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.

Big Pharma has failed: the antibiotic pipeline needs to be taken under public ownership

“Looking into the past shows that public ownership of antibiotic R&D is not as radical as it may sound. During the second world war, allied research on penicillin – the most iconic antibiotic – was publicly financed, organised and owned. In fact, the original penicillin was never patented….”

Who Owns H.I.V.-Prevention Drugs? The Taxpayers, U.S. Says – The New York Times

“After years of prodding by patient advocates, federal officials on Wednesday sued the drug maker Gilead Sciences, charging that it had infringed government patents on the idea of preventing H.I.V. with a daily pill.

The suit, by the Department of Health and Human Services, came as a pleasant shock to many critics of the company, including Democratic members of Congress who had pressed the administration to act.

It is very rare for the government to take on a drug maker over patents. But the medications made by Gilead are necessary to end the AIDS epidemic by 2030, which the Trump administration has set as a goal. That cannot be accomplished if the drugs are not made more affordable….”

The Project Jengo Saga: How Cloudflare Stood up to a Patent Troll – and Won!

“After we were sued by Blackbird, we decided that we wouldn’t roll over. We decided we would do our best to turn the incentive structure on its head and make patent trolls think twice before attempting to take advantage of the system. We created Project Jengo in an effort to remove this economic asymmetry from the litigation. In our initial blog post we suggested we could level the playing field by: (i) defending ourselves vigorously against the patent lawsuit instead of rolling over and paying a licensing fee or settling, (ii) funding awards for crowdsourced prior art that could be used to invalidate any of Blackbird’s patents, not just the one asserted against Cloudflare, and (iii) asking the relevant bar associations to investigate what we considered to be Blackbird’s violations of the rules of professional conduct for attorneys….”

The inspiring story of how Cloudflare defeated a patent troll and broke the patent-trolling business-model / Boing Boing

“In 2016, Cloudflare was targeted by a notorious patent troll called Blackbird Technologies; rather than capitulate, the company set up a fund called “Project Jengo” to pay bounties to researchers who documented prior art that could be used to invalidate the patent in question — and all of Blackbird’s patents, and began to file to have additional patents invalidated based on that crowdsourced research.

 

Not only did Cloudflare prevail in its litigation, it also seems to have taken a serious bite out of Blackbird, whose headcount has dropped precipitously, along with the number of lawsuits the company has filed. And to add insult to injury, the Cloudflare filed ethics complaints against the company’s founder (who are both lawyers) with their individual bar associations….”

WIPO General Assembly 2019: Opening statement of Knowledge Ecology International | Knowledge Ecology International

“As part of WIPO’s ongoing work on patents and health, KEI proposes that the Standing Committee on the Law of Patents (SCP) discuss the role of patents in the development of and access to new cell and gene therapies, such as CAR T treatments for cancer, or gene therapies such as Luxturna or Zolgensma. Among the topics to be considered are the extent to which patent exceptions for the treatment of humans apply, as well as the high costs and anti-competitive nature of licensing the emerging thickets of patents for these treatments….”

United States Patent: 10282424: Linking documents using citations

Abstract:  Aspects of the present disclosure relate to linking documents using citations. A server accesses a stored document in a data repository. The server determines a set of candidate citing documents that cite the stored document. The server obtains, for each candidate citing document from the set, first information representing an impact of the candidate citing document taken as a whole and second information representing a citation context within the candidate citing document. The server determines a subset of citing documents, from the set of candidate citing documents, based on the obtained first information and the obtained second information. The server provides a digital transmission of the stored document, including visible indicia of the subset of citing documents, for display at a client device.

Breaking down the walls of scientific secrecy | CBC News

Getting scooped by a competing researcher is one of a scientist’s biggest fears. And some of the most important discoveries in medical history have been tainted by competitive controversy.

Back in 1952, before he co-discovered the structure of DNA, James Watson got access to Rosalind Franklin’s revolutionary X-ray image of DNA without her knowledge.

That image, known as Photo 51, was a major clue that helped Watson and Francis Crick complete their Nobel Prize-winning discovery. The lack of credit given to Franklin remains a stain on the story of their breakthrough.

But what if Franklin had been informally publishing her research notes all along?

“She would have gotten credit instantly for her contribution,” said Susan Lamb, a historian of medicine who holds the Hannah Chair in the History of Medicine at the University of Ottawa….”

Why Pfizer didn’t report that its rheumatoid arthritis medication might prevent Alzheimer’s – The Washington Post

A team of researchers inside Pfizer made a startling find in 2015: The company’s blockbuster rheumatoid arthritis therapy Enbrel, a powerful anti-inflammatory drug, appeared to reduce the risk of Alzheimer’s disease by 64 percent.

The results were from an analysis of hundreds of thousands of insurance claims. Verifying that the drug would actually have that effect in people would require a costly clinical trial — and after several years of internal discussion, Pfizer opted against further investigation and chose not to make the data public, the company confirmed.

Researchers in the company’s division of inflammation and immunology urged Pfizer to conduct a clinical trial on thousands of patients, which they estimated would cost $80 million, to see if the signal contained in the data was real, according to an internal company document obtained by The Washington Post….

Pfizer did share the data privately with at least one prominent scientist, but outside researchers contacted by The Post believe Pfizer also should at least have published its data, making the findings broadly available to researchers.

“Of course they should. Why not?’’ said Rudolph E. Tanzi, a leading Alzheimer’s researcher and professor at Harvard Medical School and Massachusetts General Hospital. “It would benefit the scientific community to have that data out there,’’ said Keenan Walker, an assistant professor of medicine at Johns Hopkins who is studying how inflammation contributes to Alzheimer’s. “Whether it was positive data or negative data, it gives us more information to make better informed decisions.’’ …

The broader market forces that critics say discouraged Pfizer from investing in Alzheimer’s clinical trials are rooted in Enbrel’s “life cycle,’’ the 20-year period of patent exclusivity when a brand manufacturer reaps monopoly profits from a drug. By industry standards, Enbrel, an injectable biologic drug, is relatively old, with FDA approval for rheumatoid arthritis in 1998….

A medical ethics expert argued that Pfizer has a responsibility to publicize positive findings, although it is not as strong as an imperative to disclose negative findings.

“Having acquired the knowledge, refusing to disclose it to those who might act upon it hides a potential benefit, and thereby wrongs and probably harms those at risk of developing Alzheimer’s by impeding research,’’ said Bobbie Farsides, professor of clinical and biomedical ethics at Brighton and Sussex Medical School in the United Kingdom….”