Volume 6; Issue 1

Journal of Biomedical Semantics

Volume 6; Issue 1

1

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles

Kafkas, Şenay, Kim, Jee-Hyub, Pi, Xingjun, McEntyre, Johanna R

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 670 KB

english, 2015

2

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions

Hur, Junguk, Özgür, Arzucan, Xiang, Zuoshuang, He, Yongqun

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1015 KB

english, 2015

3

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns

Xiang, Zuoshuang, Zheng, Jie, Lin, Yu, He, Yongqun

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.48 MB

english, 2015

4

Similarity-based search of model organism, disease and drug effect phenotypes

Hoehndorf, Robert, Gruenberger, Michael, Gkoutos, Georgios V, Schofield, Paul N

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 336 KB

english, 2015

5

Completing the is-a structure in light-weight ontologies

Lambrix, Patrick, Wei-Kleiner, Fang, Dragisic, Zlatan

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.07 MB

english, 2015

6

Section level search functionality in Europe PMC

Kafkas, Şenay, Pi, Xingjun, Marinos, Nikos, Talo’, Francesco, Morrison, Andrew, McEntyre, Johanna R

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 759 KB

english, 2015

7

Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows

Fu, Xiao, Batista-Navarro, Riza, Rak, Rafal, Ananiadou, Sophia

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1018 KB

english, 2015

8

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment

Hastings, Janna, Jeliazkova, Nina, Owen, Gareth, Tsiliki, Georgia, Munteanu, Cristian R, Steinbeck, Christoph, Willighagen, Egon

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.89 MB

english, 2015

9

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct

Funk, Christopher S, Kahanda, Indika, Ben-Hur, Asa, Verspoor, Karin M

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

10

Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens

Smith, Cynthia L, Eppig, Janan T

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 905 KB

english, 2015

11

Development and validation of a classification approach for extracting severity automatically from electronic health records

Boland, Mary Regina, Tatonetti, Nicholas P, Hripcsak, George

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

12

Automated concept and relationship extraction for the semi-automated ontology management (SEAM) system

Doing-Harris, Kristina, Livnat, Yarden, Meystre, Stephane

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 760 KB

english, 2015

13

Capturing domain knowledge from multiple sources: the rare bone disorders use case

Groza, Tudor, Tudorache, Tania, Robinson, Peter N, Zankl, Andreas

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 536 KB

english, 2015

14

Exploring adverse drug events at the class level

Winnenburg, Rainer, Sorbello, Alfred, Bodenreider, Olivier

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.51 MB

english, 2015

15

Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT

Winnenburg, Rainer, Mortensen, Jonathan M, Bodenreider, Olivier

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 3.10 MB

english, 2015

16

Developing VISO: Vaccine Information Statement Ontology for patient education

Amith, Muhammad, Gong, Yang, Cunningham, Rachel, Boom, Julie, Tao, Cui

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1015 KB

english, 2015

17

Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies

Leroux, Hugo, Lefort, Laurent

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

18

Evaluating drug-drug interaction information in NDF-RT and DrugBank

Peters, Lee B, Bahr, Nathan, Bodenreider, Olivier

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 499 KB

english, 2015

19

Linking gene expression to phenotypes via pathway information

Papatheodorou, Irene, Oellrich, Anika, Smedley, Damian

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

20

Annotation-based feature extraction from sets of SBML models

Alm, Rebekka, Waltemath, Dagmar, Wolfien, Markus, Wolkenhauer, Olaf, Henkel, Ron

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

21

Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury

Cairelli, Michael J, Fiszman, Marcelo, Zhang, Han, Rindflesch, Thomas C

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.45 MB

english, 2015

22

Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts

Cellier, Peggy, Charnois, Thierry, Plantevit, Marc, Rigotti, Christophe, Crémilleux, Bruno, Gandrillon, Olivier, Kléma, Jiří, Manguin, Jean-Luc

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 766 KB

english, 2015

23

Implementation of linked data in the life sciences at BioHackathon 2011

Aoki-Kinoshita, Kiyoko F, Kinjo, Akira R, Morita, Mizuki, Igarashi, Yoshinobu, Chen, Yi-an, Shigemoto, Yasumasa, Fujisawa, Takatomo, Akune, Yukie, Katoda, Takeo, Kokubu, Anna, Mori, Takaaki, Nakao, Mi

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.34 MB

english, 2015

24

Development of an Ontology for Periodontitis

Suzuki, Asami, Takai-Igarashi, Takako, Nakaya, Jun, Tanaka, Hiroshi

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.24 MB

english, 2015

25

A framework for ontology-based question answering with application to parasite immunology

Asiaee, Amir H., Minning, Todd, Doshi, Prashant, Tarleton, Rick L.

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 3.89 MB

english, 2015

26

Formalizing biomedical concepts from textual definitions

Petrova, Alina, Ma, Yue, Tsatsaronis, George, Kissa, Maria, Distel, Felix, Baader, Franz, Schroeder, Michael

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 989 KB

english, 2015

27

Special issue on bio-ontologies and phenotypes

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

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 376 KB

english, 2015

28

Nanopublications for exposing experimental data in the life-sciences: a Huntington’s Disease case study

Mina, Eleni, Thompson, Mark, Kaliyaperumal, Rajaram, Zhao, Jun, van der Horst, Eelke, Tatum, Zuotian, Hettne, Kristina M, Schultes, Erik A, Mons, Barend, Roos, Marco

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.52 MB

english, 2015

29

Concept selection for phenotypes and diseases using learn to rank

Collier, Nigel, Oellrich, Anika, Groza, Tudor

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 463 KB

english, 2015

30

Region Evolution eXplorer – A tool for discovering evolution trends in ontology regions

Christen, Victor, Hartung, Michael, Groß, Anika

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.67 MB

english, 2015

31

Discovering relations between indirectly connected biomedical concepts

Weissenborn, Dirk, Schroeder, Michael, Tsatsaronis, George

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 3.69 MB

english, 2015

32

Improving the Sequence Ontology terminology for genomic variant annotation

Cunningham, Fiona, Moore, Barry, Ruiz-Schultz, Nicole, Ritchie, Graham RS, Eilbeck, Karen

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 887 KB

english, 2015

33

Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS

Zhang, Yuji, Wu, Puqiang, Luo, Yi, Tao, Cui

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.37 MB

english, 2015

34

KneeTex: an ontology–driven system for information extraction from MRI reports

Spasić, Irena, Zhao, Bo, Jones, Christopher B., Button, Kate

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

35

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development

Rabattu, Pierre-Yves, Massé, Benoit, Ulliana, Federico, Rousset, Marie-Christine, Rohmer, Damien, Léon, Jean-Claude, Palombi, Olivier

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 3.33 MB

english, 2015

36

owlcpp: a C++ library for working with OWL ontologies

Levin, Mikhail K., Cowell, Lindsay G.

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.02 MB

english, 2015

37

Ontology-based representation and analysis of host-Brucellainteractions

Lin, Yu, Xiang, Zuoshuang, He, Yongqun

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

38

Colil: a database and search service for citation contexts in the life sciences domain

Fujiwara, Toyofumi, Yamamoto, Yasunori

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 1.98 MB

english, 2015

39

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource

van Dam, Jesse CJ, Koehorst, Jasper J, Schaap, Peter J, Martins dos Santos, Vitor AP, Suarez-Diez, Maria

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.69 MB

english, 2015

40

OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research

Uciteli, Alexandr, Herre, Heinrich

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.82 MB

english, 2015

41

Ambiguity and variability of database and software names in bioinformatics

Duck, Geraint, Kovacevic, Aleksandar, Robertson, David L., Stevens, Robert, Nenadic, Goran

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 664 KB

english, 2015