Towards sustainable open access: A society publisher’s principles and pilots for transition – Legge – 2020 – Learned Publishing – Wiley Online Library

“Key points

 

New partnerships are needed to move away from paywalls and avoid article publishing charge?based publishing.
It remains difficult for small societies to negotiate with consortia, and partnerships with other societies may be a route forward.
Being open to different open access routes and using different pilots are key to learning which routes will be sustainable in the future.
While the starting position for most ‘read and publish’ offerings is based on historical spend, this will need to be re?evaluated in the longer term.
The lack of independent, universal reporting mechanisms and universally adopted persistent identifiers for institutions is a barrier to establishing agreements and one that needs a cost?effective solution….”

Towards sustainable open access: A society publisher’s principles and pilots for transition – Legge – 2020 – Learned Publishing – Wiley Online Library

“Key points

 

New partnerships are needed to move away from paywalls and avoid article publishing charge?based publishing.
It remains difficult for small societies to negotiate with consortia, and partnerships with other societies may be a route forward.
Being open to different open access routes and using different pilots are key to learning which routes will be sustainable in the future.
While the starting position for most ‘read and publish’ offerings is based on historical spend, this will need to be re?evaluated in the longer term.
The lack of independent, universal reporting mechanisms and universally adopted persistent identifiers for institutions is a barrier to establishing agreements and one that needs a cost?effective solution….”

Who Is Competing to Own Researcher Identity? – The Scholarly Kitchen

“To date, ResearchGate appears to be winning the battle to build a sector-wide identity instance for researchers, regardless of university or publisher, with Academia.edu as its primary competition. Though many have predicted the demise of these academic social networks, their continued growth cannot be dismissed. 

ResearchGate reports having 15 million members worldwide. Some portion of these “members” are presumably inactive, or active only in limited ways. Even so, there is reason to believe that ResearchGate represents a substantial share of the global scientific community. While it is difficult to know exactly what its members are doing on the platform — anything from reading articles to engaging with collaborators to searching for jobs — the amount of traffic they generate is enormous. According to data from SimilarWeb, in a recent three month period, ResearchGate’s traffic was nearly equal to that of ScienceDirect, SpringerLink, and Nature.com combined. Or, to provide another comparative, ResearchGate’s usage was almost equivalent to that of a basket of major Elsevier properties, including ScienceDirect and all its other major STM properties, including Mendeley, bepress, SSRN, and Pure. 

There is power to this scale. ResearchGate has been able to associate much of the scientific literature with its authors, enabling a variety of analytics that it is able to turn into services and in some cases to monetize. Even though ResearchGate is one of the largest sources of leakage and is therefore being sued by an array of the major publishing houses, the power of ResearchGate’s data has been sufficient to enable it to develop a partnership with  Springer Nature, at least on a pilot basis, in which Springer Nature content is freely distributed on ResearchGate. …”

Is overlay peer review the future of scholarly communications? – COAR

“You may have seen the paper published recently by COAR presenting a distributed framework for open publishing services called Pubfair (version 2, after community input), also available in Spanish.

Pubfair is a conceptual model for a modular, distributed open source publishing framework, which builds on the content contained in the network of repositories to enable the dissemination and quality-control of a range of research outputs including publications, data, and more. 

This idea is not new. It is based on the vision outlined in the COAR Next Generation Repositories report  and builds on earlier conceptual models developed by Paul Ginsparg, Herbert Van de Sompel and others. And there are already overlay journals on arXiv, such as Discrete Analysis and Advances in Combinatorics, and other platforms such as Episcience in France, that demonstrate that this can be done at a very high level of quality, for a low price.

We are proposing to expand on these initiatives by developing a highly distributed architecture for overlay services. With decentralization, comes tremendous power. It takes us beyond an environment with many silos, in which every organization maintains its own separate system; to a global, interoperable architecture for scholarly communication. This model can scale; respond to different needs and priorities related to language, region, and domain; and has the potential to set free scholarly communications….”

Knowledge Futures Group

“The Knowledge Futures Group is a non-profit technology organization where promising new projects nurtured at knowledge institutions get built to scale and compete with proprietary alternatives.

Founded at MIT, directed by educators, publishers, and technologists, and supported by a consortium of funders and partners, the KFG brings the intelligence and experience of knowledge institutions together with the product development speed and capacity of technology companies.

We build better futures….”

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery | ACS Central Science

Abstract:  Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24?594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery | ACS Central Science

Abstract:  Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24?594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

Are You Ready to ROR? An Inside Look at this New Organization Identifier Registry – The Scholarly Kitchen

“As a former full-time PID person (until recently I was ORCID’s Director of Communications), I am convinced of the important role that persistent identifiers (PIDs) play in supporting a robust, trusted, and open research information infrastructure. We already have open PIDs for research people (ORCID iDs) and research outputs (DOIs), but what about research organizations? While organization identifiers do already exist (Ringgold identifiers, for example, have been widely adopted; Digital Science’s GRID is still relatively new), until recently there has been no truly open equivalent. But that’s changing, as you will learn in this interview with the team behind the newly launched Research Organization Registry—ROR….”

 

Rescognito

“Our vision is an open environment where researchers and research professionals are recognized for a wide range of behaviors and contributions that benefit the Open Research ecosystem….

Our mission is to expand researcher recognition, to add transparency, increase effectiveness, and to improve research investment outcomes for individuals and institutions.

 

What we do: Rescognito provides a fair, open and granular platform for the recognition of a broad range research activity and good citizenship. Rescognito aims to allow researchers to openly acknowledge colleagues (and to be acknowledged by colleagues) for meaningful contributions to the research process….

The Rescognito Open Ledger draws on public information contained in researchers’ ORCID® records. ORCID iDs provide a definitive way to uniquely identify individual researchers. DOIs, grant IDs and other persistent identifiers (PIDs) are also used where available as links to appropriate contributions….”

Linked Research on the Decentralised Web

Abstract:  This thesis is about research communication in the context of the Web. I analyse literature which reveals how researchers are making use of Web technologies for knowledge dissemination, as well as how individuals are disempowered by the centralisation of certain systems, such as academic publishing platforms and social media. I share my findings on the feasibility of a decentralised and interoperable information space where researchers can control their identifiers whilst fulfilling the core functions of scientific communication: registration, awareness, certification, and archiving.

The contemporary research communication paradigm operates under a diverse set of sociotechnical constraints, which influence how units of research information and personal data are created and exchanged. Economic forces and non-interoperable system designs mean that researcher identifiers and research contributions are largely shaped and controlled by third-party entities; participation requires the use of proprietary systems.

From a technical standpoint, this thesis takes a deep look at semantic structure of research artifacts, and how they can be stored, linked and shared in a way that is controlled by individual researchers, or delegated to trusted parties. Further, I find that the ecosystem was lacking a technical Web standard able to fulfill the awareness function of research communication. Thus, I contribute a new communication protocol, Linked Data Notifications (published as a W3C Recommendation) which enables decentralised notifications on the Web, and provide implementations pertinent to the academic publishing use case. So far we have seen decentralised notifications applied in research dissemination or collaboration scenarios, as well as for archival activities and scientific experiments.

Another core contribution of this work is a Web standards-based implementation of a clientside tool, dokieli, for decentralised article publishing, annotations and social interactions. dokieli can be used to fulfill the scholarly functions of registration, awareness, certification, and archiving, all in a decentralised manner, returning control of research contributions and discourse to individual researchers.

The overarching conclusion of the thesis is that Web technologies can be used to create a fully functioning ecosystem for research communication. Using the framework of Web architecture, and loosely coupling the four functions, an accessible and inclusive ecosystem can be realised whereby users are able to use and switch between interoperable applications without interfering with existing data.

Technical solutions alone do not suffice of course, so this thesis also takes into account the need for a change in the traditional mode of thinking amongst scholars, and presents the Linked Research initiative as an ongoing effort toward researcher autonomy in a social system, and universal access to human- and machine-readable information?. Outcomes of this outreach work so far include an increase in the number of individuals self-hosting their research artifacts, workshops publishing accessible proceedings on the Web, in-the-wild experiments with open and public peer-review, and semantic graphs of contributions to conference proceedings and journals (the Linked Open Research Cloud).

Some of the future challenges include: addressing the social implications of decentralised Web publishing, as well as the design of ethically grounded interoperable mechanisms; cultivating privacy aware information spaces; personal or community-controlled on-demand archiving services; and further design of decentralised applications that are aware of the core functions of scientific communication.