Volume 5, issue 1, December 2014
51 articles in this issue
-
-
AISO: Annotation of Image Segments with Ontologies
Authors (first, second and last of 6)
- Nikhil Tej Lingutla
- Justin Preece
- Pankaj Jaiswal
- Content type: Software
- Open Access
- Published: 17 December 2014
- Article: 50
-
A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis
Authors (first, second and last of 5)
- Kim Clark
- Deepak Sharma
- Cui Tao
- Content type: Research
- Open Access
- Published: 11 December 2014
- Article: 49
-
TermGenie – a web-application for pattern-based ontology class generation
Authors (first, second and last of 8)
- Heiko Dietze
- Tanya Z Berardini
- Christopher J Mungall
- Content type: Software
- Open Access
- Published: 11 December 2014
- Article: 48
-
TopFed: TCGA tailored federated query processing and linking to LOD
Authors (first, second and last of 7)
- Muhammad Saleem
- Shanmukha S Padmanabhuni
- Helena F Deus
- Content type: Research
- Open Access
- Published: 03 December 2014
- Article: 47
-
Automatically exposing OpenLifeData via SADI semantic Web Services
Authors (first, second and last of 7)
- Alejandro RodrÃguez González
- Alison Callahan
- Mark D Wilkinson
- Content type: Software
- Open Access
- Published: 19 November 2014
- Article: 46
-
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex
Authors (first, second and last of 6)
- James P Balhoff
- Wasila M Dahdul
- Todd J Vision
- Content type: Software
- Open Access
- Published: 05 November 2014
- Article: 45
-
An effective method of large scale ontology matching
Authors
- Gayo Diallo
- Content type: Research
- Open Access
- Published: 28 October 2014
- Article: 44
-
TypOn: the microbial typing ontology
Authors (first, second and last of 9)
- Cátia Vaz
- Alexandre P Francisco
- João A Carriço
- Content type: Research
- Open Access
- Published: 18 October 2014
- Article: 43
-
Executing SADI services in Galaxy
Authors
- Mikel Egaña Aranguren
- Alejandro RodrÃguez González
- Mark D Wilkinson
- Content type: Software
- Open Access
- Published: 22 September 2014
- Article: 42
-
Structuring research methods and data with the research object model: genomics workflows as a case study
Authors (first, second and last of 19)
- Kristina M Hettne
- Harish Dharuri
- Marco Roos
- Content type: Research
- Open Access
- Published: 18 September 2014
- Article: 41
-
Making species checklists understandable to machines – a shift from relational databases to ontologies
Authors (first, second and last of 4)
- Nina Laurenne
- Jouni Tuominen
- Eero Hyvönen
- Content type: Research
- Open Access
- Published: 08 September 2014
- Article: 40
-
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology
Authors (first, second and last of 7)
- Robert W Thacker
- Maria Cristina DÃaz
- Christopher J Mungall
- Content type: Research
- Open Access
- Published: 08 September 2014
- Article: 39
-
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference
Authors (first, second and last of 5)
- Janna Hastings
- Andy Brass
- Robert Stevens
- Content type: Research
- Open Access
- Published: 03 September 2014
- Article: 38
-
CLO: The cell line ontology
Authors (first, second and last of 25)
- Sirarat Sarntivijai
- Yu Lin
- Yongqun He
- Content type: Database
- Open Access
- Published: 13 August 2014
- Article: 37
-
Standardizing adverse drug event reporting data
Authors (first, second and last of 4)
- Liwei Wang
- Guoqian Jiang
- Hongfang Liu
- Content type: Research
- Open Access
- Published: 12 August 2014
- Article: 36
-
Automated reasoning using abduction for interpretation of medical signals
Authors
- Marjan Alirezaie
- Amy Loutfi
- Content type: Research
- Open Access
- Published: 12 August 2014
- Article: 35
-
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology
Authors (first, second and last of 7)
- Wasila M Dahdul
- Hong Cui
- Melissa A Haendel
- Content type: Research
- Open Access
- Published: 11 August 2014
- Article: 34
-
Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network
Authors (first, second and last of 7)
- Yuji Zhang
- Cui Tao
- Hongfang Liu
- Content type: Research
- Open Access
- Published: 06 August 2014
- Article: 33
This is part of 1 collection: -
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data
Authors (first, second and last of 5)
- Hongyan Wu
- Toyofumi Fujiwara
- Atsuko Yamaguchi
- Content type: Research
- Open Access
- Published: 10 July 2014
- Article: 32
-
CSEO – the Cigarette Smoke Exposure Ontology
Authors (first, second and last of 8)
- Erfan Younesi
- Sam Ansari
- Manuel C Peitsch
- Content type: Research
- Open Access
- Published: 10 July 2014
- Article: 31
-
A framework for assessing the consistency of drug classes across sources
Authors
- Rainer Winnenburg
- Olivier Bodenreider
- Content type: Research
- Open Access
- Published: 09 July 2014
- Article: 30
This is part of 1 collection: -
OAE: The Ontology of Adverse Events
Authors (first, second and last of 10)
- Yongqun He
- Sirarat Sarntivijai
- Barry Smith
- Content type: Research
- Open Access
- Published: 05 July 2014
- Article: 29
-
Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications
Authors
- Tim Clark
- Paolo N Ciccarese
- Carole A Goble
- Content type: Research
- Open Access
- Published: 04 July 2014
- Article: 28
-
Why functions are not special dispositions: an improved classification of realizables for top-level ontologies
Authors
- Johannes Röhl
- Ludger Jansen
- Content type: Research
- Open Access
- Published: 02 June 2014
- Article: 27
-
Generalising semantic category disambiguation with large lexical resources for fun and profit
Authors (first, second and last of 4)
- Pontus Stenetorp
- Sampo Pyysalo
- Jun’ichi Tsujii
- Content type: Research
- Open Access
- Published: 02 June 2014
- Article: 26
This is part of 1 collection: -
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
Authors (first, second and last of 7)
- James Malone
- Andy Brown
- Robert Stevens
- Content type: Database
- Open Access
- Published: 02 June 2014
- Article: 25
-
Terminology extraction from medical texts in Polish
Authors
- Małgorzata Marciniak
- Agnieszka Mykowiecka
- Content type: Research
- Open Access
- Published: 31 May 2014
- Article: 24
This is part of 1 collection: -
An ontological modeling approach for abnormal states and its application in the medical domain
Authors (first, second and last of 5)
- Yuki Yamagata
- Kouji Kozaki
- Riichiro Mizoguchi
- Content type: Research
- Open Access
- Published: 21 May 2014
- Article: 23
-
Mining characteristics of epidemiological studies from Medline: a case study in obesity
Authors
- George Karystianis
- Iain Buchan
- Goran Nenadic
- Content type: Research
- Open Access
- Published: 19 May 2014
- Article: 22
This is part of 1 collection: -
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Authors (first, second and last of 18)
- Melissa A Haendel
- James P Balhoff
- Christopher J Mungall
- Content type: Research
- Open Access
- Published: 19 May 2014
- Article: 21
-
My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models
Authors (first, second and last of 5)
- Olivier Palombi
- Federico Ulliana
- Marie-Christine Rousset
- Content type: Research
- Open Access
- Published: 06 May 2014
- Article: 20
-
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events
Authors
- Yu Lin
- Yongqun He
- Content type: Research
- Open Access
- Published: 30 April 2014
- Article: 19
This is part of 1 collection: -
Exploitation of semantic methods to cluster pharmacovigilance terms
Authors (first, second and last of 4)
- Marie Dupuch
- Laëtitia Dupuch
- Natalia Grabar
- Content type: Research
- Open Access
- Published: 16 April 2014
- Article: 18
-
A rule-based ontological framework for the classification of molecules
Authors
- Despoina Magka
- Markus Krötzsch
- Ian Horrocks
- Content type: Research
- Open Access
- Published: 15 April 2014
- Article: 17
-
A 2013 workshop: vaccine and drug ontology studies (VDOS 2013)
Authors
- Cui Tao
- Yongqun He
- Sivaram Arabandi
- Content type: Editorial
- Open Access
- Published: 20 March 2014
- Article: 16
This is part of 1 collection: -
Thematic series on biomedical ontologies in JBMS: challenges and new directions
Authors (first, second and last of 4)
- Robert Hoehndorf
- Melissa Haendel
- Dietrich Rebholz-Schuhmann
- Content type: Review
- Open Access
- Published: 06 March 2014
- Article: 15
This is part of 1 collection: -
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
Authors (first, second and last of 17)
- Michel Dumontier
- Christopher JO Baker
- Robert Hoehndorf
- Content type: Database
- Open Access
- Published: 06 March 2014
- Article: 14
This is part of 1 collection: -
Panacea, a semantic-enabled drug recommendations discovery framework
Authors (first, second and last of 4)
- Charalampos Doulaverakis
- George Nikolaidis
- Ioannis Kompatsiaris
- Content type: Research
- Open Access
- Published: 06 March 2014
- Article: 13
-
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio
Authors (first, second and last of 4)
- Ceri E Van Slyke
- Yvonne M Bradford
- Melissa A Haendel
- Content type: Research
- Open Access
- Published: 25 February 2014
- Article: 12
This is part of 1 collection: -
Benchmarking infrastructure for mutation text mining
Authors (first, second and last of 4)
- Artjom Klein
- Alexandre Riazanov
- Christopher JO Baker
- Content type: Research
- Open Access
- Published: 25 February 2014
- Article: 11
-
Mining images in biomedical publications: Detection and analysis of gel diagrams
Authors (first, second and last of 4)
- Tobias Kuhn
- Mate Levente Nagy
- Michael Krauthammer
- Content type: Research
- Open Access
- Published: 25 February 2014
- Article: 10
This is part of 1 collection: -
Variation ontology: annotator guide
Authors
- Mauno Vihinen
- Content type: Software
- Open Access
- Published: 17 February 2014
- Article: 9
-
Semantic interestingness measures for discovering association rules in the skeletal dysplasia domain
Authors (first, second and last of 4)
- Razan Paul
- Tudor Groza
- Andreas Zankl
- Content type: Research
- Open Access
- Published: 05 February 2014
- Article: 8
-
The pathway ontology – updates and applications
Authors (first, second and last of 15)
- Victoria Petri
- Pushkala Jayaraman
- Howard J Jacob
- Content type: Research
- Open Access
- Published: 05 February 2014
- Article: 7
This is part of 1 collection: -
Synonym extraction and abbreviation expansion with ensembles of semantic spaces
Authors (first, second and last of 5)
- Aron Henriksson
- Hans Moen
- Martin Duneld
- Content type: Research
- Open Access
- Published: 05 February 2014
- Article: 6
This is part of 1 collection: -
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Authors (first, second and last of 85)
- Toshiaki Katayama
- Mark D Wilkinson
- Toshihisa Takagi
- Content type: Review
- Open Access
- Published: 05 February 2014
- Article: 5
-
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources
Authors (first, second and last of 4)
- Catia Pesquita
- João D Ferreira
- Mário J Silva
- Content type: Research
- Open Access
- Published: 17 January 2014
- Article: 4
This is part of 1 collection: -
Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time?
Authors
- Manabu Torii
- Kavishwar Wagholikar
- Hongfang Liu
- Content type: Research
- Open Access
- Published: 17 January 2014
- Article: 3
This is part of 1 collection: -
The languages of health in general practice electronic patient records: a Zipf’s law analysis
Authors (first, second and last of 4)
- Leila R Kalankesh
- John P New
- Andy Brass
- Content type: Research
- Open Access
- Published: 10 January 2014
- Article: 2
This is part of 1 collection: