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Using semantics for representing experimental protocols

Olga Giraldo, Alexander García, Federico López, Oscar Corcho
2017 Journal of Biomedical Semantics  
Our contribution is twofold; on the one hand, SMART Protocols delivers a semantic layer that represents the knowledge encoded in experimental protocols.  ...  In this paper we present "SMART Protocols", a semantic and NLP-based infrastructure for processing and enacting experimental protocols.  ...  We thank to Edna Ruckhaus for her useful discussions.  ... 
doi:10.1186/s13326-017-0160-y pmid:29132408 pmcid:PMC5683383 fatcat:a6ghxhrzgfgmfh35kziugpedkm

Sketched Reality: Sketching Bi-Directional Interactions Between Virtual and Physical Worlds with AR and Actuated Tangible UI [article]

Hiroki Kaimoto, Kyzyl Monteiro, Mehrad Faridan, Jiatong Li, Samin Farajian, Yasuaki Kakehi, Ken Nakagaki, Ryo Suzuki
2022 arXiv   pre-print
This paper introduces Sketched Reality, an approach that combines AR sketching and actuated tangible user interfaces (TUI) for bidirectional sketching interaction.  ...  We demonstrate a series of potential applications, such as tangible physics education, explorable mechanism, tangible gaming for children, and in-situ robot programming via sketching.  ...  Figure 13 represents how AR sketching can be used for pinball gaming, allowing users to sketch obstacles and play the game with a physical controller and moving physical balls.  ... 
arXiv:2208.06341v1 fatcat:wk2gn2r52bghpeidu3badrsimq

EXACT2: the semantics of biomedical protocols

Larisa N Soldatova, Daniel Nadis, Ross D King, Piyali S Basu, Emma Haddi, Véronique Baumlé, Nigel J Saunders, Wolfgang Marwan, Brian B Rudkin
2014 BMC Bioinformatics  
EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications.  ...  Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility.  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the  ... 
doi:10.1186/1471-2105-15-s14-s5 pmid:25472549 pmcid:PMC4255744 fatcat:ao5hwxozczferfmkfqzfbd3n5e

Using Semantics and NLP in the SMART Protocols Repository

Olga L. Giraldo, Alexander García Castro, Óscar Corcho
2015 International Conference on Biomedical Ontology  
In this poster we present the semantic and NLP layers in the development of our repository for experimental protocols.  ...  We have studied existing repositories for experimental protocols as well the experimental protocols themselves.  ...  We have reviewed proposed standards for representing experimental protocols, investigations, experiments, scientific documents, rhetorical structures and annotations.  ... 
dblp:conf/icbo/GiraldoGC15 fatcat:droqwu5mgfewpl2sdgiyhqhpxm

Experimental Biological Protocols with Formal Semantics [article]

Alessandro Abate, Luca Cardelli, Marta Kwiatkowska, Luca Laurenti, Boyan Yordanov
2018 arXiv   pre-print
While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics.  ...  representing the liquid-handling steps of biological protocols.  ...  Stochastic Semantics of Experimental Protocols In this Section we introduce the stochastic semantics for an experimental protocol, and show that any program defined according to Definition 1 can be mapped  ... 
arXiv:1710.08016v2 fatcat:ml2j2pqcxbeohowswfqiapub6m

Experimental Biological Protocols with Formal Semantics [chapter]

Alessandro Abate, Luca Cardelli, Marta Kwiatkowska, Luca Laurenti, Boyan Yordanov
2018 Lecture Notes in Computer Science  
While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics.  ...  together with the discrete events representing the liquid-handling steps of biological protocols.  ...  Giving to the language a formal semantics in terms of a PDMP allows us to include in our semantics the uncertainties intrinsic in the discrete operations of an experimental protocol.  ... 
doi:10.1007/978-3-319-99429-1_10 fatcat:yvmmeumrrneo3penpjkni7b4le

Nanotate: Semantically Annotating Experimental Protocols with Nanopublications

Olga L. Giraldo, Miguel Ruano, Robin A. Richardson, Remzi Celebi, Michel Dumontier, Tobias Kuhn
2022 Workshop on Semantic Web Applications and Tools for Life Sciences  
This paper addresses this problem by extracting, representing and publishing steps from experimental protocols to make them Findable, Accessible, Interoperable, and Reusable (FAIR).  ...  Such experimental protocols indicate, for each step, exactly how it should be executed, often including equipment, reagents, descriptions of critical steps, troubleshooting instructions, other kinds of  ...  The domain experts are able to infer the use of some equipment, due to the narrative; for instance, use of experimental actions like "centrifuge", and additional information such as temperature of centrifugation  ... 
dblp:conf/swat4ls/GiraldoRRCDK22 fatcat:2bgq7pwprzdqjezu3iudlzsnl4

A privacy preserving efficient protocol for semantic similarity join using long string attributes

Bilal Hawashin, Farshad Fotouhi, Traian Marius Truta
2011 Proceedings of the 4th International Workshop on Privacy and Anonymity in the Information Society - PAIS '11  
However, the existing secure protocols for similarity join methods can not be used to join tables using these long attributes.  ...  Results show that our protocol can efficiently join tables using the long attributes by considering the semantic relationships among the long string values.  ...  Section 4 represents the experimental part where we compare the previous candidate semantic methods and study the performance of our protocol upon using the best performing methods from the previous comparison  ... 
doi:10.1145/1971690.1971696 dblp:conf/edbt/HawashinFT11 fatcat:rqe2pjglujd7tmgwrm6gshfzke

CoordSS: An ontology framework for heterogeneous networks experimentation

Valentina Nejkovic, Filip Jelenkovic, Milorad Tosic, Nenad Milosevic, Zorica Nikolic
2016 Telfor Journal  
The synergy between semantic and cognitive computing is introduced as the theoretical foundation of the paper.  ...  In the framework, domain and system ontologies are adopted for formal representation of the knowledge about the context of the problem.  ...  The CoordSS OEF represents a base for a solution of coordination protocol based on semantic technologies and ontologies.  ... 
doi:10.5937/telfor1602070n fatcat:5b2d3s7frne47diueh4uj3e6gu

Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation

Max Schröder, Susanne Staehlke, Paul Groth, J. Barbara Nebe, Sascha Spors, Frank Krüger
2022 Journal of Biomedical Semantics  
The purpose of this study is to investigate whether such ELN protocols can be used to create semantic documentation of the provenance of research data by the use of ontologies and linked data methodologies  ...  Conclusions The semantic documentation of research data obtained from the ELN protocols allows for the representation of the retrospective provenance of research data in a machine-interpretable way.  ...  Acknowledgements We thank Tazin Hossain for her help with the prototypical implementation of parts of the structure-based approach.  ... 
doi:10.1186/s13326-021-00257-x pmid:35101121 pmcid:PMC8802522 fatcat:6j3vhsog3zddxavgjfycct4j7y

Ontological Clarity, Cognitive Engagement, and Conceptual Model Quality Evaluation: An Experimental Investigation

Simon Milton, Jayantha Rajapakse, Ron Weber
2012 Journal of the AIS  
a quality evaluation method designed to cognitively engage stakeholders with the semantics of the domain represented by a conceptual model.  ...  Thus, we believe that our treatment for the level of cognitive engagement evoked by the quality evaluation method did not take effect.  ...  We are indebted to participants at the Workshop for their helpful comments. We are indebted, also, to three reviewers and the senior editor for helpful comments throughout the review process.  ... 
doi:10.17705/1jais.00307 fatcat:6aklvblfunfehozj2giwet5hbe

A collaborative methodology for developing a semantic model for interlinking Cancer Chemoprevention linked-data sources

Dimitris Zeginis, Ali Hasnain, Nikolaos Loutas, Helena Futscher Deus, Ronan Fox, Konstantinos Tarabanis
2014 Semantic Web Journal  
The methodology is applied on the creation of the Cancer Chemoprevention semantic model that formally defines the fundamental entities used for annotating and describing inter-connected cancer chemoprevention  ...  of experimental data, procedures and protocols and iv) concepts to facilitate the representation of results related to virtual screening of chemopreventive agents.  ...  For example, a cluster contains the concepts "clinical trial protocol", "protocol", "experiment design protocol", "study design", "trial protocol", "experimental design" and as a representative concept  ... 
doi:10.3233/sw-130112 fatcat:6g5qaleaazdktjulp2u2tz7qxm

Protein Experimental Information Management System (PREIMS) Based on Ontology: Development and Applications

Junko Sato, Kouji Kozaki, Susumu Handa, Takashi Ikeda, Ryotaro Saka, Kohei Tomizuka, Yugo Nishiyama, Toshiyuki Okumura, Shinichi Hirai, Tadashi Ohno, Mamoru Ohta, Susumu Date (+1 others)
2013 IPSJ Transactions on Bioinformatics  
Its contents are mainly experimental protocols for the analyses of protein structures and functions, and their results.  ...  Furthermore we converted those protocols in the format of Resource Description Framework (RDF) for integration with other biological information resources.  ...  S.M. is a research fellow of the Japan Society for the Promotion of Science (JSPS).  ... 
doi:10.2197/ipsjtbio.6.9 fatcat:dtjppcpgrzapxjizctlbj3lox4

The ontology supported intelligent system for experiment search in the scientific Research center

Vladimir Cvjetkovic, Marija Djokic, Branko Arsic, Milena Curcic
2014 Kragujevac Journal of Science  
Ontologies and corresponding knowledge bases can be quite successfully used for many tasks that rely on domain knowledge and semantic structures, which should be available for machine processing and sharing  ...  According to created ontology corresponding knowledge base was made and populated with real experimental data.  ...  Using of ontology [4] , as the core component of Semantic Web, for modeling, representing and visualization of an arbitrary semantic structure of experiment, justified the expectations.  ... 
doi:10.5937/kgjsci1436095c fatcat:pwroz3xlzbbkroh4pnlyztf66e

Harmonizing semantic annotations for computational models in biology

Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba (+16 others)
2018 Briefings in Bioinformatics  
Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community.  ...  Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent.  ...  Every COMBINE initiative either uses a protocol specific to that initiative or has no established protocol for semantic annotation.  ... 
doi:10.1093/bib/bby087 pmid:30462164 fatcat:hn6gsuwefneunmk4hda6pn54zq
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