ePat: extended PROVEAN annotation tool

The 'ePat' (extended PROVEAN annotation tool) is a software tool that extends the functionality of PROVEAN: a software tool for predicting whether amino acid substitutions and indels will affect the biological function of proteins. The 'ePat' extends the conventional PROVEAN to enable the following two things. First is to calculate the pathogenicity of indel mutations with frameshift and variants near splice junctions, for which the conventional PROVEAN could not calculate the pathogenicity of these variants. Second is to use batch processing to calculate the pathogenicity of multiple variants in a variants list (VCF file) in a single step. In order to identify variants that are predicted to be functionally important from the variants list, ePat can help filter out variants that affect biological functions by utilizing not only point mutations, and indel mutations that does not cause frameshift, but also frameshift, stop gain, and splice variants.

MedTAG: a portable and customizable annotation tool for biomedical documents

Background Semantic annotators and Natural Language Processing (NLP) methods for Named Entity Recognition and Linking (NER+L) require plenty of training and test data, especially in the biomedical domain. Despite the abundance of unstructured biomedical data, the lack of richly annotated biomedical datasets poses hindrances to the further development of NER+L algorithms for any effective secondary use. In addition, manual annotation of biomedical documents performed by physicians and experts is a costly and time-consuming task. To support, organize and speed up the annotation process, we introduce MedTAG, a collaborative biomedical annotation tool that is open-source, platform-independent, and free to use/distribute. Results We present the main features of MedTAG and how it has been employed in the histopathology domain by physicians and experts to annotate more than seven thousand clinical reports manually. We compare MedTAG with a set of well-established biomedical annotation tools, including BioQRator, ezTag, MyMiner, and tagtog, comparing their pros and cons with those of MedTag. We highlight that MedTAG is one of the very few open-source tools provided with an open license and a straightforward installation procedure supporting cross-platform use. Conclusions MedTAG has been designed according to five requirements (i.e. available, distributable, installable, workable and schematic) defined in a recent extensive review of manual annotation tools. Moreover, MedTAG satisfies 20 over 22 criteria specified in the same study.

TIARA 2.0: an interactive tool for annotating discourse structure and text improvement

Discourse structure annotation aims at analysing how discourse units (e.g. sentences or clauses) relate to each other and what roles they play in the overall discourse. Several annotation tools for discourse structure have been developed. However, they often only support specific annotation schemes, making their usage limited to new schemes. This article presents TIARA 2.0, an annotation tool for discourse structure and text improvement. Departing from our specific needs, we extend an existing tool to accommodate four levels of annotation: discourse structure, argumentative structure, sentence rearrangement and content alteration. The latter two are particularly unique compared to existing tools. TIARA is implemented on standard web technologies and can be easily customised. It deals with the visual complexity during the annotation process by systematically simplifying the layout and by offering interactive visualisation, including clutter-reducing features and dual-view display. TIARA’s text-view allows annotators to focus on the analysis of logical sequencing between sentences. The tree-view allows them to review their analysis in terms of the overall discourse structure. Apart from being an annotation tool, it is also designed to be useful for educational purposes in the teaching of argumentation; this gives it an edge over other existing tools.