• Genomics & Informatics
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• v.17 no.2
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• pp.19.1-19.10
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• 2019

In this paper, we investigate cross-platform interoperability for natural language processing (NLP) and, in particular, annotation of textual resources, with an eye toward identifying the design elements of annotation models and processes that are particularly problematic for, or amenable to, enabling seamless communication across different platforms. The study is conducted in the context of a specific annotation methodology, namely machine-assisted interactive annotation (also known as human-in-the-loop annotation). This methodology requires the ability to freely combine resources from different document repositories, access a wide array of NLP tools that automatically annotate corpora for various linguistic phenomena, and use a sophisticated annotation editor that enables interactive manual annotation coupled with on-the-fly machine learning. We consider three independently developed platforms, each of which utilizes a different model for representing annotations over text, and each of which performs a different role in the process.

• Genomics & Informatics
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• v.18 no.2
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• pp.13.1-13.6
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• 2020

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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 downloadable from PubMed Central (PMC) as XML files. During the Biomedical Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotating, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnotation, a system that provides a convenient way to add PMC publications based on PMCID. Thus, this review aims to provide a tutorial overview of practicing the iterative task of named entity recognition with the PubAnnotation/PubDictionaries/TextAE ecosystem. We also describe developing a conversion tool between the Genia tagger output and the JSON format of PubAnnotation during the hackathon.

• Genomics & Informatics
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• v.18 no.2
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• pp.15.1-15.6
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• 2020

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, methods will mislabel searched text and will miss important information or identify spurious text that will frustrate users. Most tools do not capture non-contiguous entities which are separate spans of text that together refer to an entity, e.g., the entity "type 1 diabetes" in the phrase "type 1 and type 2 diabetes." This type is commonly found in biomedical texts, especially in lists, where multiple biomedical entities are named in shortened form to avoid repeating words. Most text annotation systems, that enable users to view and edit entity annotations, do not support non-contiguous entities. Therefore, experts cannot even visualize non-contiguous entities, let alone annotate them to build valuable datasets for machine learning methods. To combat this problem and as part of the BLAH6 hackathon, we extended the TextAE platform to allow visualization and annotation of non-contiguous entities. This enables users to add new subspans to existing entities by selecting additional text. We integrate this new functionality with TextAE's existing editing functionality to allow easy changes to entity annotation and editing of relation annotations involving non-contiguous entities, with importing and exporting to the PubAnnotation format. Finally, we roughly quantify the problem across the entire accessible biomedical literature to highlight that there are a substantial number of non-contiguous entities that appear in lists that would be missed by most text mining systems.

• Genomics & Informatics
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• v.18 no.2
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• pp.18.1-18.5
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• 2020

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 assess two important aspects: the relevance of the article to the research question, and whether the article's proposed approach qualifies to being an alternative method. We are currently developing a Web application to support finding alternative methods to animal experiments. The current (under development) version of the application utilizes external tools and resources for document processing, and relies on the PubAnnotation ecosystem for annotation querying, annotation storage, dictionary-based tagging of cell lines, and annotation visualization. Currently, our two PubAnnotation repositories for discourse elements contain annotations for more than 110k PubMed documents. Further, we created an annotator for cell lines that contain more than 196k terms from Cellosaurus. Finally, we are experimenting with TextAE for annotation visualization and for user feedback.

• Proceedings of the Korean Society for Language and Information Conference
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• 2007.11a
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• pp.548-556
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• 2007

We present an automatic semantic annotation system for Korean on the EXCOM (EXploration COntextual for Multilingual) platform. The purpose of natural language processing is enabling computers to understand human language, so that they can perform more sophisticated tasks. Accordingly, current research concentrates more and more on extracting semantic information. The realization of semantic processing requires the widespread annotation of documents. However, compared to that of inflectional languages, the technology in agglutinative language processing such as Korean still has shortcomings. EXCOM identifies semantic information in Korean text using our new method, the Contextual Exploration Method. Our initial system properly annotates approximately 88% of standard Korean sentences, and this annotation rate holds across text domains.

• Proceedings of the KSRS Conference
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• 2003.11a
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• pp.222-224
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• 2003

Many users want to add some their own information to data which was on the web and computer without actually needing to touch data. In remote sensing, the result data for image classification consist of image and text file in general. To overcome these inconvenience problems, we suggest the annotation method using XML language. We give the efficient annotation method which can be applied to web and viewing of image classification. We can apply the annotation for web and image classification with image and text file. The need for thesaurus construction is the lack of information for remote sensing and GIS on search engine like Empas, Naver and Google. In search engine, we can’t search the information for word which has many different names simultaneously. We select the remote sensing data from different sources and make the relation between many terms. For this process, we analyze the meaning for different terms which has similar meaning.

• Genomics & Informatics
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• v.18 no.2
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• pp.19.1-19.6
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• 2020

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 to augment the queries from the user. In the research described in this paper, we aimed to identify ontological concepts in scientific text contained in spreadsheets. We developed a tool that can handle various types of spreadsheets. Furthermore, we used the NCBO Annotator API provided by BioPortal to enhance the semantic annotation functionality to cover spreadsheet data. Table2Annotation has strengths in certain criteria such as speed, error handling, and complex concept matching.

• Proceedings of the Korean Society for Language and Information Conference
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• 2007.11a
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• pp.13-28
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• 2007

This is a speculative paper, describing a recently started effort to give a formal semantics to semantic annotation schemes. Semantic annotations are intended to capture certain semantic information in a text, which means that it only makes sense to use semantic annotations if these have a well-defined semantics. In practice, however, semantic annotation schemes are used that lack any formal semantics. In this paper we outline how existing approaches to the annotation of temporal information, semantic roles, and reference relations can be integrated in a single XML-based format and can be given a formal semantics by translating them into second-order logic. This is argued to offer an incremental aproach to the incorporation of semantic information in natural language processing that does not suffer from the problems of ambiguity and lack of robustness that are common to traditional approaches to computational semantics.

• Genomics & Informatics
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• v.18 no.2
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• pp.24.1-24.7
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• 2020

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 of Biomedical Linked Annotation Hackathon (BLAH), after a short review of 19 generic annotation tools, we adapted GATE and TextAE for annotating Twitter timelines. Although none of the tools reviewed allow the annotation of all information inherent of Twitter timelines, a few may be suitable provided the willingness by annotators to compromise on some functionality.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.8 no.1
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• pp.213-231
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• 2014

Existing image search systems allow users to search images by keywords, or by example images through content-based image retrieval (CBIR). On the other hand, users might learn more relevant textual information about an image from its text captions or surrounding contexts within documents or Web pages. Without such contexts, it's difficult to extract semantic description directly from the image content. In this paper, we propose an annotation watermarking system for users to embed text descriptions, and retrieve more relevant textual information from similar images. First, tags associated with an image are converted by two-dimensional code and embedded into the image by discrete wavelet transform (DWT). Next, for images without annotations, similar images can be obtained by CBIR techniques and embedded annotations can be extracted. Specifically, we use global features such as color ratios and dominant sub-image colors for preliminary filtering. Then, local features such as Scale-Invariant Feature Transform (SIFT) descriptors are extracted for similarity matching. This design can achieve good effectiveness with reasonable processing time in practical systems. Our experimental results showed good accuracy in retrieving similar images and extracting relevant tags from similar images.