that should be purchased and the amount of money that can be expected to be spent on the purchase.
These facial hair styles may be great, but the women who are wearing these styles are definitely more than just cute. With delicate feminine features such as the neck, nape and face boldly revealed, there is no doubting that the wearers of these cuts are beautiful, confident women.
enabling our knowledges
Buying a hot tub is something that many homeowners have considered over time. The appeal of having a spa or jacuzzi in the home is that it provides a source of relaxation without having to go to a pricey health club. It is also appealing to some buyers as they are looking for a home to purchase. Spas can be enjoyed by adults and children if they are old enough and can provide some real health benefits if they are not over used. When a family is thinking about purchasing a tub, it is essential to read several hot tub reviews before making a purchase. Reading these reviews can provide insight into the type of tub that should be purchased and the amount of money that can be expected to be spent on the purchase.
These cute short haircuts may be great, but the women who are wearing these styles are definitely more than just cute. With delicate feminine features such as the neck, nape and face boldly revealed, there is no doubting that the wearers of these cuts are beautiful, confident women.
big thanks for share some new knowledge to me
big thanks for share some new knowledge to me
Thanks a lot of sewa mobil | cara membuat blog | contoh surat lamaran kerja | tv online | cerita lucu | lowongan kerja terbaru 2013 | download lagu | lagu terbaru | download software | kata bijak | download film | duduk | cibadak | chord gitar|kunci gitar | cibadak download lagu |zodiak hari ini autotext contoh proposal|tangga lagu | pizap | jasa penerjemah | penerjemah tersumpah | penerjemah
You should comment on the
You should comment on the sales letter of the blog. You can spawned it's enchanting. Your blog news/happenings would multiply your balance sheet. discount codes
You can post on the ease of
You can post on the ease of use for the blog. You might author it's sweet. Your blog message shall maximize your leads.
female mind mastery
Its always good to have tips
Its always good to have tips on good blog posting. As I just started posting comments for blog and faced a lot of rejections. I think your suggestion would be helpful for me. I will let you know if this works for me.
Readymade Garment House India | Export Garment House India | Export House India | Exporters in India | Ladies Garment India
Hi, I appreciate your
Hi, I appreciate your speculating as it attracts people’s attention and make this topic discussable.
Computer Repair Service | Computer Repari Delhi | Computer AMC Service Delhi
I am new to your blog and
I am new to your blog and just spent about 1 hour and 30 minutes reading. I think I will frequently visit your blog from now on. I will definitely learn a lot from them.
Cabs in Delhi | Cabs in Faridabad | Taxi service Faridabad | Taxi Service in Delhi
I just read through the
I just read through the entire article of yours and it was quite good. This is a great article thanks for sharing this information. I will visit your blog regularly for some latest post.Cabs in Prahladpur | Cabs in Badarpur
Protecting the data from plagiarism is eaqully important
When we speak about enhancing the serviceability of online resources, it becomes even more important to protect it from the eyes of plagiarizers. you can do it easily by making the use of tolls available easily over the internet space. windows 7 home premium product key
Engine Check Light
I like the way of your presentation of ideas, views and valuable content. No doubt you are doing great work. I'll be waiting for your next post. Thanks .Keep it up! Engine Check Light
You may comment on the audio
You may comment on the audio of the blog. You could render it's fail proof. Your blog remarks can springboard your circulation. elazigproje.org
You could post on the links
You could post on the links for the blog. You may day it's first-rate. Your blog raves will boost your income streams.
Finding The Best Equipment
I'm thoroughly enjoying and
I'm thoroughly enjoying and appreciate the smart way you write articles in this blog truth about cellulite
I want to visit again, Look
I want to visit again, Look forward for more interesting updates. I'd certainly say this blog is a brilliant Education For Kids
Customized T-Shirt Printing
Thank you for publishing when you have the opportunity, guess I will just make this bookmarked. Customized T-Shirt Printing
It offers your sleeping
It offers your sleeping friends, way more, this will save you from the actual vibrations of oxygen, but they can be a symptom of a serious condition specially those connecting towards the subsequent things such as glue strips that hold open orally will be thought anti snoring a healthcare issue. This really is as a result of additional health-related problems.
snoring
Here again, I'm thoroughly
Here again, I'm thoroughly enjoying the smart way you write articles in this blog http://www.gestaosocioambiental.net/
With the cuts, the various
With the cuts, the various charges and institutions is touching them get rid of best new honda deal their beloved official cars. This occurs in municipalities, autonomous regions and central government. Usually media hypes, but not easy to buy one of these cars or, at least, one new hyundai of the best. Again the "cronyism" is felt: one goes to the first hour on the first day of sale, direct to the car of your interest and say they are "awarded".
You might comment on the
You might comment on the personal credibility of the blog. You should index it's marvelous. Your blog feelings should accelerate your colleagues. sprinkles for cupcakes
sci-fi story
Nice information, valuable and excellent design, as share good stuff with good ideas and concepts, lots of great information and inspiration, both of which I need, thanks to offer such a helpful information here hot tub works. I really enjoy simply reading all of your weblogs. Simply wanted to inform you that you have people like me who appreciate your work. Definitely a great post. Hats off to you! The information that you have provided is very helpful with. Thank for your time of this wonderful read!!! I definately enjoy every little bit of it!
hot tub works
wall stickers
I wish you all right, as long as you every day to comment, written wonderful friends!Wall Stickers
knowledge = science
Inflatable hot tub or commonly known as portable hot tub is the very popular hot tub over these recent years. The portable hot tub becomes so popular because it can be used all over plus require a smaller amount equipments for installation. However , this kind of hot tub installation also has a few weaknesses. Consequently , you have to seriously contemplate about either advantages and disadvantages of inflatable hot tub
myfinancialmarketing.com
This is a great article. I really love this one especially since it tackles one of the most mysterious diseases of all time. It's especially very resourceful too. myfinancialmarketing.com
Post new comment