The June 2019 issue of Genomics & Informatics was published as a special issue on the 5th Biomedical Linked Annotation Hackathon (BLAH5).
2019. 07. 01 /
The June 2019 issue of Genomics & Informatics was published as a special issue on the 5th Biomedical Linked Annotation Hackathon (BLAH5).
BLAH5, whose main organizer was DBCLS, was held at Kashiwa lab of DBCLS in February 2019, as a hackathon specialized for text mining in life sciences.
The special issue includes 1 editorial, 2 mini reviews, and 7 application notes, which are all authored based on outcomes of the BLAH5 hackathon. They are all open access papers and can be accessed online as follows:
- Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining, Jin-Dong Kim, Kevin Bretonnel Cohen, Nigel Collier, Zhiyong Lu, Fabio Rinaldi, DOI: https://doi.org/10.5808/GI.2019.17.2.e12
- Resources for assigning MeSH IDs to Japanese medical terms, Yuka Tateisi, DOI: https://doi.org/10.5808/GI.2019.17.2.e16
- A review of drug knowledge discovery using BioNLP and tensor or matrix decomposition, Mina Gachloo, Yuxing Wang, Jingbo Xia, DOI: https://doi.org/10.5808/GI.2019.17.2.e18
- Fully connecting the Observational Health Data Science and Informatics (OHDSI) initiative with the world of linked open data, Juan M. Banda, DOI: https://doi.org/10.5808/GI.2019.17.2.e13
- Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications, Leyla Garcia, Olga Giraldo, Alexander Garcia, Dietrich Rebholz-Schuhmann, DOI: https://doi.org/10.5808/GI.2019.17.2.e14
- PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts, Jordi Armengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger, DOI: https://doi.org/10.5808/GI.2019.17.2.e15
- OryzaGP: rice gene and protein dataset for named-entity recognition, Pierre Larmande, Huy Do, Yue Wang, DOI: https://doi.org/10.5808/GI.2019.17.2.e17
- Towards cross-platform interoperability for machine-assisted text annotation Richard Eckart de Castilho, Nancy Ide, Jin-Dong Kim, Jan-Christoph Klie, Keith Suderman, DOI: https://doi.org/10.5808/GI.2019.17.2.e19
- Improving methods for normalizing biomedical text entities with concepts from an ontology with (almost) no training data at BLAH5 the CONTES, Arnaud Ferré, Mouhamadou Ba, Robert Bossy, DOI: https://doi.org/10.5808/GI.2019.17.2.e20
- Improving spaCy dependency annotation and PoS tagging web service using independent NER services, Nico Colic, Fabio Rinaldi, DOI: https://doi.org/10.5808/GI.2019.17.2.e21