Reading the Tea Leaves of 2011 – Data and Technology Predictions for the Year Ahead

The beginning of a new year usually affords the opportunity to join in the predication game and to think about which topics will not only be on our radar screens on the next year, but may dominate it. I couldn’t help myself but to attempt to do the same in my particular line of work – if for no other reason, than to see how wrong I was when I will look at this again at the beginning of 2012. Here are what I think will be at least some of the big technology and data topics in 2011:

1. Big, big, big Data
2010 has been an extraordinary year when it comes to data availability. Traditional big data producers such as biology continue to generate vast amounts of sequencing and other data. Government data is pouring in from countries all over the world, be it here in the United Kingdom, in the United States and efforts to liberate and obtain government data are also starting in other countries. The Linked Open Data Cloud is growing steadily:

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Linked Open Data October 2007 - Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/

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Linked Open Data September 2010 - Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/

the current linked data cloud has about 20 billion triples in it. Britain now has, thanks to the Open Knowledge Foundation, an open bibliography. The Guardian’s Datastore is a wonderful example of a commercial company making data available. The New York Times is making an annotated corpus available. Twitter and other user-generated content also provide significant data firehoses from which one can drink and build interesting mashups and applications, such as Ben Marsh’s UK Snow Map. So that are just some examples of big data and there are several issues associated with it, that will occupy us in 2011.

2. Curation and Scalability
A lot of this big data we are talking about is “real-world” and messy. There is no nice underlying ontological model (the stuff that I am so fond of) and by necessity it is exceptionally noisy. Extracting a signal out of clean data is hard enough, but getting one out of messy data requires a great deal of effort and an even greater deal of care. And therefore the development of curation tools and methodologies will continue to be high up on the agenda of the data scientist. The development of both automated and social curation tools will be high up on the agenda. And yes, I do believe that this effort is going to become a lot more social – there are signs of this starting to happen everywhere.
However, we are now generating so much data, that the sheer amount is starting to outstrip our ability to compute it – and therefore scalability will become an issue. The fact that service providers such as Amazon are offering Cluster GPU Instances as part of the EC2 offering is highly significant in this respect. MapReduce technologies seem to be extremely popular in “Web 2.0” companies and the Hadoop ecosystem is growing extremely fast – and the ability to “make Hadoop your bitch” as an acquaintance of mine recently put it, seems to be an in-demand skill at the moment and I think for the forseeable future. And – needless to say – successful automated curation of big data,, too, requires scalable computing.

3. Discovery
Having a lot of datasets available to play with is wonderful, but what if nobody knows they are there. Even in science, it is still much much harder to discover datasets than ought to be the case. And even once you have found what you may have been looking for, it is hard to decide whether that really was what you were looking for – describing metadata is often extremely poor or not available. There is currently little collaboration between information and data providers. Data marketplaces such as Infochimps, Factual, Public Datasets on Amazon AWS or the Talis Connected Commons (to name but a few) are springing up, but there is a lot of work to do still. And is it just me or is science – the very people whose primary product is data and knowledge – is lagging far behind in developing these market places. Maybe they will develop as part of a change in the scholarly pulication landscape (journals such as Open Research Computation have a chance of leading the way here), but it is too early to tell. The increasing availablity of data will push this topic further onto the agenda in 2011.

4. An Impassioned Plea for Small Data
One thing, that will unfortunately not be on the agenda much is small data. Of course it won’t matter to you when you do stuff either at web scale or if you are someone working in Genomics. However, looking at my past existence as a laboratory-based chemist in an academic lab, a significant amount of valuable data is being produced by the lone research student who is the only one working on his project or by a small research group in a much larger department. Although there is a trend to large-scale projects in academia and away from individual small grants, small-scale data production on small scale research projects is still the reality in a significant number laboratories the world over. And the only time, this data will get published, is as a mangled PDF document in some journal supplementary – and as such is dead. And sometimes it is perfectly good data, which never gets published at all: in my previous woworkplace we found that our in-house crystallographer was sitting on several thousand structures, which were perfectly good and publishable, but had, for various reasons, never been published. And usually it is data that has been produced at great cost to both the funder as well as the student. Now small data like this is not sexy per se. But if you manage to collect lots of small data from lots of small laboratories, it becomes big data. So my plea would simply be not to forget small data, to build systems, which collect, curate and publish it and make it available to the world. It’ll be harder to convince both funders and institutions and often researchers to engage with it. But please let’s not forget it – it’s valuable.

Enough soothsaying for one blog post. But let’s get the discussion going – what are your data and technology predictions for 2011?

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The Unilever Centre @ Semantic Technology 2009

In a previous blogpost, I had already announced, that both Jim and I had been accepted to speak at Semantic Technology 2009 in San Jose.

Well, the programme for the conference is out now and looks even more mind-blowing (in a very good way) than last year. Jim and I will be speaking on Tuesday, 16th June at 14:00. Here’s our talk abstracts:

PART I | Lensfield – The Working Scientist’s Linked Data Space Elevator (Jim Downing)

The vision of Open Linked Data in long-tail science (as opposed to Big Science, high energy physics, genomics etc) is an attractive one, with the possibility of delivering abundant data without the need for massive centralization. In achieving that vision we face a number of practical challenges. The principal challenge is the steep learning curve that scientists face in dealing with URIs, web deployment, RDF, SPARQL etc. Additionally most software that could generated Linked Data runs off-web, on workstations and internal systems. The result of this is that the desktop filesystem is likely remain the arena for the production of data in the near to medium term. Lensfield is a data repository system that works with the filesystem model and abstracts semantic web complexities away from scientists who are unable to deal with them. Lensfield makes it easy for researchers to publish linked data without leaving their familiar working environment. The presentation of this system will include a demonstration of how we have extended Lensfield to produce a Linked Data publication system for small molecule data.

PART II | The Semantic Chemical World Wide Web (Nico Adams)

The development of modern new drugs, new materials and new personal care products requires the confluence of data and ideas from many different scientific disciplines and enabling scientists to ask questions of heterogeneous data sources is crucial for future innovation and progress. The central science in much of this is chemistry and therefore the development of a “semantic infrastructure” for this very important vertical is essential and of direct relevance to large industries such as the pharmaceuticals and life sciences, home and personal care and, of course, the classical chemical industry. Such an infrastructure shouls include a range of technological capabilities, from the representation of molecules and data in semantically rich form to the availability of chemistry domain ontologies and the ability to extract data from unstructured sources.

The talk will discuss the development of markup languages and ontologies for chemicals and materials (data). It will illustrate how ontologies can be used for indexing, faceted search and retrieval of chemical information and for the “axiomatisation” of chemical entities and materials beyond simple notions of chemical structure. The talk will discuss the use of linked data to generate new chemical insight and will provide a brief discussion of the use of entity extraction and natural language processing for the “semantification” of chemical information.

But that’s not all. Lezan has been accepted to present a poster and so she will be there too,, showing off her great work on the extraction and semantification of chemical reaction data from the literature. Here is her abstract:

The domain of chemistry is central to a large number of significant industries such as the pharmaceuticals and life sciences industry, the home and personal care industry as well as the “classical” chemical industry. All of these are research-intensive and any innovation is crucially dependent on the ability to connect data from heterogeneous sources: in the pharmaceutical industry, for example, the ability to link data about chemical compounds, with toxicology data, genomic and proteomic data, pathway data etc. is crucial. The availability of a semantic infrastructure for chemistry will be a significant factor for the future success of this industry. Unfortunately, virtually all current chemical knowledge and data is generated in non-semantic form and in many silos, which makes such data integration immensely difficult.

In order to address these issues, the talk will discuss several distinct, but related areas, namely chemical information extraction, information/data integration, ontology-aided information retrieval and information visualization. In particular, we demonstrate how chemical data can be retrieved from a range of unstructured sources such as reports, scientific theses and papers or patents. We will discuss how these sources can be processed using ontologies, natural language processing techniques and named-entity recognisers to produce chemical data and knowledge expressed in RDF. We will furthermore show, how this information can be searched and indexed. Particular attention will also be paid to data representation and visualisation using topic/topology maps and information lenses. At the end of the talk, attendees should have a detailed awareness of how chemical entities and data can be extracted from unstructured sources and visualised for rapid information discovery and knowledge generation.

It promises to be a great conference and I am sure our minds will go into overdrive when there….can’t wait to go! See you there!?

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(More) Triples for the World

I have taken a long hiatus from blogging for a number of reasons and still don’t have time to blog much, but something has just happened that has really excited me.
During this year’s International Semantic Web Conference in Karlsruhe (which I am still angry about not being able to attend due to time constraints), it was announced, that Freebase now produces RDF!

Now just in case you are wondering what Freebase is, here’s a description from their website:

Freebase, created by Metaweb Technologies, is an open database of the world’s information. It’s built by the community and for the community – free for anyone to query, contribute to, build applications on top of, or integrate into their websites.

Already, Freebase covers millions of topics in hundreds of categories. Drawing from large open data sets like Wikipedia, MusicBrainz, and the SEC archives, it contains structured information on many popular topics, including movies, music, people and locations – all reconciled and freely available via an open API. This information is supplemented by the efforts of a passionate global community of users who are working together to add structured information on everything from philosophy to European railway stations to the chemical properties of common food ingredients.

By structuring the world’s data in this manner, the Freebase community is creating a global resource that will one day allow people and machines everywhere to access information far more easily and quickly than they can today.

And all of this data, they are making available as RDF triples, which you can get via a simple service:

Welcome to the Freebase RDF service.

This service generates views of Freebase Topics following the principles of Linked Data. You can obtain an RDF representation of a Topic by sending a simple GET request to http://rdf.freebase.com/ns/thetopicid, where the “thetopicid” is a Freebase identifier with the slashes replaced by dots. For instance to see “/en/blade_runner” represented in RDF request http://rdf.freebase.com/ns/en.blade_runner

The /ns end-point will perform content negotiation, redirecting your client to the HTML view of the Topic if HTML is prefered (as it is in standard browsers) or redirecting you to http://rdf.freebase.com/rdf to obtain an RDF representation in N3, RDF/XML or Turtle depending on the preferences expressed in your clients HTTP Accept header.

This service will display content in Firefox if you use the Tabulator extension.

If you have questions of comments about the service please join the Freebase developer mailing list.

So now there’s DBPedia and Freebase. More triples for the world, more data, more opportunity to move ahead. In chemistry, it’s sometimes so difficult to convince people of the value of open and linked data. This sort of stuff makes me feel that we are making progress. Slowly, but inexorably. And that is exciting.