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Journal of Biomedical Semantics, Volume 13
Volume 13, Number 1, December 2022
- Sheeba Samuel
, Birgitta König-Ries
:
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach. 1 - Roberto Zanoli, Alberto Lavelli, Theresa Löffler, Nicolas Andres Perez Gonzalez, Fabio Rinaldi
:
An annotated dataset for extracting gene-melanoma relations from scientific literature. 2 - Bernd Müller
, Leyla Jael Castro
, Dietrich Rebholz-Schuhmann
:
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature. 3 - Max Schröder, Susanne Stählke, Paul Groth
, J. Barbara Nebe, Sascha Spors, Frank Krüger
:
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation. 4 - Florent Baty
, Jemima Hegermann, Tiziana Locatelli, Claudio Rüegg, Christian Gysin, Frank Rassouli, Martin H. Brutsche
:
Text mining-based measurement of precision of polysomnographic reports as basis for intervention. 5 - Raphaël Gazzotti, Catherine Faron
, Fabien Gandon, Virginie Lacroix-Hugues, David Darmon
:
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction. 6 - Nicholas Nicholson
, Francesco Giusti
, Manola Bettio, Raquel Negrao Carvalho, Nadya Dimitrova, Tadeusz Dyba, Manuela Flego, Luciana Neamtiu, Giorgia Randi, Carmen Martos
:
A multipurpose TNM stage ontology for cancer registries. 7 - Amara Tariq
, Omar Kallas, Patricia C. Balthazar
, Scott Jeffery Lee, Terry Desser, Daniel L. Rubin, Judy Wawira Gichoya, Imon Banerjee:
Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma. 8 - Rajaram Kaliyaperumal, Mark D. Wilkinson
, Pablo Alarcón Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira
, Michel Dumontier, César Henrique Bernabé, Annika Jacobsen, Clémence M. A. Le Cornec, Mario Prieto Godoy, Núria Queralt-Rosinach, Leo J. Schultze Kool, Morris A. Swertz, Philip van Damme
, K. Joeri van der Velde, Nawel Lalout
, Shuxin Zhang
, Marco Roos:
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. 9 - Zhe Yang
, Kun Jiang, Miaomiao Lou, Yang Gong, Lili Zhang, Jing Liu, Xinyu Bao, Danhong Liu, Peng Yang:
Defining health data elements under the HL7 development framework for metadata management. 10 - Marine Louarn, Fabrice Chatonnet
, Xavier Garnier, Thierry Fest, Anne Siegel
, Catherine Faron
, Olivier Dameron
:
Improving reusability along the data life cycle: a regulatory circuits case study. 11 - Núria Queralt-Rosinach, Rajaram Kaliyaperumal, César Henrique Bernabé, Qinqin Long
, Simone A. Joosten
, Henk Jan van der Wijk, Erik Flikkenschild, Kees Burger, Annika Jacobsen, Barend Mons, Marco Roos
:
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic. 12 - Lucas Emanuel Silva e Oliveira
, Ana Carolina Peters, Adalniza Moura Pucca da Silva, Caroline P. Gebeluca, Yohan Bonescki Gumiel, Lilian Mie Mukai Cintho, Deborah Ribeiro Carvalho, Sadid A. Hasan, Claudia Maria Cabral Moro:
SemClinBr - a multi-institutional and multi-specialty semantically annotated corpus for Portuguese clinical NLP tasks. 13 - Olivia Sanchez-Graillet
, Christian Witte, Frank Grimm, Philipp Cimiano
:
An annotated corpus of clinical trial publications supporting schema-based relational information extraction. 14 - Hoang-Quynh Le
, Duy-Cat Can
, Nigel Collier:
Exploiting document graphs for inter sentence relation extraction. 15 - Olivia Sanchez-Graillet
, Christian Witte, Frank Grimm, Steffen Grautoff
, Basil Ell
, Philipp Cimiano
:
Synthesizing evidence from clinical trials with dynamic interactive argument trees. 16 - Samar Binkheder
, Heng-Yi Wu, Sara K. Quinney, Shijun Zhang, Md. Muntasir Zitu, Chienwei Chiang, Lei Wang, Josette Jones, Lang Li:
PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature. 17 - Lars Vogt
, István Mikó, Thomas Bartolomaeus:
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research. 18 - Philip van Damme
, Jesualdo Tomás Fernández-Breis
, Nirupama Benis, José Antonio Miñarro-Giménez, Nicolette F. de Keizer, Ronald Cornet:
Performance assessment of ontology matching systems for FAIR data. 19 - Samar Binkheder
, Heng-Yi Wu, Sara K. Quinney, Shijun Zhang, Md. Muntasir Zitu, Chienwei Chiang, Lei Wang, Josette Jones, Lang Li:
Correction: PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature. 20 - João Cardoso
, Leyla Jael Castro
, Fajar J. Ekaputra, Marie C. Jacquemot
, Marek Suchánek, Tomasz Miksa, José Borbinha
:
DCSO: towards an ontology for machine-actionable data management plans. 21 - Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, Licong Cui:
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. 22 - John Grimes
, Piotr Szul, Alejandro Metke-Jimenez, Michael Lawley, Kylynn Loi:
Pathling: analytics on FHIR. 23 - Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale
, John Beverley
, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang
, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili
, Robert Hoehndorf
, Zoë May Pendlington
, Paola Roncaglia
, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur
, Gilbert S. Omenn, Brian D. Athey, Barry Smith:
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. 25 - Lisa Kühnel
, Juliane Fluck
:
We are not ready yet: limitations of state-of-the-art disease named entity recognizers. 26
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