Releasing 1.8 million open access publications from publisher systems for text and data mining

Text and data mining offers an opportunity to improve the way we access and analyse the outputs of academic research. But the technical infrastructure of the current scholarly communication system is not yet ready to support TDM to its full potential, even for open access outputs. To address this problem, Petr KnothNancy Pontika and Lucas Anastasiou have developed the CORE Publisher Connector, a toolkit service designed to assist text miners in accessing content though a single machine interface. The Connector aims to solve the heterogeneity among publisher APIs and assist text miners with data collection, provide a centralised point of access to all openly available scientific publications, and provide a high-performance, constantly updated access interface.

Extracting research evidence from publications | EMBL-EBI Train online

“Extracting research evidence from publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation.

This webinar took place on 5 March 2018 and is for wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically. Some prior knowledge of programmatic access and common programming languages is recommended.

The webinar covers: Available data (annotation types and sources) (1:50) API operations and parameters and web service outputs (8:08) Use case examples (16:56) How to get help (24:16)

You can download the slides from this webinar here. You can learn more about Europe PMC in our Europe PMC: Quick tour and our previous webinar Europe PMC, programmatically.

For documentation, help and support visit the Europe PMC help pages or download the developer friendly web service guide. For web service related question you can get in touch via the Google group or contact the helpdesk [at] europepmc.org”>help desk.”

MyScienceWork: The Global Scientific Platform

“Founded in 2010 by Virginie Simon, a biotech engineer and PhD in nanotechnology, and Tristan Davaille, a financial engineer with a degree in economics — MyScienceWork serves the international scientific community and the promotes easy access to scientific publications, unrestricted diffusion of knowledge and open science. Our comprehensive database includes more than 70 million scientific publications and 12 million patents.

We host a community of professional scientists and science enthusiasts from around the world who use MyScienceWork’s open network to deposit and discover scientific publications of all disciplines. Join the community! 

For Research Institutions, Scientific Publishers & private-sector R&D companies, MyScienceWork provides a suite of data-driven solutions. Learn more about our products.

Our vision for the near future is to empower research institutions and industries with more intelligence related to research fields by aggregating all available data related to research results to accelerate findings, optimize funding and research efforts, improve transparency, bridge the knowledge gap between academia and industry and avoid duplicate research.

MySciencework believes that making science more accessible will foster data sharing amongst science organizations….”

Open Data Grant Winners to Conduct Sentiment Analysis of Thousands of French Revolution Pamphlets | Newberry

“Today, you can see trends on Twitter at a glance and get immediate insights into the public discourse surrounding current events. But how can we learn about trending topics and public opinion in centuries past? The recipients of the Newberry’s Open Data Grant intend to find out. The Open Data Grant helps support innovative scholarship that applies technologies such as digital mapping, text mining, and data visualization to digitized primary sources. Joseph Harder, a chemist and data scientist, and Mimi Zhou, an expert in digital humanities studying early French literature, will use the award to complete a sentiment analysis of the Newberry’s recently digitized collection of more than 30,000 French Revolution pamphlets….”

About OpenAIRE-Advance

“OpenAIRE-Advance continues the mission of OpenAIRE to support the Open Access/Open Data mandates in Europe. By sustaining the current successful infrastructure, comprised of a human network and robust technical services, it consolidates its achievements while working to shift the momentum among its communities to Open Science, aiming to be a trusted e-Infrastructure within the realms of the European Open Science Cloud.

In this next phase, OpenAIRE-Advance strives  to empower its National Open Access Desks (NOADs) so they become a pivotal part within their own national data infrastructures, positioning OA and open science onto national agendas. The capacity building activities bring together experts on topical task groups in thematic areas (open policies, RDM, legal issues, TDM), promoting a train the trainer approach, strengthening and expanding the pan-European Helpdesk with support and training toolkits, training resources and workshops. It examines key elements of scholarly communication, i.e., co-operative OA publishing and next generation repositories, to develop essential building blocks of the scholarly commons.

On the technical level OpenAIRE-Advance focuses on the operation and maintenance of the OpenAIRE technical TRL8/9 services, and radically improves the OpenAIRE services on offer by: a) optimizing their performance and scalability, b) refining their functionality based on end-user feedback, c) repackaging them into products, taking a professional marketing approach with well-defined KPIs, d) consolidating the range of services/products into a common e-Infra catalogue to enable a wider uptake.

OpenAIREAdvance steps up its outreach activities with concrete pilots with three major RIs, citizen science initiatives, and innovators via a rigorous Open Innovation programme. Finally, viaits partnership with COAR, OpenAIRE-Advance consolidates OpenAIRE’s global roleextending its collaborations with Latin America, US, Japan, Canada, and Africa….”

Open Knowledge Finland to produce report on the openness of key scientific publishers

“To round off a great Open Access  week, we’d like to announce a new interesting project we’ve started. Continuing our efforts in the field of Open Science, Open Knowledge Finland was commissioned by CSC – IT Center for Science and the Finnish Ministry of Education and Culture to implement a Study on the Openness of Scientific Publishers.”