Open Practices and Resources for Collaborative Digital Pathology

Abstract:  In this paper, we describe open practices and open resources in the field of digital pathology with a specific focus on approaches that ease collaboration in research and education settings. Our review includes open access journals and open peer review, open-source software (libraries, desktop tools, and web applications), and open access collections. We illustrate applications and discuss current limitations and perspectives.

Strategic collaboration agreement signed between ScienceOpen and Pensoft | STM Publishing News

“The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination. The new cooperation will focus on the unified indexation, the integration of Pensoft’s ARPHA Platform content into ScienceOpen and the utilization of novel streams of scientific communication for the published materials. 

Pensoft is an independent academic publishing company, well known worldwide for bringing novelty, its cutting-edge publishing tools and commitment to open access practices. In 2013, Pensoft launched the first ever, end-to-end, XML-based, authoring, reviewing and publishing workflow, as demonstrated by the Biodiversity Data Journal (BDJ) now upgraded to the ARPHA Publishing Platform. As of today, ARPHA hosts over 50 open-access, peer-reviewed scholarly journals: the whole Pensoft portfolio in addition to titles owned by learned societies, university presses and research institutions.

As part of the strategic collaboration, all Pensoft content and journals hosted on ARPHA are indexed in the ScienceOpen’s research discovery environment, which puts it into thematic context of over 60 million articles and books. In addition, thousands of articles across more than 20 journals were integrated into a “Pensoft Biodiversity” Collection. Combined this way, the content benefits from the special infrastructure of ScienceOpen Collections, which supports thematic groups of articles and books equipped with a unique landing page, a built-in search engine and an overview of the featured content. The Collections can be reviewed, recommended and shared by users, which facilitates academic debate and increases the discoverability of the research. …”

Uses and Reuses of Scientific Data: The Data Creators’ Advantage · Harvard Data Science Review

Abstract:  Open access to data, as a core principle of open science, is predicated on assumptions that scientific data can be reused by other researchers. We test those assumptions by asking where scientists find reusable data, how they reuse those data, and how they interpret data they did not collect themselves. By conducting a qualitative meta-analysis of evidence on two long-term, distributed, interdisciplinary consortia, we found that scientists frequently sought data from public collections and from other researchers for comparative purposes such as “ground-truthing” and calibration. When they sought others’ data for reanalysis or for combining with their own data, which was relatively rare, most preferred to collaborate with the data creators. We propose a typology of data reuses ranging from comparative to integrative. Comparative data reuse requires interactional expertise, which involves knowing enough about the data to assess their quality and value for a specific comparison such as calibrating an instrument in a lab experiment. Integrative reuse requires contributory expertise, which involves the ability to perform the action, such as reusing data in a new experiment. Data integration requires more specialized scientific knowledge and deeper levels of epistemic trust in the knowledge products. Metadata, ontologies, and other forms of curation benefit interpretation for any kind of data reuse. Based on these findings, we theorize the data creators’ advantage, that those who create data have intimate and tacit knowledge that can be used as barter to form collaborations for mutual advantage. Data reuse is a process that occurs within knowledge infrastructures that evolve over time, encompassing expertise, trust, communities, technologies, policies, resources, and institutions.

Guest Post: Open Access Is a Feminist Issue – Hook & Eye

“Accountable feminist research, research that centres responsibility to the communities our research engages with or speaks to, is attentive to how its tools and methods open out or close down the possibilities for collaboration beyond the university. As a feminist scholar, I have become increasingly convinced that one of the most accountable things we can do in our work is prioritize open access….

it was a genuine shock to me when, in Spring 2019, I attended multiple conferences where colleagues in Humanities disciplines spoke of open access as neoliberalism, the scientization of research, and a devaluation of our intellectual labour. As one friend texted me in the midst of one such conferences: since when is open access neoliberal but paywalling research so that people have to pay for it isn’t? …

It is also true that many of the barriers to embracing open access are also feminist issues. The scholarly publishing world is dominated by women (as is the trade publishing world); journal editing tends to be undervalued and high labour work that is at once vital to academia and also, like most forms of service, barely counted in tenure and promotion processes….

But if we could collectively agree to the fundamental premise that open access is a feminist issue, then our conversations about labour and value and prestige would, by necessity, shift. As Kathleen Fizpatrick so succinctly puts it in Generous Thinking: A Radical Approach to Saving the University, embracing open access as a values-based approach to scholarly communication “does not just serve the goal of undoing [scholarship’s] commercialization or removing it from a market-driven, competition-based economy, but rather is a first step in facilitating public engagement with the knowledge that universities produce” (148). Can feminist scholars agree that part of the mission of publicly-funded universities should be facilitating public engagement with our work? Can we agree that pay-walling and institutionalizing research created on stolen Indigenous land perpetuates settler-colonial understandings of knowledge-as-commodity? Can we agree that the scarcity-driven models of publishing in the most “elite” and “competitive” journals or of valuing the monograph over journal articles (or journal articles over podcast episodes!) is based in a fundamentally patriarchal hierarchy of what knowledge “counts”? …”

Reflections on Global Community Biology of the Future: It is Open, Diverse, and Thriving | PLOS Synthetic Biology Community

“Community biology—a  movement that seems to democratize life sciences through access and diversity—has grown over the last decades.  This is reflected in a thriving population of community labs, like Genspace and BioCurious in the US, and Freak Lab in Thailand and Kumasi Hive in Ghana, and Co-Lab in Denmark—to name a few—that are popping up across the world. I’m reminded that community labs may be to 2019  what computer clubhouses were to the 1980s, when computers were becoming accessible to private citizens and shifting the way we interacted and communicated with technology. Community labs, too, provide an entry point for everyday people—the community—to access, tinker, and play with biology!

 

Recognizing the potential of community labs to democratize scientific knowledge on a global scale—from what I’ve heard—folks like David Kong, Maria Chavez, JJ Hastings, Scott Pownall, and other global leaders in the field, sought in different ways to convene the community as a way to network, share, and connect.  This may have sparked the first Global Community Bio Summit in 2017 and that brought together hundreds (me included) of biology enthusiasts, educators, and researchers from a number of countries collectively striving to share in the responsibility of building an open and diverse movement for community science. I attended again a few weeks ago as the Bio Summit convened for the third time and, from my experience, the event continues to grow as it draws hundreds of participants across the globe and from every continent….”

Reaping the benefits of Open Data in public health

Abstract:  Open Data is part of a broad global movement that is not only advancing science and scientific communication but also transforming modern society and how decisions are made. What began with a call for Open Science and the rise of online journals has extended to Open Data, based on the premise that if reports on data are open, then the generated or supporting data should be open as well. There have been a number of advances in Open Data over the last decade, spearheaded largely by governments. A real benefit of Open Data is not simply that single databases can be used more widely; it is that these data can also be leveraged, shared and combined with other data. Open Data facilitates scientific collaboration, enriches research and advances analytical capacity to inform decisions. In the human and environmental health realms, for example, the ability to access and combine diverse data can advance early signal detection, improve analysis and evaluation, inform program and policy development, increase capacity for public participation, enable transparency and improve accountability. However, challenges remain. Enormous resources are needed to make the technological shift to open and interoperable databases accessible with common protocols and terminology. Amongst data generators and users, this shift also involves a cultural change: from regarding databases as restricted intellectual property, to considering data as a common good. There is a need to address legal and ethical considerations in making this shift. Finally, along with efforts to modify infrastructure and address the cultural, legal and ethical issues, it is important to share the information equitably and effectively. While there is great potential of the open, timely, equitable and straightforward sharing of data, fully realizing the myriad of benefits of Open Data will depend on how effectively these challenges are addressed.

Kindness, Culture, and Caring: The Open Science Way | HASTAC

“There are lots of ways that the rational, logical, hyper-competitive, winner-take-all, zero-sum, prisoner’s dilemma, nice-guys-finish-last, single-bottom-line, annual-productivity ratchet?—?or add your adjective here?—?mindset is just wrong for sustaining the academy and bad for science. For decades now, the same neo-liberal economic schemes that have been used to reshape how governments budget their funds have also made dramatic and disturbing inroads into university budgets and governance. Open science can show how that trend is a race to the bottom for universities. What do you say, we turn around and go another way?…”

OA price and service transparency Survey

“The views of researchers, librarians, publishers, and funders about ways to increase the transparency of communications about the price of Open Access publishing services are sought in a new industry survey. The results of this survey will help to inform a collaborative project with publishers, funders, and universities to develop a framework for communications. The project is sponsored by the Wellcome Trust in partnership with UKRI on behalf of cOAlition S. You can visit the survey here ….”

The meaning of open | Research Information

“So what is open research today, and what are the near horizons of tomorrow? For Baynes the three key developments in recent years have been the growth in open access publications in journals, research data and open data, and a proliferation of tools, both from start-ups and from funders.  These are only the first steps, however, in an increasingly complex open information landscape which poses challenges to everyone working in the scholarly research lifecycle: funders must encourage open research without dictating researchers’ research practice; researchers must balance personal interest and public good with an increasingly wide range of publishing choices and funder requirements; publishers must provide both innovative services that meet researcher and funder needs without risking the value of the current system; and libraries must both help researchers navigate the complex information ecosystem and increasingly help them measure and demonstrate researchers’ contributions to it. In this rapidly changing environment it is important for organisations to be agile. This, according to Baynes, is what Springer Nature is doing, developing sustainable and agile approaches that encourage open research: ‘We are one of the largest open access publishers, but also one of the most agile. It’s not the set business model, one-size-fits-all approach, it’s very much adapting and understanding what stakeholders want. For example, understanding the barriers, challenges and motivators for researchers to make data more openly available, well described, and fair.’ …”