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Open Knowledge Maps

Note: this post first appeared on ZBW Mediatalk and has been updated to reflect the latest update of Open Knowledge Maps.

Science and research are more productive than ever. Every year, around 2.5 million research articles are published, and counting. A lot of research information is openly available: thanks to the open access movement, we can now find more than 100 million scientific outputs on the web. We have made great strides with respect to accessibility; but what about discoverability? After all, this enormous amount of knowledge is only of use to us, if it reaches the people that need it, and if it is reused as a basis for further research or transferred to practice. Here we can see a big gap. Depending on the discipline 12% to 82% of all scientific publications are never cited. This means that these publications do not serve as a basis for further research. When talking about transfer to practice, the gap is even wider: even in application-oriented disciplines such as medicine, only a small percentage of research findings ever influence practice – and even if they do so, often with a considerable delay.

Mission

What prevents knowledge transfer to practice?

One reason for this situation is that the tools for exploration and discovery of scientific knowledge are seriously lacking. Most people use search engines for this task. Search engines work very well, when you know what you want. Then, they deliver the result you are looking for – often with high precision. However, if you want to get an overview of an unknown scientific field, the list-based representation with only 10 results per page is not sufficient. With search engines, it takes a long time, before you know the main areas in a field, the most important terms, authors and journals. It can take weeks if not months – indeed in many PhD programs, the whole first year is devoted to this process. Many people in research and especially practitioners do not have that much time. Think about science journalists or patients. To summarize: there are many people out there that could benefit from scientific knowledge, if there were better tools for discovering research results.

Knowledge maps instead of lists

At Open Knowledge Maps, we intend to close this gap, to provide the missing link between accessibility and discoverability. Instead of lists, we use knowledge maps for discovery. Knowledge Maps show the main areas of a field at a glance. Relevant publications are already attached to each area. This enables users to get a quick overview of a field.

overview_heart_diseases_rund-exampleThe sub-areas also make you aware of the terminology in a field. This information alone may take weeks to find out. How much time have you already lost to searching without knowing the best search terms? In addition, the knowledge map enables users to separate the wheat from the chaff with respect to their current information need. For an ambiguous search term for example, the different meanings are sorted into separate areas.

benefits-all

Open Knowledge Maps as an openly accessible service

At Open Knowledge Maps, we are offering an openly accessible service, which allows you to create a knowledge map for any search term. Users can choose between two databases: Bielefeld Academic Search Engine (BASE) with more than 110 million scientific documents from all disciplines, and PubMed, the large biomedical database with 26 million references. We use the 100 most relevant results for a search term as reported by the respective data base as a base for our knowledge maps. The ordination and the determination of the areas is based on textual similarity of the metadata of the results. This means: the more words two documents have in common in either title, abstract, authors or journal name, the closer they are positioned on the map and the more likely they are placed in the same area. For everyone who would like to dive deeper into the algorithms used to create the map, our article Open Knowledge Maps: Creating a Visual Interface to the World’s Scientific Knowledge Based on Natural Language Processing in the journal 027.7 is worth reading.

The knowledge map for research “sugar” can be seen below. As described above, the bubbles represent the different areas. If you click on one of the bubbles, you are presented with papers related to this area. Open access articles are clearly marked and can be read within the interface. The idea is that you do not need to leave the browser tab while searching for literature. Go to Open Knowledge Maps to check out the search service.

sugar

Open Knowledge Maps brings open science to life

The “Open” in Open Knowledge Maps does not only stand for open access articles – we want to go the whole open science way and create a public good. This means that all of our software is developed open source. You can also find our development roadmap on Github and leave comments by opening an issue. The knowledge maps themselves are licensed under a Creative Commons Attribution license and can be freely shared and modified. We will also openly share the underlying data, for example as Linked Open Data. This way, we want to contribute to the open science ecosystem that our partners, including rOpenSci, ContentMine, Open Knowledge, the Internet Archive Labs and Wikimedia are creating.

We see libraries as important collaboration partners. We cooperate with the libraries of the University of Bielefeld and the Austrian Academy of Sciences. ZBW is also using software from Open Knowledge Maps in a joint project with the Know-Center. This collaboration is a win for both sides: Open Knowledge Maps is a stable, user friendly system, which enables libraries to visualize their collections of documents and to improve their discoverability. On the other hand, improvements from these projects are fed back into the software of Open Knowledge Maps, improving the system for all users.

Vision: Collaborative literature search

In the future, we want to enable collaborative literature search in Open Knowledge Maps. At the moment, most people are tackling discovery on their own. But usually someone has already walked this way before you. Unfortunately, the knowledge gained during discovery remains in people’s heads. We want to further develop Open Knowledge Maps, so that maps can be modified, extended and shared again – so that we can build on top of each other’s’ knowledge. We have created a short video to illustrate this idea:

We see libraries and librarians as central to this vision. A collaborative system cannot work without experts on knowledge curation and structuring. Together with the other stakeholders from research and society, including researchers, students, journalists, citizen scientists and many more, we want to create a system that enables us to create pathways through science for each other. So that we can all benefit from this unique knowledge.

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Note: this post was written in collaboration with Katja Mayer and first appeared on the F1000 Blog.

vienna-principles-web

In June 2016, we published the Vienna Principles: A Vision for Scholarly Communication in the 21st Century. The set of twelve principles describes the visions and foundations of a scholarly communication system that is based on the notion of openness in science, including the social sciences and humanities.

Open science demands the highest possible transparency, shareability and collaboration in knowledge production, as well as in the evaluation of scientific knowledge and impact. The principles are designed to offer a coherent frame of reference to the often controversial debates on how to improve the current system of scholarly communication.

Mindful of the fact that systems of communication shape the very core of scientific knowledge production, we set out to envision guiding principles for scientific practice that we really want. In this post, we’d like to introduce the principles and provide context on how they came about. We’ll also share our ongoing work of turning the vision into practice.

“What science becomes in any historical era depends on what we make of it” — Sandra Harding, Whose Science? Whose Knowledge? (1991)

Focusing on the benefits of openness

Our work started in Vienna during the spring of 2015, when the Open Access Network Austria (OANA) commissioned the working group “Open Access and Scholarly Communication” to sketch a vision of how open science can change scholarly communication in the long run. Over the year, we had five further meetings, each of them in a different Viennese location, hence the name “Vienna Principles”.

The group consisted of a diverse set of people, including librarians, science administrators, students and researchers from a wide range of disciplines, including arts & humanities, engineering, natural sciences and social sciences in both basic and applied contexts.

Many working group members are involved in related initiatives, such as Citizen Science Austria, Open Knowledge, Creative Commons and OpenAIRE, to name just a few, and several have a relevant professional background, including publishing and software development. The core group consisted of nine participants, but the overall work involved contributions and feedback by more than 20 people and the audiences of the 15th Annual STS Conference, Graz and the 3rd Plenary of the Open Access Network Austria.

At the beginning, there were a number of observations that were based on our own involvement in open science, and by the experience of group members that had joined the movement only very recently. Our first observation was that open science is still a fuzzy concept for many. People are often either unclear about its benefits or are overwhelmed by the challenges that come with it. Therefore, they tend to have a reserved attitude towards openness.

Our second observation was that the debate within the open science community is not necessarily focused on the benefits of openness, but mostly on what constitutes openness, how to achieve openness, and what steps to take next.

The classic debate around the “green” and the “gold” route to open access is a good example for this. In these discussions, many of the arguments carry implicit assumptions about the structures of a future scholarly communication system, besides highly emotional debates about the commodification of scientific knowledge distribution.

What do we really want?

There are currently no commonly agreed set of principles that describes the system of open scholarly communication that we want to create. Such a collection of widely shared cornerstones of the scholarly communication system would help to better guide the debate around open science. At the same time, a vision is needed that better conveys the need for openness in scholarly communication to academia and society.

For the definition of the principles, we adopted a clean slate approach. This means that we set out to describe the world that we would like to live in, if we had the chance to design it from scratch, without considering the restrictions and path dependencies of the current system.

Our aim was to be clear, concise and as comprehensive as possible, without repeating ourselves. What followed was an intense phase, where we devised and revised, expanded and reduced, split and merged. We also addressed and incorporated the valuable feedback that we received by so many.

From this, we established a set of twelve principles of scholarly communication describing the cornerstones of open scholarly communication. This is just the beginning, with this being version 1.0 and we invite everyone to comment on this version.

What next?

Our paper has been positively received. Besides hundreds of tweets linking to the publication on Zenodo and newspapers and blogs have also reported about it. This includes articles that have been partially translated into Spanish, Japanese and German. The PDF on our website has been annotated 58 times alone. We are delighted that several researchers are now trying to adopt the principles in their research and collaboration projects.

The working group, consists of 16 new active members, of which some are consolidating the latest feedback received in recent months, and others who are devising recommendations on turning each principle into reality. This allows us to study and discuss the different attitudes towards the twelve principles in a range of disciplines, especially in those fields which seem most sceptical about the principles, such as historical and art-related subjects.

We will consider stakeholder’s viewpoints, clarify legal framework conditions, and discuss incentive and reward systems to identify how the principles can be best applied throughout the institutions. In doing so, we hope to be able to illustrate the best practises and identify any obstacles to open science in the scholarly communication system.

We plan to hold group discussions and workshops with stakeholders, publisher and funders to explain how the principles could support the services they offer and articulate the capability of these principles to different stakeholders’ needs.

Furthermore, we are coordinating our efforts with other groups, such as the Force11 working group on the Scholarly Commons and SPARC Europe. By 2018, we aim to have an updated version of the Vienna Principles and several recommendations to support the adoption of open science based on the feedback obtained from the workshops and discussion groups.

We are looking forward to shaping the scholarly communication system of the future together with all of you.

I have just applied for a Shuttleworth Fellowship.

The fellowships are issued by the Shuttleworth Foundation, which describes its vision as “We would like to live in an open knowledge society with limitless possibilities for all.” I very much share this vision – it is the main reason I founded Open Knowledge Maps. Our goal is to build a visual interface to the world’s scientific knowledge in order to dramatically increase the visibility of research findings for science and society alike.

We want to provide a solution to a challenge that’s almost paradoxical: on the one hand, more research is openly available than ever, and we see considerable interest in science and technology. On the other hand, we are faced with a serious crisis of trust in scientific research, with anti-vaccination movements and climate change deniers on the rise.

I believe that the root of this problem is that it is very hard to get an “in” on research. Access does not equal discoverability or even participation. People outside academia trying to understand a research field are therefore often lost. I want to empower these people by providing better gateways into scientific research. Think: policy makers attempting to optimize decision-making by using evidence from relevant research, educators striving to convey the state-of-the-art, fact checkers trying to verify statements, or patients who would like to learn about the newest findings on their illness.

To make this happen, I believe that we need to do two things: first, improving the discoverability of research findings. Second, turning discovery into a collaborative process – thus enabling participation, and allowing people to create pathways through science for each other. Take a rare disease as an example: wouldn’t it be great, if researchers, doctors and patients would collaboratively map the newest research on this disease – and then share the results of their efforts for the benefit of patients, who don’t have access to specialists?

Enter Open Knowledge Maps: we use knowledge maps, a powerful tool for exploration and discovery. Knowledge maps provide an instant overview of a field by showing the main areas of the field at a glance, and papers related to each area (see below). In addition, knowledge maps make it possible to easily identify useful, pertinent information by separating papers into meaningful clusters – and they are exposing important concepts in the field that you would often need weeks to find out.

Examplary knowledge map for research on heart diseases

During the fellowship year, I want to explore how we can create a space for participatory discovery around these maps. How can different communities interact on a level-playing field, so that they create pathways through science for each other?

A little backstory

If you are an avid reader of this blog, you may recall that I alreay applied for a Shuttleworth Fellowship a year ago. The fellowships first caught my eye, when I learned that amazing projects like ContentMine (Peter Murray-Rust), Hypothes.is (Dan Whaley), and Koruza (Luka Mustafa) had all been enabled by a Shuttleworth Fellowship.

Back in May 2016, Open Knowledge Maps was just starting out, with an enthusiastic group of volunteers, and a prototypical service that enabled users to create a knowledge map for a topic based on the PLOS library (160,000 articles).

Since then, a lot has happened in the project.

The team has grown: I am developing Open Knowledge Maps together with nine amazing volunteers. I have also found great advisors and strong partners from the open knowledge community. We put out two major updates of our search service – pushing our coverage to 100 million scientific articles from all disciplines thanks to BASE. We’ve considerably improved the user experience based on feedback from the community, and we’ve enabled features such as  collaborative annotation thanks to Hypothes.is. And we held numerous workshops and sessions at events such as OpenCon, MozFest and re:publica, with more than 300 people in attendance.

Knowledge map for digital education. Click on the map to get to the interactive version on Open Knowledge Maps.

I am very happy that our efforts resonated with the community. Open Knowledge Maps was featured on the frontpages of reddit and HackerNews. Our user base has quickly grown: in less than a year, we saw over 100,000 vists and more than 30,000 maps have been created to date. We’ve received hundreds of enthusiastic tweets, e-mails and blog posts, motivating us to proceed with our vision.

We’ve now reached the limits of what we can do as a pure volunteer project. In order to realize the full potential of the idea, we need support. This is why I decided it’s time to give it another go. I also believe that it is a critical time that we are creating this platform in. There are several closed solutions for providing visual overviews that are being developed right now. If we do not provide an open alternative in time, we risk being stuck with proprietary solutions and wasted public money for decades.

As usual, the proposal was developed in the open. Special thanks go to Maxi Schramm, Christopher Kittel, Florian Heigl, Rufus Pollock, Antica Culina and Daniel Mietchen for comments on the draft. But I’d like to thank the Open Knowledge Maps family – team, advisors, partners and users. I am very lucky to shape this vision together with you.

You can find the full proposal on Github.

baseintegration

We have now connected Open Knowledge Maps to one of the largest academic search engines in the world: BASE. This means, you are able to visualize a research topic from 100+ million documents. And for the first time, you can search within different types of resources, including datasets and software. I would like to thank our collaborators BASE and rOpenSci for their outstanding support in making this happen!

We have also spent a lot of time improving the naming of the sub-areas to make the concepts in a field more visible – which means that this update improves our existing PubMed integration too.

In addition, we have added much more information to the site about the project and our approach. Open Knowledge Maps follows the motto “open science, all the way”. From our roadmap to our source code and our data, we publish everything under an open license that is compatible to the Open Definition.

Try it out now and let me know of any feedback you may have!

Create a visualization based on 28 million articles

Today, I am very proud to announce a milestone for Open Knowledge Maps. Thanks to an outstanding team and continued support by our partners and advisors, we have added two major content sources: the Directory of Open Access Journals (DOAJ) with more than 2.3 million articles and PubMed with more than 26.5 million articles. Taking into account a certain overlap between the two sources, we can now credibly state that one can create maps based on 28 million papers. That’s a content pool that is 175 times larger than in the previous iteration using PLOS (about 160,000 articles).

We have also completely overhauled our design & overall presentation and improved the user experience considerably. In addition, we have included the open annotation software Hypothes.is in our PDF preview.

We believe that this is a major step towards revolutionizing the way we discover research. There are many new things to try out and explore – we are looking forward to your feedback and suggestions!

Try it out now!

okmaps_start

We officially announced the launch of Open Knowledge Maps, the visual interface to the world’s scientific knowledge, with a tweet and a message to our advisors late on May 11. We had soft-launched the site more than a week before that, and a bare-bones version of the PLOS visualization service had been online since Mozfest. The website was already getting some attention, and people were using the service on a daily basis. One of the highlights was a feature on Storybench in the very early days of the project. The idea behind the announcement was to get broader feedback on the search service and the overall idea behind Open Knowledge Maps. We had come a long way since the Mozfest days, and we thought that the website was ready for a wider audience.

What was to follow though went far beyond my highest expectations. Over the next 48 hours, we saw more than 350,000 hits on openknowledgemaps.org, generated by 12,000 visitors from all over the world.

What had happened? On the morning of the next day (May 12), I noticed that the tweet had gained a lot of traction, which had translated to acitivity on the site. Lots of people were using the search service, and a new map was created every few seconds. Much to our delight, the feedback was overwhelmingly positive. We started filing all the reactions as many of them contained useful pointers for future improvements. At this point, our server was still humming along fine. Granted, you had to wait a few extra seconds on the search here and there, but nothing out of the ordinary.

During the day, news about Open Knowledge Maps spread to other channels, and at some point around noon CEST, we hit the front page of Hacker News. I immediately noticed a spike in all our parameters. We went from a map every few seconds to multiple maps being created each second. Search time began to rise and we started receive complaints about failed or endless searches. Around 3:30 pm, our server finally gave in. Hundreds of searches were running at the same time, each of them taking minutes to be processed. It was time to take the search service offline and to post our version of the “Fail Whale”. You can still find a version of this screen here.

okmaps_fail

While we frantically rewrote the search service to handle a larger amount of requests (it was back a mere 60 minutes later), the stream of positive feedback continued to roll in. Up until today, Open Knowledge Maps was mentioned in over 100 tweets, with the announcement tweet creating more than 22,000 impressions alone. You can find a collection of my favourite tweets in this collection. But it was not just Twitter – the news was shared on Facebook, blogs, and in discussion forums.

At one point, we were called “the Wikipedia of scientific knowledge”. It is clear that we still have to go a long way to really deserve this tagline, but it is encouraging that people see the potential of the idea. Needless to say, the positive feedback also sparked the ambition of the Open Knowledge Maps team of volunteers. We are currently busy improving the site and the service; the first results will be available in just a few weeks.

It was a fascinating day in the eye of the storm. I’d like to thank my awesome team for their outstanding work and our great advisors for their help in shaping Open Knowledge Maps. And I’d like to thank all of you out there for the love that you have shown for this project. It means a lot to me – Open Knowledge Maps is a project that is very close to my heart. Please continue providing feedback via social media, e-mail, or on our Github repositories. You can also sign up to the newsletter to stay on top of everything #OKMaps.

It is time to change the way we discover research, and we are off to a good start!

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