scholarly journals Converting Biomedical Text Annotated Resources into FAIR Research Objects with an Open Science Platform

2021 ◽  
Vol 11 (20) ◽  
pp. 9648
Author(s):  
Alexandros Kanterakis ◽  
Nikos Kanakaris ◽  
Manos Koutoulakis ◽  
Konstantina Pitianou ◽  
Nikos Karacapilidis ◽  
...  

Today, there are excellent resources for the semantic annotation of biomedical text. These resources span from ontologies, tools for NLP, annotators, and web services. Most of these are available either in the form of open source components (i.e., MetaMap) or as web services that offer free access (i.e., Whatizit). In order to use these resources in automatic text annotation pipelines, researchers face significant technical challenges. For open-source tools, the challenges include the setting up of the computational environment, the resolution of dependencies, as well as the compilation and installation of the software. For web services, the challenge is implementing clients to undertake communication with the respective web APIs. Even resources that are available as Docker containers (i.e., NCBO annotator) require significant technical skills for installation and setup. This work deals with the task of creating ready-to-install and run Research Objects (ROs) for a large collection of components in biomedical text analysis. These components include (a) tools such as cTAKES, NOBLE Coder, MetaMap, NCBO annotator, BeCAS, and Neji; (b) ontologies from BioPortal, NCBI BioSystems, and Open Biomedical Ontologies; and (c) text corpora such as BC4GO, Mantra Gold Standard Corpus, and the COVID-19 Open Research Dataset. We make these resources available in OpenBio.eu, an open-science RO repository and workflow management system. All ROs can be searched, shared, edited, downloaded, commented on, and rated. We also demonstrate how one can easily connect these ROs to form a large variety of text annotation pipelines.

2016 ◽  
Author(s):  
Susanne Blumesberger

Watch the VIDEO of the presentation.The Way to Open Science contains many  components. One of these  components would be open repositories based on open source software  with free access to researchers. Open access policies are essential, as are open infrastructures and open contents. Repositories can support this openness by offering open licenses, open metadata , the possibility to use open formats  and open thesauri.  Another principal point is transparency. Open peer review should be possible, and the description of processes should also be transparent. Of course, an open license should provide all data types and metadata as well.It is important to help researchers to make their results visible and accessible and to encourage them to publish in OA-Journals and use repositories for the underlying data. Open Access Policies are supporting these efforts. Open data can be freely used, modified, and shared by anyone for any purpose. In order to do so, Open Licenses are required.Also Metadata are important components of the Way  to Open Science. Metadata are data about data which should be free of all restrictions on access, structured and based on standards.Open formats are defined by a published specification and are not restricted in their use. They are mainly used by open-source software. Open Thesauruses are freely accessible for everyone without costs and with a free license.Open Processes should be documented, transparent, repeatable and reusable.An open peer review process is also  a step  forward to Open Science. Authors and referees are no longer anonymous. The whole process and the decision letters are open.Of course Open licenses allow the reuse of any work or data without any restrictions.The lecture will deal with various aspects of open science and focus on the role of repositories – with all chances and challenges.


2020 ◽  
Vol 36 (3) ◽  
pp. 263-279
Author(s):  
Isabel Steinhardt

Openness in science and education is increasing in importance within the digital knowledge society. So far, less attention has been paid to teaching Open Science in bachelor’s degrees or in qualitative methods. Therefore, the aim of this article is to use a seminar example to explore what Open Science practices can be taught in qualitative research and how digital tools can be involved. The seminar focused on the following practices: Open data practices, the practice of using the free and open source tool “Collaborative online Interpretation, the practice of participating, cooperating, collaborating and contributing through participatory technologies and in social (based) networks. To learn Open Science practices, the students were involved in a qualitative research project about “Use of digital technologies for the study and habitus of students”. The study shows the practices of Open Data are easy to teach, whereas the use of free and open source tools and participatory technologies for collaboration, participation, cooperation and contribution is more difficult. In addition, a cultural shift would have to take place within German universities to promote Open Science practices in general.


Infolib ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 34-37
Author(s):  
Anna Chulyan ◽  

The article touches upon the importance of long-term digital preservation of Armenian cultural heritage through creation of digital repositories using Open-Source Software in Armenian libraries. The research highlights the advantages of Open-Source Software in context of providing free access to digital materials, as well as its high level of functionality in order to empower libraries with new technologies for more efficient organization and dissemination of information.


2021 ◽  
Vol 15 ◽  
Author(s):  
Sanghum Woo ◽  
Jongmin Lee ◽  
Hyunji Kim ◽  
Sungwoo Chun ◽  
Daehyung Lee ◽  
...  

Brain–computer interfaces can provide a new communication channel and control functions to people with restricted movements. Recent studies have indicated the effectiveness of brain–computer interface (BCI) applications. Various types of applications have been introduced so far in this field, but the number of those available to the public is still insufficient. Thus, there is a need to expand the usability and accessibility of BCI applications. In this study, we introduce a BCI application for users to experience a virtual world tour. This software was built on three open-source environments and is publicly available through the GitHub repository. For a usability test, 10 healthy subjects participated in an electroencephalography (EEG) experiment and evaluated the system through a questionnaire. As a result, all the participants successfully played the BCI application with 96.6% accuracy with 20 blinks from two sessions and gave opinions on its usability (e.g., controllability, completeness, comfort, and enjoyment) through the questionnaire. We believe that this open-source BCI world tour system can be used in both research and entertainment settings and hopefully contribute to open science in the BCI field.


2021 ◽  
Vol 9 ◽  
Author(s):  
Mario Locati ◽  
Roberto Vallone ◽  
Matteo Ghetta ◽  
Nyall Dawson

An increasing number of web services providing convenient access to seismological data have become available in recent years. A huge effort at multiple levels was required to achieve this goal and the seismological community was engaged in the standardization of both data formats and web services. Although access to seismological data is much easier than in the past, users encounter problems because of the large number of web services, and due to the complexity of the discipline-specific data encodings. In addition, instead of adopting cross-disciplinary standards such as those by the Open Geospatial Consortium (OGC), most seismological web services created their own standards, primarily those by the International Federation of Digital Seismograph Networks (FDSN). This article introduces “QQuake,” a plugin for QGIS—the Open Source Geographic Information System—that aims at making access to seismological data easier. The plugin is based on an Open Source code available on GitHub, and it is designed in a modular and customizable way, allowing users to easily include new web services.


2018 ◽  
Vol 45 (3) ◽  
pp. 398-415 ◽  
Author(s):  
Ignacio Lizarralde ◽  
Cristian Mateos ◽  
Juan Manuel Rodriguez ◽  
Alejandro Zunino

Web Services have become essential to the software industry as they represent reusable, remotely accessible functionality and data. Since Web Services must be discovered before being consumed, many discovery approaches applying classic Information Retrieval techniques, which store and process textual service descriptions, have arisen. These efforts are affected by term mismatch: a description relevant to a query can be retrieved only if they share many words. We present an approach to improve Web Service discoverability that automatically augments Web Service descriptions and can be used on top of such existing syntactic-based approaches. We exploit Named Entity Recognition to identify entities in descriptions and expand them with information from public text corpora, for example, Wikidata, mitigating term mismatch since it exploits both synonyms and hypernyms. We evaluated our approach together with classical syntactic-based service discovery approaches using a real 1274-service dataset, achieving up to 15.06% better Recall scores, and up to 17% Precision-at-1, 8% Precision-at-2 and 4% Precision-at-3.


2011 ◽  
pp. 463-468
Author(s):  
Diego Liberati

A framework is proposed that creates, uses, communicates, and distributes information whose organizational dynamics allow it to perform a distributed cooperative enterprise in public environments even over open source systems. The approach assumes Web services as the enacting paradigm, possibly over a grid, to formalize interaction as cooperative services on various computational nodes of a network. A framework is thus proposed that defines the responsibility of e-nodes in offering services and the set of rules under which each service can be accessed by e-nodes through service invocation. By discussing a case study, the chapter will detail how specific classes of interactions can be mapped into a serviceoriented model whose implementation will be carried out in a prototypical public environment.


Author(s):  
Vincent Yen

In large organizations, typical systems portfolios consist of a mix of legacy systems, proprietary applications, databases, off-the-shelf packages, and client-server systems. Software systems integration is always an important issue and yet a very complex and difficult area in practice. Consider the software integration between two organizations on a supply chain; the level of complexity and difficulty multiply quickly. How to make heterogeneous systems work with each other within an enterprise or across the Internet is of paramount interest to businesses and industry. Web services technologies are being developed as the foundation of a new generation of business-to-business (B2B) and enterprise application integration (EAI) architectures, and important parts of components as grid (www.grid.org), wireless, and automatic computing (Kreger, 2003). Early technologies in achieving software application integration use standards such as the common object request broker architecture (CORBA) of the Object Management Group (www.omg.org), the distributed component object model (DCOM) of Microsoft, and Java/RMI, the remote method invocation mechanism. CORBA and DCOM are tightly coupled technologies, while Web services are not. Thus, CORBA and DCOM are more difficult to learn and implement than Web services. It is not surprising that the success of these standards is marginal (Chung, Lin, & Mathieu, 2003). The development and deployment of Web services requires no specific underlying technology platform. This is one of the attractive features of Web services. Other favorable views on the benefits of Web services include: a simple, lowcost EAI supporting the cross-platform sharing of functions and data; and an enabler of reducing integration complexity and time (Miller, 2003). To reach these benefits, however, Web services should meet many technology requirements and capabilities. Some of the requirements include (Zimmermann, Tomlinson & Peuser, 2003): • Automation Through Application Clients: It is required that arbitrary software applications running in different organizations have to directly communicate with each other. • Connectivity for Heterogeneous Worlds: Should be able to connect many different computing platforms. • Information and Process Sharing: Should be able to export and share both data and business processes between companies or business units. • Reuse and Flexibility: Existing application components can be easily integrated regardless of implementation details. • Dynamic Discovery of Services, Interfaces, and Implementations: It should be possible to let application clients dynamically, i.e., at runtime, look for and download service address, service binding, and service interface information. • Business Process Orchestration Without Programming: Allows orchestration of business activities into business processes, and executes such aggregated process automatically. The first five requirements are technology oriented. A solution to these requirements is XML-based Web services, or simply Web services. It employs Web standards of HTTP, URLs, and XML as the lingua franca for information and data encoding for platform independence; therefore it is far more flexible and adaptable than earlier approaches. The last requirement relates to the concept of business workflow and workflow management systems. In supply chain management for example, there is a purchase order process at the buyer’s side and a product fulfillment process at the supplier’s side. Each process represents a business workflow or a Web service if it is automated. These two Web services can be combined into one Web service that represents a new business process. The ability to compose new Web services from existing Web services is a powerful feature of Web services; however, it requires standards to support the composition process. This article will provide a simplified exposition of the underlying basic technologies, key standards, the role of business workflows and processes, and critical issues.


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