The Biomedical Informatics and the Generalized Biomedical Mechanics: The new explorations of BMKI in these fields
Main Article Content
Abstract
The paper discussed the promises and challenges in molecular biomedicines (MBMs) and their support discipline Biomedical Informatics (BMI) and investigated the possible underlying discipline the Generalized Biomedical Mechanics (GBMM) in order to seek for more understanding in MBMs. The latter is deemed to be the kingdom of phenomenology. Therefrom, a set of new concepts and principles such as the Structured Language Readable to Human and Machine, the philosophy-science interface, the semantic granule and pattern, the semi-closed or semi-isolated spaces, pan-cycle, the consuming-plus-absorbing law, the boundary principle of a ball-like cycle, the vibration-triggered pan-cycle, etc. were introduced. And also, the automatic semantic analysis and operation, the method of the expression of complex relation by ontology and the experimental project of the integration of the pan-cycle were described.
Keywords:
general biology mechanics, ontology, Biomedical Informatics, Biomedicine Knowledge Integration (BMKI), the Structured Language Readable to Human and Machine (SLRHM), Pan-cycle, knowledge engineering, molecular biomedicines, automatic semantic operations and calculations, super-complex systems, non-linearity
Article Details
How to Cite
BAO, Hanfei.
The Biomedical Informatics and the Generalized Biomedical Mechanics: The new explorations of BMKI in these fields.
Medical Research Archives, [S.l.], v. 13, n. 1, jan. 2025.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/6156>. Date accessed: 10 feb. 2025.
doi: https://doi.org/10.18103/mra.v13i1.6156.
Section
Research Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
References
1. Rita González-Márquez , Luca Schmidt, Benjamin M. Schmidt, Philipp Berens, Dmitry Kobak: The landscape of biomedical research https://www.sciencedirect.com/science/article/pii/S266638992400076X
2. 维基百科：生物資訊學, https://zh.wikipedia.org/zh-hk/%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E5%AD%A6
3. 吴春艳，王靖飞,生物信息学及其主要数学算法 https://www.dtrends.com/Chinese/bioinfo_Harbin.pdf
4. Benjamin Liu： Virtual Screening of Acetylcholinesterase-centered Inhibitors as Potential Therapies for Alzheimer’s Disease // European Journal of Biomedical and Life Sciences. 2024. №3. С. 46 - 74. URL: https://ppublishing.org/archive/publication/1209-virtual-screening-of-acetylcholinesterase-cen
5. Kevin Doxzen：Record-breaking rapid DNA sequencing.It promises timely diagnosis for thousands of rare disease cases https://www.asbmb.org/asbmb-today/science/022722/record-breaking-rapid-dna-sequencing
6. Caroline Barranco: The Human Genome Project https://www.nature.com/articles/d42859-020-00101-9
7. Hanfei Bao: (Book, In Chinese), ZheJiang University Press
8. Wikipedia：Mechanics，https://www.google.ca/search?q=mechanics+definition&sca_esv=a276a5e6dcef4cbb&sca_upv=1&ei=-ZD7ZoaxLtan0PEP2ZWE6AY&start=10&sa=N&sstk=AagrsujKOxa2uGX7oyOAwvHORuXB4iJQX8Xm5ue7fdVI27VfysW_6iA7cJ1WDYan36mwcuYVSnViHwI199fwfk0myRYbWu-kuF_RnQ&ved=2ahUKEwjGkZzHweyIAxXWEzQIHdkKAW0Q8NMDegQIChAW&biw=758&bih=337&dpr=1.78
9. Hanfei Bao: The Theory of Biomedical Knowledge Integration(Ⅰ), Chinese Journal of Medical Treatment, 2(13): 1-6, 2003
10. Hanfei Bao: The Theory of Biomedical Knowledge Integration(Ⅱ)----What is underlying the domain concepts, Chinese Journal of Medical Treatment, 2(21): 1-6, 2003
11. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅲ), Chinese Journal of Medical Treatment, Vol(3),No(7),2004
12. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅳ), Medical Information, 18(6), 545-550, 2005
13. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅴ)——The meta-dimensions and their combination of the General Linkage/Modifiers of SNOMED, Medical Information, 18(10): 1227-1232，2005
14. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅵ), Medical Information, 19(2): 183-190，2006
15. Hanfei Bao: The Theory of Biomedical Knowledge Integration (VII)----The Non-Euclid Macro-Micro Transform Law, Medical Information, 19(11), 1899-1907, 2006
16. Hanfei Bao: The Theory of Biomedical Knowledge Integration (VIII)——The Intrinsic Medical Informatics (IMI) and Meta-dimensions(MDs) of SNOMED, Medical Information, 21(7): 997-1002，2008
17. Hanfei Bao: The Theory of Biomedical Knowledge Integration (IX) ----A venture in methodology for operations on the cognitive segment in HER, Medical Information, 21(7):1003-1010,2008
18. 吴学谋：《从泛系观看世界》，中国人民大学出版社, 1990
19. Hanfei Bao: The Generalized Biology Mechanics and the Molecule Biomedicines ----BMKI and SARS-CoV-2(I) https://www.researchgate.net/publication/371157215_The_Generalized_Biology_Mechanics_and_the_Molecule_Biomedicines_----BMKI_and_SARS-CoV-2I#fullTextFileContent
20. Hanfei Bao: he Automatic Semantic Operations and Calculations in the Molecular Biomedicines ----BMKI and SARS-CoV-2 (II) https://www.researchgate.net/publication/371157176_The_Automatic_Semantic_Operations_and_Calculations_in_the_Molecular_Biomedicines_----BMKI_and_SARS-CoV-2_II
21. Hanfei Bao: A Novel Way To Express The Complicated Knowledge On The Evolvements of The Biologic Factors Of HIV-1 In Ontology ——Discussion On HIV/AIDS Ontology(12) https://www.researchgate.net/publication/316560677_A_Novel_Way_To_Express_The_Complicated_Knowledge_On_The_Evolvements_of_The_Biologic_Factors_Of_HIV-1_In_Ontology_--Discussion_On_HIVAIDS_Ontology12
22. Hanfei Bao: A Bridge Between Natural Language-And Ontology-based Biomedical Resources —-The Examples of Biomedical Knowledge Expressed by SLRHM I. The Structured Language Readable To Human And Machine (SLRHM) https://www.researchgate.net/publication/316598152_A_Bridge_Between_Natural_Language-And_Ontology-based_Biomedical_Resources_--The_Examples_of_Biomedical_Knowledge_Expressed_by_SLHMR_I_The_Structured_Language_Readable_To_Human_And_MachineSLHMR
23. Protégé: A free, open-source ontology editor and framework for building intelligent systems https://protege.stanford.edu/
24. Ilya Prigogine and Isabelle Stengers: < Order Out of Chaos: Man’s New Dialogue with Nature>, (in Chinese, translated by Qinghong Zeng, Xiaofeng Shen), Shanghai Translation Publishing House， 1988
25. Manfred Eigen: Hypercycle theory, https://en.wikipedia.org/wiki/Hypercycle_(chemistry)
26. 最小吉布斯自由能原理 https://baike.baidu.com/item/%E5%90%89%E5%B8%83%E6%96%AF%E8%87%AA%E7%94%B1%E8%83%BD/327614
27. Principle of minimum energy https://en.wikipedia.org/wiki/Principle_of_minimum_energy
28. Allison Soult：Gibbs Free Energy https://chem.libretexts.org/Bookshelves/Introductory_Chemistry/Chemistry_for_Allied_Health_(Soult)/11%3A_Properties_of_Reactions/11.05%3A_Spontaneous_Reactions_and_Free_Energy#:~:text=Spontaneous%20reactions%20release%20free%20energy,change%20and%20the%20entropy%20change.
29. Richard N. Fogoros: The Heart's Electrical System: Anatomy and Function Five components of electrical conduction make the heart beat https://www.verywellhealth.com/cardiac-electrical-system-how-the-heart-beats-1746299
30. Jason S. Rawlings, Kristin M. Rosler, Douglas A. Harrison: The JAK/STAT signaling pathway https://journals.biologists.com/jcs/article/117/8/1281/28255/The-JAK-STAT-signaling-pathway 23.
31. ThermofisherScientific: JAK/STAT Pathway https://www.thermofisher.com/ca/en/home/life-science/antibodies/antibodies-learning-center/antibodies-resource-library/cell-signaling-pathways/jak-stat-pathway.html 24.
32. Lauren Dalton and Robin Young: Cell Signaling https://open.oregonstate.education/cellbiology/chapter/cell-signaling/
33. NLM: General Principles of Cell Communication https://www.ncbi.nlm.nih.gov/books/NBK26813/
34. Reto Stricker, Raphael Eberhart, Marie-Christine Chevailler, Frank A. Quinn, PaulBischof and Rene ́ Stricker: Establishment of detailed reference values for luteinizing hormone, follicle stimulating hormone, estradiol, and progesterone during different phases of the menstrual cycle on the Abbott ARCHITECTanalyzer https://www.researchgate.net/publication/7006350_Establishment_of_detailed_reference_values_for_luteinizing_hormone_follicle_stimulating_hormone_estradiol_and_progesterone_during_different_phases_of_the_menstrual_cycle_on_the_Abbott_ARCHITECTR_analy
2. 维基百科：生物資訊學, https://zh.wikipedia.org/zh-hk/%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E5%AD%A6
3. 吴春艳，王靖飞,生物信息学及其主要数学算法 https://www.dtrends.com/Chinese/bioinfo_Harbin.pdf
4. Benjamin Liu： Virtual Screening of Acetylcholinesterase-centered Inhibitors as Potential Therapies for Alzheimer’s Disease // European Journal of Biomedical and Life Sciences. 2024. №3. С. 46 - 74. URL: https://ppublishing.org/archive/publication/1209-virtual-screening-of-acetylcholinesterase-cen
5. Kevin Doxzen：Record-breaking rapid DNA sequencing.It promises timely diagnosis for thousands of rare disease cases https://www.asbmb.org/asbmb-today/science/022722/record-breaking-rapid-dna-sequencing
6. Caroline Barranco: The Human Genome Project https://www.nature.com/articles/d42859-020-00101-9
7. Hanfei Bao:
8. Wikipedia：Mechanics，https://www.google.ca/search?q=mechanics+definition&sca_esv=a276a5e6dcef4cbb&sca_upv=1&ei=-ZD7ZoaxLtan0PEP2ZWE6AY&start=10&sa=N&sstk=AagrsujKOxa2uGX7oyOAwvHORuXB4iJQX8Xm5ue7fdVI27VfysW_6iA7cJ1WDYan36mwcuYVSnViHwI199fwfk0myRYbWu-kuF_RnQ&ved=2ahUKEwjGkZzHweyIAxXWEzQIHdkKAW0Q8NMDegQIChAW&biw=758&bih=337&dpr=1.78
9. Hanfei Bao: The Theory of Biomedical Knowledge Integration(Ⅰ), Chinese Journal of Medical Treatment, 2(13): 1-6, 2003
10. Hanfei Bao: The Theory of Biomedical Knowledge Integration(Ⅱ)----What is underlying the domain concepts, Chinese Journal of Medical Treatment, 2(21): 1-6, 2003
11. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅲ), Chinese Journal of Medical Treatment, Vol(3),No(7),2004
12. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅳ), Medical Information, 18(6), 545-550, 2005
13. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅴ)——The meta-dimensions and their combination of the General Linkage/Modifiers of SNOMED, Medical Information, 18(10): 1227-1232，2005
14. Hanfei Bao: The Theory of Biomedical Knowledge Integration (Ⅵ), Medical Information, 19(2): 183-190，2006
15. Hanfei Bao: The Theory of Biomedical Knowledge Integration (VII)----The Non-Euclid Macro-Micro Transform Law, Medical Information, 19(11), 1899-1907, 2006
16. Hanfei Bao: The Theory of Biomedical Knowledge Integration (VIII)——The Intrinsic Medical Informatics (IMI) and Meta-dimensions(MDs) of SNOMED, Medical Information, 21(7): 997-1002，2008
17. Hanfei Bao: The Theory of Biomedical Knowledge Integration (IX) ----A venture in methodology for operations on the cognitive segment in HER, Medical Information, 21(7):1003-1010,2008
18. 吴学谋：《从泛系观看世界》，中国人民大学出版社, 1990
19. Hanfei Bao: The Generalized Biology Mechanics and the Molecule Biomedicines ----BMKI and SARS-CoV-2(I) https://www.researchgate.net/publication/371157215_The_Generalized_Biology_Mechanics_and_the_Molecule_Biomedicines_----BMKI_and_SARS-CoV-2I#fullTextFileContent
20. Hanfei Bao: he Automatic Semantic Operations and Calculations in the Molecular Biomedicines ----BMKI and SARS-CoV-2 (II) https://www.researchgate.net/publication/371157176_The_Automatic_Semantic_Operations_and_Calculations_in_the_Molecular_Biomedicines_----BMKI_and_SARS-CoV-2_II
21. Hanfei Bao: A Novel Way To Express The Complicated Knowledge On The Evolvements of The Biologic Factors Of HIV-1 In Ontology ——Discussion On HIV/AIDS Ontology(12) https://www.researchgate.net/publication/316560677_A_Novel_Way_To_Express_The_Complicated_Knowledge_On_The_Evolvements_of_The_Biologic_Factors_Of_HIV-1_In_Ontology_--Discussion_On_HIVAIDS_Ontology12
22. Hanfei Bao: A Bridge Between Natural Language-And Ontology-based Biomedical Resources —-The Examples of Biomedical Knowledge Expressed by SLRHM I. The Structured Language Readable To Human And Machine (SLRHM) https://www.researchgate.net/publication/316598152_A_Bridge_Between_Natural_Language-And_Ontology-based_Biomedical_Resources_--The_Examples_of_Biomedical_Knowledge_Expressed_by_SLHMR_I_The_Structured_Language_Readable_To_Human_And_MachineSLHMR
23. Protégé: A free, open-source ontology editor and framework for building intelligent systems https://protege.stanford.edu/
24. Ilya Prigogine and Isabelle Stengers: < Order Out of Chaos: Man’s New Dialogue with Nature>, (in Chinese, translated by Qinghong Zeng, Xiaofeng Shen), Shanghai Translation Publishing House， 1988
25. Manfred Eigen: Hypercycle theory, https://en.wikipedia.org/wiki/Hypercycle_(chemistry)
26. 最小吉布斯自由能原理 https://baike.baidu.com/item/%E5%90%89%E5%B8%83%E6%96%AF%E8%87%AA%E7%94%B1%E8%83%BD/327614
27. Principle of minimum energy https://en.wikipedia.org/wiki/Principle_of_minimum_energy
28. Allison Soult：Gibbs Free Energy https://chem.libretexts.org/Bookshelves/Introductory_Chemistry/Chemistry_for_Allied_Health_(Soult)/11%3A_Properties_of_Reactions/11.05%3A_Spontaneous_Reactions_and_Free_Energy#:~:text=Spontaneous%20reactions%20release%20free%20energy,change%20and%20the%20entropy%20change.
29. Richard N. Fogoros: The Heart's Electrical System: Anatomy and Function Five components of electrical conduction make the heart beat https://www.verywellhealth.com/cardiac-electrical-system-how-the-heart-beats-1746299
30. Jason S. Rawlings, Kristin M. Rosler, Douglas A. Harrison: The JAK/STAT signaling pathway https://journals.biologists.com/jcs/article/117/8/1281/28255/The-JAK-STAT-signaling-pathway 23.
31. ThermofisherScientific: JAK/STAT Pathway https://www.thermofisher.com/ca/en/home/life-science/antibodies/antibodies-learning-center/antibodies-resource-library/cell-signaling-pathways/jak-stat-pathway.html 24.
32. Lauren Dalton and Robin Young: Cell Signaling https://open.oregonstate.education/cellbiology/chapter/cell-signaling/
33. NLM: General Principles of Cell Communication https://www.ncbi.nlm.nih.gov/books/NBK26813/
34. Reto Stricker, Raphael Eberhart, Marie-Christine Chevailler, Frank A. Quinn, PaulBischof and Rene ́ Stricker: Establishment of detailed reference values for luteinizing hormone, follicle stimulating hormone, estradiol, and progesterone during different phases of the menstrual cycle on the Abbott ARCHITECTanalyzer https://www.researchgate.net/publication/7006350_Establishment_of_detailed_reference_values_for_luteinizing_hormone_follicle_stimulating_hormone_estradiol_and_progesterone_during_different_phases_of_the_menstrual_cycle_on_the_Abbott_ARCHITECTR_analy