Tag: open science

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One place for all scholarly literature: An Open Science Prize proposal

Openly accessible scholarly literature is referred to as “the fabric and the substance of Open Science” in the present small grant proposal, submitted to the Open Science Prize contest and published in the Research Ideas and Outcomes (RIO) open access journal. However, the scholarly literature is currently quite chaotically dispersed across thousands of different websites and disconnected from its context.

To tackle this issue, authors Marcin Wojnarski, Paperity, Poland, and Debra Hanken Kurtz, DuraSpace, USA, build on the existing prototype Paperity, the first open access aggregator of scholarly journals. Their suggestion is the first global universal catalog of open access scientific literature. It is to bring together all publications by automatically harvesting both “gold” and “green” ones.

Called Paperity Central, it is to also incorporate many helpful functionalities and features, such as a wiki-type one, meant to allow for registered users to manually improve, curate and extend the catalog in a collaborative, community-controlled way.

“Manual curation will be particularly important for “green” metadata, which frequently contain missing or incorrect information; and for cataloguing those publications that are inaccessible for automatic harvesting, like the articles posted on author homepages only,” further explain the authors.

To improve on its ancestor, the planned catalog is to seamlessly add “green” publications from across repositories to the already available articles indexed from gold and hybrid journals. Paperity Central is to derive its initial part of “green” content from DSpace, the most popular repository platform worldwide, developed and stewarded by DuraSpace, and powering over 1,500 academic repositories around the world.

All items available from Paperity Central are to be assigned with globally unique permanent identifiers, thus reconnecting them to their primary source of origin. Moreover, all different types of Open Science resources related to a publication, such as author profiles, institutions, funders, grants, datasets, protocols, reviews, cited/citing works, are to be semantically linked in order to assure none of them is disconnected from its context.

Furthermore, the catalog is to perform deduplication of each entry in the same systematic and consistent way. Then, these corrections and expansions are to be transferred back to the source repositories in a feedback loop via open application programming interfaces (APIs). However, being developed from a scratch, its code will possess many distinct features setting it apart from existing wiki-type platforms, such as Wikipedia, for example.

“Every entry will consist of structured data, unlike Wikipedia pages which are basically text documents,” explain the scientists. “The catalog itself will possess internal structure, with every item being assigned to higher-level objects: journals, repositories, collections – unlike Wikipedia, where the corpus is a flat list of articles.”

In order to guarantee the correctness of the catalog, Paperity Central is to be fully transparent, meaning the history of changes is to be made public. Meanwhile, edits are to be moderated by peers, preferably journal editors or institutional repository admins overlooking the items assigned to their collections.

In their proposal, the authors note that the present development plan is only the first phase of their project. They outline the areas where the catalog is planned to be further enhanced in future. Among others, these include involvement of more repositories and platforms, fully developed custom APIs and expansion on the scholarly output types to be included in the catalog.

“If we are serious about opening up the system of scientific research, we must plant it on the foundation of open literature and make sure that this literature is properly organized and maintained: accessible for all in one central location, easily discoverable, available within its full context, annotated and semantically linked with related objects,” explain the scientists.

“Assume we want to find all articles on Zika published in 2015,” they exemplify. “We can find some of them today using services like Google Scholar or PubMed Central, but how do we know that no other exist? Or that we have not missed any important piece of literature? With the existing tools, which have incomplete and undefined coverage, we do not know and will never know for sure.”

In the spirit of their principles of openness, the authors assure that once funded, Paperity Central will be releasing its code as open source under an open license.

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Original source:

Wojnarski M, Hanken Kurtz D (2016) Paperity Central: An Open Catalog of All Scholarly Literature. Research Ideas and Outcomes 2: e8462. doi: 10.3897/rio.2.e8462

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Openly published Open Science Prize Grant Proposal builds on ContentMine and Hypothes.is to bridge scientists and facts

Public health emergencies such as the currently spreading Zika disease might be successfully necessitating open access for the available biomedical researches and their underlying data, yet filtering the right information, so that it lands in the hands of the right people, is what holds up professionals to bring the adequate measures about.

Submitted to the Open Science Prize contest, the present grant proposal, prepared with the joint efforts of scientists affiliated with Hypothes.is, ContentMine, University of Cambridge, Cottage Labs LLP and Imperial College of London, suggests a new scholarly assistant system, called amanuens.is, based on the existing ContentMine and Hypothes.is prototypes. Its aim is to combine machines and humans, so that mining critically important facts and making them available to the world can be made not only significantly faster, but also less costly. Through their publication in the open access journal Research Ideas and Outcomes (RIO), the scientists, who are also well-known open access and open data proponents, are looking for further support, feedback and collaborations.

While Hypothes.is is a mixture of software and communities, which together annotate the available literature, ContentMine are building an open source pipeline to extract facts from scientific documents, thus making the literature review process cheaper, more rigorous, continuous and transparent. The role of amanuens.is is meant to bring these two systems together.

As a result, Hypothes.is is to display ContentMine facts as annotations on the online document, therefore increasing their visibility. In turn, the large Hypothes.is community, comprising users ranging from devoted and experienced Wikipedia editors to dedicated citizen scientists, would be able to provide manually their own annotations, which could be then fed back into the ContentMine facts store.

“Facts are important – but science is performed by people – so ContentMine are partnering with Hypothes.is to bring communities together around facts in the scholarly literature,” sums up Dr Peter Murray-Rust. “Through combining machines and humans in a tight, iterating, loop, amanuens.is will be able to mine critically important facts and make them available to the world.”

In their proposal, the authors give a hypothetical, yet foreseeable example with a Hypothes.is community, centered around research and discussions regarding a bacterium, already proven to restrain some mosquitoes from transmitting various viruses, and its potential use against Zika. There, amanuens.is downloads all open access papers on Zika from a multitude of sources within 3 minutes. In a matter of a couple of seconds a total of 123 files are downloaded. Then, amanuens.is delivers a data table of the extracted data, including species, human genes, DNA primers and top word frequencies.

Within the community and thanks to the literature, made available via ContentMine, the users would be able to collaborate and build on the existing research outcomes. As a result, it could take only fifteen minutes and a brief proposal to mobilise the related scholarly resources and test for Zika resistance in infected with the virus mosquitoes.

“Finding facts to finding people took 15 minutes and this is how modern collaborative science should work,” Prof Peter Murray-Rust says about the given example. “The people then create knowledge from the facts. The knowledge creates communities. The communities explore science- and people-based solutions.”

In conclusion, the proposal states that similarly to the content and software provided by ContentMine and Hypothes.is, the outputs produced by amanuens.is will also be openly available. All of its data and annotations are to be public domain under a CC0 waiver.

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Original source:

Martone M, Murray-Rust P, Molloy J, Arrow T, MacGillivray M, Kittel C, Kasberger S, Steel G, Oppenheim C, Ranganathan A, Tennant J, Udell J (2016) ContentMine/Hypothes.is Proposal.Research Ideas and Outcomes 2: e8424. doi: 10.3897/rio.2.e8424

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An Open Science plan: Wikidata for Research

Wikidata is to databases what Wikipedia is to encyclopedias – the free version that anyone can edit. Both aim to share “the sum of all human knowledge” across the world in a multitude of languages, and while Wikidata is younger and has a smaller community, it attracts the collaboration of more than 16,000 volunteer contributors globally each month (up from 14,000 a year ago).

Meanwhile, recent years have witnessed a constantly increasing demand and support for Open Access and Open Science across professional research communities and citizen scientists. Therefore, a Horizon 2020 project plan was put together by a team of six European partners led by the Museum für Naturkunde Berlin to integrate research workflows with Wikidata into a new virtual research environment (VRE) for Open Science, called Wiki4R. The plan combined approaches to make Wikidata useful for researchers both across disciplines and for several specific use cases, e.g. chemistry.

The cross-disciplinary aspects included standard ways for handling scholarly references in Wikidata and for asking questions of Wikidata, whereas the chemical part focused on how to describe Wikidata entries for chemical topics like molecules, solvents or reactions and pathways, how to link this information to scholarly databases and publications, and how to ask chemical questions of Wikidata. These technical parts of the proposal were complemented by parts on how to bring Wikidata together with citizen science projects, on what the value proposition of openness is for institutions, and on training activities.

The grant proposal was submitted in January and ultimately rejected, but its drafters believe it contains a range of ideas that may still be worth pursuing. In fact, efforts to handle scholarly references through Wikidata are ongoing, and Wikidata can now be queried for things like a list of countries ordered by the number of their cities with a female mayor.

“The idea of a closer integration between Wikidata and research workflows is not itself rejected, and we believe that it is useful for both the research and Wikimedia communities to continue to explore the opportunities here, to pilot them and to keep talking to funders and other stakeholders about the value that such infrastructure would provide to society, so they can consider making the necessary resources available,” comments Dr. Daniel Mietchen, who spearheaded the effort.

In order to stimulate such activities, the Wiki4R proposal is among the first ones published via the new open-access journal Research Ideas & Outcomes (RIO). The innovative platform accepts submissions of scholarly works from the entire research life-cycle, including research ideas and proposals that are deemed to be valuable to scholarly research and its future.

“Our proposal focuses on the needs of open science and empowering researchers to work together across disciplines in an open environment,” explains Dr. Daniel Mietchen. “The concept of open science is central to this proposal. Open science is highly inclusive, inviting collaboration from professional peers as well as other interested parties, including citizen scientists. It is also open with respect to the process, providing access to research as it unfolds, allowing anyone to engage with it right away.”

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Original source:

Mietchen D, Hagedorn G, Willighagen E, Rico M, Gómez-Pérez A, Aibar E, Rafes K, Germain C, Dunning A, Pintscher L, Kinzler D (2015) Enabling Open Science: Wikidata for Research (Wiki4R). Research Ideas and Outcomes 1: e7573. doi: 10.3897/rio.1.e7573

 

Additional Information:

The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.

The journal harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research outputs than those traditionally made public: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform offering one of the most transparent, open and public peer-review processes.