Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature by H.-M. Müller, K. M. Van Auken, Y. Li, P. W. Sternberg

“…Conclusion Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. …”
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Meta‐analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions by Emilian Jungwirth, Katrin Panzitt, Hanns‐Ulrich Marschall, Gerhard G. Thallinger, Martin Wagner

“…All publicly available single data sets were biocurated in a standardized manner and compared on every relevant level from raw reads to affected functional pathways. …”
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Automated Recommendation of Research Keywords from PubMed That Suggest the Molecular Mechanism Associated with Biomarker Metabolites by Shinji Kanazawa, Satoshi Shimizu, Shigeki Kajihara, Norio Mukai, Junko Iida, Fumio Matsuda

“…The intended users are biocurators who have identified specific biomarker metabolites from a metabolomics study and would like to identify literature-reported molecular mechanisms that are associated with both the metabolite and their research area of interest. …”
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Text mining for identification of biological entities related to antibiotic resistant organisms by Kelle Fortunato Costa, Fabrício Almeida Araújo, Jefferson Morais, Carlos Renato Lisboa Frances, Rommel T. J. Ramos

“…However, the growing volume of biological literature increases the difficulty of the biocuration process due to the cost and time required. …”
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CardioTF, a database of deconstructing transcriptional circuits in the heart system by Yisong Zhen

“…Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. …”
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BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. by McQuilton, P, Gonzalez-Beltran, A, Rocca-Serra, P, Thurston, M, Lister, A, Maguire, E, Sansone, S

“…Driven by an international Advisory Board, the BioSharing user-base has grown by over 40% (by unique IP address), in the last year thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint RDA/Force11 working group and a collaboration with the International Society for Biocuration. In this article, we describe BioSharing, with a particular focus on community-led curation.Database URL: https://www.biosharing.org.…”

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. by McQuilton, P, Gonzalez-Beltran, A, Rocca-Serra, P, Thurston, M, Lister, A, Maguire, E, Sansone, S

“…Driven by an international Advisory Board, the BioSharing user-base has grown by over 40% (by unique IP address), in the last year thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint RDA/Force11 working group and a collaboration with the International Society for Biocuration. In this article, we describe BioSharing, with a particular focus on community-led curation.Database URL: https://www.biosharing.org.…”

Targeting Cross-Presentation as a Route to Improve the Efficiency of Peptide-Based Cancer Vaccines by Ben Wylie, Ferrer Ong, Hanane Belhoul-Fakir, Kristin Priebatsch, Heique Bogdawa, Anja Stirnweiss, Paul Watt, Paula Cunningham, Shane R. Stone, Jason Waithman

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Mechanisms of action of monoclonal antibodies in oncology integrated in IMGT/mAb-DB by Taciana Manso, Anjana Kushwaha, Nika Abdollahi, Patrice Duroux, Véronique Giudicelli, Sofia Kossida

“…The characterization of these antibodies provides a comprehensive understanding of how mAbs work in cancer.MethodsIn depth biocuration taking advantage of the abundant literature data as well as amino acid sequence analyses from mAbs managed in IMGT/2Dstructure-DB, the IMGT® protein database, allowed to define a standardized and consistent description of the MOA of mAbs targeting immune checkpoints in cancer therapy.ResultsA fine description and a standardized graphical representation of the MOA of selected mAbs are integrated within IMGT/mAb-DB highlighting two main mechanisms in cancer immunotherapy, either Blocking or Agonist. …”
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A rule-based ontological framework for the classification of molecules by Magka, D, Krötzsch, M, Horrocks, I

“…</p> <p><b>CONCLUSIONS</b>: Our proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. …”

Delving into Molecular Pathways: Analyzing the Mechanisms of Action of Monoclonal Antibodies Integrated in IMGT/mAb-DB for Myasthenia Gravis by Rebecca Golfinopoulou, Véronique Giudicelli, Taciana Manso, Sofia Kossida

“…Methods: Using available literature data combined with amino acid sequence analyses from mAbs managed in IMGT/2Dstructure-DB, the IMGT^® protein database, biocuration allowed us to define in a standardized way descriptions of MOAs of mAbs that target molecules towards MG treatment. …”
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First Plant Cell Atlas symposium report by Selena L. Rice, Elena Lazarus, Christopher Anderton, Kenneth Birnbaum, Jennifer Brophy, Benjamin Cole, Diane Dickel, David Ehrhardt, Noah Fahlgren, Margaret Frank, Elizabeth Haswell, Shao‐shan Carol Huang, Samuel Leiboff, Marc Libault, Marisa S. Otegui, Nicholas Provart, R. Glen Uhrig, Seung Y. Rhee, The Plant Cell Atlas Consortium

“…The discussions also identified the following as being essential to the PCA's success: identifying homologous cell‐type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user‐friendly data visualization and data sharing. …”
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