Volume 8, issue 1, December 2017
50 articles in this issue
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Identifying genotype-phenotype relationships in biomedical text
Authors
- Maryam Khordad
- Robert E. Mercer
- Content type: Research
- Open Access
- Published: 06 December 2017
- Article: 57
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Experiences from the anatomy track in the ontology alignment evaluation initiative
Authors (first, second and last of 4)
- Zlatan Dragisic
- Valentina Ivanova
- Patrick Lambrix
- Content type: Review
- Open Access
- Published: 04 December 2017
- Article: 56
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Matching disease and phenotype ontologies in the ontology alignment evaluation initiative
Authors (first, second and last of 10)
- Ian Harrow
- Ernesto Jiménez-Ruiz
- Arild Waaler
- Content type: Research
- Open Access
- Published: 02 December 2017
- Article: 55
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A document-centric approach for developing the tolAPC ontology
Authors (first, second and last of 4)
- Aisha Blfgeh
- Jennifer Warrender
- Phillip Lord
- Content type: Research
- Open Access
- Published: 28 November 2017
- Article: 54
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The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
Authors (first, second and last of 8)
- Vincent J. Henry
- Anne Goelzer
- Vincent Fromion
- Content type: Research
- Open Access
- Published: 23 November 2017
- Article: 53
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Using semantics for representing experimental protocols
Authors (first, second and last of 4)
- Olga Giraldo
- Alexander García
- Oscar Corcho
- Content type: Research
- Open Access
- Published: 13 November 2017
- Article: 52
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Entity recognition in the biomedical domain using a hybrid approach
Authors (first, second and last of 4)
- Marco Basaldella
- Lenz Furrer
- Fabio Rinaldi
- Content type: Research
- Open Access
- Published: 09 November 2017
- Article: 51
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Drug target ontology to classify and integrate drug discovery data
Authors (first, second and last of 22)
- Yu Lin
- Saurabh Mehta
- Stephan C. Schürer
- Content type: Research
- Open Access
- Published: 09 November 2017
- Article: 50
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Querying clinical data in HL7 RIM based relational model with morph-RDB
Authors (first, second and last of 4)
- Freddy Priyatna
- Raul Alonso-Calvo
- Oscar Corcho
- Content type: Research
- Open Access
- Published: 05 October 2017
- Article: 49
This is part of 1 collection: -
Towards refactoring the Molecular Function Ontology with a UML profile for function modeling
Authors
- Patryk Burek
- Frank Loebe
- Heinrich Herre
- Content type: Research
- Open Access
- Published: 04 October 2017
- Article: 48
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A histological ontology of the human cardiovascular system
Authors (first, second and last of 5)
- Claudia Mazo
- Liliana Salazar
- Enrique Alegre
- Content type: Research
- Open Access
- Published: 02 October 2017
- Article: 47
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Analysis and visualization of disease courses in a semantically-enabled cancer registry
Authors
- Angel Esteban-Gil
- Jesualdo Tomás Fernández-Breis
- Martin Boeker
- Content type: Research
- Open Access
- Published: 29 September 2017
- Article: 46
This is part of 1 collection: -
Simplifying drug package leaflets written in Spanish by using word embedding
Authors
- Isabel Segura-Bedmar
- Paloma Martínez
- Content type: Research
- Open Access
- Published: 29 September 2017
- Article: 45
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Semantic annotation in biomedicine: the current landscape
Authors
- Jelena Jovanović
- Ebrahim Bagheri
- Content type: Review
- Open Access
- Published: 22 September 2017
- Article: 44
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Large-scale online semantic indexing of biomedical articles via an ensemble of multi-label classification models
Authors (first, second and last of 5)
- Yannis Papanikolaou
- Grigorios Tsoumakas
- Ioannis Vlahavas
- Content type: Research
- Open Access
- Published: 22 September 2017
- Article: 43
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PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets
Authors (first, second and last of 5)
- Marija Djokic-Petrovic
- Vladimir Cvjetkovic
- David J. Wild
- Content type: Software
- Open Access
- Published: 20 September 2017
- Article: 42
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Towards achieving semantic interoperability of clinical study data with FHIR
Authors
- Hugo Leroux
- Alejandro Metke-Jimenez
- Michael J. Lawley
- Content type: Research
- Open Access
- Published: 19 September 2017
- Article: 41
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Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data
Authors (first, second and last of 8)
- Alokkumar Jha
- Yasar Khan
- Ratnesh Sahay
- Content type: Research
- Open Access
- Published: 19 September 2017
- Article: 40
This is part of 1 collection: -
Predicting activities of daily living for cancer patients using an ontology-guided machine learning methodology
Authors (first, second and last of 5)
- Hua Min
- Hedyeh Mobahi
- Janusz Wojtusiak
- Content type: Research
- Open Access
- Published: 16 September 2017
- Article: 39
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Design of an extensive information representation scheme for clinical narratives
Authors (first, second and last of 4)
- Louise Deléger
- Leonardo Campillos
- Aurélie Névéol
- Content type: Research
- Open Access
- Published: 11 September 2017
- Article: 37
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Ontology-based specification, identification and analysis of perioperative risks
Authors (first, second and last of 14)
- Alexandr Uciteli
- Juliane Neumann
- Heinrich Herre
- Content type: Research
- Open Access
- Published: 06 September 2017
- Article: 36
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RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Authors (first, second and last of 7)
- Samuel Lampa
- Egon Willighagen
- Ola Spjuth
- Content type: Software
- Open Access
- Published: 04 September 2017
- Article: 35
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Discovering associations between adverse drug events using pattern structures and ontologies
Authors (first, second and last of 6)
- Gabin Personeni
- Emmanuel Bresso
- Adrien Coulet
- Content type: Research
- Open Access
- Published: 22 August 2017
- Article: 29
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An ontology-driven tool for structured data acquisition using Web forms
Authors (first, second and last of 5)
- Rafael S. Gonçalves
- Samson W. Tu
- Mark A. Musen
- Content type: Software
- Open Access
- Published: 01 August 2017
- Article: 26
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Towards a more molecular taxonomy of disease
Authors
- Jisoo Park
- Benjamin J. Hescott
- Donna K. Slonim
- Content type: Research
- Open Access
- Published: 27 July 2017
- Article: 25
This is part of 1 collection: -
Ontological interpretation of biomedical database content
Authors (first, second and last of 4)
- Filipe Santana da Silva
- Ludger Jansen
- Stefan Schulz
- Content type: Research
- Open Access
- Published: 26 June 2017
- Article: 24
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Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets
Authors
- Aleksandra Gruca
- Marek Sikora
- Content type: Research
- Open Access
- Published: 26 June 2017
- Article: 23
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Disease Compass– a navigation system for disease knowledge based on ontology and linked data techniques
Authors (first, second and last of 5)
- Kouji Kozaki
- Yuki Yamagata
- Kazuhiko Ohe
- Content type: Research
- Open Access
- Published: 19 June 2017
- Article: 22
This is part of 1 collection: -
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation
Authors (first, second and last of 6)
- Marcos Martínez-Romero
- Clement Jonquet
- Mark A. Musen
- Content type: Research
- Open Access
- Published: 07 June 2017
- Article: 21
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Literature evidence in open targets - a target validation platform
Authors
- Şenay Kafkas
- Ian Dunham
- Johanna McEntyre
- Content type: Software
- Open Access
- Published: 06 June 2017
- Article: 20
This is part of 1 collection: -
Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies
Authors (first, second and last of 6)
- Deepak K. Sharma
- Harold R. Solbrig
- Guoqian Jiang
- Content type: Research
- Open Access
- Published: 05 June 2017
- Article: 19
This is part of 1 collection: -
Dead simple OWL design patterns
Authors (first, second and last of 4)
- David Osumi-Sutherland
- Melanie Courtot
- Christopher Mungall
- Content type: Software
- Open Access
- Published: 05 June 2017
- Article: 18
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Modulated evaluation metrics for drug-based ontologies
Authors
- Muhammad Amith
- Cui Tao
- Content type: Research
- Open Access
- Published: 24 April 2017
- Article: 17
This is part of 1 collection: -
Learning from biomedical linked data to suggest valid pharmacogenes
Authors (first, second and last of 6)
- Kevin Dalleau
- Yassine Marzougui
- Adrien Coulet
- Content type: Research
- Open Access
- Published: 20 April 2017
- Article: 16
This is part of 1 collection: -
MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank
Authors
- Yuqing Mao
- Zhiyong Lu
- Content type: Research
- Open Access
- Published: 17 April 2017
- Article: 15
This is part of 1 collection: -
SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature
Authors (first, second and last of 5)
- Behrouz Bokharaeian
- Alberto Diaz
- Ramyar Chavoshinejad
- Content type: Research
- Open Access
- Published: 07 April 2017
- Article: 14
This is part of 1 collection: -
BioFed: federated query processing over life sciences linked open data
Authors (first, second and last of 8)
- Ali Hasnain
- Qaiser Mehmood
- Dietrich Rebholz-Schuhmann
- Content type: Research
- Open Access
- Published: 15 March 2017
- Article: 13
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Ontology-based literature mining of E. coli vaccine-associated gene interaction networks
Authors
- Junguk Hur
- Arzucan Özgür
- Yongqun He
- Content type: Research
- Open Access
- Published: 14 March 2017
- Article: 12
This is part of 1 collection: -
Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data
Authors
- The Knowledge Base workgroup of the Observational Health Data Sciences and Informatics (OHDSI) collaborative
- Content type: Software
- Open Access
- Published: 07 March 2017
- Article: 11
This is part of 1 collection: -
Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
Authors (first, second and last of 10)
- William R. Hogan
- Josh Hanna
- Chris Delcher
- Content type: Research
- Open Access
- Published: 03 March 2017
- Article: 10
This is part of 1 collection: -
Optimization on machine learning based approaches for sentiment analysis on HPV vaccines related tweets
Authors (first, second and last of 5)
- Jingcheng Du
- Jun Xu
- Cui Tao
- Content type: Research
- Open Access
- Published: 03 March 2017
- Article: 9
This is part of 1 collection: -
12 years on – Is the NLM medical text indexer still useful and relevant?
Authors
- James Mork
- Alan Aronson
- Dina Demner-Fushman
- Content type: Research
- Open Access
- Published: 23 February 2017
- Article: 8
This is part of 1 collection: -
Evaluating the effect of annotation size on measures of semantic similarity
Authors
- Maxat Kulmanov
- Robert Hoehndorf
- Content type: Research
- Open Access
- Published: 13 February 2017
- Article: 7
This is part of 1 collection: -
Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus
Authors (first, second and last of 4)
- Vianney Jouhet
- Fleur Mougin
- Frantz Thiessard
- Content type: Research
- Open Access
- Published: 07 February 2017
- Article: 6
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SAFE: SPARQL Federation over RDF Data Cubes with Access Control
Authors (first, second and last of 7)
- Yasar Khan
- Muhammad Saleem
- Ratnesh Sahay
- Content type: Research
- Open Access
- Published: 01 February 2017
- Article: 5
This is part of 1 collection: -
Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy
Authors (first, second and last of 11)
- Ferdinand Dhombres
- Paul Maurice
- Jean-Marie Jouannic
- Content type: Research
- Open Access
- Published: 31 January 2017
- Article: 4
This is part of 1 collection: -
Consolidating drug data on a global scale using Linked Data
Authors
- Milos Jovanovik
- Dimitar Trajanov
- Content type: Research
- Open Access
- Published: 21 January 2017
- Article: 3
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Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources
Authors
- Mark E Sharp
- Content type: Research
- Open Access
- Published: 10 January 2017
- Article: 2
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An ontological analysis of medical Bayesian indicators of performance
Authors (first, second and last of 4)
- Adrien Barton
- Jean-François Ethier
- Anita Burgun
- Content type: Research
- Open Access
- Published: 03 January 2017
- Article: 1
This is part of 1 collection: