Constructing knowledge graphs and their biomedical applications

Computational and Structural Biotechnology Journal
David N Nicholson, Casey S Greene

Abstract

Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomedical knowledge graphs have often been constructed by integrating databases that were populated by experts via manual curation, but we are now seeing a more robust use of automated systems. A number of techniques are used to represent knowledge graphs, but often machine learning methods are used to construct a low-dimensional representation that can support many different applications. This representation is designed to preserve a knowledge graph's local and/or global structure. Additional machine learning methods can be applied to this representation to make predictions within genomic, pharmaceutical, and clinical domains. We frame our discussion first around knowledge graph construction and then around unifying representational learning techniques and unifying applications. Advances in machine learning for biomedicine are creating new opportunities across many domains, and we note potential avenues for future work...Continue Reading

References

Oct 23, 1997·Neural Computation·S Hochreiter, J Schmidhuber
Nov 21, 2000·Journal of Microbiological Methods·I A Basheer, M Hajmeer
Dec 23, 2000·Science·J B TenenbaumJ C Langford
Apr 7, 2005·Artificial Intelligence in Medicine·Razvan BunescuYuk Wah Wong
Dec 5, 2006·Bioinformatics·Katrin FundelRalf Zimmer
Feb 13, 2007·BMC Bioinformatics·Sampo PyysaloTapio Salakoski
May 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kwang-Il GohAlbert-László Barabási
Jul 25, 2007·Bioinformatics·William A BaumgartnerLawrence Hunter
Dec 1, 2007·Nucleic Acids Research·David S WishartMurtaza Hassanali
May 13, 2008·Journal of Biomedical Informatics·François BelleauJean Morissette
Jan 1, 2009·Nature Methods·Michael E CusickMarc Vidal
Nov 26, 2009·Nature Methods·Lukasz SalwinskiHenning Hermjakob
Oct 5, 2010·PLoS Computational Biology·Raoul FrijtersWynand Alkema
Nov 26, 2010·Journal of Biomedical Informatics·Aurélie NévéolZhiyong Lu
Dec 1, 2010·Nucleic Acids Research·Donna MaglottTatiana Tatusova
Dec 2, 2010·Pacific Symposium on Biocomputing·Jang H Lee, Graciela H Gonzalez
Dec 15, 2011·Journal of Biomedical Informatics·Sachin Mathur, Deendayal Dinakarpandian
Mar 22, 2012·Database : the Journal of Biological Databases and Curation·Rafal RakSophia Ananiadou
Jul 11, 2012·BMC Bioinformatics·Michael BadaLawrence E Hunter
Aug 4, 2012·PLoS Computational Biology·Bin ChenDavid J Wild
Sep 21, 2012·Clinical Pharmacology and Therapeutics·M Whirl-CarrilloT E Klein
Dec 4, 2012·Nucleic Acids Research·Andrea FranceschiniLars J Jensen
Dec 4, 2012·Nucleic Acids Research·Andrew Chatr-AryamontriMike Tyers
Mar 21, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hua WangFeiping Nie
Nov 15, 2013·BMC Bioinformatics·Hee-Jin LeeJong C Park
Dec 3, 2013·Nucleic Acids Research·Michael KuhnPeer Bork
May 23, 2014·Database : the Journal of Biological Databases and Curation·Yifan PengK Vijay-Shanker
Jun 14, 2014·Database : the Journal of Biological Databases and Curation·Ingrid M KeselerPeter D Karp
Jul 24, 2014·Database : the Journal of Biological Databases and Curation·Dongseop KwonW John Wilbur
Oct 30, 2014·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Dec 3, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Jürgen Schmidhuber
Dec 9, 2014·Methods : a Companion to Methods in Enzymology·Sune Pletscher-FrankildLars Juhl Jensen
Apr 4, 2015·Database : the Journal of Biological Databases and Curation·Catalina O TudorCecilia N Arighi
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jun 17, 2015·Computational and Mathematical Methods in Medicine·Wen DaiPeng Lu
Aug 19, 2015·Journal of Biomedical Informatics·Min SongKeun Young Kang
Sep 5, 2015·Bioinformatics·Emily K MalloryRuss B Altman
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Manabu ToriiK Vijay-Shanker
Sep 26, 2015·PLoS Computational Biology·Gang LiK Vijay-Shanker
Dec 10, 2015·PLoS Computational Biology·Varsha D BadalIlya A Vakser

❮ Previous
Next ❯

Citations

Dec 29, 2020·Environmental Health Perspectives·Anne E ThessenMelissa A Haendel
Feb 12, 2021·Briefings in Bioinformatics·Alisa PavelDario Greco
Feb 6, 2021·JACC. Cardiovascular Imaging·Partho P Sengupta, Y S Chandrashekhar
Mar 21, 2021·Clinical and Translational Science·Karamarie FechoStanley C Ahalt
May 19, 2021·Database : the Journal of Biological Databases and Curation·Santiago Timón-ReinaRafael Martínez-Tomás
Jun 3, 2021·Pharmaceutics·Kevin McCoyCassie S Mitchell
Jul 3, 2021·Diagnostics·Nora El-RashidyShaker El-Sappagh

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Landau-Kleffner Syndrome

Landau Kleffner syndrome (LKS), also called infantile acquired aphasia, acquired epileptic aphasia, or aphasia with convulsive disorder, is a rare childhood neurological syndrome characterized by the sudden or gradual development of aphasia (the inability to understand or express language) and an abnormal electroencephalogram. Discover the latest research on LKS here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.