In?silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases – Chatterjee – – PROTEOMICS – Wiley Online Library

Abstract:  Blood protein markers have been studied for the clinical management of cancer. Due to the large number of the proteins existing in blood, it is often necessary to pre-select potential protein markers before experimental studies. However, to date there is a lack of automated method for in-silico selection of cancer blood proteins that integrates the information from both genetic and proteomic studies in a cancer-specific manner. In this work, we synthesized both genomic and proteomic information from several open access databases and established a bioinformatic pipeline for in-silico selection of blood plasma proteins overexpressed in specific type of cancer. We demonstrated the workflow of this pipeline with an example of breast cancer, while the methodology was applicable for other cancer types. With this pipeline we obtained 10 candidate biomarkers for breast cancer. The proposed pipeline provides a useful and convenient tool for in-silico selection of candidate blood protein biomarkers for a variety of cancer research.

 

NISO Announces New Project to Integrate Publisher and Repository Workflows | NISO website

“The National Information Standards Organization (NISO) today announced that its Voting Members have approved work on a new project, Integrating Publisher and Repository Workflows to Improve Research Data-Article Links. 

With widespread support for open data from many government entities, publishers, funders, and other stakeholders, research data is increasingly being deposited, published, and cited. However, there are still a number of barriers — technical as well as cultural. This new project aims to address some of the technical issues by making linking between data and other research objects with their associated literature both easier and more consistent. The new NISO Working Group on Integrating Publisher and Repository Workflows to Improve Research Data-Article Links will develop a Recommended Practice for how publisher and repository systems should interoperate, so that link creation happens automatically.

Building on industry efforts such as the RDA/WDS Scholarly Link Exchange (Scholix),  JATS4R Recommendations on Data Citations and Data Availability Statements, this project aims to define the information required at each end of the bidirectional link between datasets and other research works, including what notifications are needed. The goal is to create a Recommended Practice that platform providers of all sizes can aspire to meet.

The Working Group’s remit will include defining the required metadata, building a terminology of events and of citation/link types for data/article relationships, and agreeing what information needs to be exchanged and in which direction.  …”

4Science Webinar: ORCID Integration with DSpace 7 and DSpace-CRIS 7 – 4Science

“Why: The ORCID permanent identifier is a powerful, widely adopted means of linking people unambiguously to their publications, projects, institutions and more, and distinguishing each researcher across the globe.

However, the full power of ORCID within the research infrastructure is only unleashed through ORCID-enabled systems. Different levels of integration are evident across different systems, and therefore there are different degrees of automation, intervention and verification to be aware of….”

Wellcome Trust awards PLOS a grant to test ways to increase sharing and discovery of research data – The Official PLOS Blog

“PLOS has been awarded a grant from the Wellcome Trust’s 2021 Open Research Fund to accelerate development and testing of new solutions that promote and reward open science. PLOS Pathogens will be piloting the latest version of the Dryad data repository, provided free of charge to authors and integrated into the publishing experience, along with prominent visual links on publications designed to incentivise open research practices….”

Something old, something new: Figshare’s new ORCID integration is here

“We’re big fans of ORCID here at Figshare. Our first ORCID integration was released way back in 2013 when we were “Alpha launch partners”. We’ve made a few changes to the integration along the way, of course. We’re very pleased to say that as of September 2021 and in collaboration with our friends and development partners at Singapore Institute of Technology, we are launching a new ORCID integration with significantly improved functionality!…”

 

Books Contain Multitudes: Exploring Experimental Publishing · COPIM

“Books contain multitudes: Exploring Experimental Publishing is a three-part research and scoping report created to support the Experimental Publishing and Reuse Work Package (WP 6) of the COPIM project. It also serves as a resource for the scholarly community, especially for authors and publishers interested in pursuing more experimental forms of book publishing.

COPIM (Community-led Open Publication Infrastructures for Monographs) is a 3-year project led by Coventry University as part of an international partnership of researchers, universities, librarians, open access (OA) book publishers and infrastructure providers and is funded by The Research England Development Fund and Arcadia—a charitable fund of Lisbet Rausing and Peter Baldwin. COPIM is building community-owned, open systems and infrastructures to enable OA book publishing to flourish, delivering major improvements in the infrastructures used by OA book publishers and those publishers making a transition to OA. The project addresses the key technological, structural, and organisational hurdles—around funding, production, dissemination, discovery, reuse, and archiving—that are standing in the way of the wider adoption and impact of OA books. COPIM will realign OA book publishing away from competing commercial service providers to a more horizontal and cooperative knowledge-sharing approach.

As part of seven connected Work Packages, COPIM will work on 1) integrated capacity-building amongst presses; 2) access to and development of consortial, institutional, and other funding channels; 3) development and piloting of appropriate business models; 4) cost reductions achieved by economies of scale; 5) mutually supportive governance models; 6) integration into library, repository, and digital learning environments; 7) the re-use of and experimentation with OA books; 8) the effective and robust archiving of OA content; and 9) knowledge transfer to stakeholders through various pilots….”

Books Contain Multitudes: Exploring Experimental Publishing · COPIM

“Books contain multitudes: Exploring Experimental Publishing is a three-part research and scoping report created to support the Experimental Publishing and Reuse Work Package (WP 6) of the COPIM project. It also serves as a resource for the scholarly community, especially for authors and publishers interested in pursuing more experimental forms of book publishing.

COPIM (Community-led Open Publication Infrastructures for Monographs) is a 3-year project led by Coventry University as part of an international partnership of researchers, universities, librarians, open access (OA) book publishers and infrastructure providers and is funded by The Research England Development Fund and Arcadia—a charitable fund of Lisbet Rausing and Peter Baldwin. COPIM is building community-owned, open systems and infrastructures to enable OA book publishing to flourish, delivering major improvements in the infrastructures used by OA book publishers and those publishers making a transition to OA. The project addresses the key technological, structural, and organisational hurdles—around funding, production, dissemination, discovery, reuse, and archiving—that are standing in the way of the wider adoption and impact of OA books. COPIM will realign OA book publishing away from competing commercial service providers to a more horizontal and cooperative knowledge-sharing approach.

As part of seven connected Work Packages, COPIM will work on 1) integrated capacity-building amongst presses; 2) access to and development of consortial, institutional, and other funding channels; 3) development and piloting of appropriate business models; 4) cost reductions achieved by economies of scale; 5) mutually supportive governance models; 6) integration into library, repository, and digital learning environments; 7) the re-use of and experimentation with OA books; 8) the effective and robust archiving of OA content; and 9) knowledge transfer to stakeholders through various pilots….”

Toward Easy Deposit: Lowering the Barriers of Green Open Access with Data Integration and Automation

Abstract:  This article describes the design and development of an interoperable application that supports green open access with long-term sustainability and improved user experience of article deposit. The lack of library resources and the unfriendly repository user interface are two significant barriers that hinder green open access. Tasked to implement the open access mandate, librarians at an American research university developed a comprehensive system called Easy Deposit 2 to automate the support workflow of green open access. Easy Deposit 2 is a web application that is able to harvest new publications, to source manuscripts on behalf of the library, and to facilitate self-archiving to a university’s institutional repository. The article deposit rate increased from 7.40% to 25.60% with the launch of Easy Deposit 2. The results show that a computer system can implement routine tasks to support green open access with success. Recent developments in digital repository provide new opportunities for innovation, such as Easy Deposit 2, in supporting open access. Academic librarians are vital in promoting “openness” in scholarly communication, such as transparency and diversity in the sharing of publication data.

 

ORCID-ShareYourPaper.org Integration in the Works – Cal schol.com

“[T]here’s nothing specific to announce yet, but the creativity and enthusiasm on both sides is very, very promising. I’d wager to say we will see some really cool ORCID-Shareyourpaper.org integrations in place in the not too distant future.”

ORCID-ShareYourPaper.org Integration in the Works – Cal schol.com

“[T]here’s nothing specific to announce yet, but the creativity and enthusiasm on both sides is very, very promising. I’d wager to say we will see some really cool ORCID-Shareyourpaper.org integrations in place in the not too distant future.”

Europe PMC Integrates Smart Citations from scite – scite – Medium

“scite, an award-winning citation analysis platform, and Europe PMC, an open science discovery tool that provides access to a worldwide collection of life science publications, have partnered to display what scite calls smart citations on the Europe PMC platform.

Smart citations advance regular citations by providing more contextual information beyond the information that one study references another. Specifically, smart citations provide the excerpt of text surrounding the citation, the section of the article in which the reference is mentioned, and indicate whether the citing study provides supporting or contradicting evidence. As a result, one can evaluate a study of interest much faster….”

Case study: Doing more with ORCID – UK ORCID Support

“The University of Cambridge research repository (Apollo), uses ORCID IDs as a unique identifier for researchers.  When a researcher submits a dataset to Apollo, a DOI is minted for the dataset through the DataCite service.   By including the ORCID in the metadata submitted to DataCite, DataCite then populates the ORCID registry entry for the researcher (with their permission) with information about the dataset, using an ‘auto-update’ feature. 

The result is that a link is created between the researcher and their data, through the ORCID ID identifying the researcher, and the DOI for the data assigned by DataCite. The persistent identifiers are used to connect researchers and their achievements, improving visibility and discoverability across different systems.  The workflow reduces duplication of effort in entering information and avoids input or identification errors….”

Integration of Machine Learning and Open Access Geospatial Data for Land Cover Mapping

Abstract:  In-time and accurate monitoring of land cover and land use are essential tools for countries to achieve sustainable food production. However, many developing countries are struggling to efficiently monitor land resources due to the lack of financial support and limited access to adequate technology. This study aims at offering a solution to fill in such a gap in developing countries, by developing a land cover solution that is free of costs. A fully automated framework for land cover mapping was developed using 10-m resolution open access satellite images and machine learning (ML) techniques for the African country of Lesotho. Sentinel-2 satellite images were accessed through Google Earth Engine (GEE) for initial processing and feature extraction at a national level. Also, Food and Agriculture Organization’s land cover of Lesotho (FAO LCL) data were used to train a support vector machine (SVM) and bagged trees (BT) classifiers. SVM successfully classified urban and agricultural lands with 62 and 67% accuracy, respectively. Also, BT could classify the two categories with 81 and 65% accuracy, correspondingly. The trained models could provide precise LC maps in minutes or hours. they can also be utilized as a viable solution for developing countries as an alternative to traditional geographic information system (GIS) methods, which are often labor intensive, require acquisition of very high-resolution commercial satellite imagery, time consuming and call for high budgets. 

 

Unpaywall extension adds 200,000th active user – Impactstory blog

“We’re thrilled to announce that we’re now supporting over 200,000 active users of the Unpaywall extension for Chrome and Firefox!

The extension, which debuted nearly two years ago, helps users find legal, open access copies of paywalled scholarly articles. Since its release, the extension has been used more than 45 million times, finding an open access copy in about half of those. …

However, although the extension gets the press, the database powering the extension is the real star. There are millions of people using the Unpaywall database every day:

  • We deliver nearly one million OA papers every day to users worldwide via our open API…that’s 10 papers every second!
  • Over 1,600 academic libraries use our SFX integration to automatically find and deliver OA copies of articles when they have no subscription access.
  • If you’re using an academic discovery tool, it probably includes Unpaywall data…we’re integrated into Web of Science, Europe PubMed Central, WorldCat, Scopus, Dimensions, and many others.
  • Our data is used to inform and monitor OA policy at organizations like the US NIH, UK Research and Innovation, the Swiss National Science Foundation, the Wellcome Trust, the European Open Science Monitor, and many others.

The Unpaywall database gets information from over 50,000 academic journals and 5000 scholarly repositories and archives, tracking OA status for more than 100 million articles. You can access this data for free using our open API, or user our free web-based query tool. Or if you prefer, you can just download the whole database for free….”