Scalable Construction of a Lung Cancer Knowledge Base: Profiling Semantic Reasoning in LLMs.

Yalbi Itzel Balderas-Martínez Yalbi I. Balderas-Martínez

Cesar Felipe Martínez Cisneros Jesús Ulises Quiroz Bautista Claudia Anahí Guzmán Solano Bogdan Kaleb García Rivera Iván García-Pacheco Yalbi Itzel Balderas-Martínez Kolawole John Adebayo Ignacio Arroyo-Fernández Scalable Construction of a Lung Cancer Knowledge Base: Profiling Semantic Reasoning in LLMs. 2026 January abs/2601.02604 CoRR https://doi.org/10.48550/arXiv.2601.02604 db/journals/corr/corr2601.html#abs-2601-02604 streams/journals/corr

Yalbi Itzel Balderas-Martínez José Armando Sánchez-Rojas Arturo Téllez-Velázquez Flavio Juárez-Martínez Raúl Cruz-Barbosa Enrique Guzmán-Ramírez Iván García-Pacheco Ignacio Arroyo-Fernández Semantic Reasoning Using Standard Attention-Based Models: An Application to Chronic Disease Literature. 162 2025 9 Big Data Cogn. Comput. 6 https://doi.org/10.3390/bdcc9060162 db/journals/bdcc/bdcc9.html#BalderasMartinezSTJCGGA25 streams/journals/bdcc

Cesar Felipe Martínez Cisneros Jesús Ulises Quiroz Bautista Claudia Anahí Guzmán Solano Bogdan Kaleb García Rivera Iván García-Pacheco Yalbi Itzel Balderas-Martínez Kolawole John Adebayo Ignacio Arroyo-Fernández Scalable Construction of a Lung Cancer Knowledge Base: Profiling Semantic Reasoning in LLMs. 1-6 2025 ENC https://doi.org/10.1109/ENC68268.2025.11311861 conf/enc/2025 db/conf/enc/enc2025.html#CisnerosBSRGBAA25 streams/conf/enc

Ignacio Arroyo-Fernández José Armando Sánchez-Rojas Arturo Téllez-Velázquez Flavio Juárez-Martínez Raúl Cruz-Barbosa Enrique Guzmán-Ramírez Yalbi Itzel Balderas-Martínez Common Sense Knowledge Learning for Open Vocabulary Neural Reasoning: A First View into Chronic Disease Literature. 2021 abs/2111.13781 CoRR https://arxiv.org/abs/2111.13781 db/journals/corr/corr2111.html#abs-2111-13781

Yalbi Itzel Balderas-Martínez Fabio Rinaldi 0001 Gabriela Contreras Hilda Solano-Lira Mishael Sánchez-Pérez Julio Collado-Vides Moisés Selman Annie Pardo Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. bax030 2017 2017 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bax030 https://www.wikidata.org/entity/Q33787495 db/journals/biodb/biodb2017.html#Balderas-Martinez17

Qinghua Wang 0003 Shabbir Syed-Abdul Lara Almeida Sophia Ananiadou Yalbi I. Balderas-Martínez Riza Batista-Navarro David Campos 0001 Lucy Chilton Hui-Jou Chou Gabriela Contreras Laurel Cooper Hong-Jie Dai Barbra Ferrell Juliane Fluck Socorro Gama-Castro Nancy George Georgios V. Gkoutos Afroza Khanam Irin Lars Juhl Jensen Silvia Jimenez Toni Rose Jue Ingrid M. Keseler Sumit Madan Sérgio Matos Peter McQuilton Marija Milacic Matthew E. Mort Jeyakumar Natarajan Evangelos Pafilis Emiliano Pereira Shruti Rao Fabio Rinaldi 0001 Karen Rothfels David Salgado Raquel M. Silva Onkar Singh Raymund Stefancsik Chu-Hsien Su Suresh Subramani Hamsa D. Tadepally Loukia Tsaprouni Nicole A. Vasilevsky Xiaodong Wang 0008 Andrew Chatr-aryamontri Stanley J. F. Laulederkind Sherri Matis-Mitchell Johanna R. McEntyre Sandra E. Orchard Sangya Pundir Raul Rodriguez-Esteban Kimberly Van Auken Zhiyong Lu Mary L. Schaeffer Cathy H. Wu Lynette Hirschman Cecilia N. Arighi Overview of the interactive task in BioCreative V. 2016 2016 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baw119 https://www.wikidata.org/entity/Q30002351 https://orkg.org/orkg/resource/R162489 db/journals/biodb/biodb2016.html#WangAAABBCCCCCD16

Ernesto Pérez-Rueda Silvia Tenorio-Salgado Alejandro Huerta-Saquero Yalbi I. Balderas-Martínez Gabriel Moreno-Hagelsieb The functional landscape bound to the transcription factors of Escherichia coli K-12. 93-103 2015 58 Comput. Biol. Chem. https://doi.org/10.1016/j.compbiolchem.2015.06.002 https://www.wikidata.org/entity/Q45998576 db/journals/candc/candc58.html#Perez-RuedaTHBM15

Fabio Rinaldi 0001 Oscar Lithgow-Serrano Alejandra López-Fuentes Socorro Gama-Castro Yalbi I. Balderas-Martínez Hilda Solano-Lira Julio Collado-Vides An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database. 25-31 2015 52 Polibits https://doi.org/10.17562/PB-52-3 db/journals/polibits/polibits52.html#RinaldiLLGBSC15

Socorro Gama-Castro Fabio Rinaldi 0001 Alejandra López-Fuentes Yalbi Itzel Balderas-Martínez Simon Clematide Tilia Renate Ellendorff Alberto Santos-Zavaleta Hernani Marques-Madeira Julio Collado-Vides Assisted curation of regulatory interactions and growth conditions of OxyR in <i>E. coli</i> K-12. 2014 2014 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bau049 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207228/ https://www.wikidata.org/entity/Q34392527 db/journals/biodb/biodb2014.html#Gama-CastroRLBCESMC14

Heladia Salgado Martín Peralta-Gil Socorro Gama-Castro Alberto Santos-Zavaleta Luis Muñiz-Rascado Jair S. García-Sotelo Verena Weiss Hilda Solano-Lira Irma Martínez-Flores Alejandra Medina-Rivera Gerardo Salgado-Osorio Shirley Alquicira-Hernández Kevin Alquicira-Hernández Alejandra López-Fuentes Liliana Porrón-Sotelo Araceli M. Huerta César Bonavides-Martínez Yalbi Itzel Balderas-Martínez Lucia Pannier Maricela Olvera Aurora Labastida Verónica Jiménez-Jacinto Leticia Vega-Alvarado Victor del Moral-Chávez Alfredo Hernández-Alvarez Enrique Morett Julio Collado-Vides RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. 203-213 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1201 https://www.wikidata.org/entity/Q30579774 db/journals/nar/nar41.html#SalgadoPGSMGWSMMSAALPHBBPOLJVMHMC13

Kolawole John Adebayo Lara Almeida Kevin Alquicira-Hernández Shirley Alquicira-Hernández Sophia Ananiadou Cecilia N. Arighi Ignacio Arroyo-Fernández Kimberly Van Auken Riza Theresa Batista-NavarroRiza Batista-Navarro Jesús Ulises Quiroz Bautista César Bonavides-Martínez David Campos 0001 Andrew Chatr-aryamontri Lucy Chilton Hui-Jou Chou Cesar Felipe Martínez Cisneros Simon Clematide Julio Collado-Vides Gabriela Contreras Laurel Cooper Raúl Cruz-Barbosa Hong-Jie Dai Tilia EllendorffTilia Renate Ellendorff Barbra Ferrell Juliane Fluck Socorro Gama-Castro Iván García-Pacheco Jair Santiago García-SoteloJair S. García-Sotelo Nancy George Georgios V. Gkoutos Enrique Guzmán 0001Enrique Guzmán-Ramírez Alfredo Hernández-Alvarez Lynette Hirschman Araceli M. Huerta Alejandro Huerta-Saquero Afroza Khanam Irin Lars Juhl Jensen Silvia Jimenez Verónica Jiménez-Jacinto Flavio Juárez-Martínez Toni Rose Jue Ingrid M. Keseler Aurora Labastida Stanley J. F. Laulederkind Oscar Lithgow-Serrano Alejandra López-Fuentes Zhiyong Lu Sumit Madan Hernani Marques-Madeira Irma Martínez-Flores Sherri Matis-Mitchell Sérgio Matos Johanna R. McEntyre Peter McQuilton Alejandra Medina-Rivera Victor del Moral-Chávez Gabriel Moreno-Hagelsieb Enrique Morett Matthew E. Mort Luis Muñiz-Rascado Jeyakumar Natarajan Maricela Olvera Sandra E. Orchard Marija Orlic-MilacicMarija Milacic Evangelos Pafilis Lucia Pannier Annie Pardo Martín Peralta-Gil Emiliano Pereira Ernesto Pérez-Rueda Liliana Porrón-Sotelo Sangya Pundir Shruti Rao Fabio Rinaldi 0001 Bogdan Kaleb García Rivera Raul Rodriguez-Esteban Karen Rothfels David Salgado Heladia Salgado Gerardo Salgado-Osorio Mishael Sánchez-Pérez José Armando Sánchez-Rojas Alberto Santos-Zavaleta Mary L. Schaeffer Moisés Selman Syed Abdul ShabbirShabbir Syed-Abdul Raquel M. Silva Onkar Singh Claudia Anahí Guzmán Solano Hilda Solano-Lira Raymund Stefancsik Chu-Hsien Su Suresh Subramani Hamsa D. Tadepally Arturo Téllez-Velázquez Silvia Tenorio-Salgado Loukia Tsaprouni Nicole A. Vasilevsky Leticia Vega-Alvarado Qinghua Wang 0003 Xiaodong Wang 0008 Verena Weiss Cathy H. Wu