Methods getting their chance to shine – Apollo wants your methods!

Supporting Open Research,

By Dr. Kim Clugston, Research Data Co-ordinator, Office of Scholarly Communication

Underlying all research data is always an effective and working method and this applies across all disciplines from STEMM to the Arts, Humanities and Social Sciences. Methods are a detailed description of the tools that are used in research and can come in many forms depending on the type of research. Methods are often overlooked rather than being seen as an integral research output in their own right. Traditionally, published journals include a materials and methods section, which is often a summary due to restrictions on word limits making it difficult for other researchers to reproduce the results or replicate the study. There can sometimes be an option to submit the method as “supplementary material”, but this is not always the case. There are specific journals that publish methods and may be peer-reviewed but not all are open access, rendering them hidden behind a paywall. The last decade has seen the creation of “protocol” repositories, some with the ability to comment, adapt and even insert videos. Researchers at the University of Cambridge, from all disciplines – arts, humanities, social sciences and STEMM fields – can now publish their method openly in Apollo, our institutional repository. In this blog, we discuss why it is important to publish methods openly and how the University’s researchers and students can do this in Apollo.

The protocol sharing repository, Protocols.io, was founded in 2012. Protocols can be uploaded to the platform or created within it; they can be shared privately with others or made public. The protocols can be dynamic and interactive (rather than a static document) and can be annotated, which is ideal for highlighting information that could be key to an experiment’s success. Collaboration, adaptation and reuse are possible by creating a fork (an editable clone of a version) that can be compared with any existing versions of the same protocol. Protocols.io currently hosts nearly 16,000 public protocols, showing that there is a support for this type of platform. In July this year it was announced that Protocols.io was acquired by Springer Nature. Their press statement aims to reassure that Protocols.io mission and vision will not change with the acquisition, despite Springer Nature already hosting the world’s largest collection of published protocols in the form of SpringerProtocols along with their own version of a free and open repository, Protocol Exchange. This begs the question of whether a major commercial publisher is monopolising the protocol space, and if they are, is this or will this be a problem? At the moment there do not appear to be any restrictions on exporting/transferring protocols from Protocols.io and hopefully this will continue. This is a problem often faced by researchers using proprietary Electronic Research Notebooks (ERNs), where it can be difficult to disengage from one platform and laborious to transfer notebooks to another, all while ensuring that data integrity is maintained. Because of this, researchers may feel locked into using a particular product. Time will tell how the partnership between Protocols.io and Springer Nature develops and whether the original mission and vision of Protocols.io will remain. Currently, their Open Research plan enables researchers to make an unlimited number of protocols public, with the number of private protocols limited to two (paid plans offer more options and features).

Bio-protocol exchange (under the umbrella of Bio-protocol Journal) is a platform for researchers to find, share and discuss life science protocols with protocol search and webinars. Protocols can be submitted either to Bio-protocol or as a preprint, researchers can ask authors questions, and fork to modify and share the protocol while crediting the original author. They also have an interesting ‘Request a Protocol’ (RaP) service that searches more than 6 million published research papers for protocols or allows you to request one if you are unable to find what you are looking for. A useful feature is that you can ask the community or the original authors of the protocol any question you may have about the protocol. Bio-protocol exchange published all protocols free of charge to their authors since their launch in 2011, with substantial financial backing of their founders. Unfortunately,  it was announced that protocol articles submitted to Bio-protocol after March 1 2023 will be charged an Article Processing Charge (APC) of $1200. Researchers who do not want to pay the APC can still post a protocol for free in the Bio-protocol Preprint Repository where they will receive a DOI but will not have gone through the journal’s peer review process.

As methods are integral to successful research, it is a positive move to see the creation and growth of platforms supporting protocol development and sharing. Currently, these tend to cater for research in the sciences, and serve the important role of supporting research reproducibility. Yet, methods exist across all disciplines – arts, humanities, social sciences as well as STEMM – and we see the term ‘method’ rather than ‘protocol’ as more inclusive of all areas of research.

Apollo (Cambridge University’s repository) has now joined the growing appreciation within the research community of recognising the importance of detailing and sharing methodologies. Researchers at the University can now use their Symplectic Elements account to deposit a method into Apollo. Not only does this value the method as an output in its own right, it provides the researcher with a DOI and a publication that can be automatically updated to their ORCID profile (if ORCID is linked to their Elements account). In May this year, Apollo was awarded CoreTrustSeal certification, reinforcing the University’s commitment to preserving research outputs in the long-term and should give researchers confidence that they are depositing their work in a trustworthy digital repository.

The first method to be deposited into Apollo in this way was authored by Professor John Suckling and colleagues. Professor Suckling is Director of Research in Psychiatric Neuroimaging in the Department of Psychiatry. His published method relates to an interesting project combining art and science to create artwork that aims to represent hallucinatory experiences in individuals with diagnosed psychotic or neurodegenerative disorders. He is no stranger to depositing in Apollo; in fact, he has one of the most downloaded datasets in Apollo after depositing the Mammographic Image Analysis Society database in Apollo in 2015. This record contains the images of 322 digital mammograms from a database complied in 1992. Professor Suckling is an advocate of open research and was a speaker at the Open Research at Cambridge conference in 2021.

An interesting and exciting new platform which aims to change research culture and the way researchers are recognised is Octopus. Founded by University of Cambridge researcher Dr Alexandra Freeman, Octopus is free to use for all and is funded by UKRI and developed by Jisc. Researchers can publish instantly all research outputs without word limit constraints, which can often stifle the details. Research outputs are not restricted to articles but also include, for example, code, methods, data, videos and even ideas or short pieces of work. This serves to incentivise the importance of all research outputs. Octopus aims to level up the current skew toward publishing more sensationalist work and encourages publishing all work, such as negative findings, which are often of equal value to science but often get shelved in what is termed the ‘file drawer’ problem. A collaborative research community is encouraged to work together on pieces of a puzzle, with credit given to individual researchers rather than a long list of authors. The platform supports reproducibility, transparency, accountability and aims to allow research the best chance to advance more quickly. Through Octopus, authors retain copyright and apply a Creative Commons licence to their work; the only requirement is that published work is open access and allows derivatives. It is a breath of fresh air in the current rigid publishing structure.

Clear and transparent methods underpin research and are fundamental to the reliability, integrity and advancement of research. Is the research landscape beginning to change to allow open methods, freely published, to take centre stage and for methods to be duly recognised and rewarded as a standalone research output? We certainly hope so. The University of Cambridge is committed to supporting open research, and past and present members who have conducted research at the University can share these outputs openly in Apollo. If you would like to publish a method in Apollo, please submit it here or if you have any queries email us at info@data.cam.ac.uk.

There will be an Octopus workshop at the Open Research for Inclusion: Spotlighting Different Voices in Open Research at Cambridge on Friday 17th November 2023 at Downing College.

Cambridge Open Research Conference 2023: The stage is set

Open Research at Cambridge Conference, Supporting Open Research

By Nicola Swann and Mandy Wigdorowitz, Office of Scholarly Communication, Cambridge University Libraries

The programme is ready, spaces are nearly full, and we are nearing Cambridge University Libraries’ annual conference on Open Research (OR), taking place at Downing College or online on Friday 17 November 2023. This year’s theme is Open Research for Inclusion: Spotlighting Different Voices in Open Research at Cambridge.

OR is designed to promote equity and inclusion by ensuring that research is accessible to all, regardless of research background, location, or affiliation. The conference will acknowledge that OR can look different in different areas, with the common goal of advancing knowledge and understanding. Giving a voice to OR from diverse perspectives can propel learning, collaboration, and allow us to learn from one another’s approaches to openness.

“The conference looks fantastic! It’s a really fabulous mix of papers and speakers, and really exciting in terms of moving Open Research conversations into different disciplinary practices. It is the first programme I’ve seen that truly integrates research and open into a joint conversation. It’s brilliant!”

Dr Jessica Gardner, University Librarian & Director of Library Services, Cambridge University Libraries

This blog post highlights the speakers who will be joining us on the day and the topics they will explore. We’re delighted to host OR experts who will show the value of open practices in typically under-represented disciplines and contexts. These include the Arts, Humanities, and Social Sciences, the GLAM sector (Galleries, Libraries, Archives, and Museums), and research from and about the Global South.

The day starts with a welcome address from Professor Anne Ferguson-Smith CBE FRS FMedSci, Pro-Vice-Chancellor for Research and International Partnerships and the Arthur Balfour Professor of Genetics, who is a key proponent of OR – see her views about OR on the Office of Scholarly Communication’s (OSC) website. Our Keynote speaker, Dr Siddharth Soni, Isaac Newton Trust Fellow at Cambridge Digital Humanities and affiliated lecturer at the Faculty of English, will then addresses us with a talk on Common Ground, Common Duty: Open Humanities and the Global South, providing an account of how to think against neoliberal conceptions of the ‘open’ and to reimagine what openness might look like if the Global South was viewed as a common ground space for building an open and international university culture.

Dr Stefania Merlo from the McDonald Institute for Archaeological Research and Dr Rebecca Roberts from the McDonald Institute for Archaeological Research and Fitzwilliam Museum will further explore the theme of the Global South in their practical perspective on how they managed the curation of digital archives for heritage management from their work on the projects: Mapping Africa’s Endangered Archaeological Sites and Monuments (MAEASaM) and Mapping Archaeological Heritage in South Asia (MAHSA).

We will then change pace with an OR panel session comprising panellists with diverse backgrounds and expertise who will address registrants’ pre-submitted questions. There will be engaging insights and debate amongst the panellists, led by Bertrand Russell Professor of Philosophy, Professor Alexander Bird. He will share the platform with Philosophy of Science Professor, Professor Anna Alexandrova, Psychiatry PhD student Luisa Fassi, Cambridge University Libraries (CUL) Interim Head of Open Research Services Dr Sacha Jones, Cambridge University Press & Assessment’s Research Data Manager Dr Kiera McNeice, and Cambridge’s Head of Research Culture Liz Simmonds.

The spotlight switches to the GLAM sector in the afternoon, with a second panel chaired by CUL’s Scholarly Communication Specialist Dr Samuel Moore. This panel brings together experts who will showcase their diverse work in the GLAM sector, from software development and museum practices to infrastructure and archiving support. The panel includes Dr Mary Chester-Kadwell, CUL’s Senior Software Developer and Lead Research Software Engineer at Cambridge Digital Humanities, Isaac Newton Trust Research Associate in Conservation Dr Ayesha Fuentes from the Museum of Archaeology and Anthropology, Dr Agustina Martinez-Garcia, CUL’s Head of OR Systems, and Dr Amelie Roper, CUL’s Head of Research. They will each expand on specialist areas, including OR code and data practices in digital humanities, collections research, teaching and learning collections care, and OR infrastructure. 

In a workshop session, Tim Fellows, Product Manager for Octopus, will outline how Octopus is an alternative publishing model that can foster OR. To round the day off, Professor Joanna Page, Director of CRASSH and Professor of Latin American Studies, will present on the considerations of OR and the coloniality of knowledge with a specific focus on the questions of possession and access.

In true Cambridge tradition, a drinks reception will bring the event to a close, allowing attendees a chance to mingle and continue the discussions.

Make sure to book your place so you don’t miss out. Take a look at the programme to register and join researchers, students, librarians, administrators, and publishers across the University of Cambridge at every career stage. Get in touch if you have any queries info@osc.cam.ac.uk.

The Data Picture

Library and training matters, Uncategorized

I was recently named one of “the next generation of [library] leaders” as part of the CILIP 125, having been recognised as an individual who contributes energy and knowledge to improving and impacting their organisation. My area of expertise, and thus recognition, lies with the use of data within libraries. As a data analyst for the Office of Scholarly Communications at Cambridge University Library, my role focuses on empowering decisions with data driven understanding – such as supporting the Springer Nature negotiations. To develop my understanding of data, and its role within a wider organisation, further, I engage with data beyond the library – such as the Big Data London conference and the Carruthers and Jackson Data Leaders’ Summer School. Reflecting on the use of data in the wider world, what can be expected of the library and data?

The summer school provided practical advice, proven methodologies, and guidance that could apply across a variety of businesses. The course is designed to provide insight on the workflow of data officers, and their role within an organisation – no matter its stage of data maturity and literacy. Over the course of the ten weeks, leading experts discussed the role of a chief data officer (CDO), both as a business development opportunity, and as a career path for individuals. It explored the risk and governance of data within an organisation, and the final weeks focused strongly on the role of people and teams associated with data.

Peter Jackson and Caroline Carruthers addressed the differing types of CDO and described a pendulum between ‘risk aversion’ and ‘value added’. Understanding the balance between secure and proper data governance (GDPR for example) and providing value through data (such as setting up automation). The pendulum of risk to reward is relevant to many roles, including those within the library. Understanding the need to divide time and energy between creating policies and getting decision making results, is just as relevant to my role as a chief data officer. In my role I have supported decision making staff through data production, but equally, to instil a culture of data, time and energy must be dedicated to risk aversion, through tasks of researching data management, preparing training sessions for data storage, and supporting staff in data preparation.

Another important concept introduced was the DIKW pyramid – Data, Information, Knowledge, Wisdom – for understanding the value created from data. The base of the pyramid is (raw) Data, which can be processed into (useful) Information. This Information is data with meaning and a purpose and can be organised into (insightful) knowledge. Knowledge combines experiences, values, insights, and contextual information, which can then transcend to (integral) Wisdom. Wisdom is considered a deeper understanding with ethical implications and the ability to define ‘why’. The DIKW pyramid provided a frame of thought for presenting and approaching future data projects. Understanding the requirement to provide, data, information or knowledge, to better support a decision-making team.

To develop communication skills, expert Scott Taylor, known as The Data Whisperer, spoke about the three V’s for data storytelling: Vocabulary, Voice and Vision. Combining an accessible vocabulary, with a common voice will illuminate the business vision, and why that is important. This overarching concept for an organisations data approach can be scaled down to support individual data workers, to provide value – which should either grow, improve or protect the business case. Understanding how to communicate the data is a key skill as “Hardware comes and goes, software comes and goes, but data remains”. And that data that remains should be used to either grow, improve or protect the business, such that data gathered should be usable data!

At Big Data London, the organisation Women in Data hosted conversations about nurturing a culture of learning within data teams. Pulling from their experiences from minority backgrounds, the speakers highlighted the power in upskilling, sharing skills across teams and being an advocate on oneself and skills. As for what to upskill, data literacy was a hot topic across the conference. Data literacy, also called data fluency and data confidence, is the combination of ability, skills and confidence surround data and its uses. Data literacy enables more efficient work, and begs the question, what is the base level of data literacy / confidence across the library? Librarians use data daily; checking in/out material, answering students’ queries, or tracking the use of space, but are all librarians confident to use that data? This is an area I hope to explore further at the CUL, to ensure staff can use the data they have to support decisions.

Engaging with the world of data provides a big picture of the possibilities within the library. Conversations of AI (Artificial Intelligence), data policies and maturity, and shiny-new databases, software, and services, demonstrate the growing adoption of data, and therefore, libraries should follow suit. Actively taking snippets of larger conversations, developing ideas within the library space, and exploring the possibilities with data will help libraries thrive in this world of technological growth.