[1] A.S. Behr, D. Chernenko, D. Kossmann, A. Neyyathala, S. Hanf, S.A. Schunk, N. Kockmann, Generating knowledge graphs through text mining of catalysis research related literature, Catal. Sci. Technol. 14 (19) (2024) 5699-5713. [2] Z.Y. Zhang, S.M. Ma, S.S. Zheng, Z.W. Nie, B.X. Wang, K. Lei, S.N. Li, F. Pan, Semantic knowledge graph as a companion for catalyst recommendation, Natl. Sci. Open (2024) 20230040. [3] A.L. Lamprecht, L. Garcia, M. Kuzak, C. Martinez, R. Arcila, E. Martin Del Pico, V. Dominguez Del Angel, S. van de Sandt, J. Ison, P.A. Martinez, P. McQuilton, A. Valencia, J. Harrow, F. Psomopoulos, J.L. Gelpi, N. Chue Hong, C. Goble, S. Capella-Gutierrez, Towards FAIR principles for research software, Data Sci. 3 (1) (2020) 37-59. [4] C.H. Wang, Y.Q. Yang, J.S. Song, X.F. Nan, Research progresses and applications of knowledge graph embedding technique in chemistry, J. Chem. Inf. Model. 64 (19) (2024) 7189-7213. [5] A. Hogan, E. Blomqvist, M. Cochez, C. d'Amato, G. de Melo, C. Gutierrez, S. Kirrane, J. E. L. Gayo, R. Navigli, S. Neumaier, A.-C. N. Ngomo, A. Polleres, S. M. Rashid, A. Rula, L. Schmelzeisen. Knowledge graphs. arXiv [cs.AI]. 2020. doi:10.1145/3447772. [6] C.Y. Peng, F. Xia, M. Naseriparsa, F. Osborne, Knowledge graphs: opportunities and challenges, Artif. Intell. Rev. (2023) 1-32. [7] S. Auer, V. Kovtun, M. Prinz, A. Kasprzik, M. Stocker, M.E. Vidal, Towards a knowledge graph for science,In:Proceedings of the 8th International Conference on Web Intelligence, Mining and Semantics. Novi Sad Serbia. ACM, 2018. [8] L. Ehrlinger, W. Woss. Towards a definition of knowledge graphs. SEMANTICS. 2016. Available: https://ceur-ws.org/Vol-1695/paper4.pdf. [9] Ontologies. [cited 18 Feb 2025]. Available: https://nfdi4cat.org/en/services/ontology-collection/. [10] M. Hofer, D. Obraczka, A. Saeedi, H. Kopcke, E. Rahm, Construction of knowledge graphs: current state and challenges, Information 15 (8) (2024) 509. [11] N. Kertkeidkachorn, R. Ichise. T2KG: An end-to-end system for creating knowledge Graph from unstructured text. 2017. Available: https://cdn.aaai.org/ocs/ws/ws0328/15129-68427-1-PB.pdf. [12] D. Buscaldi, D. Dessi, E. Motta, F. Osborne, D. Reforgiato Recupero, Mining scholarly publications for scientific knowledge graph construction. The Semantic Web: ESWC 2019 Satellite Events. Springer International Publishing, (2019), pp -12. [13] Y. Gao, L.D. Wang, X.Q. Chen, Y. Du, B. Wang, Revisiting electrocatalyst design by a knowledge graph of Cu-based catalysts for CO2 reduction, ACS Catal. 13 (13) (2023) 8525-8534. [14] A. Oarga, M. Hart, A.M. Bran, M. Lederbauer, P. Schwaller. Scientific knowledge graph and ontology generation using open large language models. Neurips 2024 Workshop Foundation Models for Science: Progress, Opportunities, and Challenges. 2024. Available: https://openreview.net/pdf?id=kHsfqBhZjC. [15] Y. Zhang, C. Wang, M. Soukaseum, D.G. Vlachos, H. Fang, Unleashing the power of knowledge extraction from scientific literature in catalysis, J. Chem. Inf. Model. 62 (14) (2022) 3316-3330. [16] K.T. Winther, M.J. Hoffmann, J.R. Boes, O. Mamun, M. Bajdich, T. Bligaard, Catalysis-Hub.org, an open electronic structure database for surface reactions, Sci. Data 6 (1) (2019) 75. [17] L. Pascazio, S. Rihm, A. Naseri, S. Mosbach, J. Akroyd, M. Kraft, Chemical species ontology for data integration and knowledge discovery, J. Chem. Inf. Model. 63 (21) (2023) 6569-6586. [18] V. Lopez, L. Hoang, M. Martinez-Galindo, R. Fernandez-Diaz, M.L. Sbodio, R. Ordonez-Hurtado, M. Zayats, N. Mulligan, J. Bettencourt-Silva, Enhancing foundation models for scientific discovery via multimodal knowledge graph representations, J. Web Semant. 84 (2025) 100845. [19] M.J. Buehler, Accelerating scientific discovery with generative knowledge extraction, graph-based representation, and multimodal intelligent graph reasoning, arXiv [cs.LG]. 2024. Available: http://arxiv.org/abs/2403.11996 . [20] X. Wang, B.Y. Meng, H. Chen, Y. Meng, K. Lv, W.W. Zhu, TIVA-KG: A multimodal knowledge graph with text, image, video and audio,In:Proceedings of the 31st ACM International Conference on Multimedia. Ottawa ON Canada. ACM, 2023. [21] V. Venugopal, E. Olivetti, MatKG: an autonomously generated knowledge graph in Material Science, Sci. Data 11 (1) (2024) 217. [22] A. Bordes, N. Usunier, A. Garcia-Duran, J. Weston, O. Yakhnenko. Translating embeddings for modeling multi-relational data. In: Burges CJ, Bottou L, Welling M, Ghahramani Z, Weinberger KQ, editors. Advances in Neural Information Processing Systems. Curran Associates, Inc.; 2013. Available: https://papers.nips.cc/paper/5071-translating-embeddings-for-modeling-multi-relational-data.pdf. [23] T. Trouillon, J. Welbl, S. Riedel, E. Gaussier, G. Bouchard, Complex embeddings for simple link prediction, In: Proceedings of the 33rd International Conference on Machine Learning (Proceedings of Machine Learning Research, 48, 2071 - 2080) (2016). PMLR. arXiv:1606.06357 [cs.AI]. [24] A.S. Behr, H. Borgelt, N. Kockmann, Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management, J. Cheminform. 16 (1) (2024) 16. [25] A.S. Behr, H. Borgelt, N. Kockmann, Reac4Cat-ontology: harnessing the power of ontological description logic in catalysis research as aPractical approach to knowledge inferences, Datenbank-Spektrum 24 (2) (2024) 139-150. [26] N. Huskova, Y. Dikova, T. Petrenko, T. Bonisch, Improvement of data and metadata quality in catalysis research: a use case-driven methodology, Catal. Today 446 (2025) 115111. [27] X. Wang, V. Hu, X.C. Song, S. Garg, J.F. Xiao, J.W. Han, ChemNER: Fine-grained chemistry named entity recognition with ontology-guided distant supervision,In:Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing. Online and Punta Cana, Dominican Republic. Stroudsburg, PA, USAACL, 2021. [28] A.S. Behr, M. Volkenrath, N. Kockmann, Ontology extension with NLP-based concept extraction for domain experts in catalytic sciences, Knowl. Inf. Syst. 65 (12) (2023) 5503-5522. [29] W.J. Liu, P. Zhou, Z. Zhao, Z.R. Wang, Q. Ju, H.T. Deng, P. Wang, K-BERT: enabling language representation with knowledge graph, Proc. AAAI Conf. Artif. Intell. 34 (3) (2020) 2901-2908. [30] L. Weston, V. Tshitoyan, J. Dagdelen, O. Kononova, A. Trewartha, K.A. Persson, G. Ceder, A. Jain, Named entity recognition and normalization applied to large-scale information extraction from the materials science literature, J. Chem. Inf. Model. 59 (9) (2019) 3692-3702. [31] R. Tran, J. Lan, M. Shuaibi, B.M. Wood, S. Goyal, A. Das, J. Heras-Domingo, A. Kolluru, A. Rizvi, N. Shoghi, A. Sriram, F. Therrien, J. Abed, O. Voznyy, E.H. Sargent, Z. Ulissi, C.L. Zitnick, The open catalyst 2022 (OC22) dataset and challenges for oxide electrocatalysts, ACS Catal. 13 (5) (2023) 3066-3084. [32] S.L. Scott, T.B. Gunnoe, P. Fornasiero, C.M. Crudden, To err is human; to reproduce takes time, ACS Catal. 12 (6) (2022) 3644-3650. [33] ChEBI. [cited 22 Feb 2025]. https://www.ebi.ac.uk/chebi/. [34] RXNO - ontology lookup service. [cited 22 Feb 2025]. Available: https://www.ebi.ac.uk/ols4/ontologies/rxno. [35] L. Takahashi, K. Takahashi, Visualizing scientists' cognitive representation of materials data through the application of ontology, J. Phys. Chem. Lett. 10 (23) (2019) 7482-7491. [36] I. Beltagy, K. Lo, A. Cohan. SciBERT, A pretrained language model for scientific text, In: Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (Volume 1, pp. 3615 - 3620). Association for Computational Linguistics. DOI: 10.18653/v1/D19-1371. arXiv: 1903.10676 [cs.CL], 2019, http://arxiv.org/abs/1903.10676. [37] D. Dessi, F. Osborne, D. Reforgiato Recupero, D. Buscaldi, E. Motta, SCICERO: a deep learning and NLP approach for generating scientific knowledge graphs in the computer science domain, Knowl. Based Syst. 258 (2022) 109945. [38] M.D.L. Tosi, J.C. dos Reis, SciKGraph: a knowledge graph approach to structure a scientific field, J. Informetr. 15 (1) (2021) 101109. [39] Y.W. Zhang, F.Y. Chen, Z.Y. Liu, Y.Z. Ju, D.L. Cui, J.Y. Zhu, X. Jiang, X. Guo, J. He, L. Zhang, X.T. Zhang, Y.J. Su, A materials terminology knowledge graph automatically constructed from text corpus, Sci. Data 11 (1) (2024) 600. [40] L. Wang, J. Ren, B. Xu, J. Li, W. Luo, F. Xia. MODEL: Motif-based deep feature learning for link prediction. arXiv [cs.SI]. 2020. doi:10.1109/TCSS.2019.2962819. [41] L. Yao, C. Mao, Y. Luo. KG-BERT: BERT for knowledge graph completion. arXiv [cs.CL]. 2019. Available: http://arxiv.org/abs/1909.03193. [42] A. Khan, Knowledge graphs querying, SIGMOD Rec. 52 (2) (2023) 18-29. [43] B.Z. Liu, X. Wang, P.K. Liu, S.Z. Li, Q. Fu, Y.P. Chai, UniKG: A Unified Interoperable Knowledge Graph Database System,In:2021 IEEE 37th International Conference on Data Engineering (ICDE). 2021. Chania, Greece. IEEE, 2021. [44] Comparing cypher with SQL. In: Neo4j Graph Data Platform [Internet]. [cited 22 Feb 2025], https://neo4j.com/docs/getting-started/cypher-intro/cypher-sql/. [45] Text2Cypher: Bridging natural language and graph databases. [cited 22 Feb 2025], https://arxiv.org/html/2412.10064v1. [46] Z. Zhong, L.Q. Zhong, Z.Z. Sun, Q.Y. Jin, Z.C. Qin, X.F. Zhang, SyntheT2C: generating synthetic data for fine-tuning large language models on the Text2Cypher task, arXiv [cs.AI]. 2024. Available: http://arxiv.org/abs/2406.10710. [47] B.B. Komecoglu, B. Yilmaz, Knowledge-augmented large language model prompting for cypher query construction, 2024 9th International Conference on Computer Science and Engineering (UBMK). October 26-28, 2024, Antalya, Turkiye. IEEE, (2024) 187-192. [48] M.A. Rodriguez. The Gremlin graph traversal machine and language. arXiv [cs.DB]. 2015. doi:10.1145/2815072.2815073. [49] Y. Liang, T. Xie, G. Peng, Z. Huang, Y. Lan, W. Qian. NAT-NL2GQL: a novel multi-agent framework for translating natural language to graph query language. arXiv [cs.CL]. 2024. Available: http://arxiv.org/abs/2412.10434. [50] G. Vargas-Solar, K. Dao, J.-A. Espinosa-Oviedo, Translating data science queries from natural language into graph analytics queries using NLDS-QL, In: Ioannina, Greece, 28-31 March 2023 (CEUR Workshop Proceedings, Vol. 3379, Paper 6, pp. 1 - 6). EDBT-ICDT, 2023, https://ceur-ws.org/Vol-3379/DARLI-AP_2023_6.pdf. [51] L. Nie, S. Cao, J.X. Shi, J. Sun, Q.W. Tian, L. Hou, J.Z. Li, J.D. Zhai, GraphQ IR: unifying the semantic parsing of graph query languages with one intermediate representation, In: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Abu Dhabi, UAE, pp. 5848 - 5865. Association for Computational Linguistics.arXiv: 2205.12078 [cs.CL], 2022, http://arxiv.org/abs/2205.12078. [52] P. Ghiasnezhad Omran, K. Taylor, S. Rodríguez Méndez, A. Haller, Learning SHACL shapes from knowledge graphs, Semant. Web 14 (1)101–121. [53] J.Y. Chen, F. Lecue, J.Z. Pan, S.M. Deng, H.J. Chen, Knowledge graph embeddings for dealing with concept drift in machine learning, J. Web Semant. 67 (2021) 100625. [54] D. Garay-Ruiz, C. Bo, Chemical reaction network knowledge graphs: the OntoRXN ontology, J. Cheminform. 14 (1) (2022) 29. [55] A. Kondinski, P. Rutkevych, L. Pascazio, D.N. Tran, F. Farazi, S. Ganguly, M. Kraft, Knowledge graph representation of zeolitic crystalline materials, Digit. Discov. 3 (10) (2024) 2070-2084. [56] H. Han, Y. Wang, H. Shomer, K. Guo, J. Ding, Y. Lei, M. Halappanavar, R. A. Rossi, S. Mukherjee, X. Tang, Q. He,Z. Hua, B. Long, T. Zhao, N. Shah, A. Javari, Y. Xia, J. Tang. Retrieval-augmented generation with graphs (GraphRAG). arXiv [cs.IR]. 2024. Available: http://arxiv.org/abs/2501.00309. [57] G. Perkovic, A. Drobnjak, I. Boticki, Hallucinations in LLMs: understanding and addressing challenges, 2024 47th MIPRO ICT and Electronics Convention (MIPRO). May 20-24, 2024, Opatija, Croatia. IEEE, (2024) 2084-2088. [58] G. Agrawal, T. Kumarage, Z. Alghamdi, H. Liu, Can knowledge graphs reduce hallucinations in LLMs? : a survey, In: Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL 2024), Volume 1 - Long Papers, Mexico City, Mexico, pp. 3947 - 3960. Association for Computational Linguistics.arXiv: 2311.07914 [cs.CL], 2023, http://arxiv.org/abs/2311.07914. [59] H. Abu-Rasheed, C. Weber, M. Fathi, Knowledge graphs as context sources for LLM-based explanations of learning recommendations, 2024 IEEE Global Engineering Education Conference (EDUCON). May 8-11, 2024, Kos Island, Greece. IEEE, (2024) 1-5. [60] Y.X. Dong, S. Wang, H.Y. Zheng, J.J. Chen, Z.H. Zhang, C.H. Wang, Advanced RAG models with graph structures: optimizing complex knowledge reasoning and text generation, in:2024 5th International Symposium on Computer Engineering and Intelligent Communications (ISCEIC). Wuhan, China. IEEE, (2024) 626-630. [61] Β. Τσακαλ?κη?. Augmentation of large language model capabilities with knowledge graphs. Πανεπιστ?μιο Δυτικ?? Αττικ??; 2024. doi:10.26265/POLYNOE-5908. [62] A. Saleh, G. Tur, Y. Saygin. SG-RAG: Multi-hop question answering with large Language Models through Knowledge Graphs. ICNLSP. 2024. Available: https://aclanthology.org/2024.icnlsp-1.45.pdf. [63] A. Kau, X. He, A. Nambissan, A. Astudillo, H. Yin, A. Aryani. Combining knowledge graphs and large language models. arXiv [cs.CL]. 2024. Available: http://arxiv.org/abs/2407.06564. [64] C. Feng, X. Zhang, Z. Fei. Knowledge solver: teaching LLMs to search for domain knowledge from knowledge graphs. arXiv [cs.CL]. 2023. Available: http://arxiv.org/abs/2309.03118. [65] K.K.Y. Ng, I. Matsuba, P.C. Zhang, RAG in health care: a novel framework for improving communication and decision-making by addressing LLM limitations, Nejm Ai 2 (1) (2025) 2400380. [66] S. Schimmler, T. Bonisch, M.T. Horsch, T. Petrenko, B. Schembera, V. Kushnarenko, NFDI4Cat: local and overarching data infrastructures. E-Science-Tage 2021: Share Your Research Data. 2022. doi:10.11588/heibooks.979.c137. [67] C. Wulf, P. Matthias Beller, D.I. Thomas Boenisch, P. Olaf Deutschmann, D. Schirin Hanf, P. Norbert Kockmann, D.I. Ralph Kraehnert, P. Mehtap Oezaslan, D. Stefan Palkovits, D. Sonja Schimmler, D.S.A. Schunk, P. Kurt Wagemann, D. David Linke, A unified research data infrastructure for catalysis research-challenges and concepts, ChemCatChem 13 (14) (2021) 3223-3236. [68] K.M. Jablonka, L. Patiny, B. Smit, Making the collective knowledge of chemistry open and machine actionable, Nat. Chem. 14 (4) (2022) 365-376. [69] S. Ji, S. Pan, E. Cambria, P. Marttinen, P.S. Yu, A survey on knowledge graphs: representation, acquisition and applications, IEEE Transactions on Neural Networks and Learning Systems 33 (2) 494–514. |