@article{Borkowski:et:al:2026,
  author = "C. Borkowski and G. Abrami and D. Terefe and D. Baumartz and A. Mehler",
  title = "DUUIgateway: A Web Service for Platform-independent, Ubiquitous Big Data NLP",
  year = 2026,
  journal = "SoftwareX",
  volume = 34,
  pages = "102549",
  keywords = "duui",
  doi = "https://doi.org/10.1016/j.softx.2026.102549",
  url = "https://www.sciencedirect.com/science/article/pii/S2352711026000439"
}


@inproceedings{Dahmann:et:al:2026,
  author = "T. Dahmann and J. Schneider and P. Stephan and G. Abrami and A. Mehler",
  title = "Towards the Generation and Application of Dynamic Web-Based Visualization of UIMA-based Annotations for Big-Data Corpora with the Help of Unified Dynamic Annotation Visualizer",
  year = 2026,
  booktitle = "Proceedings of the 15th International Conference on Language Resources and Evaluation (LREC 2026)",
  keywords = "nlp, uima, annotations, dynamic visualization, uce",
  note = "accepted"
}


@inproceedings{Hammerla:et:al:2025a,
  author = "L. Hammerla and A. Mehler and G. Abrami",
  title = "Standardizing Heterogeneous Corpora with DUUR: A Dual Data- and Process-Oriented Approach to Enhancing NLP Pipeline Integration",
  year = 2025,
  booktitle = "Proceedings of the 14th International Joint Conference on Natural Language Processing and the 4th Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics",
  publisher = "The Asian Federation of Natural Language Processing and The Association for Computational Linguistics",
  pages = "1410-1425",
  keywords = "duui",
  url = "https://aclanthology.org/2025.findings-ijcnlp.87/",
  isbn = "979-8-89176-303-6"
}


@inproceedings{Boenisch:et:al:2025,
  author = "K. Bönisch and G. Abrami and A. Mehler",
  title = "Towards Unified, Dynamic and Annotation-based Visualisations and Exploration of Annotated Big Data Corpora with the Help of Unified Corpus Explorer",
  year = 2025,
  booktitle = "Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (System Demonstrations)",
  publisher = "Association for Computational Linguistics",
  pages = "522-534",
  url = "https://aclanthology.org/2025.naacl-demo.42/",
  note = "Best Demo Award",
  isbn = "979-8-89176-191-9"
}


@article{Aldana-Martín2025a,
  author = "J. F. Aldana-Martín and D. J. Russell and C. A. Martínez-Muñoz and C. Driller and S. Lesch and I. Navas-Delgado",
  title = "Advancing soil biology research: Empowering European databases with ontological frameworks for enhanced data integration of soil biodiversity data",
  year = 2025,
  journal = "Ecological Informatics",
  volume = 91,
  doi = "10.1016/j.ecoinf.2025.103356"
}


@inproceedings{Abrami:et:al:2025:b,
  author = "G. Abrami and D. Baumartz and A. Mehler",
  title = "DUUI: A Toolbox for the Construction of a new Kind of Natural Language Processing",
  year = 2025,
  booktitle = "Proceedings of the DHd 2025: Under Construction. Geisteswissenschaften und Data Humanities",
  publisher = "Zenodo",
  pages = "446-448",
  keywords = "duui",
  doi = "10.5281/zenodo.14943128",
  url = "https://doi.org/10.5281/zenodo.14943128"
}


@article{Abrami:et:al:2025:a,
  author = "G. Abrami and M. Genios and F. Fitzermann and D. Baumartz and A. Mehler",
  title = "Docker Unified UIMA Interface: New perspectives for NLP on big data",
  year = 2025,
  journal = "SoftwareX",
  volume = 29,
  pages = "102033",
  keywords = "duui, docker, kubernetes, uima, distributed nlp",
  doi = "https://doi.org/10.1016/j.softx.2024.102033",
  url = "https://www.sciencedirect.com/science/article/pii/S2352711024004047"
}


@inproceedings{Abrami:Mehler:2024,
  author = "G. Abrami and A. Mehler",
  title = "Efficient, uniform and scalable parallel NLP pre-processing with DUUI: Perspectives and Best Practice for the Digital Humanities",
  year = 2024,
  booktitle = "Digital Humanities Conference 2024 - Book of Abstracts (DH 2024)",
  publisher = "Zenodo",
  pages = "15-18",
  month = "Aug",
  keywords = "duui",
  doi = "10.5281/zenodo.13761079",
  url = "https://doi.org/10.5281/zenodo.13761079"
}


@inproceedings{Konca:et:al:2024,
  author = "M. Konca and A. Lücking and A. Mehler",
  title = "{G}erman {SRL}: Corpus Construction and Model Training",
  year = 2024,
  booktitle = "Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)",
  publisher = "ELRA and ICCL",
  pages = "7717-7727",
  month = "May",
  url = "https://aclanthology.org/2024.lrec-main.682"
}


@inproceedings{Luecking:et:al:2024,
  author = "A. Lücking and G. Abrami and L. Hammerla and M. Rahn and D. Baumartz and S. Eger and A. Mehler",
  title = "Dependencies over Times and Tools ({D}o{TT})",
  year = 2024,
  booktitle = "Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)",
  publisher = "ELRA and ICCL",
  pages = "4641-4653",
  month = "May",
  url = "https://aclanthology.org/2024.lrec-main.415"
}


@inproceedings{Leonhardt:et:al:2023,
  author = "A. Leonhardt and G. Abrami and D. Baumartz and A. Mehler",
  title = "Unlocking the Heterogeneous Landscape of Big Data {NLP} with {DUUI}",
  year = 2023,
  booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2023",
  publisher = "Association for Computational Linguistics",
  pages = "385-399",
  keywords = "duui",
  url = "https://aclanthology.org/2023.findings-emnlp.29"
}


@inproceedings{Luecking:Stoeckel:Abrami:Mehler:2022,
  author = "A. Lücking and M. Stoeckel and G. Abrami and A. Mehler",
  title = "I still have Time(s): Extending {HeidelTime} for {German} Texts",
  year = 2022,
  booktitle = "Proceedings of the 13th Language Resources and Evaluation Conference",
  url = "https://aclanthology.org/2022.lrec-1.505"
}


@inproceedings{Fischer:et:al:2021,
  author = "P. Fischer and A. Smajic and G. Abrami and A. Mehler",
  title = "Multi-Type-TD-TSR - Extracting Tables from Document Images using a Multi-stage Pipeline for Table Detection and Table Structure Recognition: from OCR to Structured Table Representations",
  year = 2021,
  booktitle = "Proceedings of the 44th German Conference on Artificial Intelligence",
  url = "https://www.springerprofessional.de/multi-type-td-tsr-extracting-tables-from-document-images-using-a/19711570"
}


@article{Luecking:et:al:2021,
  author = "A. Lücking and C. Driller and M. Stoeckel and G. Abrami and A. Pachzelt and A. Mehler",
  title = "Multiple Annotation for Biodiversity: Developing an annotation framework among biology, linguistics and text technology",
  year = 2021,
  journal = "Language Resources and Evaluation",
  keywords = "biofid",
  doi = "10.1007/s10579-021-09553-5"
}


@inproceedings{Pachzelt2021a,
  author = "A. Pachzelt and G. Kasperek and A. Lücking and G. Abrami and C. Driller",
  title = "Semantic Search in Legacy Biodiversity Literature: Integrating data from different data infrastructures",
  year = 2021,
  journal = "Biodiversity Information Science and Standards",
  publisher = "Pensoft Publishers",
  volume = 5,
  pages = "e74251",
  month = "Sep",
  doi = "10.3897/biss.5.74251",
  url = "https://doi.org/10.3897/biss.5.74251"
}


@inproceedings{Abrami:et:al:2021,
  author = "G. Abrami and A. Henlein and A. Lücking and A. Kett and P. Adeberg and A. Mehler",
  title = "Unleashing annotations with TextAnnotator: Multimedia, multi-perspective document views for ubiquitous annotation",
  year = 2021,
  booktitle = "Proceedings of the Seventeenth Joint ACL - ISO Workshop on Interoperable Semantic Annotation (ISA-17)",
  month = "Jun",
  url = "https://iwcs2021.github.io/proceedings/isa/pdf/2021.isa-1.7.pdf"
}


@article{Driller2020c,
  author = "C. Driller and M. Koch and G. Abrami and W. Hemati and A. Lücking and A. Mehler and A. Pachzelt and G. Kasperek",
  title = "Fast and Easy Access to Central European Biodiversity Data with BIOfid",
  year = 2020,
  journal = "Biodiversity Information Science and Standards",
  publisher = "Pensoft Publishers",
  month = "Oct",
  doi = "10.3897/biss.4.59157"
}


@inproceedings{Driller2019a,
  author = "C. Driller and M. Koch and G. Abrami and M. Stoeckel and A. Pachzelt and G. Kasperek",
  title = "Tracing back biodiversity to the 19th century via text mining",
  year = 2020,
  journal = "World Biodiversity Forum, Davos, Switzerland, February 23-28",
  month = "Feb"
}


@inproceedings{Driller2020a,
  author = "C. Driller and M. Koch and G. Abrami and M. Stoeckel and A. Pachzelt and G. Kasperek",
  title = "Mobilising Biodiversity Knowledge By Mining Heritage Literature",
  year = 2020,
  journal = "World Biodiversity Forum, Davos, Switzerland, February 23-28",
  month = "Feb"
}


@inproceedings{Abrami:Mehler:Stoeckel:2020,
  author = "G. Abrami and A. Mehler and M. Stoeckel",
  title = "TextAnnotator: A web-based annotation suite for texts",
  year = 2020,
  booktitle = "Proceedings of the Digital Humanities 2020",
  url = "https://dh2020.adho.org/wp-content/uploads/2020/07/547_TextAnnotatorAwebbasedannotationsuitefortexts.html"
}


@inproceedings{Abrami:Stoeckel:Mehler:2020,
  author = "G. Abrami and M. Stoeckel and A. Mehler",
  title = "TextAnnotator: A UIMA based tool for simultaneous and collaborative annotation of texts",
  year = 2020,
  booktitle = "12th International Conference on Language Resources and Evaluation (LREC 2020)",
  publisher = "European Language Resources Association",
  pages = "891–900",
  url = "http://www.lrec-conf.org/proceedings/lrec2020/pdf/2020.lrec-1.112.pdf"
}


@inproceedings{Henlein:Mehler:2020,
  author = "A. Henlein and A. Mehler",
  title = "On the Influence of Coreference Resolution on Word Embeddings in Lexical-semantic Evaluation Tasks",
  year = 2020,
  booktitle = "12th International Conference on Language Resources and Evaluation (LREC 2020)",
  url = "http://www.lrec-conf.org/proceedings/lrec2020/pdf/2020.lrec-1.4.pdf"
}


@inproceedings{Hildebrand:Hemati:Mehler:2020,
  author = "J. Hildebrand and W. Hemati and A. Mehler",
  title = "Recognizing Sentence-level Logical Document Structures with the Help of Context-free Grammars",
  year = 2020,
  booktitle = "12th International Conference on Language Resources and Evaluation (LREC 2020)",
  url = "http://www.lrec-conf.org/proceedings/lrec2020/pdf/2020.lrec-1.650.pdf"
}


@inproceedings{Koch2019a,
  author = "M. Koch and T. Hörnschemeyer",
  title = "Biodiversity of the apterygote hexapods - a global assessment",
  year = 2020,
  journal = "26th International Congress of Entomology, Helsinki, Finland, July 19-24",
  url = "https://submit.peerageofscience.org/conference/ICE_2020/109837"
}


@inproceedings{Stoeckel:Hemati:Mehler:2019,
  author = "M. Stoeckel and W. Hemati and A. Mehler",
  title = "When Specialization Helps: Using Pooled Contextualized Embeddings to Detect Chemical and Biomedical Entities in {S}panish",
  year = 2019,
  booktitle = "Proceedings of The 5th Workshop on BioNLP Open Shared Tasks",
  publisher = "Association for Computational Linguistics",
  month = "Nov",
  doi = "10.18653/v1/D19-5702",
  url = "https://www.aclweb.org/anthology/D19-5702"
}


@inproceedings{Driller2019b,
  author = "C. Driller and G. Abrami and M. Koch and G. Kasperek and A. Pachzelt and A. Mehler",
  title = "Accessing knowledge from legacy biodiversity literature",
  year = 2019,
  journal = "Biodiversity Next, Leiden, Netherlands, October 22-25",
  month = "Oct"
}


@inproceedings{Koch2019c,
  author = "M. Koch and C. Driller and I. Mikó and M. Yoder",
  title = "Exploring biodiversity knowledge by ontologies",
  year = 2019,
  journal = "Biodiversity Next, Leiden, Netherlands, October 22-25",
  month = "Oct"
}


@inproceedings{Driller2019a,
  author = "C. Driller and G. Abrami and M. Stoeckel and M. Koch and G. Kasperek",
  title = "Tracing back biodiversity to the 19th century via text mining",
  year = 2019,
  journal = "49th Annual Meeting of the Ecological Society of Germany, Austria and Switzerland, Münster, Germany; September 9-13",
  month = "Sep"
}


@inproceedings{Koch2019b,
  author = "M. Koch and C. Driller and C. Weiland and T. Hörnschemeyer",
  title = "Modern information technologies for the study of myriapod biodiversity",
  year = 2019,
  journal = "18th International Congress of Myriapodology, Budapest, Hungary, August 25-31",
  month = "Aug"
}


@inproceedings{Abrami:et:al:2019,
  author = "G. Abrami and A. Mehler and A. Lücking and E. Rieb and P. Helfrich",
  title = "{TextAnnotator}: A flexible framework for semantic annotations",
  year = 2019,
  booktitle = "Proceedings of the Fifteenth Joint ACL - ISO Workshop on Interoperable Semantic Annotation, (ISA-15)",
  month = "May",
  url = "https://www.texttechnologylab.org/wp-content/uploads/2019/04/TextAnnotator_IWCS_G%C3%B6teborg.pdf"
}


@article{Hemati:Mehler:2019b,
  author = "W. Hemati and A. Mehler",
  title = "{CRFVoter}: gene and protein related object recognition using a conglomerate of CRF-based tools",
  year = 2019,
  journal = "Journal of Cheminformatics",
  volume = 11,
  number = 1,
  month = "Mar",
  doi = "10.1186/s13321-019-0343-x",
  url = "https://doi.org/10.1186/s13321-019-0343-x"
}


@article{Hemati:Mehler:2019a,
  author = "W. Hemati and A. Mehler",
  title = "{LSTMVoter}: chemical named entity recognition using a conglomerate of sequence labeling tools",
  year = 2019,
  journal = "Journal of Cheminformatics",
  volume = 11,
  number = 1,
  month = "Jan",
  doi = "10.1186/s13321-018-0327-2",
  url = "https://doi.org/10.1186/s13321-018-0327-2"
}


@inproceedings{Ahmed:Stoeckel:Driller:Pachzelt:Mehler:2019,
  author = "S. Ahmed and M. Stoeckel and C. Driller and A. Pachzelt and A. Mehler",
  title = "BIOfid Dataset: Publishing a German Gold Standard for Named Entity Recognition in Historical Biodiversity Literature",
  year = 2019,
  booktitle = "Proceedings of the 23rd Conference on Computational Natural Language Learning (CoNLL)",
  publisher = "Association for Computational Linguistics",
  note = "accepted"
}


@inproceedings{Hemati:Mehler:Uslu:Abrami:2019,
  author = "W. Hemati and A. Mehler and T. Uslu and G. Abrami",
  title = "Der TextImager als Front- und Backend für das verteilte NLP von Big Digital Humanities Data",
  year = 2019,
  booktitle = "Proceedings of the 6th Digital Humanities Conference in the German-speaking Countries, DHd 2019"
}


@inproceedings{Stoeckel:Hemati:Mehler:2019,
  author = "M. Stoeckel and W. Hemati and A. Mehler",
  title = "When Specialization Helps: Using Pooled Contextualized Embeddings to Detect Chemical and Biomedical Entities in Spanish",
  year = 2019,
  booktitle = "Proceedings of the International Workshop on BioNLP Open Shared Tasks (BioNLP-OST) 2019",
  publisher = "Association for Computational Linguistics SIGDAT and Asian Federation of Natural Language Processing",
  note = "accepted"
}


@inproceedings{Uslu:Mehler:Baumartz:2019,
  author = "T. Uslu and A. Mehler and D. Baumartz",
  title = "Computing Classifier-based Embeddings with the Help of text2ddc",
  year = 2019,
  booktitle = "Proceedings of the 20th International Conference on Computational Linguistics and Intelligent Text Processing, (CICLing 2019)"
}


@inproceedings{Uslu:Mehler:Schulz:Baumartz:2019,
  author = "T. Uslu and A. Mehler and C. Schulz and D. Baumartz",
  title = "{BigSense}: a Word Sense Disambiguator for Big Data",
  year = 2019,
  booktitle = "Proceedings of the Digital Humanities 2019, (DH2019)"
}


@inproceedings{Abrami:et:al:2018,
  author = "G. Abrami and A. Mehler and P. Helfrich and E. Rieb",
  title = "{TextAnnotator}: A Browser-based Framework for Annotating Textual Data in Digital Humanities",
  year = 2018,
  booktitle = "Proceedings of the Digital Humanities Austria 2018"
}


@inproceedings{Abrami:et:al:2018,
  author = "G. Abrami and A. Mehler",
  title = "A UIMA Database Interface for Managing NLP-related Text Annotations",
  year = 2018,
  booktitle = "Proceedings of the 11th edition of the Language Resources and Evaluation Conference, May 7 - 12"
}


@inproceedings{Ahmed:Mehler:2018,
  author = "S. Ahmed and A. Mehler",
  title = "Resource-Size matters: Improving Neural Named Entity Recognition with Optimized Large Corpora",
  year = 2018,
  booktitle = "Proceedings of the 17th IEEE International Conference on Machine Learning and Applications (ICMLA)"
}


@inproceedings{Baumartz:Uslu:Mehler:2018,
  author = "D. Baumartz and T. Uslu and A. Mehler",
  title = "{LTV}: Labeled Topic Vector",
  year = 2018,
  booktitle = "Proceedings of {COLING 2018}, the 27th International Conference on Computational Linguistics: System Demonstrations, August 20-26",
  publisher = "The COLING 2018 Organizing Committee"
}


@article{10.3897/biss.2.25876,
  author = "C. Driller and M. Koch and M. Schmidt and C. Weiland and T. Hörnschemeyer and T. Hickler and G. Abrami and S. Ahmed and R. Gleim and W. Hemati and T. Uslu and A. Mehler and A. Pachzelt and J. Rexhepi and T. Risse and J. Schuster and G. Kasperek and A. Hausinger",
  title = "Workflow and Current Achievements of BIOfid, an Information Service Mobilizing Biodiversity Data from Literature Sources",
  year = 2018,
  journal = "Biodiversity Information Science and Standards",
  publisher = "Pensoft Publishers",
  volume = 2,
  doi = "10.3897/biss.2.25876",
  url = "https://doi.org/10.3897/biss.2.25876"
}


@inproceedings{Helfrich:et:al:2018,
  author = "P. Helfrich and E. Rieb and G. Abrami and A. Lücking and A. Mehler",
  title = "TreeAnnotator: Versatile Visual Annotation of Hierarchical Text Relations",
  year = 2018,
  booktitle = "Proceedings of the 11th edition of the Language Resources and Evaluation Conference, May 7 - 12"
}


@inproceedings{KasperekSchmidt2018,
  author = "G. Kasperek and M. Schmidt",
  title = "A Specialised Information Service for Biodiversity Research, involving large-scale data mobilisation by mining German biodiversity literature",
  year = 2018,
  booktitle = "XIX International Botanical Congress (IBC2017), July 23-29"
}


@inproceedings{Kett:et:al:2018,
  author = "A. Kett and G. Abrami and A. Mehler and C. Spiekermann",
  title = "{Resources2City Explorer}: A System for Generating Interactive Walkable Virtual Cities out of File Systems",
  year = 2018,
  booktitle = "Proceedings of the 31st ACM User Interface Software and Technology Symposium"
}


@article{10.3897/biss.2.25585,
  author = "M. Koch and C. Driller and M. Schmidt and T. Hörnschemeyer and C. Weiland and Miko I and M. Yoder and T. Hickler",
  title = "Current progress in the development of taxonomic and anatomical ontologies within the scope of BIOfid",
  year = 2018,
  journal = "Biodiversity Information Science and Standards",
  publisher = "Pensoft Publishers",
  volume = 2,
  doi = "10.3897/biss.2.25585",
  url = "https://doi.org/10.3897/biss.2.25585"
}


@inproceedings{Uslu:Mehler:2018,
  author = "T. Uslu and A. Mehler",
  title = "{PolyViz}: a Visualization System for a Special Kind of Multipartite Graphs",
  year = 2018,
  booktitle = "Proceedings of the IEEE VIS 2018"
}


@inproceedings{Uslu:et:al:2018,
  author = "T. Uslu and A. Mehler and D. Baumartz and A. Henlein and W. Hemati",
  title = "{fastSense}: An Efficient Word Sense Disambiguation Classifier",
  year = 2018,
  booktitle = "Proceedings of the 11th edition of the Language Resources and Evaluation Conference, May 7 - 12"
}


@inproceedings{Weiland:et:al:2018,
  author = "C. Weiland and C. Driller and M. Koch and M. Schmidt and G. Abrami and S. Ahmed and A. Mehler and A. Pachzelt and G. Kasperek and A. Hausinger and T. Hörnschemeyer",
  title = "{BioFID}, a platform to enhance accessibility of biodiversity data",
  year = 2018,
  booktitle = "Proceedings of the 10th International Conference on Ecological Informatics"
}


@inproceedings{Hemati:Mehler:Uslu:2017,
  author = "W. Hemati and A. Mehler and T. Uslu",
  title = "{CRFVoter}: Chemical Entity Mention, Gene and Protein Related Object recognition using a conglomerate of CRF based tools",
  year = 2017,
  booktitle = "BioCreative V.5. Proceedings"
}


@article{10.3897/tdwgproceedings.1.19803,
  author = "M. Koch and G. Kasperek and T. Hörnschemeyer and A. Mehler and C. Weiland and A. Hausinger",
  title = "Setup of BIOfid, a new Specialised Information Service for Biodiversity Research",
  year = 2017,
  journal = "Biodiversity Information Science and Standards",
  publisher = "Pensoft Publishers",
  volume = 1,
  doi = "10.3897/tdwgproceedings.1.19803",
  url = "https://doi.org/10.3897/tdwgproceedings.1.19803"
}