ASAP awards – Interview with Mark Costello

ASAP Finalist Announcement 600x600Mark Costello, a researcher at the Institute of Marine Science and Leigh Marine Laboratory (University of Auckland in New Zealand) was nominated for his work with WoRMS of which he was founding chair. The site provides a database of scientific names for all marine species. Species are sometimes described with different scientific names, and the site helps disambiguate these names and also provides or links to information about each species.

Q: How did the project come about

M.Costello
Courtesy of ASAP awards

MC: When I was in Ireland 1990’s I was involved in workshops developing policies for biodiversity – the main barrier was lack of coordination of species names. This meant we couldn’t merge datasets easily enough. In 1996 I put in a proposal to create an inventory of science species names which was funded by the European Commission. Since 2004, the Flemish Government has funded the hosting of the database. Once the infrastructure was secure and professionally managed, then getting the info into it became possible. People were motivated because this was a permanent website with permanent support from the Flanders Marine Institute (VLIZ). It started as a clean-up exercise.

Q: What is special about the site?

MC: By providing naming information about species, it helps people navigate the scientific literature where alternative names may be used, but it also links to information about the species.

Q: What did you learn from working on WoRMS?

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Courtesy of Mark Costello

MC: There were unexpected patterns that were discovered from the data. We discovered that the number of species being described over time has been increasing at a linear rate. When you look at the authors there are now about 3-5 times more people discovering species than ever before – so taxonomists are not really disappearing as many people have said. The number of species discovered per author is, however, declining. That it is taking more people to discover species than it did before suggests that we have discovered most species on Earth (at least half, perhaps 2/3), not only a small fraction as some have speculated. We found also that science is doing better, conservation is working.

Q: What was people’s response?

MC: Word of mouth helped – there was an element of trust. We only know the people we know – but when you look globally you start to get a different picture than when you look at your own community. The taxonomy is curated by specialists, and people are now more trusting about online collaboration than when we started. But it was important to have a long – term commitment to supporting these databases to make the system sustainable so that the databases are shareable.

According to their stats page, In 2007 the site had received 37,221 unique visitors and by 2012 this number had risen to 817,335 unique visitors and 30,423,583 page views. The material is provided under a CC-BY, although permission needs to be sought for the re-distribution of the entire database, and it seems too to download the entire database too. I asked Mark about that.

MC: I don’t think that the CC-BY is a hindrance for sharing the data or reusing. We provide a clear citation for the data. We want the source to be cited because we consider it a scholarly publication. And users concerned about quality assurance of their sources can then cite it as an ‘authoritative’ rather than anonymous resource. When you combine the data into a new set, people that want to use this new group or want to replicate need to know where the original data came from. Otherwise they would be having to start from scratch. The citation solves this problem.

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Courtesy of Mark Costello

MC: The request was put there originally because databases change over time and we were worried that there would be multiple copies which could create confusion as to what is the best source. It also was a way of not having to deal with data flow issues if too many people were downloading the entire database at the same time. We also needed safeguarding from attacks of sending constant queries to the database. But it is also a good way of knowing and tracking who your users are, so we can provide the list of organisations that use the database when we are out looking for funding and support.

Q: What would you like to see next?

MC: I would love to have all species on Earth in a quality approved database and see what we could then discover about the species. We learned a lot from querying this database, and we could learn a lot more if we had all species in there.

Even if you are not interested in digging into the data, the site is a great place to get to know our underwater neighbours. I encourage you to visit the site.

ASAP Awards Finalists announced

Earlier this year, nominations opened for the Accelerating Science Awards Program (ASAP). Backed by major sponsors like Google, PLOS and the Wellcome Trust, and a number of other organisations, this award seeks to “build awareness and encourage the use of scientific research — published through Open Access — in transformative ways.” From their website:ASAP Finalist Announcement 300x250

The Accelerating Science Award Program (ASAP) recognizes individuals who have applied scientific research – published through Open Access – to innovate in any field and benefit society.

The list of finalists is impressive, as is the work they have been doing taking advantage of Open Access research results. I am sure the judges did not have an easy job. How does one choose the winners?

In the end, this has been the promise of Open Access: that once the information is put out there it will be used beyond its original purpose, in innovative ways. From the use of cell phone apps to help diagnose HIV in low income communities, to using mobile phones as microscopes in education, to helping cure malaria, the finalists are a group of people that the Open Access movement should feel proud of. They represent everything we believed that could be achieved when the barriers to access to scientific information were lowered to just access to the internet.

The finalists have exploited Open Access in a variety of ways, and I was pleased to see a few familiar names in the finalists list. I spoke to three of the finalists, and you can read what Mat Todd, Daniel Mietchen and Mark Costello had to say elsewhere.

One of the finalist is Mat Todd from University of Sydney, whose work I have stalked for a while now. Mat has been working on an open source approach to drug discovery for malaria. His approach goes against everything we are always told: that unless one patents one’s discovery there are no chances that the findings will be commercialised to market a pharmaceutical product. For those naysayers out there, take a second look here.

 

A different approach to fighting disease was led by Nikita Pant Pai, Caroline Vadnais, Roni Deli-Houssein and Sushmita Shivkumar tackling HIV. They developed a smartphone app to help circumvent the need to go to a clinic to get an HIV test avoiding the possible discrimination that may come with it. But with the ability to test for HIV with home testing, then what was needed was a way to provide people with the information and support that would normally be provided face to face. Smartphones are increasingly becoming a tool that healthcare is exploring and exploiting. The hope is that HIV infection rates could be reduced by diminishing the number of infected people that are unaware of their condition.

 

What happens when different researchers from different parts of the world use different names for the same species? This is an issue that Mark Costello came across – and decided to do something about it. What he did was become part of the WoRMS project – a database that collects the knowledge of individual species. The site receives about 90,000 visitors per month. The data in the WoRMS database is curated and available under CC-BY. You can read more about Mark Costello here.

 

We’ve all heard about ecotourism. For it to work, it needs to go hand in hand with conservation. But how do you calculate the value (in terms of revenue) that you can put on a species based on ecotourism? This is what Ralf Buckley, Guy Castley, Clare Morrison, Alexa Mossaz, Fernanda de Vasconcellos Pegas, Clay Alan Simpkins and Rochelle Steven decided to calculate. Using data that was freely available they were able to calculate to what extent the populations of threatened species were dependent on money that came from ecotourism. This provides local organisations the information they need to meet their conservation targets within a viable revenue model.

 

Many research papers are rich in multimedia – but many times these multimedia files are published in the “supplementary” section of the article (yes – that part that we don’t tend to pay much attention to!). These multimedia files, when published under open access, offer the opportunity to exploit them in broader contexts, such as to illustrate Wikipedia pages. That is what Daniel Mietchen, Raphael Wimmer and Nils Dagsson Moskopp set out to do. They created a bot called Open Access Media Importer (OAMI) that harvests the multimedia files from articles in PubMed Central. The bot also uploaded these files to Wikimedia Commons, where they now illustrate more than 135 Wikipedia pages. You can read more about it here.

 

Saber Iftekhar Khan, Eva Schmid and Oliver Hoeller were nominated for developing a low weight microscope that uses the camera of a smartphone. The microscope is relatively small, and many of its parts are printed on a 3D printer. For teaching purposes it has two advantages. Firstly, it is mobile, which means that you can go hiking with your class and discover the world that lives beyond your eyesight. Secondly, because the image of the specimen is seen through the camera function on your phone or ipod, several students can look at an image at the same time, which, as anyone who teaches knows, is a major plus. To do this with standard microscopes would cost a lot of money in specialised cameras and monitors. Being able to do this at a relative low cost can provide students with a way of engaging with science that may be completely different from what they were offered before.

Three top awards will be announced at the beginning of Open Access Week on October 21st. Good luck to all!