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Journal articles on the topic 'Annotation tool'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Islamaj, Rezarta, Dongseop Kwon, Sun Kim, and Zhiyong Lu. "TeamTat: a collaborative text annotation tool." Nucleic Acids Research 48, W1 (2020): W5—W11. http://dx.doi.org/10.1093/nar/gkaa333.

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Abstract Manually annotated data is key to developing text-mining and information-extraction algorithms. However, human annotation requires considerable time, effort and expertise. Given the rapid growth of biomedical literature, it is paramount to build tools that facilitate speed and maintain expert quality. While existing text annotation tools may provide user-friendly interfaces to domain experts, limited support is available for figure display, project management, and multi-user team annotation. In response, we developed TeamTat (https://www.teamtat.org), a web-based annotation tool (loca

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Rau, Pei-Luen Patrick, and Sho-Hsen Chen. "A Study of Electronic Annotation on Web Documents." Proceedings of the Human Factors and Ergonomics Society Annual Meeting 46, no. 5 (2002): 680–84. http://dx.doi.org/10.1177/154193120204600517.

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This study develops an electronic annotation system, allowing users to annotate on hypertexts, to build up knowledge structure, and to browse instructions provided by the system administrator or the instructor electronically. The electronic annotation system is a distributed World Wide Web application based on HTTP access and allows annotations on HTML documents. The major functions of the electronic annotation system include highlighting texts, inserting and editing annotations, and organizing and presenting annotations hierarchically. The five interactive components of the electronic annotat

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Groh, Florian, Dominik Schörkhuber, and Margrit Gelautz. "A tool for semi-automatic ground truth annotation of traffic videos." Electronic Imaging 2020, no. 16 (2020): 200–1. http://dx.doi.org/10.2352/issn.2470-1173.2020.16.avm-150.

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We have developed a semi-automatic annotation tool – “CVL Annotator” – for bounding box ground truth generation in videos. Our research is particularly motivated by the need for reference annotations of challenging nighttime traffic scenes with highly dynamic lighting conditions due to reflections, headlights and halos from oncoming traffic. Our tool incorporates a suite of different state-of-the-art tracking algorithms in order to minimize the amount of human input necessary to generate high-quality ground truth data. We focus our user interface on the premise of minimizing user interaction a

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Saklofske, Jon. "brat Rapid Annotation Tool. Web-based annotation and visualization tool." Renaissance and Reformation 42, no. 2 (2019): 180–89. http://dx.doi.org/10.7202/1065133ar.

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Al-Bukhitan, Saeed, Tarek Helmy, and Mohammed Al-Mulhem. "Semantic Annotation Tool for Annotating Arabic Web Documents." Procedia Computer Science 32 (2014): 429–36. http://dx.doi.org/10.1016/j.procs.2014.05.444.

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Misirli, Goksel, Matteo Cavaliere, William Waites, et al. "Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization." Bioinformatics 32, no. 6 (2015): 908–17. http://dx.doi.org/10.1093/bioinformatics/btv660.

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Abstract Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling

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Lima, Phyllipe, Eduardo Guerra, and Paulo Meirelles. "Annotation Sniffer: A tool to Extract Code Annotations Metrics." Journal of Open Source Software 5, no. 47 (2020): 1960. http://dx.doi.org/10.21105/joss.01960.

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Dijkshoorn, Chris, Victor De Boer, Lora Aroyo, and Guus Schreiber. "Accurator: Nichesourcing for Cultural Heritage." Human Computation 6 (June 2, 2019): 12–41. http://dx.doi.org/10.15346/hc.v6i1.91.

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With the increase of cultural heritage data published online, the usefulness of data in this open context hinges on the quality and diversity of descriptions of collection objects. In many cases, existing descriptions are not sufficient for retrieval and research tasks, resulting in the need for more specific annotations. However, eliciting such annotations is a challenge since it often requires domain-specific knowledge. Where crowdsourcing can be successfully used to execute simple annotation tasks, identifying people with the required expertise might prove troublesome for more complex and d

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Chehab, Khalil, Anis Kalboussi, and Ahmed Hadj Kacem. "Study of Healthcare Annotation Systems." International Journal of E-Health and Medical Communications 12, no. 3 (2021): 74–89. http://dx.doi.org/10.4018/ijehmc.20210501.oa5.

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The annotation practice is an almost daily activity used by healthcare professionals (PHC) to analyze patients' records, collaborate, share knowledge, and communicate. These annotations are generated within a healthcare cycle. Similarly, this cycle represents the life cycle of annotations in the patient record. The exponential increase in the number of medical annotation systems made the choice of a system by a PHC difficult, in a well-defined context (biology, radiology) and according to his/her needs to the functionalities offered by these tools. Therefore, the authors propose two taxonomies

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Gayoso-Cabada, Joaquín, María Goicoechea-de-Jorge, Mercedes Gómez-Albarrán, Amelia Sanz-Cabrerizo, Antonio Sarasa-Cabezuelo, and José-Luis Sierra. "Ontology-Enhanced Educational Annotation Activities." Sustainability 11, no. 16 (2019): 4455. http://dx.doi.org/10.3390/su11164455.

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Information and communications technology and technology-enhanced learning have unquestionably transformed traditional teaching–learning processes and are positioned as key factors to promote quality education, one of the basic sustainable development goals of the 2030 agenda. Document annotation, which was traditionally carried out with pencil and paper and currently benefits from digital document annotation tools, is a representative example of this transformation. Using document annotation tools, students can enrich the documents with annotations that highlight the most relevant aspects of

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Liu, Chia-Hsin, Bing-Ching Ho, Chun-Ling Chen, et al. "ePIANNO: ePIgenomics ANNOtation tool." PLOS ONE 11, no. 2 (2016): e0148321. http://dx.doi.org/10.1371/journal.pone.0148321.

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Gil de Gómez Pérez, David, and Roman Bednarik. "POnline: An Online Pupil Annotation Tool Employing Crowd-sourcing and Engagement Mechanisms." Human Computation 6 (December 10, 2019): 176–91. http://dx.doi.org/10.15346/hc.v6i1.99.

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Pupil center and pupil contour are two of the most important features in the eye-image used for video-based eye-tracking. Well annotated databases are needed in order to allow benchmarking of the available- and new pupil detection and gaze estimation algorithms. Unfortunately, creation of such a data set is costly and requires a lot of efforts, including manual work of the annotators. In addition, reliability of manual annotations is hard to establish with a low number of annotators. In order to facilitate progress of the gaze tracking algorithm research, we created an online pupil annotation

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Conesa, Ana, and Stefan Götz. "Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics." International Journal of Plant Genomics 2008 (April 30, 2008): 1–12. http://dx.doi.org/10.1155/2008/619832.

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Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotat

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Timonen, Oskari, Mikko Särkkä, Tibor Fülöp, Anton Mattsson, Juha Kekäläinen, and Jussi Paananen. "Varanto: variant enrichment analysis and annotation." Bioinformatics 35, no. 17 (2019): 3154–56. http://dx.doi.org/10.1093/bioinformatics/btz046.

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Abstract Summary Genome-wide association studies (GWAS) aim to identify associations of genetic variations such as single-nucleotide polymorphisms (SNPs) to a specific trait or a disease. Identifying common themes such as pathways, biological processes and diseases associations is needed to further explore and interpret these results. Varanto is a novel web tool for annotating, visualizing and analyzing human genetic variations using diverse data sources. Varanto can be used to query a set of input variations, retrieve their associated variation and gene level annotations, perform annotation e

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Agius, Phaedra, Heather Geiger, and Nicolas Robine. "SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions." Bioinformatics 35, no. 22 (2019): 4843–45. http://dx.doi.org/10.1093/bioinformatics/btz452.

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Abstract Motivation The association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions (SJs), with an efficient visualization tool that highlights SJ details such as frame-shifts and annotation support for individual samples or a sample cohort. Results Using publicly available samples, we show that the tissue specificity inherent in splicing signatures is maintained with the Relative Read Support scoring method in SCANVIS, and

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Otto, Thomas D., Gary P. Dillon, Wim S. Degrave, and Matthew Berriman. "RATT: Rapid Annotation Transfer Tool." Nucleic Acids Research 39, no. 9 (2011): e57-e57. http://dx.doi.org/10.1093/nar/gkq1268.

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Ramos, Alex H., Lee Lichtenstein, Manaswi Gupta, et al. "Oncotator: Cancer Variant Annotation Tool." Human Mutation 36, no. 4 (2015): E2423—E2429. http://dx.doi.org/10.1002/humu.22771.

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18

Darwin, Ian. "AnnaBot: A Static Verifier for Java Annotation Usage." Advances in Software Engineering 2010 (December 20, 2010): 1–7. http://dx.doi.org/10.1155/2010/540547.

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This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in 2004 and have become widely used in recent years due to their introduction in the Java Enterprise Edition 5,

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Rydell, Christopher, and Joakim Lindblad. "CytoBrowser: a browser-based collaborative annotation platform for whole slide images." F1000Research 10 (March 22, 2021): 226. http://dx.doi.org/10.12688/f1000research.51916.1.

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We present CytoBrowser, an open-source (GPLv3) JavaScript and Node.js driven environment for fast and accessible collaborative online visualization, assessment, and annotation of very large microscopy images, including, but not limited to, z-stacks (focus stacks) of cytology or histology whole slide images. CytoBrowser provides a web-based viewer for high-resolution zoomable images and facilitates easy remote collaboration, with options for joint-view visualization and simultaneous collaborative annotation of very large datasets. It delivers a unique combination of functionalities not found in

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Gayoso-Cabada, Joaquín, Antonio Sarasa-Cabezuelo, and José-Luis Sierra-Rodríguez. "A review of annotation classification tools in the educational domain." Open Computer Science 9, no. 1 (2019): 299–307. http://dx.doi.org/10.1515/comp-2019-0021.

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AbstractAn annotation consists of a portion of information that is associated with a piece of content in order to explain something about the content or to add more information. The use of annotations as a tool in the educational field has positive effects on the learning process. The usual way to use this instrument is to provide students with contents, usually textual, with which they must associate annotations. In most cases this task is performed in groups of students who work collaboratively. This process encourages analysis and understanding of the contents since they have to understand

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Fuoli, Matteo. "A stepwise method for annotating appraisal." Functions of Language 25, no. 2 (2018): 229–58. http://dx.doi.org/10.1075/fol.15016.fuo.

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Abstract Despite a growing awareness of methodological issues, the literature on appraisal has not so far provided adequate answers to some of the key challenges involved in reliably identifying and classifying evaluative language expressions. This article presents a stepwise method for the manual annotation of appraisal in text that is designed to optimize reliability, replicability and transparency. The procedure consists of seven steps, from the creation of a context-specific annotation manual to the statistical analysis of the quantitative data derived from the manually-performed annotatio

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Hu, Yang, Wenyang Zhou, Jun Ren, et al. "Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology." BioMed Research International 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/4130861.

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Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations b

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Bayerl, Petra Saskia, and Karsten Ingmar Paul. "Identifying Sources of Disagreement: Generalizability Theory in Manual Annotation Studies." Computational Linguistics 33, no. 1 (2007): 3–8. http://dx.doi.org/10.1162/coli.2007.33.1.3.

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Many annotation projects have shown that the quality of manual annotations often is not as good as would be desirable for reliable data analysis. Identifying the main sources responsible for poor annotation quality must thus be a major concern. Generalizability theory is a valuable tool for this purpose, because it allows for the differentiation and detailed analysis of factors that influence annotation quality. In this article we will present basic concepts of Generalizability Theory and give an example for its application based on published data.

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Zheng, Yuanshui, Min Wu, Elodia Cole, and Etta D. Pisano. "Online annotation tool for digital mammography1." Academic Radiology 11, no. 5 (2004): 566–72. http://dx.doi.org/10.1016/s1076-6332(03)00726-8.

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Lindvall, Martin, Alexander Sanner, Fredrik Petré, et al. "TissueWand, a rapid histopathology annotation tool." Journal of Pathology Informatics 11, no. 1 (2020): 27. http://dx.doi.org/10.4103/jpi.jpi_5_20.

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Sangkuhl, Katrin, Michelle Whirl‐Carrillo, Ryan M. Whaley, et al. "Pharmacogenomics Clinical Annotation Tool (Pharm CAT )." Clinical Pharmacology & Therapeutics 107, no. 1 (2019): 203–10. http://dx.doi.org/10.1002/cpt.1568.

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Klein, Teri E., and Marylyn D. Ritchie. "PharmCAT: A Pharmacogenomics Clinical Annotation Tool." Clinical Pharmacology & Therapeutics 104, no. 1 (2017): 19–22. http://dx.doi.org/10.1002/cpt.928.

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Hu, Qiang, ZhiGang Wang, and ZhengGuo Zhang. "FSim: A Novel Functional Similarity Search Algorithm and Tool for Discovering Functionally Related Gene Products." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/509149.

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Background. During the analysis of genomics data, it is often required to quantify the functional similarity of genes and their products based on the annotation information from gene ontology (GO) with hierarchical structure. A flexible and user-friendly way to estimate the functional similarity of genes utilizing GO annotation is therefore highly desired.Results. We proposed a novel algorithm using a level coefficient-weighted model to measure the functional similarity of gene products based on multiple ontologies of hierarchical GO annotations. The performance of our algorithm was evaluated

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Oscanoa, Jorge, Lavanya Sivapalan, Emanuela Gadaleta, Abu Z. Dayem Ullah, Nicholas R. Lemoine, and Claude Chelala. "SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)." Nucleic Acids Research 48, W1 (2020): W185—W192. http://dx.doi.org/10.1093/nar/gkaa420.

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Abstract SNPnexus is a web-based annotation tool for the analysis and interpretation of both known and novel sequencing variations. Since its last release, SNPnexus has received continual updates to expand the range and depth of annotations provided. SNPnexus has undergone a complete overhaul of the underlying infrastructure to accommodate faster computational times. The scope for data annotation has been substantially expanded to enhance biological interpretations of queried variants. This includes the addition of pathway analysis for the identification of enriched biological pathways and mol

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Steuernagel, Burkhard, Kamil Witek, Simon G. Krattinger, et al. "The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire." Plant Physiology 183, no. 2 (2020): 468–82. http://dx.doi.org/10.1104/pp.19.01273.

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Chen, Yu-Hua, and Radovan Bruncak. "Transcribear – Introducing a secure online transcription and annotation tool." Digital Scholarship in the Humanities 35, no. 2 (2019): 265–75. http://dx.doi.org/10.1093/llc/fqz016.

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Abstract Reliable high-quality transcription and/or annotation (a.k.a. ‘coding’) is essential for research in a variety of areas in Humanities and Social Sciences which make use of qualitative data such as interviews, focus groups, classroom observations, or any other audio/video recordings. A good tool can facilitate the work of transcription and annotation because the process is notoriously time-consuming and challenging. However, our survey indicates that few existing tools can accommodate the requirements for transcription and annotation (e.g. audio/video playback, spelling checks, keyboar

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Nilsson, Daniel, and Björn Andersson. "A graphical tool for parasite genome annotation." Computer Methods and Programs in Biomedicine 73, no. 1 (2004): 55–60. http://dx.doi.org/10.1016/s0169-2607(02)00162-1.

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Shaikh-Lesko, Rina. "Web annotation tool Hypothesis hits a milestone." Nature 569, no. 7755 (2019): 295. http://dx.doi.org/10.1038/d41586-019-01427-9.

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Otlu, Burçak, Can Firtina, Sündüz Keleş, and Oznur Tastan. "GLANET: genomic loci annotation and enrichment tool." Bioinformatics 33, no. 18 (2017): 2818–28. http://dx.doi.org/10.1093/bioinformatics/btx326.

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Yakunin, Alexander F., Adelinda A. Yee, Alexei Savchenko, Aled M. Edwards, and Cheryl H. Arrowsmith. "Structural proteomics: a tool for genome annotation." Current Opinion in Chemical Biology 8, no. 1 (2004): 42–48. http://dx.doi.org/10.1016/j.cbpa.2003.12.003.

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Piasecki, Michael, and Bora Beran. "A semantic annotation tool for hydrologic sciences." Earth Science Informatics 2, no. 3 (2009): 157–68. http://dx.doi.org/10.1007/s12145-009-0031-x.

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Huang, Po-Jung, Chi-Ching Lee, Bertrand Chin-Ming Tan, et al. "Vanno: A Visualization-Aided Variant Annotation Tool." Human Mutation 36, no. 2 (2015): 167–74. http://dx.doi.org/10.1002/humu.22684.

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Milchevskaya, Vladislava, Grischa Tödt, and Toby James Gibson. "A Tool to Build Up-To-Date Gene Annotations for Affymetrix Microarrays." Genomics and Computational Biology 3, no. 2 (2017): 38. http://dx.doi.org/10.18547/gcb.2017.vol3.iss2.e38.

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Genome-wide expression profiling and genotyping is widely applied in functional genomics research, ranging from stem cell studies to cancer, in drug response studies, and in clinical diagnostics. The Affymetrix GeneChip microarrays represent the most popular platform for such assays. Nevertheless, due to rapid and continuous improvement of the knowledge about the genome, the definition of many of the genes and transcripts change, and new genes are discovered. Thus the original probe information is out-dated for a number of Affymetrix platforms, and needs to be re-defined. It has been demonstra

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Tickotsky, Nili, and Moti Moskovitz. "Protein Activation in Periapical Reaction to Iodoform Containing Root Canal Sealer." Journal of Clinical Pediatric Dentistry 41, no. 6 (2017): 450–55. http://dx.doi.org/10.17796/1053-4628-41.6.6.

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Objectives: An association between root canal sealers and periapical lesions in primary dentition has been suggested, yet the chemical-protein interactions that may be involved in it have not been studied. The present study explored root sealer components' effect on periapical tissue proteins using bioinformatics tools. Study design: For each chemical component of Endoflas F.S. root sealing material we identified the known and predicted target proteins, using STITCH (search tool for interactions of chemicals http://stitch.embl.de/). Identified target proteins were grouped into functional categ

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Letunic, Ivica, and Peer Bork. "Interactive Tree Of Life (iTOL) v4: recent updates and new developments." Nucleic Acids Research 47, W1 (2019): W256—W259. http://dx.doi.org/10.1093/nar/gkz239.

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Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding t

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Fang, Li Yong, Xu Dong Yin, Hai Huang Zhang, and Hui Li. "Design and Implementation of 2D Elevation Annotation in Hydropower Project Designbased on CATIA/CAA." Applied Mechanics and Materials 501-504 (January 2014): 2093–96. http://dx.doi.org/10.4028/www.scientific.net/amm.501-504.2093.

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When CATIA software is used for hydropowerproject design, elevation annotation in 2D drafting workbench is a complicated process that brought extremely inconvenience to designers. In order to solve the problem, a method of 2D elevation annotation based on UDF(user defined feature) is proposed in this paper. Then, a 2D elevation annotation tool based on proposed method is developed and implemented through CAA(Component Application Architecture) development tool of CATIA V5R19 software.At last,several annotation results are illustrated and the developed tool is proven to meet the demands of 2D e

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Bertino, Andrea C., and Heather Staines. "Enabling A Conversation Across Scholarly Monographs through Open Annotation." Publications 7, no. 2 (2019): 41. http://dx.doi.org/10.3390/publications7020041.

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The digital format opens up new possibilities for interaction with monographic publications. In particular, annotation tools make it possible to broaden the discussion on the content of a book, to suggest new ideas, to report errors or inaccuracies, and to conduct open peer reviews. However, this requires the support of the users who might not yet be familiar with the annotation of digital documents. This paper will give concrete examples and recommendations for exploiting the potential of annotation in academic research and teaching. After presenting the annotation tool of Hypothesis, the art

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Aasman, Susan, Liliana Melgar Estrada, Tom Slootweg, and Rob Wegter. "Tales of a Tool Encounter." Audiovisual Data in Digital Humanities 7, no. 14 (2018): 73. http://dx.doi.org/10.18146/2213-0969.2018.jethc154.

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This article explores the affordances and functionalities of the Dutch CLARIAH research infrastructure – and the integrated video annotation tool – for doing media historical research with digitised audiovisual sources from television archives. The growing importance of digital research infrastructures, archives and tools, has enticed media historians to rethink their research practices more and more in terms of methodological transparency, tool criticism and reflection. Moreover, also questions related to the heuristics and hermeneutics of our scholarly work need to be reconsidered. The artic

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Tsiliki, Georgia, Konstantinos Tsaramirsis, and Sophia Kossida. "AmalgamScope: Merging Annotations Data across the Human Genome." BioMed Research International 2014 (2014): 1–5. http://dx.doi.org/10.1155/2014/893501.

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The past years have shown an enormous advancement in sequencing and array-based technologies, producing supplementary or alternative views of the genome stored in various formats and databases. Their sheer volume and different data scope pose a challenge to jointly visualize and integrate diverse data types. We present AmalgamScope a new interactive software tool focusing on assisting scientists with the annotation of the human genome and particularly the integration of the annotation files from multiple data types, using gene identifiers and genomic coordinates. Supported platforms include ne

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Zhang, Wei. "NLR-Annotator: A Tool for De Novo Annotation of Intracellular Immune Receptor Repertoire." Plant Physiology 183, no. 2 (2020): 418–20. http://dx.doi.org/10.1104/pp.20.00525.

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Ouyang, Wei, Trang Le, Hao Xu, and Emma Lundberg. "Interactive biomedical segmentation tool powered by deep learning and ImJoy." F1000Research 10 (February 24, 2021): 142. http://dx.doi.org/10.12688/f1000research.50798.1.

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Deep learning-based methods play an increasingly important role in bioimage analysis. User-friendly tools are crucial for increasing the adoption of deep learning models and efforts have been made to support them in existing image analysis platforms. Due to hardware and software complexities, many of them have been struggling to support re-training and fine-tuning of models which is essential to avoid overfitting and hallucination issues when working with limited training data. Meanwhile, interactive machine learning provides an efficient way to train models on limited training data. It works

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Ernst, Madeleine, Kyo Bin Kang, Andrés Mauricio Caraballo-Rodríguez, et al. "MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools." Metabolites 9, no. 7 (2019): 144. http://dx.doi.org/10.3390/metabo9070144.

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Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a dat

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Hackenberg, M., and R. Matthiesen. "Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists." Bioinformatics 24, no. 11 (2008): 1386–93. http://dx.doi.org/10.1093/bioinformatics/btn178.

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Baur, Tobias, Alexander Heimerl, Florian Lingenfelser, et al. "eXplainable Cooperative Machine Learning with NOVA." KI - Künstliche Intelligenz 34, no. 2 (2020): 143–64. http://dx.doi.org/10.1007/s13218-020-00632-3.

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Abstract In the following article, we introduce a novel workflow, which we subsume under the term “explainable cooperative machine learning” and show its practical application in a data annotation and model training tool called NOVA. The main idea of our approach is to interactively incorporate the ‘human in the loop’ when training classification models from annotated data. In particular, NOVA offers a collaborative annotation backend where multiple annotators join their workforce. A main aspect is the possibility of applying semi-supervised active learning techniques already during the annota

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Coetzee, Simon G., Zachary Ramjan, Huy Q. Dinh, Benjamin P. Berman, and Dennis J. Hazelett. "StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation." F1000Research 7 (February 22, 2018): 214. http://dx.doi.org/10.12688/f1000research.13535.1.

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Genome annotation is critical to understand the function of disease variants, especially for clinical applications. To meet this need there are segmentations available from public consortia reflecting varying unsupervised approaches to functional annotation based on epigenetics data, but there remains a need for transparent, reproducible, and easily interpreted genomic maps of the functional biology of chromatin. We introduce a new methodological framework for defining a combinatorial epigenomic model of chromatin state on a web database, StateHub. In addition, we created an annotation tool fo

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