Towards the automation of Knowledge Graph
construction using Large Language Models
Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel, NLP4KGC: 3rd International Workshop on Natural
Language Processing for Knowledge Graph Creation in conjunction with SEMANTiCS 2024 Conference, 2024 (To
appear)
Integrating domain knowledge for enhanced concept
model explainability in Plant Disease classification
Jihen Amara, Sheeba Samuel, Birgitta König-Ries, The 21st European Semantic Web Conference, ESWC In-Use
Track, 2024 (Paper)
Computational reproducibility of Jupyter
notebooks
from biomedical publications
Sheeba Samuel, Daniel Mietchen, GigaScience, 2024 (Paper)
From human experts to machines: An LLM supported
approach to ontology and knowledge graph construction
Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel, 2024 (Preprint)
FAIR Jupyter: a knowledge graph approach to
semantic sharing and granular exploration of a computational notebook reproducibility dataset
Sheeba Samuel, Daniel Mietchen, 2024 (Preprint)
Evaluating the method reproducibility of deep
learning models in the
biodiversity domain
Waqas Ahmed, Vamsi Krishna Kommineni, Birgitta König-Ries, Jitendra Gaikwad, Luiz M. R. Gadelha Jr., Sheeba
Samuel, 2024 (Preprint)
Dagstuhl Seminar 23372 - Working Group:
Applications
Klaus Eckelt, Sheeba Samuel, David Koop, Kiran Gadhave, Dominik Moritz, Dagstuhl Seminar 23372 -
Human-Centered Approaches for Provenance in Automated Data Science, 2024 (Paper)
Data Provenance for Reproducible Research
Sheeba Samuel, Dagstuhl Seminar 23372 - Human-Centered Approaches for Provenance in Automated Data Science,
2024 (Paper)
The role of Ontology Matching in Ontology Network
Development
Sheeba Samuel, Birgitta König-Ries, Alsayed Algergawy, The 18th International Workshop on Ontology Matching
co-located with the 22nd International Semantic Web Conference ISWC-2023, 2023 (Paper)
Concept explainability for plant diseases
classification
Jihen Amara, Birgitta König-Ries, Sheeba Samuel, VISAPP, 2023 (Paper, Preprint, Bibtex)
MLProvLab: Provenance Management for Data Science
Notebooks
Dominik Kerzel, Birgitta König-Ries, Sheeba Samuel, DE4DS Workshop co-located with BTW 2023 , 2023 (Paper, Bibtex)
MLProvCodeGen: A Tool for Provenance Data Input
and Capture of Customizable Machine Learning Scripts
Tarek Al Mustafa, Birgitta König-Ries, Sheeba Samuel, BTW 2023 Student Program, 2023 (Paper, Bibtex)
Computational reproducibility of Jupyter
notebooks
from biomedical publications
Sheeba Samuel, Daniel Mietchen, GigaScience, 2023 (Preprint,
Accepted, to appear)
Reproducible Domain-Specific Knowledge Graphs in
the Life Sciences: a
Systematic Literature Review
Samira Babalou, Sheeba Samuel, Birgitta König-Ries, [arXiv preprint], 2023 (Preprint)
How Reproducible are the Results Gained with the Help of Deep Learning Methods in Biodiversity Research? Waqas Ahmed, Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel, Biodiversity Information Science and Standards, TDWG, 9-13th October 2023, Australia (Abstract)
Computational reproducibility of Jupyter
notebooks from biomedical publications
Sheeba Samuel, Daniel Mietchen, [arXiv preprint], 2022 (Paper)
End-to-End Provenance Representation for the
Understandability and Reproducibility of Scientific Experiments using a Semantic Approach
Sheeba Samuel, Birgitta König-Ries, Journal of Biomedical Semantics, 2022 (Paper, Bibtex)
A collaborative semantic-based provenance
management platform for reproducibility.
Sheeba Samuel, Birgitta König-Ries, PeerJ Computer Science, 2022 (Paper, Bibtex)
Toward a Framework for Integrative, FAIR, and
Reproducible Management of Data on the Dynamic Balance of Microbial Communities
Luiz Gadelha, Martin Hohmuth, Mahnoor Zulfiqar, David Schöne, Sheeba Samuel, Maria Sorokina, Christoph
Steinbeck, Birgitta König-Ries, Proc. 2022 IEEE 18th International Conference on eScience (eScience). IEEE,
2022 (Paper, preprint, Bibtex)
BiodivNERE: Gold standard corpora for named
entity recognition and relation extraction in the biodiversity domain
Nora Abdelmageed, Felicitas Löffler, Leila Feddoul, Alsayed Algergawy, Sheeba Samuel, Jitendra Gaikwad,
Anahita Kazem, Birgitta König-Ries,
Biodiversity Data Journal, 2022 (Paper, Bibtex)
[RE] Nondeterminism and Instability in Neural
Network Optimization
Waqas Ahmed, Sheeba Samuel, ML Reproducibility Challenge 2021, ReScience journal, 2022 (Paper, Bibtex)
Towards Tracking Provenance from Machine Learning
Notebooks.
Dominik Kerzel, Sheeba Samuel, Birgitta König-Ries, 13th International Conference on Knowledge Discovery and
Information Retrieval (KDIR), 2021 (Paper, Bibtex)
Towards an Ontology Network for the
reproducibility of scientific studies.
Sheeba Samuel, Alsayed Algergawy, Birgitta König-Ries, 8th International Workshop on Ontologies and
Conceptual Modeling, co-located with FOIS, 2021 (Paper, Slides, Bibtex)
A Data-driven Approach for Core Biodiversity
Ontology Development.
Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel, Birgitta König-Ries, Third International Workshop on
Semantics for Biodiversity, co-located with ICBO, 2021 (Paper, Bibtex)
Capturing and Semantically Describing Provenance
to Tell the Story of R Scripts.
Maria Luiza Mondelli, Sheeba Samuel, Birgitta König-Ries, Luiz M. R. Gadelha Jr., ReWords, co-located with
17th IEEE e-Science 2021 (Paper, Bibtex)
ReproduceMeGit: A Visualization Tool for
Analyzing Reproducibility of Jupyter Notebooks.
Sheeba Samuel, Birgitta König-Ries, Provenance and Annotation of Data and Processes - 8th and 9th
International
Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021 (Paper, Bibtex)
Machine Learning Pipelines: Provenance,
Reproducibility and FAIR Data Principles.
Sheeba Samuel, Frank Löffler, Birgitta König-Ries, Provenance and Annotation of Data and Processes - 8th and
9th International
Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021 (Paper, Bibtex)
Understanding experiments and research practices
for reproducibility: an exploratory study
Sheeba Samuel, Birgitta König-Ries, PeerJ 9:e11140, 2021(Paper, Bibtex)
BiodivOnto: Towards a Core Ontology for
Biodiversity
Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel, Birgitta König-Ries, 18th Extended Semantic Web
Conference (ESWC) 2021 Poster Track, 6-10 June, 2021 (Paper, Bibtex)
A virtual “Werkstatt” for digitization in the
sciences
Sheeba Samuel, Maha Shadaydeh, Sebastian Böcker, Bernd Brügmann, Solveig Franziska Bucher, Volker Deckert,
Joachim Denzler, Peter Dittrich, Ferdinand von Eggeling, Daniel Güllmar, Orlando Guntinas-Lichius, Birgitta
König-Ries, Frank Löffler, Lutz Maicher, Manja Marz, Mirco Migliavacca, Jürgen R. Reichenbach, Markus
Reichstein, Christine Römermann, Andrea Wittig,
Research Ideas and Outcomes Journal 2020 (Paper)
ReproduceMeGit: A Visualization Tool for
Analyzing Reproducibility of Jupyter Notebooks.
Sheeba Samuel, Birgitta König-Ries, ProvenanceWeek 2020 (Paper,
Slides, Bibtex)
Machine Learning Pipelines: Provenance,
Reproducibility and FAIR Data Principles.
Sheeba Samuel, Frank Löffler, Birgitta König-Ries, ProvenanceWeek 2020 (Paper, Slides, Bibtex)
Contributions to Open Science for Understandability, Reproducibility and Reuse of Scientific Experiments, Birgitta König-Ries, Sheeba Samuel, Microverse Symposium 2020 [Abstract]
Towards Integrative Data Management for Research on the Dynamic Balance of Microbial Communities, Maria Sorokina, Martin Hohmuth, David Schöne, Sheeba Samuel, Roman Gerlach, Aurélie Jost, Christoph Steinbeck, Birgitta König-Ries, Microverse Symposium 2020 [Abstract]
A Provenance-based Semantic Approach to Support
Understandability, Reproducibility, and Reuse of Scientific Experiments
Sheeba Samuel, PhD Dissertation, Friedrich Schiller University Jena, Germany
(Thesis, PhD Defense Slides, Bibtex)
The Story of an Experiment:A Provenance-based
Semantic Approach towards Research Reproducibility
Sheeba Samuel, Kathrin Groeneveld, Frank Taubert, Daniel Walther, Tom Kache, Teresa Langenstück, Birgitta
König-Ries, H. Martin Bücker and Christoph Biskup,
The 11th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences
(SWAT4HCLS 2018), 3-6 December, 2018, antwerp, Belgium
(Preprint, Slides, Paper, Bibtex)
ProvBook: Provenance-based Semantic Enrichment of
Interactive Notebooks for Reproducibility
Sheeba Samuel, Birgitta König-Ries, The 17th International Semantic Web Conference (ISWC) 2018 Demo Track,
8-12 October, 2018, Monterey, California, USA (Demo, Paper, Bibtex)
Combining P-Plan and the REPRODUCE-ME Ontology to
Achieve Semantic Enrichment of Scientific Experiments using Interactive Notebooks
Sheeba Samuel, Birgitta König-Ries, 15th Extended Semantic Web Conference (ESWC) 2018 Poster Track, 3-7
June, 2018, Heraklion, Crete, Greece (Paper, Bibtex)
Provenance-based Semantic Approach for the Reproducibility of Scientific Experiments ICEI2018 - The 10th International Conference on Ecological Informatics, September 27, 2018 [Abstract] (Paper)
REPRODUCE-ME: Ontology-based Data Access for
Reproducibility of Microscopy Experiments
Sheeba Samuel, Birgitta König-Ries, 14th Extended Semantic Web Conference (ESWC) 2018 Poster Track, 28 May-1
June, 2017, Portoroz, Slovenia (Paper, Bibtex)
Integrative Data Management for Reproducibility
of Microscopy Experiments
Sheeba Samuel, 14th Extended Semantic Web Conference (ESWC) 2018 PhD Symposium, 28 May-1 June, 2017,
Portoroz, Slovenia (Paper, Bibtex)
Towards reproducibility of microscopy
experiments
Sheeba Samuel, Frank Taubert, Daniel Walther, Birgitta König-Ries, H Martin Bücker, D-Lib Magazine 23.1/2
(2017) (Paper, Bibtex)
Hadoop Compatible Framework for Discovering
Network
Topology and Detecting Hardware Failures
Ventrapragada, Anusha, Sheeba Samuel, Varsha Raja Vidya, Shwetha Muralidharan, and Shrisha Rao, In 2012
Third International Conference on Services in Emerging Markets (pp. 58-64). IEEE 2012. (Paper, Bibtex)
