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Journal articles on the topic 'Annotation via web'

Author: Grafiati

Published: 25 May 2024

Last updated: 31 July 2025

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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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Mazhoud, Omar, Anis Kalboussi, and Ahmed Hadj Kacem. "Educational Recommender System based on Learner’s Annotative Activity." International Journal of Emerging Technologies in Learning (iJET) 16, no. 10 (2021): 108. http://dx.doi.org/10.3991/ijet.v16i10.19955.

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In recent years, Educational Recommender Systems (ERSs) have attracted great attention as a solution towards addressing the problem of information overload in e-learning environments and providing relevant recommendations to online learners. These systems play a key role in helping learners to find educational resources relevant and pertinent to their profiles and context. So, it is necessary to identify information that helps learner’s profile definition and in identifying requests and interests. In this context, we suggest to take advantage of the annotation activity used usually in the lear

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Wang, Han, Xinxiao Wu, and Yunde Jia. "Video Annotation via Image Groups from the Web." IEEE Transactions on Multimedia 16, no. 5 (2014): 1282–91. http://dx.doi.org/10.1109/tmm.2014.2312251.

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Tschöpe, Okka, Lutz Suhrbier, Anton Güntsch, and Walter Berendsohn. "AnnoSys – an online tool for sharing annotations to enhance data quality." Biodiversity Information Science and Standards 1 (August 15, 2017): e20315. https://doi.org/10.3897/tdwgproceedings.1.20315.

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AnnoSys is a web-based open-source information system that enables users to correct and enrich specimen data published in data portals, thus enhancing data quality and documenting research developments over time. This brings the traditional annotation workflows for specimens to the Internet, as annotations become visible to researchers who subsequently observe the annotated specimen. During its first phase, the AnnoSys project developed a fully functional prototype of an annotation data repository for complex and cross-linked XML-standardized data in the ABCD (Access to biological collection d

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Ma, Zhigang, Feiping Nie, Yi Yang, Jasper R. R. Uijlings, and Nicu Sebe. "Web Image Annotation Via Subspace-Sparsity Collaborated Feature Selection." IEEE Transactions on Multimedia 14, no. 4 (2012): 1021–30. http://dx.doi.org/10.1109/tmm.2012.2187179.

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Wei, Chih-Hsuan, Alexis Allot, Robert Leaman, and Zhiyong Lu. "PubTator central: automated concept annotation for biomedical full text articles." Nucleic Acids Research 47, W1 (2019): W587—W593. http://dx.doi.org/10.1093/nar/gkz389.

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AbstractPubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) is a web service for viewing and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art text mining systems for genes/proteins, genetic variants, diseases, chemicals, species and cell lines, all available for immediate download. PTC annotates PubMed (29 million abstracts) and the PMC Text Mining subset (3 million full text articles). The new PTC web interface allows users to build full text document collections and visualize concept

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Lelong, Sebastien, Xinghua Zhou, Cyrus Afrasiabi, et al. "BioThings SDK: a toolkit for building high-performance data APIs in biomedical research." Bioinformatics 38, no. 7 (2022): 2077–79. http://dx.doi.org/10.1093/bioinformatics/btac017.

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Abstract Summary To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info and MyChem.info for integrating annotations on genes, variants and chemical compounds, respectively. These APIs are used b

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Park, Yeon-Ji, Min-a. Lee, Geun-Je Yang, Soo Jun Park, and Chae-Bong Sohn. "Biomedical Text NER Tagging Tool with Web Interface for Generating BERT-Based Fine-Tuning Dataset." Applied Sciences 12, no. 23 (2022): 12012. http://dx.doi.org/10.3390/app122312012.

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In this paper, a tagging tool is developed to streamline the process of locating tags for each term and manually selecting the target term. It directly extracts the terms to be tagged from sentences and displays it to the user. It also increases tagging efficiency by allowing users to reflect candidate categories in untagged terms. It is based on annotations automatically generated using machine learning. Subsequently, this architecture is fine-tuned using Bidirectional Encoder Representations from Transformers (BERT) to enable the tagging of terms that cannot be captured using Named-Entity Re

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Hu, Mengqiu, Yang Yang, Fumin Shen, Luming Zhang, Heng Tao Shen, and Xuelong Li. "Robust Web Image Annotation via Exploring Multi-Facet and Structural Knowledge." IEEE Transactions on Image Processing 26, no. 10 (2017): 4871–84. http://dx.doi.org/10.1109/tip.2017.2717185.

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Wang, Han, Xiabi Liu, Xinxiao Wu, and Yunde Jia. "Cross-domain structural model for video event annotation via web images." Multimedia Tools and Applications 74, no. 23 (2014): 10439–56. http://dx.doi.org/10.1007/s11042-014-2175-z.

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Barrett, Kristian, Cameron J. Hunt, Lene Lange, and Anne S. Meyer. "Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes." Nucleic Acids Research 48, W1 (2020): W110—W115. http://dx.doi.org/10.1093/nar/gkaa375.

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Abstract The CUPP platform includes a web server for functional annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based on a novel peptide-based similarity assessment algorithm, i.e. protein grouping according to Conserved Unique Peptide Patterns (CUPP). This online platform is open to all users and there is no login requirement. The web server allows the user to perform genome-based annotation of carbohydrate active enzymes to CAZy families, CAZy subfamilies, CUPP groups and EC numbers (function) via assessment of peptide-motifs by CUPP. The web server is intended for funct

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Palowitch, John, Hamidreza Alvari, Mehran Kazemi, Tanvir Amin, and Filip Radlinski. "SocialQuotes: Learning Contextual Roles of Social Media Quotes on the Web." Proceedings of the International AAAI Conference on Web and Social Media 19 (June 7, 2025): 1453–70. https://doi.org/10.1609/icwsm.v19i1.35882.

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Web authors frequently embed social media to support and enrich their content, creating the potential to derive webbased, cross-platform social media representations that can enable more effective social media retrieval systems and richer scientific analyses. As a step toward such capabilities, we introduce a novel language modeling framework that enables automatic annotation of roles that social media entities play in their embedded web context. Using related communication theory, we liken social media embeddings to quotes, formalize the page context as structured natural language signals, an

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Lachmann, Alexander, Kaeli A. Rizzo, Alon Bartal, Minji Jeon, Daniel J. B. Clarke, and Avi Ma’ayan. "PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices." PeerJ 11 (February 27, 2023): e14927. http://dx.doi.org/10.7717/peerj.14927.

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Background Gene-gene co-expression correlations measured by mRNA-sequencing (RNA-seq) can be used to predict gene annotations based on the co-variance structure within these data. In our prior work, we showed that uniformly aligned RNA-seq co-expression data from thousands of diverse studies is highly predictive of both gene annotations and protein-protein interactions. However, the performance of the predictions varies depending on whether the gene annotations and interactions are cell type and tissue specific or agnostic. Tissue and cell type-specific gene-gene co-expression data can be usef

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Cornwell, Peter. "Progress with Repository-based Annotation Infrastructure for Biodiversity Applications." Biodiversity Information Science and Standards 7 (September 14, 2023): e112707. https://doi.org/10.3897/biss.7.112707.

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Rapid development since the 1980s of technologies for analysing texts, has led not only to widespread employment of text 'mining', but also to now-pervasive large language model artificial intelligence (AI) applications. However, building new, concise, data resources from historic, as well as contemporary scientific literature, which can be employed efficiently at scale by automation and which have long-term value for the research community, has proved more elusive.Efforts at codifying analyses, such as the Text Encoding Initiative (TEI), date from the early 1990s and were initially driven by

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Wang, Jiyao, Philippe Youkharibache, Dachuan Zhang, et al. "iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures." Bioinformatics 36, no. 1 (2019): 131–35. http://dx.doi.org/10.1093/bioinformatics/btz502.

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Abstract Motivation Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. Results iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/anno

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König, Matthias. "cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK." F1000Research 5 (July 18, 2016): 1736. http://dx.doi.org/10.12688/f1000research.9211.1.

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Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information. Despite the importance for computational modelling there has been no simple solution to visualize the kinetic data from SABIO-RK. In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape. The kinetic information is accessible via a combination of graph structure and annotation

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Gil-de-la-Fuente, Alberto, Maricruz Mamani-Huanca, María C. Stroe, et al. "Aspergillus Metabolome Database for Mass Spectrometry Metabolomics." Journal of Fungi 7, no. 5 (2021): 387. http://dx.doi.org/10.3390/jof7050387.

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The Aspergillus Metabolome Database is a free online resource to perform metabolite annotation in mass spectrometry studies devoted to the genus Aspergillus. The database was created by retrieving and curating information on 2811 compounds present in 601 different species and subspecies of the genus Aspergillus. A total of 1514 scientific journals where these metabolites are mentioned were added as meta-information linked to their respective compounds in the database. A web service to query the database based on m/z (mass/charge ratio) searches was added to CEU Mass Mediator; these queries can

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Backes, Paul G., Kam S. Tso, and Gregory K. Tharp. "The Web Interface for Telescience." Presence: Teleoperators and Virtual Environments 8, no. 5 (1999): 531–39. http://dx.doi.org/10.1162/105474699566440.

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The Web Interface for Telescience (WITS) is an Internet-based tool that enables members of geographically distributed science teams to participate in daily planetary lander and rover mission planning. WITS enables the viewing of downlinked images and results in various ways, terrain-feature measurement and annotation, and the planning of daily mission activities. WITS is written in the Java language and is accessible by mission scientists and the general public via a Web browser. The public can use WITS to plan and simulate their own rover missions. WITS was used during the 1997 Mars Pathfinde

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Christoforou, Evgenia, Gianluca Demartini, and Jahna Otterbacher. "Generative AI in Crowdwork for Web and Social Media Research: A Survey of Workers at Three Platforms." Proceedings of the International AAAI Conference on Web and Social Media 18 (May 28, 2024): 2097–103. http://dx.doi.org/10.1609/icwsm.v18i1.31452.

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Crowdsourcing plays an important role in Web and social media research, from data annotation, to online experiments and user surveys. With the emergence of Generative AI (GenAI), researchers are considering how models and tools such as GPT might replace crowdwork. Many have already evaluated GPT on annotation tasks. However, it is less clear how GenAI might impact other types of tasks, or to what extent crowdworkers have already incorporated it into their work processes. Thus, we asked crowdworkers directly regarding their use of GenAI, via a survey at two points in time, across three commerci

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Ruta, Michele, Floriano Scioscia, Maria Di Summa, Saverio Ieva, Eugenio Di Sciascio, and Marco Sacco. "Semantic Matchmaking for Kinect-Based Posture and Gesture Recognition." International Journal of Semantic Computing 08, no. 04 (2014): 491–514. http://dx.doi.org/10.1142/s1793351x14400169.

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Innovative analysis methods applied to data extracted by off-the-shelf peripherals can provide useful results in activity recognition without requiring large computational resources. In this paper a framework is proposed for automated posture and gesture recognition, exploiting depth data provided by a commercial tracking device. The detection problem is handled as a semantic-based resource discovery. A general data model and the corresponding ontology provide the formal underpinning for posture and gesture annotation via standard Semantic Web languages. Hence, a logic-based matchmaking, explo

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Alexander, John, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas, and Peristera Paschou. "Variant Ranker: a web-tool to rank genomic data according to functional significance." BMC Bioinformatics 18, no. 1 (2017): 341. https://doi.org/10.1186/s12859-017-1752-3.

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<strong>Background: </strong>The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. <i>Variant Ranker</i> allows researchers to rank identified variants and determine the most confident variants for experimental validation.<strong>Results: </strong>We describe <i>Variant Ranker</i>, a user-friendly simple web-based tool for ranking, filtering and annotation of coding and non-coding variants. <i>Variant Ranker</i> facilitates the identification of causal variants based on nov

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Sejdiu, Besmir, Florije Ismaili, and Lule Ahmedi. "Integration of Semantics Into Sensor Data for the IoT." International Journal on Semantic Web and Information Systems 16, no. 4 (2020): 1–25. http://dx.doi.org/10.4018/ijswis.2020100101.

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The internet of things (IoT) as an evolving technology represents an active scientific research field in recognizing research challenges associated with its application in various domains, ranging from consumer convenience, smart energy, and resource saving to IoT enterprises. Sensors are crucial components of IoT that relay the collected data in the form of the data stream for further processing. Interoperability of various connected digital resources is a key challenge in IoT environments. The enrichment of raw sensor data with semantic annotations using concept definitions from ontologies e

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Dimitrova, Mariya, Georgi Zhelezov, Teodor Georgiev, and Lyubomir Penev. "The Pensoft Annotator: A new tool for text annotation with ontology terms." Biodiversity Information Science and Standards 4 (September 28, 2020): e59042. https://doi.org/10.3897/biss.4.59042.

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IntroductionDigitisation of biodiversity knowledge from collections, scholarly literature and various research documents is an ongoing mission of the Biodiversity Information Standards (TDWG) community. Organisations such as the Biodiversity Heritage Library make historical biodiversity literature openly available and develop tools to allow biodiversity data reuse and interoperability. For instance, Plazi transforms free text into machine-readable formats and extracts collection data and feeds it into the Global Biodiversity Information Facility (GBIF) and other aggregators. All of these digit

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Macklin, James, David Shorthouse, and Falko Glöckler. "I Know Something You Don't Know: The annotation saga continues…" Biodiversity Information Science and Standards 7 (September 14, 2023): e112715. https://doi.org/10.3897/biss.7.112715.

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Over the past 20 years, the biodiversity informatics community has pursued components of the digital annotation landscape with varying degrees of success. We will provide an historical overview of the theory, the advancements made through a few key projects, and will identify some of the ongoing challenges and opportunities. The fundamental principles remain unchanged since annotations were first proposed. Someone (or something): (1) has an enhancement to make elsewhere from the source where original data or information are generated or transcribed; (2) wishes to broadcast these statements to

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Kumagai, Masahiko, Daiki Nishikawa, Yoshihiro Kawahara, et al. "TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data." DNA Research 26, no. 6 (2019): 445–52. http://dx.doi.org/10.1093/dnares/dsz022.

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Abstract Recent revolutionary advancements in sequencing technologies have made it possible to obtain mass quantities of genome-scale sequence data in a cost-effective manner and have drastically altered molecular biological studies. To utilize these sequence data, genome-wide association studies (GWASs) have become increasingly important. Hence, there is an urgent need to develop a visualization tool that enables efficient data retrieval, integration of GWAS results with diverse information and rapid public release of such large-scale genotypic and phenotypic data. We developed a web-based ge

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Kempa, Matúš, John Edmondson, Hans Walter Lack, Janka Smatanová, and Karol Marhold. "František Nábělek’s Iter Turcico-Persicum 1909–1910 – database and digitized herbarium collection." PhytoKeys 75 (December 1, 2016): 69–79. https://doi.org/10.3897/phytokeys.75.9780.

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The Czech botanist František Nábělek (1884−1965) explored the Middle East in 1909-1910, visiting what are now Israel, Palestine, Jordan, Syria, Lebanon, Iraq, Bahrain, Iran and Turkey. He described four new genera, 78 species, 69 varieties and 38 forms of vascular plants, most of these in his work Iter Turcico-Persicum (1923−1929). The main herbarium collection of Iter Turcico-Persicum comprises 4163 collection numbers (some with duplicates), altogether 6465 specimens. It is currently deposited in the herbarium SAV. In addition, some fragments and duplicates are found in B, E, W and WU. The wh

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Ausland, Catherine, Jinfang Zheng, Haidong Yi, et al. "dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates." Nucleic Acids Research 49, no. D1 (2020): D523—D528. http://dx.doi.org/10.1093/nar/gkaa742.

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Abstract PULs (polysaccharide utilization loci) are discrete gene clusters of CAZymes (Carbohydrate Active EnZymes) and other genes that work together to digest and utilize carbohydrate substrates. While PULs have been extensively characterized in Bacteroidetes, there exist PULs from other bacterial phyla, as well as archaea and metagenomes, that remain to be catalogued in a database for efficient retrieval. We have developed an online database dbCAN-PUL (http://bcb.unl.edu/dbCAN_PUL/) to display experimentally verified CAZyme-containing PULs from literature with pertinent metadata, sequences,

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Abhishek, Dutta, Gupta Ankush, and Zisserman Andrew. "VGG Image Annotator." June 15, 2018. https://doi.org/10.5281/zenodo.1312088.

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VGG Image Annotator (VIA) is a manual image annotation tool to define and describe regions in an image. The region shape can be rectangle, circle, ellipse, polygon, polyline, or a single point. Region descriptions can be plain text or a set of predefined options presented to manual annotators as checkbox, dropdown menu, radio buttons or image list. This tool supports bulk update of annotations corresponding to a large set of images (e.g. frames extracted from a video). VIA is an open source project developed solely using HTML, CSS and Javascript and therefore runs in most modern web browsers w

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Beyvers, Sebastian, Lukas Jelonek, Alexander Goesmann, and Oliver Schwengers. "Bakta Web – rapid and standardized genome annotation on scalable infrastructures." Nucleic Acids Research, April 24, 2025. https://doi.org/10.1093/nar/gkaf335.

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Abstract The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, the usage of command line software tools and the interpretation of result files in various formats might be challenging and pose technical barriers. Here, we present the recent updates on the Bakta web server, a user-friendly web interface for conducting and visualizing annotations using Bakta without requiring command line expertise or local comp

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Nobusada, Tomoe, Chi Wai Yip, Saumya Agrawal, et al. "Update of the FANTOM web resource: enhancement for studying noncoding genomes." Nucleic Acids Research, November 27, 2024. http://dx.doi.org/10.1093/nar/gkae1047.

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Abstract The FANTOM web resource (https://fantom.gsc.riken.jp/) has been a unique resource for studying mammalian genomes, which is built on the research activities conducted in the international collaborative project FANTOM (Functional ANnoTation Of the Mammalian genome). In recent updates, we expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs). The former was derived from the large-scale lncRNA perturbations in induced pluripotent stem cells (iPSCs) and integrative analysis of Hi-C data conducted in the sixth iteration of the project (FANTOM

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Schwengers, Oliver, Lukas Jelonek, Marius Alfred Dieckmann, Sebastian Beyvers, Jochen Blom, and Alexander Goesmann. "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification." Microbial Genomics 7, no. 11 (2021). http://dx.doi.org/10.1099/mgen.0.000685.

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Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes. However, results of existing command-line software pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes. Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into accou

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Qurban, A. Memon, and A. Khoja Shakeel. "Academic Program Administration via Semantic Web – A Case Study." January 29, 2009. https://doi.org/10.5281/zenodo.1059938.

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Generally, administrative systems in an academic environment are disjoint and support independent queries. The objective in this work is to semantically connect these independent systems to provide support to queries run on the integrated platform. The proposed framework, by enriching educational material in the legacy systems, provides a value-added semantics layer where activities such as annotation, query and reasoning can be carried out to support management requirements. We discuss the development of this ontology framework with a case study of UAE University program administration to sho

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Hur, Junguk, Larson Danes, Dakota Krout, Jui‐Hua Hsieh, and Scott Auerbach. "Tox21 Enricher: Web‐based chemical and functional enrichment analysis tool for Tox21 toxicity screening platform." FASEB Journal 31, S1 (2017). http://dx.doi.org/10.1096/fasebj.31.1_supplement.613.1.

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Humans are exposed to tens of thousands of chemicals that are used in our daily life, some at levels that may pose a health risk. For many of these chemicals, there are limited toxicological information which makes risk assessment impossible. The United States Toxicology Testing in the 21st Century (Tox21) program was established to develop more efficient and human relevant toxicity assessment methods. The Tox21 program is currently screening over 10,000 chemicals, the Tox21 10K library, using quantitative high‐throughput screening (qHTS) of assays that measure effects on toxicity pathways. To

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Beenu, Yadav. "Microposts Ontology Construction Via Concept Extraction." July 12, 2019. https://doi.org/10.5281/zenodo.3333542.

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The social networking website Facebook offers to its users a feature called “status updates” (or just “status”), which allows users to create Microposts directed to all their contacts, or a subset thereof. Readers can respond to Microposts, or in addition to that also click a “Like” button to show their appreciation for a certain Micropost. Adding semantic meaning in the sense of unambiguous intended ideas to such Microposts. We can make a start towards semantic web by adding semantic annotation to web resources. Ontology are used to specify meaning of annot

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Mitchell, Joshua M., Yuanye Chi, Shujian Zheng, Maheshwor Thapa, Eric Wang, and Shuzhao Li. "Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web." Journal of the American Society for Mass Spectrometry, September 30, 2024. http://dx.doi.org/10.1021/jasms.4c00175.

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Midlik, Adam, Sebastian Bittrich, Jennifer R. Fleming, et al. "MolViewSpec: a Mol* extension for describing and sharing molecular visualizations." Nucleic Acids Research, May 6, 2025. https://doi.org/10.1093/nar/gkaf370.

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Abstract Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Sce

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Mudge, Jonathan M., Sílvia Carbonell-Sala, Mark Diekhans, et al. "GENCODE 2025: reference gene annotation for human and mouse." Nucleic Acids Research, November 20, 2024. http://dx.doi.org/10.1093/nar/gkae1078.

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Abstract GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq expe

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Dolin, Robert, Bret S. E. Heale, Rohan Gupta, et al. "Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR‐formatted genomic variants." Learning Health Systems, August 30, 2023. http://dx.doi.org/10.1002/lrh2.10385.

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AbstractIntroductionVariant annotation is a critical component in next‐generation sequencing, enabling a sequencing lab to comb through a sea of variants in order to hone in on those likely to be most significant, and providing clinicians with necessary context for decision‐making. But with the rapid evolution of genomics knowledge, reported annotations can quickly become out‐of‐date. Under the ONC Sync for Genes program, our team sought to standardize the sharing of dynamically annotated variants (e.g., variants annotated on demand, based on current knowledge). The computable biomedical knowl

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Vieira, Ana Odete Santos, and G. J. Shepherd. "A new species of Lobelia (Campanulaceae) from Brazil." June 5, 1998. https://doi.org/10.5281/zenodo.10959049.

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This record enriches the publication "A new species of Lobelia (Campanulaceae) from Brazil" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via the Arcadia Fund corpus repository.

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Vieira, Ana Odete Santos, and G. J. Shepherd. "A new species of Lobelia (Campanulaceae) from Brazil." June 5, 1998. https://doi.org/10.5281/zenodo.10959104.

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This record enriches the publication "A new species of Lobelia (Campanulaceae) from Brazil" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via the Arcadia Fund corpus repository.

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Lammers, Thomas G. "Nemacladoideae, a New Subfamily of Campanulaceae." June 5, 1998. https://doi.org/10.5281/zenodo.10959106.

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This record enriches the publication "Nemacladoideae, a New Subfamily of Campanulaceae" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via the Arcadia Fund corpus repository.

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Cornwell, Peter. "Progress with Repository-based Annotation Infrastructure for Biodiversity Applications." Biodiversity Information Science and Standards 7 (September 14, 2023). http://dx.doi.org/10.3897/biss.7.112707.

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Rapid development since the 1980s of technologies for analysing texts, has led not only to widespread employment of text 'mining', but also to now-pervasive large language model artificial intelligence (AI) applications. However, building new, concise, data resources from historic, as well as contemporary scientific literature, which can be employed efficiently at scale by automation and which have long-term value for the research community, has proved more elusive. Efforts at codifying analyses, such as the Text Encoding Initiative (TEI), date from the early 1990s and were initially driven by

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Lucinda, Paulo Henrique Franco, and Roberto E. Reis. "Systematics of the subfamily Poeciliinae Bonaparte (Cyprinodontiformes: Poeciliidae), with an emphasis on the tribe Cnesterodontini Hubbs." June 5, 2005. https://doi.org/10.5281/zenodo.10959191.

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This record enriches the publication "Systematics of the subfamily Poeciliinae Bonaparte (Cyprinodontiformes: Poeciliidae), with an emphasis on the tribe Cnesterodontini Hubbs" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation u

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Koerber, Stefan, Thomas O. Litz, and Wilson S. Serra. "CLOFFUY - update 5 - supplement to Checklist of the Freshwater Fishes of Uruguay." June 5, 2023. https://doi.org/10.5281/zenodo.10959205.

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This record enriches the publication "CLOFFUY - update 5 - supplement to Checklist of the Freshwater Fishes of Uruguay" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via the Arcadia Fun

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Jara, Carlos G., and Víctor L. Palacios. "Two new species of Aegla Leach (Crustacea: Decapoda: Anomura: Aeglidae) from southern Chile." June 5, 1999. https://doi.org/10.5281/zenodo.10959027.

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This record enriches the publication "Two new species of Aegla Leach (Crustacea: Decapoda: Anomura: Aeglidae) from southern Chile" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via the

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Coelho, Guilherme Peres, João Ricardo Vieira Iganci, and Silvia Teresinha Sfoggia Miotto. "Siphocampylus nebularis (Campanulaceae, Lobelioideae), a New Endemic Species from the Atlantic Forest in Southern Brazil." June 5, 2020. https://doi.org/10.5281/zenodo.10959053.

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This record enriches the publication "Siphocampylus nebularis (Campanulaceae, Lobelioideae), a New Endemic Species from the Atlantic Forest in Southern Brazil" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotati

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Schilling, Edward E., Aaron Floden, Jayne Lampley, Thomas S. Patrick, and Susan B. Farmer. "A New Species of Trillium (Melanthiaceae) from Central Georgia and its Phylogenetic Position in subgenus Sessilium." June 5, 2019. https://doi.org/10.5281/zenodo.10959057.

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This record enriches the publication "A New Species of Trillium (Melanthiaceae) from Central Georgia and its Phylogenetic Position in subgenus Sessilium" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Dat

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Freitas, Joelcio, Favio González, and Anderson Alves-Araújo. "Aristolochia lorenae, a New Cauliflorous Aristolochia (Aristolochiaceae) from the Brazilian Amazonian Forest." June 5, 2019. https://doi.org/10.5281/zenodo.10959059.

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This record enriches the publication "Aristolochia lorenae, a New Cauliflorous Aristolochia (Aristolochiaceae) from the Brazilian Amazonian Forest" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Mode

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Lucas, Dióber Borges, and Ilsi lob Boldrini. "Eryngium irgangii (Apiaceae, Saniculoideae): A New Species From the Southern Brazilian Highlands." June 5, 2018. https://doi.org/10.5281/zenodo.10959073.

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This record enriches the publication "Eryngium irgangii (Apiaceae, Saniculoideae): A New Species From the Southern Brazilian Highlands" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via

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Coelho, Guilherme Peres, and Silvia Teresinha Sfoggia Miotto. "A New Species of Buddleja (Scrophulariaceae) From Southern Brazil." June 5, 2017. https://doi.org/10.5281/zenodo.10959075.

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This record enriches the publication "A New Species of Buddleja (Scrophulariaceae) From Southern Brazil" to improve its Data Commons accessibility. It demonstrates the generation of DataCite metadata using Data Futures <em>annostor</em> which improves discovery and at the same time creates a platform for further identification of taxonomic information. In addition to a preview-able PDF for the publication, individual page imagery is attached as PNG files—providing a coordinate framework for taxonomic treatment annotation using Web Annotation Data Model (WADM) via the Arcadia Fund corpus reposi

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