Map as a Knowledge Base (MapKB), A Free and Open Source Geospatial Semantic Technology System Prototype

This chapter presents an ontology-based document management system developed for the Romanian public institutions. The system meets both general and specific requirements for this type of organization. The system has a three-tier architecture. FileZilla ftp server version 0.9.37 was used as application server. Jess Expert System Shell version 7.0p1 was the solution in developing knowledge base of the system and MySQL open-source server, version 5.0.51 is chosen for data tier. The system ontology is developed using the Protégé environment. The system is validated and deployed at Ploiesti City Hall. Employees from different departments (town planning, taxes etc.) working with the system provided validation information.

Download Full-text

Reactome and ORCID—fine-grained credit attribution for community curation

Database ◽

10.1093/database/baz123 ◽

2019 ◽

Vol 2019 ◽

Cited By ~ 2

Author(s):

Guilherme Viteri ◽

Lisa Matthews ◽

Thawfeek Varusai ◽

Marc Gillespie ◽

Marija Milacic ◽

...

Keyword(s):

Community Engagement ◽

Knowledge Base ◽

Open Source ◽

Open Data ◽

Web Interface ◽

Domain Experts ◽

Fine Grained ◽

Community Curation ◽

The Web ◽

Pathway Level

Abstract Reactome is a manually curated, open-source, open-data knowledge base of biomolecular pathways. Reactome has always provided clear credit attribution for authors, curators and reviewers through fine-grained annotation of all three roles at the reaction and pathway level. These data are visible in the web interface and provided through the various data download formats. To enhance visibility and credit attribution for the work of authors, curators and reviewers, and to provide additional opportunities for Reactome community engagement, we have implemented key changes to Reactome: contributor names are now fully searchable in the web interface, and contributors can ‘claim’ their contributions to their ORCID profile with a few clicks. In addition, we are reaching out to domain experts to request their help in reviewing and editing Reactome pathways through a new ‘Contribution’ section, highlighting pathways which are awaiting community review. Database URL: https://reactome.org

Download Full-text

Implementing an open source knowledge base

IEEE Software ◽

10.1109/ms.2005.155 ◽

2005 ◽

Vol 22 (6) ◽

pp. 92-95 ◽

Cited By ~ 7

Author(s):

B. Donnellan ◽

B. Fitzgerald ◽

B. Lake ◽

J. Sturdy

Keyword(s):

Knowledge Base ◽

Open Source

Download Full-text

A Platform for Oncogenomic Reporting and Interpretation

10.1101/2021.04.13.439667 ◽

2021 ◽

Author(s):

Caralyn Reisle ◽

Laura Williamson ◽

Erin Pleasance ◽

Anna Davies ◽

Brayden Pellegrini ◽

...

Keyword(s):

Knowledge Base ◽

Open Source ◽

Unmet Need ◽

Genomic Data ◽

Molecular Data ◽

Data Sets ◽

Precision Oncology ◽

Analytic Framework ◽

Manual Curation ◽

Rate Limiting

AbstractManual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we created the Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework created to facilitate the interpretation and reporting of somatic variants in cancer. PORI is unique in its integration of reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents one of the first open-source platform alternatives to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 TCGA tumours to the graph knowledge base, revealing that 88.2% have at least one potentially targetable alteration, and making available reports describing select individual samples.

Download Full-text

A Rule-Based Model for Compliance of Medical Devices Applied to the European Market

International Journal of Extreme Automation and Connectivity in Healthcare ◽

10.4018/ijeach.2019070104 ◽

2019 ◽

Vol 1 (2) ◽

pp. 56-78 ◽

Cited By ~ 1

Author(s):

Sofia Almpani ◽

Petros Stefaneas ◽

Harold Boley ◽

Theodoros Mitsikas ◽

Panayiotis Frangos

Keyword(s):

Knowledge Base ◽

Open Source ◽

Medical Devices ◽

Feedback Loop ◽

European Market ◽

Conformity Assessment ◽

Rule Based ◽

Consumer Interest ◽

Regulatory Frameworks

There is a growing producer and consumer interest in medical devices and the commensurate need for regulatory frameworks to ensure the quality of medical devices marketed locally and globally. This work focuses on formalizing the clauses enacted by Regulation (EU) 2017/745 for risk-based classification and class-based conformity assessment regarding marketability of medical devices. The resulting knowledge base (KB) represents clauses in Positional-Slotted Object-Applicative (PSOA) RuleML by integrating F-logic-like frames with Prolog-like relationships for atoms used as facts and in the conclusions and conditions of rules. Rules can apply polyadic functions, define polyadic relations, and augment conclusions with actions and conditions with events. The PSOA RuleML-implemented Medical Devices Rules KB was tested by querying in the open-source Java-implemented PSOATransRun system, which has provided a feedback loop for refinement and extension. This prototype can contribute to the licensing process of stakeholders and the registration of medical devices with a CE conformity mark.

Download Full-text

Wikidata as a knowledge graph for the life sciences

eLife ◽

10.7554/elife.52614 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 10

Author(s):

Andra Waagmeester ◽

Gregory Stupp ◽

Sebastian Burgstaller-Muehlbacher ◽

Benjamin M Good ◽

Malachi Griffith ◽

...

Keyword(s):

Knowledge Base ◽

Open Source ◽

Genetic Variants ◽

Life Sciences ◽

Drug Repurposing ◽

Chemical Compounds ◽

Knowledge Graph ◽

Biomedical Ontologies ◽

Biomedical Knowledge ◽

Fair Principles

Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.

Download Full-text