The Case for an Institutionally Owned Knowledge Infrastructure

“Academic journals, the dominant dissemination platforms of scientific knowledge, have not been able to take advantage of the linking, transparency, dynamic communication and decentralized authority and review that the internet enables. Many other knowledge-driven sectors, from journalism to law, suffer from a similar bottleneck — caused not by a lack of technological capacity, but rather by an inability to design and implement efficient, open and trustworthy mechanisms of information dissemination.

Fortunately, growing dissatisfaction with current knowledge-sharing infrastructures has led to a more nuanced understanding of the requisite features that such platforms must provide. With such an understanding, higher education institutions around the world can begin to recapture the control and increase the utility of the knowledge they produce….

But signs suggest that the bright future envisioned in the early days of the internet is still within reach. Increasing awareness of, and dissatisfaction with, the many bottlenecks that the commercial monopoly on research information has imposed are stimulating new strategies for developing the future’s knowledge infrastructures. One of the most promising is the shift toward infrastructures created and supported by academic institutions, the original creators of the information being shared, and nonprofit consortia like the Collaborative Knowledge Foundation and the Center for Open Science….

The Case for an Institutionally Owned Knowledge Infrastructure

“Academic journals, the dominant dissemination platforms of scientific knowledge, have not been able to take advantage of the linking, transparency, dynamic communication and decentralized authority and review that the internet enables. Many other knowledge-driven sectors, from journalism to law, suffer from a similar bottleneck — caused not by a lack of technological capacity, but rather by an inability to design and implement efficient, open and trustworthy mechanisms of information dissemination.

Fortunately, growing dissatisfaction with current knowledge-sharing infrastructures has led to a more nuanced understanding of the requisite features that such platforms must provide. With such an understanding, higher education institutions around the world can begin to recapture the control and increase the utility of the knowledge they produce….

But signs suggest that the bright future envisioned in the early days of the internet is still within reach. Increasing awareness of, and dissatisfaction with, the many bottlenecks that the commercial monopoly on research information has imposed are stimulating new strategies for developing the future’s knowledge infrastructures. One of the most promising is the shift toward infrastructures created and supported by academic institutions, the original creators of the information being shared, and nonprofit consortia like the Collaborative Knowledge Foundation and the Center for Open Science….

Here’s What You Can Do with Your Overhead · punctum books

“As punctum books over the last few years has tried to develop a sustainable model of scholar-led open-access publishing, and has devoted a considerable amount of resources to advocating for the common goods of public scholarship and knowledge, we have increasingly encountered arguments, both open and veiled, that somehow our practice would not be “replicable,” “scalable,” or, indeed, “sustainable.” These arguments often depart from the assumption that we—in one way or the other—are not playing by the rules of the academic publishing game. And because we would be rigging the game, our publishing model could reasonably never gain any traction, let alone serve as a model for others.

Some of these arguments suggest that we have poured our own supposed personal (or family) resources into punctum, and that this would give us an unfair advantage over traditional legacy publishers. If we choose to disregard the reality of the sizable endowments for certain university presses and the obscene profit margins of commercial players, it is indeed the case that for many years we have worked for salaries below the industry standard. However, we never made the claim that the scholar-led open-access model that punctum advocates necessitates such below-market remuneration levels; on the contrary, we believe that with the current money that is already in the system, all scholarly publishers, editors, and authors can be paid a reasonable living wage. We don’t assume that any open-access scholar-led publishing house that were to follow the model we are developing would have to make the same financial sacrifices we did in our early years—that, indeed, would be unsustainable and unreplicable….”

Here’s What You Can Do with Your Overhead · punctum books

“As punctum books over the last few years has tried to develop a sustainable model of scholar-led open-access publishing, and has devoted a considerable amount of resources to advocating for the common goods of public scholarship and knowledge, we have increasingly encountered arguments, both open and veiled, that somehow our practice would not be “replicable,” “scalable,” or, indeed, “sustainable.” These arguments often depart from the assumption that we—in one way or the other—are not playing by the rules of the academic publishing game. And because we would be rigging the game, our publishing model could reasonably never gain any traction, let alone serve as a model for others.

Some of these arguments suggest that we have poured our own supposed personal (or family) resources into punctum, and that this would give us an unfair advantage over traditional legacy publishers. If we choose to disregard the reality of the sizable endowments for certain university presses and the obscene profit margins of commercial players, it is indeed the case that for many years we have worked for salaries below the industry standard. However, we never made the claim that the scholar-led open-access model that punctum advocates necessitates such below-market remuneration levels; on the contrary, we believe that with the current money that is already in the system, all scholarly publishers, editors, and authors can be paid a reasonable living wage. We don’t assume that any open-access scholar-led publishing house that were to follow the model we are developing would have to make the same financial sacrifices we did in our early years—that, indeed, would be unsustainable and unreplicable….”

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….”

 

Transitioning punctum books to Open Source Infrastructure · punctum books

“Without open source digital infrastructure, open access publishing has no long-term chance of truly remaining open, that is, not only free to read but also free to write, free to edit, and free to publish. Without a commitment to make, as much as possible, the entire book production pipeline open, the decision of who gets to write and who gets to read will always remain beholden to actors that do not consider the public good their first priority.

An overarching profit motive of any of the vendors that punctum books uses as part of its pipeline posits a risk for our open access ideal: we are as weak as our most commercial link. Furthermore, the implementation of GDPR in the European Union obliges us to be much more careful with what happens with the personal data of our authors and readers – and rightfully so. Like knowledge, privacy is a public good that is at odds with the idea of profit maximalization. The open source community, on the contrary, embraces the public sharing of knowledge while safeguarding the human right to privacy.

Our first step was to find a replacement of the technically most complicated part of the book production process, the book design itself. This brought us to the good folks of Editoria, who are very close to cracking the nut of creating an open source online collaborative environment for the editing of scholarly texts combined with an output engine that creates well designed EPUB, HTML, PDF, and ICML output formats.

Through the COPIM project of Scholarled, punctum books was also already involved in the development of a metadata database and management system (under the codenames Thoth and Hapi) that will be the first free and open source system to generate ONIX, MARC, and KBART records….”

Transitioning punctum books to Open Source Infrastructure · punctum books

“Without open source digital infrastructure, open access publishing has no long-term chance of truly remaining open, that is, not only free to read but also free to write, free to edit, and free to publish. Without a commitment to make, as much as possible, the entire book production pipeline open, the decision of who gets to write and who gets to read will always remain beholden to actors that do not consider the public good their first priority.

An overarching profit motive of any of the vendors that punctum books uses as part of its pipeline posits a risk for our open access ideal: we are as weak as our most commercial link. Furthermore, the implementation of GDPR in the European Union obliges us to be much more careful with what happens with the personal data of our authors and readers – and rightfully so. Like knowledge, privacy is a public good that is at odds with the idea of profit maximalization. The open source community, on the contrary, embraces the public sharing of knowledge while safeguarding the human right to privacy.

Our first step was to find a replacement of the technically most complicated part of the book production process, the book design itself. This brought us to the good folks of Editoria, who are very close to cracking the nut of creating an open source online collaborative environment for the editing of scholarly texts combined with an output engine that creates well designed EPUB, HTML, PDF, and ICML output formats.

Through the COPIM project of Scholarled, punctum books was also already involved in the development of a metadata database and management system (under the codenames Thoth and Hapi) that will be the first free and open source system to generate ONIX, MARC, and KBART records….”