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Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies [article]

Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa Haendel, Nomi L. Harris, William R Hogan, Charles Tapley Hoyt (+15 others)
2022 arXiv   pre-print
The Ontology Development Kit (ODK) provides a set of standardised, customisable, and automatically executable workflows, and packages all required tooling in a single Docker image.  ...  Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardising release practices and metadata, and establishing shared quality standards  ...  13/19 (RDF/XML, OBO Flat File, OBO Graphs JSON) and metadata (version IRIs, licence information and more) to make ontologies more FAIR and interoperable. Funding  ... 
arXiv:2207.02056v1 fatcat:hciy653pqjhcvjwrkhe57lx7wm

A framework for developing engineering design ontologies within the aerospace industry

I.O. Sanya, E.M. Shehab
2014 International Journal of Production Research  
This paper presents a framework for developing engineering design ontologies within the aerospace industry.  ...  The major benefit of this approach is in the reduction of man-hours required for maintaining engineering design ontologies.  ...  Acknowledgements The authors would like to thank the Engineering and Physical Research Council (EPSRC) and case study organisation for funding this research project.  ... 
doi:10.1080/00207543.2014.965352 fatcat:n6i3q77v5faetp7ljvqaytrypa

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
The eSysbio project explored ways of developing a workbench for collaborative data analysis, accessible in various ways for users with various tasks and expertise.  ...  The EDAM ontology aimed at enumerating and organising concepts within bioinformatics, including operations and types of data.  ...  Developing tools together as a toolkit, if designed carefully, may also make it easier to develop them further, which is a feature of good maintainability.  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

Corbel Review Of Identifier Schemes, Standards And Interoperability Maps And Proposed Harmonization Strategy

Carol Goble, Helen Parkinson, Simon Jupp, Renzo Kottmann, Jan-Willem Boiten, Frank Oliver Glöckner, Eleanor Williams, Jason Swedlow, Morris Swertz, David van Enckevort, Nick Juty, Anna Gaulton
2017 Zenodo  
We summarise community activities in this space (Appendix 1), provide two checklists for: (i) RI identifier strategy and (ii) identifier harmonisation of common entities and services for identity use cases  ...  We also define priorities and document existing services that can be adopted, or extended in support of CORBEL.  ...  It is hard to make a definitive recommendation without discussion with the ontology owners for the non maintained ontology.  ... 
doi:10.5281/zenodo.376236 fatcat:jnrelmcl5vd7vnr4butpx2g6me

A viewpoint-based case-based reasoning approach utilising an enterprise architecture ontology for experience management

Andreas Martin, Sandro Emmenegger, Knut Hinkelmann, Barbara Thönssen
2016 Enterprise Information Systems  
This ontological representation, containing historical cases and specific enterprise domain knowledge, is applied in a new ontology-based case-based reasoning approach.  ...  In this section we introduce the main concepts starting with a brief overview on CBR, followed by related work concerning enterprise ontologies and enterprise architecture frameworks.  ...  Acknowledgement We would like to thank Helmar Steinmann, Thorsten Herb and Holger Aumann, from the ELO Digital Office CH AG for their project support and for providing us with the use case.  ... 
doi:10.1080/17517575.2016.1161239 fatcat:64tqz4hvrrdhfm4tuhb3kdnlqm

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
Marco Masseroli, and Dr. Fernando Palluzzi for numerous discussions regarding the data model. This work was supported by a PRIN awarded to Prof. Stefano Ceri.  ...  A continuation of this work is planned within the scope of a collaboration with Roche Pharmaceuticals, Basel, Switzerland. Acknowledgements The project team at Syngenta.  ...  This package is used by a web page that we developed using the PrimeFaces toolkit.  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie

NFDI4Ing - the National Research Data Infrastructure for Engineering Sciences

Robert H. Schmitt, Verena Anthofer, Sören Auer, Sait Başkaya, Christian Bischof, Torsten Bronger, Florian Claus, Florian Cordes, Évariste Demandt, Thomas Eifert, Bernd Flemisch, Matthias Fuchs (+39 others)
2020 Zenodo  
A broad consensus on typical methods and workflows in engineering research has been established: The archetypes.  ...  It offers a unique method-oriented and user-centred approach in order to make engineering research data FAIR – findable, accessible, interoperable, and re-usable. NFDI4Ing has been founded in 2017.  ...  Measure CC-5 "Standardisation" (KIT, DLR) To establish successful services for the community there is a need to develop standards.  ... 
doi:10.5281/zenodo.4015201 fatcat:qud4tskyyjfrhcnkt4qjufaeyi

NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

Christoph Steinbeck, Oliver Koepler, Felix Bach, Sonja Herres-Pawlis, Nicole Jung, Johannes Liermann, Steffen Neumann, Matthias Razum, Carsten Baldauf, Frank Biedermann, Thomas Bocklitz, Franziska Boehm (+18 others)
2020 Research Ideas and Outcomes  
To this end, the overarching objective is the development and maintenance of a national research data infrastructure for the research domain of chemistry in Germany, and to enable innovative and easy to  ...  Identify and recommend open data standards in key areas of chemistry, in order to support the FAIR principles for research data. Finally, develop standards, if there is a lack.  ...  team at the KIT and merged and general implementation for all subdisciplines will be developed.  ... 
doi:10.3897/rio.6.e55852 fatcat:fvde2vhzyfc27ieavgkzjhxlaa

Survey of Context Provisioning Middleware

Michael Knappmeyer, Saad Liaquat Kiani, Eike Steffen Reetz, Nigel Baker, Ralf Tonjes
2013 IEEE Communications Surveys and Tutorials  
Development Kits (SDK).  ...  Dominant market forces, including Apple, Google and Microsoft, not only build and equip smartphones but also entire software ecosystems that include software development kits and software distribution  ... 
doi:10.1109/surv.2013.010413.00207 fatcat:xlt33n5zmvdyjlxhk4kowwz6qe

SSHOC D1.4 Second Annual Progress & Activity Report

Martina Drascic, Ivana Ilijasic Versic, Libby Bishop, Mathilde Steinsvåg Hansen, Mari Kleemola, Irena Vipavc Brvar, Ana Inkret, Alexander König, Daan Broeder, Maria Eskevich, Kea Tijdens, Darja Fišer (+41 others)
2021 Zenodo  
The report starts with a general plan for the SSHOC project in Year 2 (2020), and lists the main objectives set up to be achieved.  ...  The section also contains a reference to the deviations from the DoA that happened in this period, and risk assessment status.  ...  and developing the SSHOC trainer directory, a registry for finding trainers in the social sciences and humanities The Training Discovery Toolkit was released in April 2020 and is meant as a discovery  ... 
doi:10.5281/zenodo.4633680 fatcat:v2ttk2eavjf7pe2o4swjeef7xm

D3.2: EOSC Open Science Monitor specifications [article]

George Papastefanatos, Elli Papadopoulou, Marios Meimaris, Leo Mack, Rahul Thorat
2018 Zenodo  
This deliverable first presents an overview of existing efforts that have so far been introduced for the monitoring of Open Science, then provides the vision of the EOSCpilot for such a framework, and  ...  This document provides the specifications of the Open Science Monitor Framework of the EOSCpilot, for monitoring of Open science trends and impact in EOSC.  ...  In addition, a variety of tools have been developed which have their technical and conceptual background in these metrics. • Open Data Certificate 66 is a free online tool developed and maintained by the  ... 
doi:10.5281/zenodo.3387563 fatcat:orepnx6xyvd3hkcqiee4fdmgk4

D1.5 Final Annual Progress & Activity Report

Martina Drascic, Ivana Ilijasic Versic, Vanja Komljenovic, Anne Sofie Fink, Panagiota Starida, Mari Kleemola, Irena Vipavc Brvar, Veronika Heider, Libby Bishop, Mathilde Steinsvaag Hansen, Vigdis Kvalheim, Alexander König (+3 others)
2022 Zenodo  
The report starts with a general plan for the SSHOC project in Year 3 (2021), and lists the main objectives set up to be achieved.  ...  The section also contains a reference to the deviations from the DoA that happened in this period, and risk assessment status.  ...  Importantly, the presence of a landing page in almost all cases allowed for building up a test sample made up of a very diverse dataset from those repositories for which we want to build standardised and  ... 
doi:10.5281/zenodo.6567240 fatcat:odpitdyarrdxrgn2r7v66ytl4i

PARTHENOS D2.3 Report on the assessment of data policies and standardization

Steven Krauwer, Sara Di Giorgio, Karolien Verbrugge, Claus Spiecker, Christos Chatzimichail, Emiliano Degl'Innocenti, Hélène Gautier, Roberta Giacomi, Lina Henriksen, Klaus Illmayer, Antonio Davide Madonna, Maurizio Sanesi
2017 Zenodo  
requirements for implementation carried out by WP3, 4, 5, 6, 7 and 8 of the PARTHENOS project.  ...  The document provides collect needs and experiences from the project constituencies (research communities, ESFRI and non-ESFRI Research Infrastructures, other projects) and to organize and feed them as  ...  The aim of the BackBone Thesaurus is to develop a model and a proposal of how existing thesauri and ontologies will become interoperable and can be maintained in a sustainable and scalable way.  ... 
doi:10.5281/zenodo.2662524 fatcat:kovfreaafrdfdlmzhgka6nshdq


Ch. Elsner, D. Häckl, H. van der Slikke, V. Della Mea, T.N. Arvanitis, H. Wiesmeth
2007 Technology and Health Care  
Results: Transinsight developed GoPubMed, a biomedical search engine which uses background knowledge for searches and leads faster to much better search results.  ...  We deal with 16 Million documents and 120,000 ontology terms.  ...  to the particularities of the biomedical sublanguage and an ontology of the Greek biomedical terminology.  ... 
doi:10.3233/thc-2007-15503 fatcat:bjb5zxdzwncrdkdufkdzathke4

A semantic-driven framework for IT support of clinical laboratory standards

Fatima Sabiu Maikore
The SmartSOP framework consists of three main components, the Ontology for Clinical Laboratory SOP (OCL-SOP), the translation engine that converts free text SOPs to a standardised format, and a mobile  ...  In this thesis, we present the SmartSOP framework, a semantic-driven framework, that supports the representation of clinical laboratory procedure concepts in a standardised format for use within software  ...  Ontologies for the biomedical domain The Open Biomedical Ontologies (OBO) exists as an umbrella body for ontology developers in the domain of life sciences [121] .  ... 
doi:10.25602/gold.00030139 fatcat:beehbfjhjbeixhbnadvtuiybcy
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