Works in Journal of Biomedical Semantics, 2016, Vol 7

Results: 61

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0097-6

By:

Buttigieg, Pier Luigi;
Pafilis, Evangelos;
Lewis, Suzanna E.;
Schildhauer, Mark P.;
Walls, Ramona L.;
Mungall, Christopher J.

Publication type:

Article

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0107-8

By:

Hoehndorf, Robert;
Alshahrani, Mona;
Gkoutos, Georgios V.;
Gosline, George;
Groom, Quentin;
Hamann, Thomas;
Kattge, Jens;
de Oliveira, Sylvia Mota;
Schmidt, Marco;
Sierra, Soraya;
Smets, Erik;
Vos, Rutger A.;
Weiland, Claus

Publication type:

Article

Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0098-5

By:

Hogan, William R.;
Ceusters, Werner

Publication type:

Article

TrhOnt: building an ontology to assist rehabilitation processes.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0104-y

By:

Berges, Idoia;
Antón, David;
Bermúdez, Jesús;
Goñi, Alfredo;
Illarramendi, Arantza

Publication type:

Article

Expansion of medical vocabularies using distributional semantics on Japanese patient blogs.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0093-x

By:

Ahltorp, Magnus;
Skeppstedt, Maria;
Kitajima, Shiho;
Henriksson, Aron;
Rzepka, Rafal;
Araki, Kenji

Publication type:

Article

tESA: a distributional measure for calculating semantic relatedness.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0109-6

By:

Rybinski, Maciej;
Aldana-Montes, José Francisco

Publication type:

Article

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0108-7

By:

Verspoor, Karin;
Oellrich, Anika;
Collier, Nigel;
Groza, Tudor;
Rocca-Serra, Philippe;
Soldatova, Larisa;
Dumontier, Michel;
Shah, Nigam

Publication type:

Article

TNM-O: ontology support for staging of malignant tumours.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0106-9

By:

Boeker, Martin;
França, Fábio;
Bronsert, Peter;
Schulz, Stefan

Publication type:

Article

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0100-2

By:

Jie Zheng;
Harris, Marcelline R.;
Masci, Anna Maria;
Yu Lin;
Hero, Alfred;
Smith, Barry;
Yongqun He

Publication type:

Article

Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0091-z

By:

Duque-Ramos, Astrid;
Quesada-Martínez, Manuel;
Iniesta-Moreno, Miguela;
Fernández-Breis, Jesualdo Tomás;
Stevens, Robert

Publication type:

Article

Dione: An OWL representation of ICD-10-CM for classifying patients' diseases.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0105-x

By:

del Mar Roldán-García, María;
García-Godoy, María Jesús;
Aldana-Montes, José F.

Publication type:

Article

The early bird catches the term: combining twitter and news data for event detection and situational awareness.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0103-z

By:

Thapen, Nicholas;
Simmie, Donal;
Hankin, Chris

Publication type:

Article

Can SNOMED CT be squeezed without losing its shape?

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0101-1

By:

López-García, Pablo;
Schulz, Stefan

Publication type:

Article

A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0102-0

By:

Mutowo, Prudence;
Bento, A. Patrícia;
Dedman, Nathan;
Gaulton, Anna;
Hersey, Anne;
Lomax, Jane;
Overington, John P.

Publication type:

Article

Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0095-8

By:

Pozza, Giandomenico;
Borgo, Stefano;
Oltramari, Alessandro;
Contalbrigo, Laura;
Marangon, Stefano

Publication type:

Article

Towards natural language question generation for the validation of ontologies and mappings.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0089-6

By:

Abacha, Asma Ben;
Dos Reis, Julio Cesar;
Mrabet, Yassine;
Pruski, Cédric;
Da Silveira, Marcos

Publication type:

Article

Making adjustments to event annotations for improved biological event extraction.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0094-9

By:

Baek, Seung-Cheol;
Park, Jong C.

Publication type:

Article

The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0092-y

By:

Hogan, William R.;
Wagner, Michael M.;
Brochhausen, Mathias;
Levander, John;
Brown, Shawn T.;
Millett, Nicholas;
DePasse, Jay;
Hanna, Josh

Publication type:

Article

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0090-0

By:

Slater, Luke;
Gkoutos, Georgios V.;
Schofield, Paul N.;
Hoehndorf, Robert

Publication type:

Article

The ontology of medically related social entities: recent developments.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0087-8

By:

Hicks, Amanda;
Hanna, Josh;
Welch, Daniel;
Brochhausen, Mathias;
Hogan, William R.

Publication type:

Article

PhenoImageShare: an image annotation and query infrastructure.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0072-2

By:

Adebayo, Solomon;
McLeod, Kenneth;
Tudose, Ilinca;
Osumi-Sutherland, David;
Burdett, Tony;
Baldock, Richard;
Burger, Albert;
Parkinson, Helen

Publication type:

Article

COMODI: an ontology to characterise differences in versions of computational models in biology.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0080-2

By:

Scharm, Martin;
Waltemath, Dagmar;
Mendes, Pedro;
Wolkenhauer, Olaf

Publication type:

Article

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0088-7

By:

Diehl, Alexander D.;
Meehan, Terrence F.;
Bradford, Yvonne M.;
Brush, Matthew H.;
Dahdul, Wasila M.;
Dougall, David S.;
Yongqun He;
Osumi-Sutherland, David;
Ruttenberg, Alan;
Sarntivijai, Sirarat;
Van Slyke, Ceri E.;
Vasilevsky, Nicole A.;
Haendel, Melissa A.;
Blake, Judith A.;
Mungall, Christopher J.

Publication type:

Article

Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0086-9

By:

Scuba, William;
Tharp, Melissa;
Mowery, Danielle;
Tseytlin, Eugene;
Yang Liu;
Drews, Frank A.;
Chapman, Wendy W.

Publication type:

Article

A corpus of potentially contradictory research claims from cardiovascular research abstracts.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0083-z

By:

Alamri, Abdulaziz;
Stevenson, Mark

Publication type:

Article

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0079-8

By:

Iyappan, Anandhi;
Kawalia, Shweta Bagewadi;
Raschka, Tamara;
Hofmann-Apitius, Martin;
Senger, Philipp

Publication type:

Article

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0067-z

By:

Bolleman, Jerven T.;
Mungall, Christopher J.;
Strozzi, Francesco;
Baran, Joachim;
Dumontier, Michel;
Bonnal, Raoul J. P.;
Buels, Robert;
Hoehndorf, Robert;
Fujisawa, Takatomo;
Katayama, Toshiaki;
Cock, Peter J. A.

Publication type:

Article

Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0084-y

By:

Mowery, Danielle L.;
South, Brett R.;
Christensen, Lee;
Jianwei Leng;
Peltonen, Laura-Maria;
Salanterä, Sanna;
Suominen, Hanna;
Martinez, David;
Velupillai, Sumithra;
Elhadad, Noémie;
Savova, Guergana;
Pradhan, Sameer;
Chapman, Wendy W.

Publication type:

Article

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0081-1

By:

Leung, Tiffany I.;
Dumontier, Michel

Publication type:

Article

Functional coherence metrics in protein families.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0076-y

By:

Bastos, Hugo P.;
Sousa, Lisete;
Clarke, Luka A.;
Couto, Francisco M.

Publication type:

Article

Large scale biomedical texts classification: a kNN and an ESA-based approaches.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0073-1

By:

Dramé, Khadim;
Mougin, Fleur;
Diallo, Gayo

Publication type:

Article

DermO; an ontology for the description of dermatologic disease.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0085-x

By:

Fisher, Hannah M.;
Hoehndorf, Robert;
Bazelato, Bruno S.;
Dadras, Soheil S.;
King Jr., Lloyd E.;
Gkoutos, Georgios V.;
Sundberg, John P.;
Schofield, Paul N.

Publication type:

Article

The cellular microscopy phenotype ontology.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0074-0

By:

Jupp, Simon;
Malone, James;
Burdett, Tony;
Heriche, Jean-Karim;
Williams, Eleanor;
Ellenberg, Jan;
Parkinson, Helen;
Rustici, Gabriella

Publication type:

Article

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0057-1

By:

Masashi Yokochi;
Naohiro Kobayashi;
Ulrich, Eldon L.;
Akira R. Kinjo;
Takeshi Iwata;
Yannis E. Ioannidis;
Livny, Miron;
Markley, John L.;
Haruki Nakamura;
Chojiro Kojima;
Toshimichi Fujiwara

Publication type:

Article

The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0071-3

By:

Read, Warren J.;
Demetriou, George;
Nenadic, Goran;
Ruddock, Noel;
Stevens, Robert;
Winter, Jerry

Publication type:

Article

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0069-x

By:

Guo, Abra;
Racz, Rebecca;
Junguk Hur;
Yu Lin;
Zuoshuang Xiang;
Lili Zhao;
Rinder, Jordan;
Guoqian Jiang;
Qian Zhu;
Yongqun He

Publication type:

Article

Inferring gene-to-phenotype and gene-to-disease relationships at Mouse Genome Informatics: challenges and solutions.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0054-4

By:

Bello, Susan M.;
Eppig, Janan T.

Publication type:

Article

Erratum to: Towards exergaming commons: composing the exergame ontology for publishing open game data.

Published in:: Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0082-0
Publication type:: Article

Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0056-2

By:

Jingcheng Du;
Yi Cai;
Yong Chen;
Cui Tao

Publication type:

Article

Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0065-1

By:

Mowery, Danielle L.;
Chapman, Brian E.;
Conway, Mike;
South, Brett R.;
Madden, Erin;
Keyhani, Salomeh;
Chapman, Wendy W.

Publication type:

Article

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0064-2

By:

Jingshan Huang;
Gutierrez, Fernando;
Strachan, Harrison J.;
Dejing Dou;
Weili Huang;
Smith, Barry;
Blake, Judith A.;
Eilbeck, Karen;
Natale, Darren A.;
Yu Lin;
Bin Wu;
de Silva, Nisansa;
Xiaowei Wang;
Zixing Liu;
Borchert, Glen M.;
Ming Tan;
Ruttenberg, Alan

Publication type:

Article

Developing a web-based SKOS editor.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-015-0043-z

By:

Conway, Mike;
Khojoyan, Artem;
Fana, Fariba;
Scuba, William;
Castine, Melissa;
Mowery, Danielle;
Chapman, Wendy;
Jupp, Simon

Publication type:

Article

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0070-4

By:

Mehryary, Farrokh;
Kaewphan, Suwisa;
Kai Hakala;
Ginter, Filip

Publication type:

Article

OBIB-a novel ontology for biobanking.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0068-y

By:

Brochhausen, Mathias;
Jie Zheng;
Birtwell, David;
Williams, Heather;
Masci, Anna Maria;
Ellis, Helena Judge;
Stoeckert Jr., Christian J.

Publication type:

Article

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

Published in:

2016

By:

Gupta, Samir;
Ross, Karen E.;
Tudor, Catalina O.;
Wu, Cathy H.;
Schmidt, Carl J.;
Vijay-Shanker, K.

Publication type:

Product Review

VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0062-4

By:

Yu Lin;
Jie Zheng;
Yongqun He

Publication type:

Article

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0066-0

By:

Jingshan Huang;
Eilbeck, Karen;
Smith, Barry;
Blake, Judith A.;
Dejing Dou;
Weili Huang;
Natale, Darren A.;
Ruttenberg, Alan;
Jun Huan;
Zimmermann, Michael T.;
Guoqian Jiang;
Yu Lin;
Bin Wu;
Strachan, Harrison J.;
Yongqun He;
Shaojie Zhang;
Xiaowei Wang;
Zixing Liu;
Borchert, Glen M.;
Ming Tan

Publication type:

Article

Modularising ontology and designing inference patterns to personalise health condition assessment: the case of obesity.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0049-1

By:

Sojic, Aleksandra;
Terkaj, Walter;
Contini, Giorgia;
Sacco, Marco

Publication type:

Article

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0051-7

By:

Sarntivijai, Sirarat;
Vasant, Drashtti;
Jupp, Simon;
Saunders, Gary;
Bento, A. Patrícia;
Gonzalez, Daniel;
Betts, Joanna;
Hasan, Samiul;
Koscielny, Gautier;
Dunham, Ian;
Parkinson, Helen;
Malone, James

Publication type:

Article

Extracting drug-enzyme relation from literature as evidence for drug drug interaction.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0052-6

By:

Yaoyun Zhang;
Heng-Yi Wu;
Jingcheng Du;
Jun Xu;
Jingqi Wang;
Cui Tao;
Lang Li;
Hua Xu

Publication type:

Article