Revisiting 2019, setting goals for 2020, and reflecting upon open science

“The major objectives of the Jornal Brasileiro de Pneumologia (JBP, Brazilian Journal of Pulmonology) are to disseminate Brazilian research in the field of respiratory diseases and related areas, to expand the internationalization of the journal, and to act as one of the major sources of updates for the members of the Sociedade Brasileira de Pneumologia e Tisiologia (Brazilian Thoracic Society), increasingly reaching out to our readers. The JBP will celebrate its 45th anniversary in 2020. Since its inception, it has matured in the dissemination of knowledge by monitoring the developments and occasional events occurring in the field of pulmonology, continuing to be the leading Latin American journal in the field. The secondary and indirect objectives that should be highlighted are to increase the interest of recent graduates in the field and to promote the development of new researchers in related areas….

In Plan S,5 organized by an international coalition, as well as in presentations in various forums and publications by the SciELO Program, it has been suggested that open practices of scientific communication be adopted over the next five years. This scientific model includes open and unrestricted access to all peer-reviewed publications, acceptance of manuscripts previously deposited on a preprint server, adoption of the continuous publication modality, making all research content available in detail, and the possibility of open peer review.5-8 However, although most of the proposals put forth have been in agreement regarding open communication, which will certainly contribute to the progress of science, establish greater transparency in editorial processes, and democratize access to information, there are still certain questions about the universal adoption of this policy, even within the international scientific community, especially regarding the possibility of opening the peer review process (i.e., disclosing the identity of the reviewers to the authors). Certainly, there are advantages to an open peer review process, because it will increase the importance of the reviewers and promote a trend toward improvement of the quality of the evaluations, because all of the participants are likely to be more careful in carrying out their part in the process and to venture out of their comfort zone. However, there are potential negative aspects of this process, including a higher risk that reviewers will decline to participate in the peer review process (given that it has already been difficult to find reviewers in the various areas of knowledge using the traditional model) and a potential risk of “retaliation” by authors in the event of negative reviews regarding the manuscript in question….”

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology

Abstract:  The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

 

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology

Abstract:  The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

 

São Paulo Statement on Open Access | National Research Foundation

The representatives of African Open Science Platform, AmeLICA, cOAlition S, OA2020, and SciELO – five of the major worldwide Open Access initiatives – met on 01 May 2019 during the annual meeting of the Global Research Council (GRC) in Sao Paulo. They are united in their common mission of making knowledge available and accessible wherever it can have the greatest impact and help solve humanity’s challenges regardless of where it was produced.

The combined effect of the five initiatives has generated a new momentum in the push towards universal, full and immediate Open Access.

The Five Initiatives jointly state that:

  • They consider that scholarly and scientific knowledge is a global public good. When generated by public funds, free access to it is a universal right.
  • They share one common ultimate objective: providing universal, unrestricted, and immediate Open Access to scholarly information, including use and re-use by humans and machines.
  • They share the belief that this common goal can be achieved through a variety of approaches.
  • They will pursue points of alignment among their approaches and ways to co-operate towards reaching the shared objective.
  • They seek an active dialogue with all stakeholders, including researchers, research funders, universities, libraries, publishers, learned societies, governments, and citizens to take into account the diversity of the global scholarly community….”

São Paulo Statement on Open Access

“The representatives of African Open Science Platform, AmeLICA, cOAlition S, OA2020, and SciELO – five of the major worldwide Open Access initiatives – met on 1 May 2019 during the annual meeting of the Global Research Council in São Paulo, Brazil. They are united in their common mission of making knowledge available and accessible wherever it can have the greatest impact and help solve humanity’s challenges regardless of where it was produced. The combined effect of the five initiatives has generated a new momentum in the push towards universal, full, and immediate Open Access….”

São Paulo Statement on Open Access | Plan S

The representatives of African Open Science PlatformAmeLICA, cOAlition S, OA2020, and SciELO – five of the major worldwide Open Access initiatives – met on 1 May 2019 during the annual meeting of the Global Research Council in São Paulo, Brazil. They are united in their common mission of making knowledge available and accessible wherever it can have the greatest impact and help solve humanity’s challenges regardless of where it was produced.

The combined effect of the five initiatives has generated a new momentum in the push towards universal, full, and immediate Open Access.

The Five Initiatives Jointly State That:

  • They consider that scholarly and scientific knowledge is a global public good. When generated by public funds, free access to it is a universal right.
  • They share one common ultimate objective: providing universal, unrestricted, and immediate Open Access to scholarly information, including use and re-use by humans and machines.
  • They share the belief that this common goal can be achieved through a variety of approaches.
  • They will pursue points of alignment among their approaches and ways to co-operate towards reaching the shared objective.
  • They seek an active dialogue with all stakeholders, including researchers, research funders, universities, libraries, publishers, learned societies, governments, and citizens to take into account the diversity of the global scholarly community.

Discovering Patterns in Brazilian Open Data using OrientDB

“Here in Brazil, our deputies have a monthly quota to perform their job. Let’s say that some deputy needs to buy a flight ticket or buy gas to the car in order to go to a meeting, he or she can use this monthly quota to do that. However, this money is public, therefore there are some rules to use it. One specific rule caught my attention, and it says that the deputies cannot use the money to buy a product or a service with companies that he or she is a partner, or a relative until third degree is a partner. With that information in mind I wondered if it would be possible to discover whether a deputy was using this quota illegally….

To perform all that I decided to use a graph oriented database. I chose OrientDB as the DBMS because of the query language derived from SQL. In the next sections I will explain the whole process to achieve those goals….”

Google Arts & Culture Digitizes Artifacts Following Brazil Museum Fire

“Earlier this year, 20 million irreplaceable artifacts housed by Brazil’s National Museumwere lost in a fire. As the museum did not have a platform for viewing most of these works digitally, many people feared that their memory would be lost forever. However, thanks to a two-year-old project spearheaded by Google, a lucky selection of these priceless pieces will live a second life online.

 

In 2016, Google Arts & Culture teamed up with the Museu Nacional in an effort to digitize its collections. Using Street View imagery, the initial goal of this undertaking was “to bring their collection online—so that anyone, anywhere in the world could see and learn about these ancient artifacts.” Since the fire, however, this project has served a much greater purpose.

With a couple clicks of a mouse, users are transported to the museum as it once stood. Featuring high-resolution photographs that offer 360-degree views of both the artifacts and the galleries they once inhabited, this invaluable project lets users wander through the lost museum and wade through some of its destroyed objects. Ancient sculptures, scientific specimens, and Luzia, the oldest fossilized human remains found in the Americas, are just some of the pieces immortalized in this virtual treasure trove….”

Google Virtual Tour Preserves Collections Destroyed in Brazil Museum Fire | Smart News | Smithsonian

“In early September, a fire roared through the 200-year-old National Museum of Brazil in Rio de Janeiro, destroying up to 90 percent of its precious collections. The extent of the damages was “incalculable,” Brazil President Michel Temer stated on Twitter at the time. “Two hundred years of work, research and knowledge have been lost.”

 

While it is true that little can be done to restore so many of the museum’s irreplaceable specimens and artifacts, a recently launched Google Arts & Culture project hopes to see the institution live on in the digital realm. As Kelly Richman-Abodou reports for My Modern Met, Street View imagery has made it possible to take a virtual tour of the museum as it stood before tragedy struck.

In what would prove to be a fortuitous collaboration, Google started working with the National Museum of Brazil in 2016 to digitize the museum’s collections and capture its interior through “high-resolution photography, photogrammetry, 3D laser scanning, and virtual and augmented reality,” writes Chance Coughenour, program manager of Google Arts & Culture, in a blog post. Google has embarked on similar projects with many other museums and heritage sites, but its partnership with the National Museum of Brazil has become particularly important in the wake of the fire….”