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Editor’s introduction to the special issue of the 6th Biomedical Linked Annotation Hackathon (BLAH6)

Kim JD, Cohen KB, Rinaldi F, Lu Z, Collier N, Park HS

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Choosing preferable labels for the Japanese translation of the Human Phenotype Ontology

Ninomiya K, Takatsuki T, Kushida T, Yamamoto Y, Ogishima S

The Human Phenotype Ontology (HPO) is the de facto standard ontology to describe human phenotypes in detail, and it is actively used, particularly in the field of rare disease diagnoses....
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A proof-of-concept study of extracting patient histories for rare/intractable diseases from social media

Yamaguchi A, Queralt-Rosinach N

The amount of content on social media platforms such as Twitter is expanding rapidly. Simultaneously, the lack of patient information seriously hinders the diagnosis and treatment of rare/intractable diseases. However,...
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An empirical evaluation of electronic annotation tools for Twitter data

Weissenbacher D, O'Connor K, Hiraki AT, Kim JD, Gonzalez-Hernandez G

Despite a growing number of natural language processing shared-tasks dedicated to the use of Twitter data, there is currently no ad-hoc annotation tool for the purpose. During the 6th edition...
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open-japanese-mesh: assigning MeSH UIDs to Japanese medical terms via open Japanese-English glossaries

Yamada R, Tatieisi Y

The Medical Subject Headings (MeSH) system is a controlled vocabulary for indexing biomedical documents that is used for document retrieval and other natural language processing purposes. However, although the original...
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WTO, an ontology for wheat traits and phenotypes in scientific publications

Nédellec C, Ibanescu L, Bossy R, Sourdille P

Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop. The need to improve...
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Using the PubAnnotation ecosystem to perform agile text mining on Genomics & Informatics: a tutorial review

Nam HJ, Yamada R, Park HS

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository. The full-text publications of volumes 10 through 17 are also directly...
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SciBabel: a system for crowd-sourced validation of automatic translations of scientific texts

Soares F, Rebechi R, Stevenson M

Scientific research is mostly published in English, regardless of the researcher's nationality. However, this growing practice impairs or hinders the comprehension of professionals who depend on the results of these...
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Improving accessibility and distinction between negative results in biomedical relation extraction

Sousa D, Lamurias A, Couto FM

Accessible negative results are relevant for researchers and clinicians not only to limit their search space but also to prevent the costly re-exploration of research hypotheses. However, most biomedical relation...
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Enabling a fast annotation process with the Table2Annotation tool

Larmande P, Jibril KM

In semantic annotation, semantic concepts are linked to natural language. Semantic annotation helps in boosting the ability to search and access resources and can be used in information retrieval systems...
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Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods

Neves M

Finding publications that propose alternative methods to animal experiments is an important but time-consuming task since researchers need to perform various queries to literature databases and screen many articles to...
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Social Media Mining Toolkit (SMMT)

Tekumalla R, Banda JM

There has been a dramatic increase in the popularity of utilizing social media data for research purposes within the biomedical community. In PubMed alone, there have been nearly 2,500 publication...
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Extending TextAE for annotation of non-contiguous entities

Lever J, Altman R, Kim JD

Named entity recognition tools are used to identify mentions of biomedical entities in free text and are essential components of high-quality information retrieval and extraction systems. Without good entity recognition,...
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