Category Archives: oa.metadata

Seven principles for scientific publishing – International Science Council

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“Principle I: Universal open access

The record of published science is a vital source of ideas, observations, evidence and data that provide fuel and inspiration for further enquiry, and is a profound part of the edifice of human knowledge.

That record, including the back catalogues of publishers, should be regarded as a global public good, openly and perennially free to read by citizens, researchers and all societal stakeholders….

Principle II: Open licensing

The progress of science depends on the ability to access and interrogate evidence and conclusions from past work. Open licences help to promote accountability and traceability, permit authors to continue to derive benefit from their work and maximize the extent to which the work can be built on by others. Yet when submitting to journals, authors may be required to transfer copyright to publishers.

As new technologies enhance the capacity to interrogate the whole record of science to discover new knowledge, pathways to access the resources that could facilitate such discovery should be open to all, unrestricted by licensing or ability to pay….”

Are we there yet?: Publishing meta(data) standards to help scholars get from point A to point B

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“Most are familiar with registering Digital Object Identifiers (DOIs), a type of Persistent Identifier (PID), to create lasting records for online research outputs. Registering DOIs for journal articles and other scholarly content and adding DOI links to references when possible is one of the best steps publishers can take to support research linking and discovery. But publishers shouldn’t stop at creating DOIs for articles. There are many other PIDs to consider adding to article-level metadata to support research discovery, assessment, and reuse. Additional PIDs can also expand the potential reach of content outputs when included in metadata registered with discovery services like Crossref.

During the NISO Plus session “Linked Data and the Future of Information Sharing,” Christian Herzog, CEO of Dimensions, and Shelley Stall, Senior Director of Data Leadership at the American Geophysical Union, spoke to emerging PIDs for linking research outputs by not only the content referenced in them but also the scholars, institutions, and funders associated with them. Among the PIDs they said all publishers should consider adding to their metadata are:

ORCID identifiers for authors and their history of research contributions
Institutional IDs such as those developed by GRID, which is the seed data set for the community-led ROR open research organization identifier registry
Grant IDs and funder IDs, such as those in The Open Funder Registry…”

Evolution of Standardization and Dissemination of Cryo-EM Structures and Data Jointly by the Community, PDB and EMDB – Journal of Biological Chemistry

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“Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.

 

FAIR and open multilingual clinical trials in Wikidata and Wikipedia

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Abstract:  This project seeks to conduct language translation on metadata labels for research publications, attribution data, and clinical trials information to make data about medical research queriable in underserved languages through Wikidata and the Linked Open Web. This project has the benefit of distributing content through Wikipedia and Wikidata, which already have an annual userbase of a billion users and which already have established actionable standards to practice diversity, inclusion, openness, FAIRness, and transparency about program development. The impact will be localized access to basic research information in various Global South languages to integrate with existing community efforts for establishing the same. Although Wikidata development in this direction seems inevitable, the cultural and social exchange required to establish global multilingual research partnerships could begin now with support rather than later as a second phase effort for including the developing world. Wikipedia and Wikidata are established forums with an existing active userbase for multilingual research collaboration, but the research practices there still are immature. By applying metadata expertise through this project, we will elevate the current amateur development with more stable Linked Open Data compatibility to English language databases. Using the wiki distribution and discussion platform to develop the global conversation about data sharing will set good precedents for the trend of global research collaboration.

 

Leveraging Open Science to Accelerate Research | NEJM

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The United States has mobilized the full force of its clinical research enterprise to address the Covid-19 pandemic, allocating billions of dollars to support timely research. As of January 2021, for example, the National Institutes of Health (NIH) had issued nearly a thousand awards cumulatively worth roughly $2 billion to support Covid-19 projects ranging from the development of medical products (including diagnostics and vaccines) to evaluations of population-specific risk factors and outcomes.1 Such initiatives, which have yielded new technologies and important evidence, illustrate the value of robust scientific infrastructure.

Feasibility study: Open Knowledge Base

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“However, the current landscape of research infrastructures presents two main issues. First, academic independence is threatened since overviews, evaluations and assessments of scholarship depend on citation databases governed by private enterprises. Second, where metadata on scholarly communications is available in public infrastructures, this metadata is fragmented and lacking in quality and/or coverage. As such, the core values of an open knowledge base (OKB) can be summarised as related to two concerns. First, to protect academic independence by opening up the metadata and metrics underlying assessments of scholarship and becoming less dependent on private enterprises for providing data and software. Second, to improve and enhance the quality and coverage of metadata available in the Dutch landscape of infrastructures on scholarly communications. By incorporating metadata on scholarly communications in an open infrastructure that not only digests but enriches and redistributes metadata, we posit that an OKB may establish a feedback loop, see figure above. Through such a feedback loop, metadata coverage and quality are improved in the OKB by integrating, harmonising and enriching metadata from multiple sources including participating CRISs, open infrastructures (e.g., CrossRef, Orcid, ROR) and research intelligence services. These improvements and enrichments are fed back into institutional CRISs to improve metadata and subsequently overviews and reports at the local institutional level. To this end, the OKB posits two proposals. First, a technological proposal of an open data layer that is interoperable and that prevents vertical integration by separating the data from the services. Second, a governance proposal to develop and maintain this technology and create buy-in from research institutes.”

Improving Domain Repository Connectivity: Establishing a Baseline — Metadata Game Changer

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“As I have been working with domain repositories to understand and describe their practices and apply for Core Trust Seal certification, I have been struck by the close, long-term relationships that these repositories form with their communities. In some cases, like UNAVCO, the repository is an integral part of an extensive community support system that extends from proposal planning and writing, through project initiation and implementation, data collection, management, and archive, to publication of results and access to data by other community members. Scientists, engineers, logistics specialists, data managers, software developers, and educators work together to create and extend our understanding of the shape of the earth and how it changes (the science of Geodesy). 

The UNAVCO Community described the responsibilities of players in open science communities during 2012 (https://doi.org/10.1029/2012EO260006) and developed an open data policy based on those responsibilities. These responsibilities included identifying datasets with PIDs and connecting data to papers with citations, that is, establishing an important element of the PID Graph: connections between papers and data.

I introduced the concept of Connectivity last month and have been thinking about it ever since. Connectivity measures how well research objects or collections of research objects are connected to the global research web, represented by the PID Graph. These connections depend on identifiers for all kinds of research objects. I am initially focusing on people, identified by ORCIDs, and organizations, identified by RORs.

As the breadth of identifiers and connections continues to expand, I made the leap from the strong connections between real people and organizations in the UNAVCO Community and connections between these entities in the PID Graph. Specifically, I wondered if the multitudinous real-world connections could help populate identifiers in the metadata and related connections in the PID Graph. I begin the exploration of this question here with UNAVCO datasets described in DataCite….”

HighWire at 25: Anurag Acharya (Google Scholar) looks back – Highwire Press

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“In the early 2000s, my role at Google was running web indexing: the system that crawls the web, making pages and content discoverable and accessible through search. Nowadays, there’s an assumption that looking for something via Google searches everything, but that wasn’t the case in the early days. Part of my role was to expand the index by reaching out to many different types of organizations – government, business, publishers – to make sure their web sites were included in the index.

A key group among these was scholarly publishers hosting journals and conferences. Having grown up on a university campus, scholarly articles had been all around and I wanted to make sure that they were as easy to find as everything else.

As a part of this, I reached out to HighWire to explore the possibility of indexing the hosted journals. I remember our first call in the Fall of 2002 with John Sack, Todd McGee and several others. A few quick calls, a couple of meetings in person and we were off….”

Search Scholarly Materials Preserved in the Internet Archive – Internet Archive Blogs

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“IA Scholar is a simple, access-oriented interface to content identified across several Internet Archive collections, including web archives, archive.org files, and digitized print materials. The full text of articles is searchable for users that are hunting for particular phrases or keywords. This complements our existing full-text search index of millions of digitized books and other documents on archive.org.

The service builds on Fatcat, an open catalog we have developed to identify at-risk and web-published open scholarly outputs that can benefit from long-term preservation, additional metadata, and perpetual access. Fatcat includes resources that may be useful to librarians and archivists, such as bulk metadata dumps, a read/write API, command-line tool, and file-level archival metadata. If you are interested in collaborating with us, or are a researcher interested in text analysis applications, we have a public chat channel or can be contacted by email at info@archive.org.

IA Scholar marks a milestone in our work initiated in 2018 to leverage the automation and scale of web and API harvesting in providing open infrastructure for the preservation of and perpetual access to scholarly materials from the public web. We particularly want to thank the Mellon Foundation for their original and ongoing support of this work, our many current partners, and the other collaborators, contributors, and volunteers.

All of this is possible because of the incredible open research ecosystem built and collectively maintained by Open Access advocates. Thank you to the DOAJ and other groups for helping catalog open access journals which has aided preservation. Thank you to the Biodiversity Heritage Library and its supporters for digitizing print journal literature. And thank you to the many other organizations we have worked with, integrated, or whose services we have utilized, including open web indices (Unpaywall, CORE, CiteseerX, Microsoft Academic, Semantic Scholar), directories of open journals (DOAJ, ROAD SHERPA/ROMEO, JURN, Wikidata), and open bibliographic catalogs (Crossref, Datacite, J-STAGE, Pubmed, dblp). 

IA Scholar is built from open source software components, and is itself released as Free Software. The website has been translated into eight languages (so far!) by generous volunteers….”

CHORUS Forum: Making the Future of Open Research Work – CHORUS

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“There are many ways that infrastructure players (like CHORUS) can support the scholarly communications community as stakeholders work together to advance innovation in open science. Publishers are introducing new models to make more content open access. How do they connect metadata about their customers, researchers, and articles to make these models work? What infrastructure is needed to make new models for open access a success for librarians as well as for publishers? What elements do funders, researchers, and institutions need to make the future of open research work?

This CHORUS Forum event will look at the complexities and commonalities of several new models for open research, and discuss how can we as a community build on the progress made so far in an interoperable and open ecosystem.

Our speakers and panelists are a diverse group of funders, institutions, researchers, and publishers, who will share their case studies and participate in panel discussions. There will be time for Q&A, so bring your questions and your ideas for collaboration as we address “Making the Future of Open Research Work”….”