{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T14:16:10Z","timestamp":1773843370820,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":50,"publisher":"ACM","license":[{"start":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T00:00:00Z","timestamp":1683676800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2023,5,10]]},"DOI":"10.1145\/3603765.3603771","type":"proceedings-article","created":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T18:13:45Z","timestamp":1697566425000},"page":"37-42","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Applying BioBERT to Extract Germline Gene-Disease Associations for Building a Knowledge Graph from the Biomedical Literature"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4061-1880","authenticated-orcid":false,"given":"Armando D.","family":"Diaz Gonzalez","sequence":"first","affiliation":[{"name":"Department of Computing Science, Charleston Southern University, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4084-6484","authenticated-orcid":false,"given":"Kevin S.","family":"Hughes","sequence":"additional","affiliation":[{"name":"Department of Surgery, Medical University of South Carolina, United States"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0945-3105","authenticated-orcid":false,"given":"Songhui","family":"Yue","sequence":"additional","affiliation":[{"name":"Department of Computing Science, Charleston Southern University, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3631-7782","authenticated-orcid":false,"given":"Sean T.","family":"Hayes","sequence":"additional","affiliation":[{"name":"Department of Computing Science, Charleston Southern University, United States"}]}],"member":"320","published-online":{"date-parts":[[2023,10,17]]},"reference":[{"key":"e_1_3_2_1_1_1","unstructured":"J Abreu\u00a0Vicente. 2022. drAbreu\/bioBERT-NER-BC2GM_corpus. https:\/\/huggingface.co\/drAbreu\/bioBERT-NER-BC2GM_corpus  J Abreu\u00a0Vicente. 2022. drAbreu\/bioBERT-NER-BC2GM_corpus. https:\/\/huggingface.co\/drAbreu\/bioBERT-NER-BC2GM_corpus"},{"key":"e_1_3_2_1_2_1","unstructured":"J Abreu\u00a0Vicente. 2022. drAbreu\/bioBERT-NER-NCBI_disease. https:\/\/huggingface.co\/drAbreu\/bioBERT-NER-NCBI_disease  J Abreu\u00a0Vicente. 2022. drAbreu\/bioBERT-NER-NCBI_disease. https:\/\/huggingface.co\/drAbreu\/bioBERT-NER-NCBI_disease"},{"key":"e_1_3_2_1_3_1","volume-title":"The Role of Natural Language Processing during the COVID-19 Pandemic: Health Applications, Opportunities, and Challenges. Healthcare 10, 11","author":"Al-Garadi Mohammed\u00a0Ali","year":"2022","unstructured":"Mohammed\u00a0Ali Al-Garadi , Yuan-Chi Yang , and Abeed Sarker . 2022. The Role of Natural Language Processing during the COVID-19 Pandemic: Health Applications, Opportunities, and Challenges. Healthcare 10, 11 ( 2022 ). https:\/\/doi.org\/10.3390\/healthcare10112270 10.3390\/healthcare10112270 Mohammed\u00a0Ali Al-Garadi, Yuan-Chi Yang, and Abeed Sarker. 2022. The Role of Natural Language Processing during the COVID-19 Pandemic: Health Applications, Opportunities, and Challenges. Healthcare 10, 11 (2022). https:\/\/doi.org\/10.3390\/healthcare10112270"},{"key":"e_1_3_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2020.2973928"},{"key":"e_1_3_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.18517\/ijaseit.6.6.1367"},{"key":"#cr-split#-e_1_3_2_1_6_1.1","doi-asserted-by":"crossref","unstructured":"Iz Beltagy Kyle Lo and Arman Cohan. 2019. SciBERT: A Pretrained Language Model for Scientific Text. (2019). https:\/\/doi.org\/10.48550\/ARXIV.1903.10676 Publisher: arXiv. 10.48550\/ARXIV.1903.10676","DOI":"10.18653\/v1\/D19-1371"},{"key":"#cr-split#-e_1_3_2_1_6_1.2","doi-asserted-by":"crossref","unstructured":"Iz Beltagy Kyle Lo and Arman Cohan. 2019. SciBERT: A Pretrained Language Model for Scientific Text. (2019). https:\/\/doi.org\/10.48550\/ARXIV.1903.10676 Publisher: arXiv.","DOI":"10.18653\/v1\/D19-1371"},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/jamiaopen\/ooac043"},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1007\/0-387-25739-X_8"},{"key":"e_1_3_2_1_9_1","volume-title":"Exploring the Link between Germline and Somatic Genetic Alterations in Breast Carcinogenesis. PLOS ONE 5, 11","author":"Bonifaci N\u00faria","year":"2010","unstructured":"N\u00faria Bonifaci , Bohdan G\u00f3rski , Bartlomiej Masoj\u0107 , Dominika Woko\u0142orczyk , Anna Jakubowska , Tadeusz D\u0119bniak , Antoni Berenguer , Jordi Serra\u00a0Musach , Joan Brunet , Joaqu\u00edn Dopazo , Steven\u00a0 A Narod , Jan Lubi\u0144ski , Conxi L\u00e1zaro , Cezary Cybulski , and Miguel\u00a0Angel Pujana . 2010. Exploring the Link between Germline and Somatic Genetic Alterations in Breast Carcinogenesis. PLOS ONE 5, 11 ( 2010 ), 1\u20138. https:\/\/doi.org\/10.1371\/journal.pone.0014078 Publisher : Public Library of Science . 10.1371\/journal.pone.0014078 N\u00faria Bonifaci, Bohdan G\u00f3rski, Bartlomiej Masoj\u0107, Dominika Woko\u0142orczyk, Anna Jakubowska, Tadeusz D\u0119bniak, Antoni Berenguer, Jordi Serra\u00a0Musach, Joan Brunet, Joaqu\u00edn Dopazo, Steven\u00a0A Narod, Jan Lubi\u0144ski, Conxi L\u00e1zaro, Cezary Cybulski, and Miguel\u00a0Angel Pujana. 2010. Exploring the Link between Germline and Somatic Genetic Alterations in Breast Carcinogenesis. PLOS ONE 5, 11 (2010), 1\u20138. https:\/\/doi.org\/10.1371\/journal.pone.0014078 Publisher: Public Library of Science."},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.26615\/978-954-452-071-7_009"},{"key":"#cr-split#-e_1_3_2_1_11_1.1","unstructured":"Seyone Chithrananda Gabriel Grand and Bharath Ramsundar. 2020. ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction. (2020). https:\/\/doi.org\/10.48550\/ARXIV.2010.09885 Publisher: arXiv. 10.48550\/ARXIV.2010.09885"},{"key":"#cr-split#-e_1_3_2_1_11_1.2","unstructured":"Seyone Chithrananda Gabriel Grand and Bharath Ramsundar. 2020. ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction. (2020). https:\/\/doi.org\/10.48550\/ARXIV.2010.09885 Publisher: arXiv."},{"key":"e_1_3_2_1_12_1","volume-title":"A method for named entity normalization in biomedical articles: Application to diseases and plants. BMC Bioinformatics 18","author":"Cho Hyejin","year":"2017","unstructured":"Hyejin Cho , Wonjun Choi , and Hyunju Lee . 2017. A method for named entity normalization in biomedical articles: Application to diseases and plants. BMC Bioinformatics 18 ( 2017 ). https:\/\/doi.org\/10.1186\/s12859-017-1857-8 10.1186\/s12859-017-1857-8 Hyejin Cho, Wonjun Choi, and Hyunju Lee. 2017. A method for named entity normalization in biomedical articles: Application to diseases and plants. BMC Bioinformatics 18 (2017). https:\/\/doi.org\/10.1186\/s12859-017-1857-8"},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0258626"},{"key":"e_1_3_2_1_14_1","volume-title":"BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding.","author":"Devlin Jacob","year":"2018","unstructured":"Jacob Devlin , Ming-Wei Chang , Kenton Lee , and Kristina Toutanova . 2018 . BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding. (2018). https:\/\/doi.org\/10.48550\/ARXIV.1810.04805 Publisher : arXiv. 10.48550\/ARXIV.1810.04805 Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2018. BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding. (2018). https:\/\/doi.org\/10.48550\/ARXIV.1810.04805 Publisher: arXiv."},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2013.12.006"},{"key":"e_1_3_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac957"},{"key":"e_1_3_2_1_17_1","volume-title":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","author":"Fukuda Ken","year":"1998","unstructured":"Ken Fukuda , Akihiro Tamura , Tatsuhiko Tsunoda , and Toshihisa Takagi . 1998 . Toward information extraction: identifying protein names from biological papers . Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1998), 707\u2013718. Ken Fukuda, Akihiro Tamura, Tatsuhiko Tsunoda, and Toshihisa Takagi. 1998. Toward information extraction: identifying protein names from biological papers. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1998), 707\u2013718."},{"key":"e_1_3_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1162\/coli.2006.32.1.83"},{"key":"e_1_3_2_1_19_1","volume-title":"SemEval-2018 Task 7: Semantic Relation Extraction and Classification in Scientific Papers","author":"G\u00e1bor Kata","year":"1865","unstructured":"Kata G\u00e1bor , Davide Buscaldi , Anne-Kathrin Schumann , Behrang QasemiZadeh , Ha\u00effa Zargayouna , and Thierry Charnois . 2018. SemEval-2018 Task 7: Semantic Relation Extraction and Classification in Scientific Papers . Association for Computational Linguistics , New Orleans , Louisiana, 679\u2013688. https:\/\/doi.org\/10. 1865 3\/v1\/S18-1111 10.18653\/v1 Kata G\u00e1bor, Davide Buscaldi, Anne-Kathrin Schumann, Behrang QasemiZadeh, Ha\u00effa Zargayouna, and Thierry Charnois. 2018. SemEval-2018 Task 7: Semantic Relation Extraction and Classification in Scientific Papers. Association for Computational Linguistics, New Orleans, Louisiana, 679\u2013688. https:\/\/doi.org\/10.18653\/v1\/S18-1111"},{"key":"e_1_3_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007022"},{"key":"e_1_3_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2015.07.010"},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz682"},{"key":"#cr-split#-e_1_3_2_1_23_1.1","unstructured":"Jing Li Aixin Sun Jianglei Han and Chenliang Li. 2018. A Survey on Deep Learning for Named Entity Recognition. (2018). https:\/\/doi.org\/10.48550\/ARXIV.1812.09449 Publisher: arXiv. 10.48550\/ARXIV.1812.09449"},{"key":"#cr-split#-e_1_3_2_1_23_1.2","unstructured":"Jing Li Aixin Sun Jianglei Han and Chenliang Li. 2018. A Survey on Deep Learning for Named Entity Recognition. (2018). https:\/\/doi.org\/10.48550\/ARXIV.1812.09449 Publisher: arXiv."},{"key":"e_1_3_2_1_24_1","volume-title":"BioRED: a rich biomedical relation extraction dataset. Briefings in Bioinformatics 23, 5","author":"Luo Ling","year":"2022","unstructured":"Ling Luo , Po-Ting Lai , Chih-Hsuan Wei , Cecilia\u00a0 N Arighi , and Zhiyong Lu. 2022. BioRED: a rich biomedical relation extraction dataset. Briefings in Bioinformatics 23, 5 ( 2022 ). https:\/\/doi.org\/10.1093\/bib\/bbac282 10.1093\/bib Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia\u00a0N Arighi, and Zhiyong Lu. 2022. BioRED: a rich biomedical relation extraction dataset. Briefings in Bioinformatics 23, 5 (2022). https:\/\/doi.org\/10.1093\/bib\/bbac282"},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.5555\/972470.972475"},{"key":"#cr-split#-e_1_3_2_1_26_1.1","doi-asserted-by":"crossref","unstructured":"Nicolas Matentzoglu Damien Goutte-Gattat Shawn Zheng\u00a0Kai Tan James\u00a0P Balhoff Seth Carbon Anita\u00a0R Caron William\u00a0D Duncan Joe\u00a0E Flack Melissa Haendel Nomi\u00a0L Harris William\u00a0R Hogan Charles\u00a0Tapley Hoyt Rebecca\u00a0C Jackson Hyeongsik Kim Huseyin Kir Martin Larralde Julie\u00a0A McMurry James\u00a0A Overton Bjoern Peters Clare Pilgrim Ray Stefancsik Sofia M\u00a0C Robb Sabrina Toro Nicole\u00a0A Vasilevsky Ramona Walls Christopher\u00a0J Mungall and David Osumi-Sutherland. 2022. Ontology Development Kit: a toolkit for building maintaining and standardizing biomedical ontologies. Database 2022 (2022). https:\/\/doi.org\/10.1093\/database\/baac087 10.1093\/database","DOI":"10.1093\/database\/baac087"},{"key":"#cr-split#-e_1_3_2_1_26_1.2","doi-asserted-by":"crossref","unstructured":"Nicolas Matentzoglu Damien Goutte-Gattat Shawn Zheng\u00a0Kai Tan James\u00a0P Balhoff Seth Carbon Anita\u00a0R Caron William\u00a0D Duncan Joe\u00a0E Flack Melissa Haendel Nomi\u00a0L Harris William\u00a0R Hogan Charles\u00a0Tapley Hoyt Rebecca\u00a0C Jackson Hyeongsik Kim Huseyin Kir Martin Larralde Julie\u00a0A McMurry James\u00a0A Overton Bjoern Peters Clare Pilgrim Ray Stefancsik Sofia M\u00a0C Robb Sabrina Toro Nicole\u00a0A Vasilevsky Ramona Walls Christopher\u00a0J Mungall and David Osumi-Sutherland. 2022. Ontology Development Kit: a toolkit for building maintaining and standardizing biomedical ontologies. Database 2022 (2022). https:\/\/doi.org\/10.1093\/database\/baac087","DOI":"10.1093\/database\/baac087"},{"key":"e_1_3_2_1_27_1","volume-title":"Comparison of biomedical relationship extraction methods and models for knowledge graph creation. Journal of Web Semantics 75 (Jan","author":"Milo\u0161evi\u0107 Nikola","year":"2023","unstructured":"Nikola Milo\u0161evi\u0107 and Wolfgang Thielemann . 2023. Comparison of biomedical relationship extraction methods and models for knowledge graph creation. Journal of Web Semantics 75 (Jan . 2023 ), 100756. https:\/\/doi.org\/10.1016\/j.websem.2022.100756 Publisher : Elsevier BV. 10.1016\/j.websem.2022.100756 Nikola Milo\u0161evi\u0107 and Wolfgang Thielemann. 2023. Comparison of biomedical relationship extraction methods and models for knowledge graph creation. Journal of Web Semantics 75 (Jan. 2023), 100756. https:\/\/doi.org\/10.1016\/j.websem.2022.100756 Publisher: Elsevier BV."},{"key":"e_1_3_2_1_28_1","volume-title":"Moara: A Java library for extracting and normalizing gene and protein mentions. BMC bioinformatics 11","author":"Neves Mariana","year":"2010","unstructured":"Mariana Neves , Jos\u00e9-Mar\u00eda Carazo , and Alberto Pascual-Montano . 2010 . Moara: A Java library for extracting and normalizing gene and protein mentions. BMC bioinformatics 11 (2010), 157. https:\/\/doi.org\/10.1186\/1471-2105-11-157 10.1186\/1471-2105-11-157 Mariana Neves, Jos\u00e9-Mar\u00eda Carazo, and Alberto Pascual-Montano. 2010. Moara: A Java library for extracting and normalizing gene and protein mentions. BMC bioinformatics 11 (2010), 157. https:\/\/doi.org\/10.1186\/1471-2105-11-157"},{"key":"e_1_3_2_1_29_1","volume-title":"Counterfactual Examples, and Zero-Shot Evaluation. In BCB \u201921","author":"Noh Jiho","unstructured":"Jiho Noh and Ramakanth Kavuluru . 2021. Joint Learning for Biomedical NER and Entity Normalization: Encoding Schemes , Counterfactual Examples, and Zero-Shot Evaluation. In BCB \u201921 . Association for Computing Machinery , New York, NY, USA. https:\/\/doi.org\/10.1145\/3459930.3469533 Journal Abbreviation : BCB \u201921. 10.1145\/3459930.3469533 Jiho Noh and Ramakanth Kavuluru. 2021. Joint Learning for Biomedical NER and Entity Normalization: Encoding Schemes, Counterfactual Examples, and Zero-Shot Evaluation. In BCB \u201921. Association for Computing Machinery, New York, NY, USA. https:\/\/doi.org\/10.1145\/3459930.3469533 Journal Abbreviation: BCB \u201921."},{"key":"#cr-split#-e_1_3_2_1_30_1.1","unstructured":"Sachin Pawar Girish\u00a0K Palshikar and Pushpak Bhattacharyya. 2017. Relation Extraction : A Survey. (2017). https:\/\/doi.org\/10.48550\/ARXIV.1712.05191 Publisher: arXiv. 10.48550\/ARXIV.1712.05191"},{"key":"#cr-split#-e_1_3_2_1_30_1.2","unstructured":"Sachin Pawar Girish\u00a0K Palshikar and Pushpak Bhattacharyya. 2017. Relation Extraction : A Survey. (2017). https:\/\/doi.org\/10.48550\/ARXIV.1712.05191 Publisher: arXiv."},{"key":"e_1_3_2_1_31_1","volume-title":"Open questions: How many genes do we have?BMC Biology 16, 1 (Aug","author":"Salzberg L","year":"2018","unstructured":"Steven\u00a0 L Salzberg . 2018. Open questions: How many genes do we have?BMC Biology 16, 1 (Aug . 2018 ). https:\/\/doi.org\/10.1186\/s12915-018-0564-x Publisher : BioMed Central . 10.1186\/s12915-018-0564-x Steven\u00a0L Salzberg. 2018. Open questions: How many genes do we have?BMC Biology 16, 1 (Aug. 2018). https:\/\/doi.org\/10.1186\/s12915-018-0564-x Publisher: BioMed Central."},{"key":"e_1_3_2_1_32_1","volume-title":"Christian W\u00a0B Bachem, and Richard Finkers.","author":"Singh Gurnoor","year":"2021","unstructured":"Gurnoor Singh , Evangelia\u00a0 A Papoutsoglou , Frederique Keijts-Lalleman , Bilyana Vencheva , Mark Rice , Richard G\u00a0F Visser , Christian W\u00a0B Bachem, and Richard Finkers. 2021 . Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait. BMC Plant Biology 21, 1 (April 2021). https:\/\/doi.org\/10.1186\/s12870-021-02943-5 Publisher : Springer Verlag . 10.1186\/s12870-021-02943-5 Gurnoor Singh, Evangelia\u00a0A Papoutsoglou, Frederique Keijts-Lalleman, Bilyana Vencheva, Mark Rice, Richard G\u00a0F Visser, Christian W\u00a0B Bachem, and Richard Finkers. 2021. Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait. BMC Plant Biology 21, 1 (April 2021). https:\/\/doi.org\/10.1186\/s12870-021-02943-5 Publisher: Springer Verlag."},{"key":"e_1_3_2_1_33_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-s2-s2"},{"key":"#cr-split#-e_1_3_2_1_34_1.1","unstructured":"Ashish Vaswani Noam Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan\u00a0N Gomez Lukasz Kaiser and Illia Polosukhin. 2017. Attention Is All You Need. (2017). https:\/\/doi.org\/10.48550\/ARXIV.1706.03762 Publisher: arXiv. 10.48550\/ARXIV.1706.03762"},{"key":"#cr-split#-e_1_3_2_1_34_1.2","unstructured":"Ashish Vaswani Noam Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan\u00a0N Gomez Lukasz Kaiser and Illia Polosukhin. 2017. Attention Is All You Need. (2017). https:\/\/doi.org\/10.48550\/ARXIV.1706.03762 Publisher: arXiv."},{"key":"e_1_3_2_1_35_1","doi-asserted-by":"publisher","DOI":"10.1007\/s40747-022-00806-6"},{"key":"e_1_3_2_1_36_1","volume-title":"Classifying Relations for Biomedical Named Entity Disambiguation","author":"Wang Xinglong","unstructured":"Xinglong Wang , Jun\u2019ichi Tsujii , and Sophia Ananiadou . 2009. Classifying Relations for Biomedical Named Entity Disambiguation . Association for Computational Linguistics , Singapore , 1513\u20131522. https:\/\/aclanthology.org\/D09-1157 Xinglong Wang, Jun\u2019ichi Tsujii, and Sophia Ananiadou. 2009. Classifying Relations for Biomedical Named Entity Disambiguation. Association for Computational Linguistics, Singapore, 1513\u20131522. https:\/\/aclanthology.org\/D09-1157"},{"key":"e_1_3_2_1_37_1","volume-title":"COLING \u201992","author":"Webster J","unstructured":"Jonathan\u00a0 J Webster and Chunyu Kit . 1992. Tokenization as the Initial Phase in NLP . In COLING \u201992 . Association for Computational Linguistics , USA, 1106\u20131110. https:\/\/doi.org\/10.3115\/992424.992434 Journal Abbreviation: COLING \u201992. 10.3115\/992424.992434 Jonathan\u00a0J Webster and Chunyu Kit. 1992. Tokenization as the Initial Phase in NLP. In COLING \u201992. Association for Computational Linguistics, USA, 1106\u20131110. https:\/\/doi.org\/10.3115\/992424.992434 Journal Abbreviation: COLING \u201992."},{"key":"e_1_3_2_1_38_1","volume-title":"BioPortal: Enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic acids research 39","author":"Whetzel Patricia","year":"2011","unstructured":"Patricia Whetzel , Natasha Noy , Nigam Shah , Paul Alexander , Csongor Nyulas , Tania Tudorache , and Mark Musen . 2011. BioPortal: Enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic acids research 39 ( 2011 ), W541\u20135. https:\/\/doi.org\/10.1093\/nar\/gkr469 10.1093\/nar Patricia Whetzel, Natasha Noy, Nigam Shah, Paul Alexander, Csongor Nyulas, Tania Tudorache, and Mark Musen. 2011. BioPortal: Enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic acids research 39 (2011), W541\u20135. https:\/\/doi.org\/10.1093\/nar\/gkr469"},{"key":"e_1_3_2_1_39_1","volume-title":"Hing-Fung Ting, and Tak\u00a0Wah Lam.","author":"Wu Ye","year":"2019","unstructured":"Ye Wu , Ruibang Luo , Henry C\u00a0M Leung , Hing-Fung Ting, and Tak\u00a0Wah Lam. 2019 . RENET : A Deep Learning Approach for Extracting Gene-Disease Associations from Literature. Ye Wu, Ruibang Luo, Henry C\u00a0M Leung, Hing-Fung Ting, and Tak\u00a0Wah Lam. 2019. RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature."},{"key":"#cr-split#-e_1_3_2_1_40_1.1","unstructured":"Jie Yang Soyeon\u00a0Caren Han and Josiah Poon. 2021. A Survey on Extraction of Causal Relations from Natural Language Text. (2021). https:\/\/doi.org\/10.48550\/ARXIV.2101.06426 Publisher: arXiv. 10.48550\/ARXIV.2101.06426"},{"key":"#cr-split#-e_1_3_2_1_40_1.2","unstructured":"Jie Yang Soyeon\u00a0Caren Han and Josiah Poon. 2021. A Survey on Extraction of Causal Relations from Natural Language Text. (2021). https:\/\/doi.org\/10.48550\/ARXIV.2101.06426 Publisher: arXiv."},{"key":"e_1_3_2_1_41_1","volume-title":"S10 (July","author":"Yang Xi","year":"2021","unstructured":"Xi Yang , Chengkun Wu , Goran Nenadic , Wei Wang , and Kai Lu. 2021. Mining a stroke knowledge graph from literature. BMC Bioinformatics 22 , S10 (July 2021 ). https:\/\/doi.org\/10.1186\/s12859-021-04292-4 Publisher : Springer Nature . 10.1186\/s12859-021-04292-4 Xi Yang, Chengkun Wu, Goran Nenadic, Wei Wang, and Kai Lu. 2021. Mining a stroke knowledge graph from literature. BMC Bioinformatics 22, S10 (July 2021). https:\/\/doi.org\/10.1186\/s12859-021-04292-4 Publisher: Springer Nature."},{"key":"e_1_3_2_1_42_1","volume-title":"An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). Journal of Biomedical Semantics 11","author":"Zhu Qian","year":"2020","unstructured":"Qian Zhu , Dac-Trung Nguyen , Ivan Grishagin , Noel Southall , Eric Sid , and Anne Pariser . 2020. An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). Journal of Biomedical Semantics 11 ( 2020 ). https:\/\/doi.org\/10.1186\/s13326-020-00232-y 10.1186\/s13326-020-00232-y Qian Zhu, Dac-Trung Nguyen, Ivan Grishagin, Noel Southall, Eric Sid, and Anne Pariser. 2020. An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). Journal of Biomedical Semantics 11 (2020). https:\/\/doi.org\/10.1186\/s13326-020-00232-y"},{"key":"e_1_3_2_1_43_1","volume-title":"HerbKG: Constructing a Herbal-Molecular Medicine Knowledge Graph Using a Two-Stage Framework Based on Deep Transfer Learning. Frontiers in Genetics 13","author":"Zhu Xian","year":"2022","unstructured":"Xian Zhu , Yueming Gu , and Zhifeng Xiao . 2022. HerbKG: Constructing a Herbal-Molecular Medicine Knowledge Graph Using a Two-Stage Framework Based on Deep Transfer Learning. Frontiers in Genetics 13 ( 2022 ). https:\/\/doi.org\/10.3389\/fgene.2022.799349 10.3389\/fgene.2022.799349 Xian Zhu, Yueming Gu, and Zhifeng Xiao. 2022. HerbKG: Constructing a Herbal-Molecular Medicine Knowledge Graph Using a Two-Stage Framework Based on Deep Transfer Learning. Frontiers in Genetics 13 (2022). https:\/\/doi.org\/10.3389\/fgene.2022.799349"}],"event":{"name":"ICISDM 2023: 2023 the 7th International Conference on Information System and Data Mining","location":"Atlanta USA","acronym":"ICISDM 2023"},"container-title":["2023 the 7th International Conference on Information System and Data Mining (ICISDM)"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3603765.3603771","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3603765.3603771","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T16:37:22Z","timestamp":1750178242000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3603765.3603771"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,10]]},"references-count":50,"alternative-id":["10.1145\/3603765.3603771","10.1145\/3603765"],"URL":"https:\/\/doi.org\/10.1145\/3603765.3603771","relation":{},"subject":[],"published":{"date-parts":[[2023,5,10]]},"assertion":[{"value":"2023-10-17","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}