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Easy-to-use Semantic Search of Pharmacological Data

Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis
2016 Workshop on Semantic Web Applications and Tools for Life Sciences  
To overcome these limitations, we have set up a novel pharmacological search facility that combines data from multiple RDF sources and uses PepeSearch to formulate queries.  ...  We demonstrate this search system that is currently being tested with clinicians as a means for exploring the knowledge contained in these databases, to create flexible queries and to support decision-making  ...  To overcome these limitations we are working on providing an easy-to-use search facility of pharmacological data.  ... 
dblp:conf/swat4ls/Esteban-GilF16a fatcat:izi6ufwnrvcexaic7x456cumhm

OpenPHACTS Explorer 2: Bringing the Web to the Semantic Web

Ian Dunlop, Rishi Ramgolam, Steve Pettifer, Alasdair J. G. Gray, James M. Eales, Carole A. Goble, Jan Velterop
2013 Workshop on Semantic Web Applications and Tools for Life Sciences  
It provides a UI layer on top of the Open PHACTS linked data cache and also provides a javascript library to facilitate easy access to the Open PHACTS API.  ...  The Open PHACTS Explorer is a web application that supports drug discovery via the Open PHACTS API without requiring knowledge of SPARQL or the RDF data being searched.  ...  Introduction A common criticism of the semantic web and linked data is the lack of end-user tools available [1] .  ... 
dblp:conf/swat4ls/DunlopRPGEGV13 fatcat:xpxhuhlxdncqnbujh35irbctpq

Towards interoperability of information sources within a hospital Intranet

S Aymard, D Fieschi, F Volot, M Joubert, M Fieschi
1998 Proceedings. AMIA Symposium  
The project ARIANE is devoted to provide end-users with an easy to use and natural access to information databases.  ...  Information is usually available in heterogeneous data format and various legacy sources. Interoperability appears to be a major approach for applications to access information.  ...  Many thanks to Microsoft™ France for its helpful assistance.  ... 
pmid:9929297 pmcid:PMC2232205 fatcat:gffqqzc4nvhxheyywln6225bte

Drug Encyclopedia – Linked Data Application for Physicians [chapter]

Jakub Kozák, Martin Nečaský, Jaroslav Pokorný
2015 Lecture Notes in Computer Science  
In this paper we present an application called Drug Encyclopedia which is built on the top of the data mart represented as Linked Data and enables physicians to search and browse clinically relevant information  ...  We describe the development driven by requirements, data mart creation, application evaluation and discuss the lessons learned.  ...  Semantic technologies enable us to easily implement the above mentioned configuration of the search.  ... 
doi:10.1007/978-3-319-25010-6_3 fatcat:syjsq2jdr5c7pgwmws26icwswq

DisGeNET: from MySQL to Nanopublication, Modelling Gene-Disease Associations for the Semantic Web

Núria Queralt-Rosinach, Laura Inés Furlong
2012 Workshop on Semantic Web Applications and Tools for Life Sciences  
DisGeNET is a relational gene-disease database that has been converted to RDF in order to make gene-disease association data available for Semantic Web projects such as Open PHACTS.  ...  In this paper, the conversion of DisGeNET from MySQL to RDF and their modelization to the nanopublication data format is presented, and we discuss the challenges encountered throughout the process.  ...  The research leading to these results has received support from the IMI Joint Undertaking under grant agreement n • 115191, Open PHACTS, resources of which are composed of financial contribution from the  ... 
dblp:conf/swat4ls/Queralt-RosinachF12 fatcat:4i6e44rfuzbcvfv4kecv6yvoue

Semantic Queries Expedite MedDRA Terms Selection Thanks to a Dedicated User Interface: A Pilot Study on Five Medical Conditions

Julien Souvignet, Gunnar Declerck, Béatrice Trombert-Paviot, Hadyl Asfari, Marie-Christine Jaulent, Cédric Bousquet
2019 Frontiers in Pharmacology  
Our objective was to compare user performances when using a new kind of user interface enabling semantic queries versus classical methods, and evaluating term selection improvement in MedDRA.  ...  Results: OntoADR Query Tools allows the user to search in MedDRA: One may enter search criteria by selecting one semantic property from a dropdown list and one or more SNOMED CT concepts related to the  ...  ACKNOWLEDGMENTS We kindly acknowledge the eight users who have participated in the comparison of OQT and MWB: Florelle Bellet, Marie-Noelle Beyens, Lucienne Clavel, Virginie Fulda, Claire Guy, Agnès Lillo-Le  ... 
doi:10.3389/fphar.2019.00050 pmid:30792654 pmcid:PMC6374626 fatcat:d3h7zdxh5vdenimvolnmp6t2ju

A Nanopublication Framework for Biological Networks using Cytoscape.js

Jim McCusker, Rui Yan, Kusum Solanki, John S. Erickson, Cynthia Chang, Michel Dumontier, Jonathan S. Dordick, Deborah L. McGuinness
2014 International Conference on Biomedical Ontology  
A semantic web service API is provided that enables search, traversal, and provides composite probabilities for the resulting graph of biological entities using the SADI web service framework and Nanopublications  ...  In our efforts to create a systematic approach to discovering new uses for existing drugs, we have developed Repurposing Drugs with Semantics (ReDrugS).  ...  ACKNOWLEDGMENTS A special thanks to Pascale Gaudet, who, with Michel Dumontier, evaluated the experimental methods and evidence codes listed in the Protein/Protein Interaction Ontology and Gene Ontology  ... 
dblp:conf/icbo/McCuskerYSECDDM14 fatcat:qtshz3fbyfcvdfiydh3qu3flyi

Semantic relations for interpreting DNA microarray data

Dimitar Hristovski, Andrej Kastrin, Borut Peterlin, Thomas C Rindflesch
2009 AMIA Annual Symposium Proceedings  
However, results are not easy to interpret.  ...  Our proposal enhances current methods in this regard and uses semantic relations extracted from biomedical text with the SemRep information extraction system.  ...  We use Lucene for fast searching and then used the data stored in MySQL when needed. The tools for searching are web-based and are developed with the Ruby on Rails application development framework.  ... 
pmid:20351860 pmcid:PMC2815475 fatcat:vyqh4zjob5cwlp6lc2nejloifm

An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies

Oriol López-Massaguer, Ferran Sanz, Manuel Pastor, John Hancock
2017 Bioinformatics  
The tool extracts data from the 'Open Pharmacological Space' (OPS) developed by the Open PHACTS project, using as input a valid name of the biological target.  ...  We describe an application (Collector) for obtaining series of compounds annotated with bioactivity data, ready to be used for the development of quantitative structure-activity relationships (QSAR) models  ...  by integrating relevant data sources using semantic web technologies (Allemang and Hendler, 2011; Berners-Lee et al., 2001; Parsons, 2009 ).  ... 
doi:10.1093/bioinformatics/btx566 pmid:28968713 fatcat:njm4w2twrrhjtffgzz57u5iefa

Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research

David J. Wild, Ying Ding, Amit P. Sheth, Lee Harland, Eric M. Gifford, Michael S. Lajiness
2012 Drug Discovery Today  
Recent Semantic Web technologies such as RDF and SPARQL are technical enablers of systems chemical biology, facilitating the deployment of advanced algorithms for searching and mining large integrated  ...  as chemogenomics, are central to emerging new paradigms of drug discovery such as drug repurposing and personalized medicine.  ...  Semantically integrated networks of data Why semantic networks are useful There are two key advantages of using integrated networks of data from multiple datasets over searching those datasets individually  ... 
doi:10.1016/j.drudis.2011.12.019 pmid:22222943 fatcat:ihung2o5cnhrjbytslxfm2lxx4

Biomedical question answering using semantic relations

Dimitar Hristovski, Dejan Dinevski, Andrej Kastrin, Thomas C Rindflesch
2015 BMC Bioinformatics  
The tool has some extensions that make it especially useful for interpretation of DNA microarray results.  ...  up to the end of 2012).  ...  Acknowledgements This study was supported in part by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.  ... 
doi:10.1186/s12859-014-0365-3 pmid:25592675 pmcid:PMC4307891 fatcat:oqid5twg4zh6pixtwsoo2rvrzm

Electronic Medical Record Search Engine (EMERSE): An Information Retrieval Tool for Supporting Cancer Research

David A. Hanauer, Jill S. Barnholtz-Sloan, Mark F. Beno, Guilherme Del Fiol, Eric B. Durbin, Oksana Gologorskaya, Daniel Harris, Brett Harnett, Kensaku Kawamoto, Benjamin May, Eric Meeks, Emily Pfaff (+2 others)
2020 JCO Clinical Cancer Informatics  
Search terms for two of the sites were characterized using the natural language processing tool MetaMap to determine to which semantic types the terms could be mapped.  ...  Many user-entered search queries could not be mapped to a semantic type, but the most common semantic type for terms that did match was "disease or syndrome," followed by "pharmacologic substance."  ...  Relevance Information retrieval systems such as EMERSE have the potential to be powerful and easy-to-use software tools for supporting cancer research.  ... 
doi:10.1200/cci.19.00134 pmid:32412846 pmcid:PMC7265780 fatcat:eig3tsystzgphaxaln6hr5vfsq

Supporting infobuttons with terminological knowledge

J J Cimino, G Elhanan, Q Zeng
1997 Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium  
We make use of knowledge in our terminology, the Medical Entities Dictionary (MED) to assist with the selection of appropriate queries and resources, as well as the translation of patient data to forms  ...  We have developed several prototype applications which integrate clinical systems with on-line information resources by using patient data to drive queries in response to user information needs.  ...  Elhanan is supported in part by National Library of Medicine training grant LM07079. The authors thank Socrates Socratous for programming support. References  ... 
pmid:9357682 pmcid:PMC2233544 fatcat:55p7ug5y6nd5fj2jz22nz7edeu

Survey of NLP in Pharmacology: Methodology, Tasks, Resources, Knowledge, and Tools [article]

Dimitar Trajanov, Vangel Trajkovski, Makedonka Dimitrieva, Jovana Dobreva, Milos Jovanovik, Matej Klemen, Aleš Žagar, Marko Robnik-Šikonja
2022 arXiv   pre-print
The main objective of this work is to survey the recent use of NLP in the field of pharmacology.  ...  It has been used extensively, from intelligent searches through thousands of medical documents to finding traces of adversarial drug interactions in social media.  ...  The work in this paper was partially financed by the Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University in Skopje.  ... 
arXiv:2208.10228v1 fatcat:76kwzhx53fbfpowwjie5neeicu

A New Semantic Resource Description Framework for Medical Diagnosis based on Gene Ontology

2020 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
Semantic-Based medical informatics system is an interdisciplinary deflect of bioinformatics research, where a dealing to knowledge discovery of proper diagnosis of disease leads to more attention about  ...  Due to this limited citation information force to develop a new dimension of the semantic web-based medical diagnosis system.  ...  Drug: The drug is a combination of chemical, pharmacological and pharmaceutical data used to target sequence, structure, and pathway information for docking complete drug [14] . c).  ... 
doi:10.35940/ijitee.c8324.019320 fatcat:3yqa4n44frc2njk2imx23r3miq
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